@article{mahindroo_narayan_modgil_kaur_shahi_sharma_jain_thakur_mohan_taneja_2024, title={Antimicrobial resistance in food-borne pathogens at the human-animal interface: Results from a large surveillance study in India}, volume={18}, ISSN={["2352-7714"]}, DOI={10.1016/j.onehlt.2024.100677}, abstractNote={The burden of foodborne diseases and antimicrobial resistance carried by key foodborne pathogens in India is unknown due to a lack of an integrated surveillance system at the human-animal interface. We present data from the WHO-AGISAR (Advisory Group on Integrated Surveillance of Antimicrobial Resistance), India project. Concurrent human and animal sampling was done across a large area across north India. Community-acquired diarrhea cases (n = 1968) of all age groups were included. Cross-sectional sampling of stool/ intestinal contents (n = 487) and meat samples (n = 419) from food-producing animals was done at farms, retail shops, and slaughterhouses. Pathogens were cultured and identified, and antimicrobial susceptibility was performed. Over 80% of diarrhoeal samples were obtained from moderate to severe diarrhea patients, which yielded EAEC (5%), ETEC (4.84%), EPEC (4.32%), and Campylobacter spp. (2%). A high carriage of EPEC (32.11%) and Campylobacter spp. (24.72%) was noted in food animals, but the prevalence of ETEC (2%) and EAEC (1%) was low. Atypical EPEC (aEPEC, 84.52%, p ≤0.0001) were predominant and caused milder diarrhea. All EPEC from animal/poultry were aEPEC. Overall, a very high level of resistance was observed, and the MDR rate ranged from 29.2% in Campylobacter spp., 53.6% in EPEC, and 59.8% in ETEC. Resistance to piperacillin-tazobactam, cefepime, ceftriaxone, and co-trimoxazole was significantly higher in human strains. In contrast, resistance to ciprofloxacin, aminoglycosides, and tetracycline was higher in animal strains, reflecting the corresponding usage in human and animal sectors. ESBL production was commoner in animal isolates than in humans, indicating high use of third-generation cephalosporins in the animal sector. C. hyointestinalis is an emerging zoonotic pathogen, first time reported from India. In one of the most extensive studies from India, a high burden of key foodborne pathogens with MDR and ESBL phenotypes was found in livestock, poultry, and retail meat.}, journal={ONE HEALTH}, author={Mahindroo, Jaspreet and Narayan, Chandradeo and Modgil, Vinay and Kaur, Harpreet and Shahi, Varun and Sharma, Bhawna and Jain, Ruby and Thakur, Siddhartha and Mohan, Balvinder and Taneja, Neelam}, year={2024}, month={Jun} }
 @article{aworh_thakur_gensler_harrell_harden_fedorka-cray_jacob_2024, title={Characteristics of antimicrobial resistance in <i>Escherichia coli</i> isolated from retail meat products in North Carolina}, volume={19}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0294099}, abstractNote={Background Escherichia coli is commonly used as an indicator for antimicrobial resistance (AMR) in food, animal, environment, and human surveillance systems. Our study aimed to characterize AMR in E. coli isolated from retail meat purchased from grocery stores in North Carolina, USA as part of the National Antimicrobial Resistance Monitoring System (NARMS). Methods Retail chicken (breast, n=96; giblets, n=24), turkey (n=96), and pork (n=96) products were purchased monthly from different counties in North Carolina during 2022. Label claims on packages regarding antibiotic use were recorded at collection. E. coli was isolated from meat samples using culture-based methods and isolates were characterized for antimicrobial resistance using whole genome sequencing. Multi-locus sequence typing, phylogroups, and a single nucleotide polymorphism (SNP)-based maximum-likelihood phylogenic tree were generated. Data were analyzed statistically to determine differences between antibiotic use claims and meat type. Results Of 312 retail meat samples, 138 (44.2%) were positive for E. coli, with turkey (78/138; 56.5%) demonstrating the highest prevalence. Prevalence was lower in chicken (41/138; 29.7%) and pork (19/138;13.8%). Quality sequence data was available from 84.8% (117/138) of the E. coli isolates, which included 72 (61.5%) from turkey, 27 (23.1%) from chicken breast, and 18 (15.4%) from pork. Genes associated with AMR were detected in 77.8% (91/117) of the isolates and 35.9% (42/117) were defined as MDR (≥3 distinct classes of antimicrobials). Commonly observed AMR genes included tetB (35%), tetA (24.8%), aph(3’’)-lb (24.8%), and blaTEM-1 (20.5%), the majority of which originated from turkey isolates. Antibiotics use claims had no statistical effect on MDR E. coli isolates from the different meat types (X2=2.21, p =0.33). MDR was observed in isolates from meat products with labels indicating “no claims” (n=29; 69%), “no antibiotics ever” (n=9; 21.4%), and “organic” (n=4; 9.5%). Thirty-four different replicon types were observed. AMR genes were carried on plasmids in 17 E. coli isolates, of which 15 (88.2%) were from turkey and two (11.8%) from chicken. Known sequence types (STs) were described for 81 E. coli isolates, with ST117 (8.5%), ST297 (5.1%), and ST58 (3.4%) being the most prevalent across retail meat types. The most prevalent phylogroups were B1 (29.1%) and A (28.2%). Five clonal patterns were detected among isolates. Conclusions E. coli prevalence and the presence of AMR and MDR were highest in turkey retail meat. The lack of an association between MDR E. coli in retail meat and antibiotic use claim, including those with no indication of antimicrobial use, suggests that additional research is required to understand the origin of resistance. The presence of ST117, an emerging human pathogen, warrants further surveillance. The isolates were distinctly diverse suggesting an instability in population dynamics.}, number={1}, journal={PLOS ONE}, author={Aworh, Mabel Kamweli and Thakur, Siddhartha and Gensler, Catherine and Harrell, Erin and Harden, Lyndy and Fedorka-Cray, Paula J. and Jacob, Megan}, year={2024}, month={Jan} }
 @article{abdelrahim_harrell_fedorka-cray_jacob_thakur_2024, title={Phenotypic and Genotypic Characterizations of Antimicrobial-Resistant <i>Escherichia coli</i> Isolates from Diverse Retail Meat Samples in North Carolina During 2018-2019}, volume={1}, ISSN={["1556-7125"]}, DOI={10.1089/fpd.2023.0093}, abstractNote={Surveillance of antimicrobial-resistant pathogens in U.S. retail meats is conducted to identify potential risks of foodborne illness. In this study, we conducted a phenotypic and genotypic analysis of Escherichia coli recovered from a diverse range of retail meat types during 2018-2019 in North Carolina. The investigation was conducted as part of the National Antimicrobial Resistance Monitoring System (NARMS). Retail meat sampling and E. coli isolation were performed in accordance with NARMS retail meat isolation protocols. We used the Sensititre™ broth microdilution system to determine phenotypic resistance to 14 antimicrobial agents and the Illumina next-generation sequencing platform for genotypic resistance profiling. The highest prevalence of E. coli isolates was found in ground turkey (n = 57, 42.9%) and chicken (n = 27, 20.3%), followed by ground beef (n = 25, 18.9%) and pork (n = 24, 18%). The isolates were divided into seven different phylogroups using the Clermont typing tool, with B1 (n = 59, 44.4%) and A (n = 39, 29.3%) being the most dominant, followed by B2 (n = 14, 10.5%), D (n = 7, 5.3%), F (n = 6, 4.5%), E (n = 3, 2.3%), and C (n = 2, 1.5%). Using multilocus sequence typing (MLST), 128 Sequence types (STs) were identified indicating high diversity. Phenotypic and genotypic resistance was observed toward aminoglycosides, sulfonamides, beta-lactams, macrolides, tetracyclines, phenicols, and fluoroquinolones. Ground turkey samples were more resistant to the panel of tested antimicrobials than chicken, beef, or pork (p < 0.05). All isolates were found to be susceptible to meropenem. A high percentage of turkey isolates (n = 16, 28%) were multidrug-resistant (MDR) compared with 18.5% of chicken (n = 5), 8.4% of pork (n = 2), and 8% of beef isolates (n = 2). This study highlights the benefit of surveillance to identify MDR E. coli for epidemiologic tracking and is a comprehensive report of the phenotypic and genotypic characterization of E. coli isolated from retail meats in North Carolina.}, journal={FOODBORNE PATHOGENS AND DISEASE}, author={Abdelrahim, Afaf and Harrell, Erin and Fedorka-Cray, Paula J. and Jacob, Megan and Thakur, Siddhartha}, year={2024}, month={Jan} }
 @article{grinevich_harden_thakur_callahan_2024, title={Serovar-level identification of bacterial foodborne pathogens from full-length 16S rRNA gene sequencing}, volume={2}, ISSN={["2379-5077"]}, url={https://doi.org/10.1128/msystems.00757-23}, DOI={10.1128/msystems.00757-23}, abstractNote={ABSTRACT The resolution of variation within species is critical for interpreting and acting on many microbial measurements. In the key foodborne pathogens Salmonella and Escherichia coli, the primary subspecies classification scheme used is serotyping: differentiating variants within these species by surface antigen profiles. Serotype prediction from whole-genome sequencing (WGS) of isolates is now seen as comparable or preferable to traditional laboratory methods where WGS is available. However, laboratory and WGS methods depend on an isolation step that is time-consuming and incompletely represents the sample when multiple strains are present. Community sequencing approaches that skip the isolation step are, therefore, of interest for pathogen surveillance. Here, we evaluated the viability of amplicon sequencing of the full-length 16S rRNA gene for serotyping Salmonella enterica and E. coli. We developed a novel algorithm for serotype prediction, implemented as an R package (Seroplacer), which takes as input full-length 16S rRNA gene sequences and outputs serovar predictions after phylogenetic placement into a reference phylogeny. We achieved over 89% accuracy in predicting Salmonella serotypes on in silico test data and identified key pathogenic serovars of Salmonella and E. coli in isolate and environmental test samples. Although serotype prediction from 16S rRNA gene sequences is not as accurate as serotype prediction from WGS of isolates, the potential to identify dangerous serovars directly from amplicon sequencing of environmental samples is intriguing for pathogen surveillance. The capabilities developed here are also broadly relevant to other applications where intraspecies variation and direct sequencing from environmental samples could be valuable. IMPORTANCE In order to prevent and stop outbreaks of foodborne pathogens, it is important that we can detect when pathogenic bacteria are present in a food or food-associated site and identify connections between specific pathogenic bacteria present in different samples. In this work, we develop a new computational technology that allows the important foodborne pathogens Escherichia coli and Salmonella enterica to be serotyped (a subspecies level classification) from sequencing of a single-marker gene, and the 16S rRNA gene often used to surveil bacterial communities. Our results suggest current limitations to serotyping from 16S rRNA gene sequencing alone but set the stage for further progress that we consider likely given the rapid advance in the long-read sequencing technologies and genomic databases our work leverages. If this research direction succeeds, it could enable better detection of foodborne pathogens before they reach the public and speed the resolution of foodborne pathogen outbreaks.}, journal={MSYSTEMS}, author={Grinevich, Dmitry and Harden, Lyndy and Thakur, Siddhartha and Callahan, Benjamin}, editor={Langille, Morgan G. I.Editor}, year={2024}, month={Feb} }
 @article{hull_harrel_harden_thakur_2023, title={Detection of resistance and virulence plasmids in Campylobacter coli and Campylobacter jejuni isolated from North Carolina food animal production, 2018-2019}, volume={116}, ISSN={["1095-9998"]}, DOI={10.1016/j.fm.2023.104348}, abstractNote={Campylobacter remains the leading cause of bacterial foodborne illness in the U.S. and worldwide. Campylobacter plasmids may play a significant role in antimicrobial resistance (AMR) and virulence factor distribution, and potentially drive rapid adaptation. C. coli (n = 345) and C. jejuni (n = 199) isolates collected from live cattle, swine, turkey, and chickens, poultry carcasses at production, and retail meat in N.C. were analyzed to determine plasmid prevalence, extrachromosomal virulence and AMR genes, and the phylogeny of assembled plasmids. Putative plasmids ranging from <2 kb to 237kb were identified with virulence factors present in 66.1% (228/345) C. coli and 88.4% (176/199) C. jejuni plasmids (promoting adherence, invasion, exotoxin production, immune modulation, chemotaxis, mobility, and the type IV secretion system). AMR genes were identified in 21.2% (73/345) C. coli and 28.1% C. jejuni plasmids (conferring resistance to tetracyclines, aminoglycosides, beta-lactams, nucleosides, and lincosamides). Megaplasmids (>100 kb) were present in 25.7% (140/544) of the isolates and carried genes previously recognized to be involved with interspecies recombination. Our study highlights the extensive distribution and diversity of Campylobacter plasmids in food animal production and their role in the dissemination of biomedically important genes. Characterizing Campylobacter plasmids within the food animal production niche is important to understanding the epidemiology of potential emerging strains.}, journal={FOOD MICROBIOLOGY}, author={Hull, Dawn M. and Harrel, Erin and Harden, Lyndy and Thakur, Siddhartha}, year={2023}, month={Dec} }
 @article{walker_harden_suyemoto_thakur_jacob_borst_2023, title={Draft Genome Sequences of Escherichia coli and Enterococcus faecalis Coisolated from Polymicrobial Extraintestinal Infections of Chickens and Turkeys}, volume={2}, ISSN={["2576-098X"]}, DOI={10.1128/mra.01163-22}, abstractNote={Coinfections by avian pathogenic Escherichia coli (APEC) and Enterococcus faecalis in poultry with colisepticemia have become increasingly recognized. Here, we report draft genome sequences of 18 APEC and 18 E. faecalis strains coisolated from lesions of diseased poultry. ABSTRACT Coinfections by avian pathogenic Escherichia coli (APEC) and Enterococcus faecalis in poultry with colisepticemia have become increasingly recognized. Here, we report draft genome sequences of 18 APEC and 18 E. faecalis strains coisolated from lesions of diseased poultry.}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Walker, Grayson K. and Harden, Lyndy and Suyemoto, M. Mitsu and Thakur, Siddhartha and Jacob, Megan and Borst, Luke B.}, year={2023}, month={Feb} }
 @article{walker_harden_suyemoto_thakur_jacob_borst_2023, title={Draft genome sequences of 12 Escherichia coli co-isolated with Enterococcus spp. from dogs with polybacterial bacteriuria at a veterinary hospital}, volume={8}, ISSN={["2576-098X"]}, DOI={10.1128/MRA.00262-23}, abstractNote={ABSTRACT Escherichia coli are frequently co-isolated with Enterococcus spp. from urine cultures of dogs with urinary tract infections (UTIs). Uropathogenic E. coli (UPEC) are augmented by Enterococcus in polymicrobial UTIs. We report the draft genome sequences of 12 UPEC co-isolated with Enterococcus spp. from canine urinary tract infections.}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Walker, Grayson K. and Harden, Lyndy and Suyemoto, M. Mitsu and Thakur, Siddhartha and Jacob, Megan and Borst, Luke B.}, year={2023}, month={Aug} }
 @article{muyyarikkandy_parzygnat_thakur_2023, title={Uncovering changes in microbiome profiles across commercial and backyard poultry farming systems}, volume={11}, ISSN={["2165-0497"]}, url={https://doi.org/10.1128/spectrum.01682-23}, DOI={10.1128/spectrum.01682-23}, abstractNote={ABSTRACT The microbiome profiles of poultry production systems significantly impact bird health, welfare, and the environment. This study investigated the influence of broiler-rearing systems on the microbiome composition of commercial and backyard chicken farms and their environment over time. Understanding these effects is vital for optimizing animal growth, enhancing welfare, and addressing human and environmental health implications. We collected and analyzed various samples from commercial and backyard farms, revealing significant differences in microbial diversity measurements between the two systems. Backyard farms exhibited higher alpha diversity measurements in soil and water samples, while commercial farms showed higher values for litter and feeder samples. The differences in microbial diversity were also reflected in the relative abundance of various microbial taxa. In backyard farms, Proteobacteria levels increased over time, while Firmicutes levels decreased. Campilobacterota, including the major poultry foodborne pathogen Campylobacter, increased over time in commercial farm environments. Furthermore, Bacteroides, associated with improved growth performance in chickens, were more abundant in backyard farms. Conversely, pathogenic Acinetobacter was significantly higher in backyard chicken fecal and feeder swab samples. The presence of Brevibacterium and Brachybacterium, associated with low-performing broiler flocks, was significantly higher in commercial farm samples. The observed differences in microbial composition and diversity suggest that farm management practices and environmental conditions significantly affect poultry health and welfare and have potential implications for human and environmental health. Understanding these relationships can inform targeted interventions to optimize poultry production, improve animal welfare, and mitigate foodborne pathogens and antimicrobial resistance risks. IMPORTANCE The microbiome of poultry production systems has garnered significant attention due to its implications on bird health, welfare, and overall performance. The present study investigates the impact of different broiler-rearing systems, namely, commercial (conventional) and backyard (non-conventional), on the microbiome profiles of chickens and their environment over time. Understanding the influence of these systems on microbiome composition is a critical aspect of the One-Health concept, which emphasizes the interconnectedness of animal, human, and environmental health. Our findings demonstrate that the type of broiler production system significantly affects both the birds and their environment, with distinct microbial communities associated with each system. This study reveals the presence of specific microbial taxa that differ in abundance between commercial and backyard poultry farms, providing valuable insights into the management practices that may alter the microbiome in these settings. Furthermore, the dynamic changes in microbial composition over time observed in our study highlight the complex interplay between the poultry gut microbiome, environmental factors, and production systems. By identifying the key microbial players and their fluctuations in commercial and backyard broiler production systems, this research offers a foundation for developing targeted strategies to optimize bird health and welfare while minimizing the potential risks to human and environmental health. The results contribute to a growing body of knowledge in the field of poultry microbiome research and have the potential to guide future improvements in poultry production practices that promote a sustainable and healthy balance between the birds, their environment, and the microbial communities they host. The microbiome of poultry production systems has garnered significant attention due to its implications on bird health, welfare, and overall performance. The present study investigates the impact of different broiler-rearing systems, namely, commercial (conventional) and backyard (non-conventional), on the microbiome profiles of chickens and their environment over time. Understanding the influence of these systems on microbiome composition is a critical aspect of the One-Health concept, which emphasizes the interconnectedness of animal, human, and environmental health. Our findings demonstrate that the type of broiler production system significantly affects both the birds and their environment, with distinct microbial communities associated with each system. This study reveals the presence of specific microbial taxa that differ in abundance between commercial and backyard poultry farms, providing valuable insights into the management practices that may alter the microbiome in these settings. Furthermore, the dynamic changes in microbial composition over time observed in our study highlight the complex interplay between the poultry gut microbiome, environmental factors, and production systems. By identifying the key microbial players and their fluctuations in commercial and backyard broiler production systems, this research offers a foundation for developing targeted strategies to optimize bird health and welfare while minimizing the potential risks to human and environmental health. The results contribute to a growing body of knowledge in the field of poultry microbiome research and have the potential to guide future improvements in poultry production practices that promote a sustainable and healthy balance between the birds, their environment, and the microbial communities they host.}, number={5}, journal={MICROBIOLOGY SPECTRUM}, author={Muyyarikkandy, Muhammed Shafeekh and Parzygnat, Jessica and Thakur, Siddhartha}, editor={Steven, BlaireEditor}, year={2023} }
 @article{gomes_moreno_silva_thakur_la ragione_mather_moreno_2022, title={Characterization of Salmonella enterica Contamination in Pork and Poultry Meat from Sao Paulo/Brazil: Serotypes, Genotypes and Antimicrobial Resistance Profiles}, volume={11}, ISSN={["2076-0817"]}, url={https://www.mdpi.com/2076-0817/11/3/358}, DOI={10.3390/pathogens11030358}, abstractNote={Salmonellosis is a zoonosis of major relevance to global public health. Here we present the assessment of Salmonella enterica contamination in pork and poultry meat sold at retail markets in São Paulo, Brazil. A total of 780 meat samples (386 poultry meat and 394 pork samples) were collected from 132 markets. From these, 57 samples (7.3%) were positive for S. enterica isolation, including 32 (8.3%) poultry meat and 25 (6.3%) pork samples. S. enterica isolates were further characterized for serotyping, antimicrobial resistance and genotyping by amplified fragment length polymorphism and pulsed field gel electrophoresis. Antimicrobial resistance analysis demonstrated two main profiles: pork isolates were more resistant to macrolides, β-lactams, tetracycline, phenicols, and fluoroquinolones, and poultry meat isolates presented higher resistance to fluoroquinolones, sulfonamides, tetracycline, and β-lactams. A total of 72.4% of poultry meat isolates were identified as S. Heidelberg, while most of pork isolates were S. Typhimurium (31.7%) and S. Give (16.7%). Genotyping resulted in most clusters consisting exclusively of pork or poultry meat, no cross-contamination was detected, and a tendency to differentiate isolates according to their serotypes and markets of origin. High resistance rates to critically important antimicrobials reinforce the importance of controlling Salmonella contamination in meat production chains.}, number={3}, journal={PATHOGENS}, author={Gomes, Vasco T. M. and Moreno, Luisa Z. and Silva, Ana Paula S. and Thakur, Siddhartha and La Ragione, Roberto M. and Mather, Alison E. and Moreno, Andrea M.}, year={2022}, month={Mar} }
 @article{atlaw_keelara_correa_foster_gebreyes_aidara-kane_harden_thakur_fedorka-cray_2022, title={Evidence of sheep and abattoir environment as important reservoirs of multidrug-resistant Salmonella and extended-spectrum beta-lactamase Escherichia coli}, volume={363}, ISSN={["1879-3460"]}, url={http://dx.doi.org/10.1016/j.ijfoodmicro.2021.109516}, DOI={10.1016/j.ijfoodmicro.2021.109516}, abstractNote={The increase in antimicrobial-resistant (AMR) foodborne pathogens, including E. coli and Salmonella in animals, humans, and the environment, is a growing public health concern. Among animals, cattle, pigs, and chicken are reservoirs of these pathogens worldwide. There is a knowledge gap on the prevalence and AMR of foodborne pathogens in small ruminants (i.e., sheep and goats). This study investigates the prevalence and antimicrobial resistance of extended-spectrum beta-lactamase (ESBL) E. coli and Salmonella from sheep and their abattoir environment in North Carolina. We conducted a year-round serial cross-sectional study and collected a total of 1128 samples from sheep (n = 780) and their abattoir environment (n = 348). Sheep samples consisted of feces, cecal contents, carcass swabs, and abattoir resting area feces. Environmental samples consisted of soil samples, lairage swab, animal feed, and drinking water for animals. We used CHROMAgar EEC with 4 μg/ml of Cefotaxime for isolating ESBL E. coli, and ESBL production was confirmed by double-disk diffusion test. Salmonella was isolated and confirmed using standard methods. All of the confirmed isolates were tested against a panel of 14 antimicrobials to elucidate susceptibility profiles. The prevalence of ESBL E. coli and Salmonella was significantly higher in environmental samples (47.7% and 65.5%) compared to the sheep samples (19.5% and 17.9%), respectively (P < 0.0001). We recovered 318 ESBL E. coli and 368 Salmonella isolates from sheep and environmental samples. More than 97% (310/318) of ESBL E. coli were multidrug-resistant (MDR; resistant to ≥3 classes of antimicrobials). Most Salmonella isolates (77.2%, 284/368) were pansusceptible, and 10.1% (37/368) were MDR. We identified a total of 24 different Salmonella serotypes by whole genome sequencing (WGS). The most common serotypes were Agona (19.8%), Typhimurium (16.2%), Cannstatt (13.2%), Reading (13.2%), and Anatum (9.6%). Prevalence and percent resistance of ESBL E. coli and Salmonella isolates varied significantly by season and sample type (P < 0.0001). The co-existence of ESBL E. coli in the same sample was associated with increased percent resistance of Salmonella to Ampicillin, Chloramphenicol, Sulfisoxazole, Streptomycin, and Tetracycline. We presumed that the abattoir environment might have played a great role in the persistence and dissemination of resistant bacteria to sheep as they arrive at the abattoir. In conclusion, our study reaffirms that sheep and their abattoir environment act as important reservoirs of AMR ESBL E. coli and MDR Salmonella in the U.S. Further studies are required to determine associated public health risks.}, journal={International Journal of Food Microbiology}, publisher={Elsevier BV}, author={Atlaw, N.A. and Keelara, S. and Correa, M. and Foster, D. and Gebreyes, W. and Aidara-Kane, A. and Harden, L. and Thakur, S. and Fedorka-Cray, P.J.}, year={2022}, month={Feb}, pages={109516} }
 @article{vliet_thakur_prada_mehat_la ragione_2022, title={Genomic Screening of Antimicrobial Resistance Markers in UK and US Campylobacter Isolates Highlights Stability of Resistance over an 18-Year Period}, volume={4}, ISSN={["1098-6596"]}, DOI={10.1128/aac.01687-21}, abstractNote={Campylobacter jejuni and Campylobacter coli are important bacterial causes of human foodborne illness. Despite several years of reduced antibiotics usage in livestock production in the United Kingdom (UK) and United States (US), a high prevalence of antimicrobial resistance (AMR) persists in Campylobacter. ABSTRACT Campylobacter jejuni and Campylobacter coli are important bacterial causes of human foodborne illness. Despite several years of reduced antibiotics usage in livestock production in the United Kingdom (UK) and United States (US), a high prevalence of antimicrobial resistance (AMR) persists in Campylobacter. Both countries have instigated genome sequencing-based surveillance programs for Campylobacter, and in this study, we have identified AMR genes in 32,256 C. jejuni and 8,776 C. coli publicly available genome sequences to compare the prevalence and trends of AMR in Campylobacter isolated in the UK and US between 2001 and 2018. AMR markers were detected in 68% of C. coli and 53% of C. jejuni isolates, with 15% of C. coli isolates being multidrug resistant (MDR), compared to only 2% of C. jejuni isolates. The prevalence of aminoglycoside, macrolide, quinolone, and tetracycline resistance remained fairly stable from 2001 to 2018 in both C. jejuni and C. coli, but statistically significant differences were observed between the UK and US. There was a statistically significant higher prevalence of aminoglycoside and tetracycline resistance for US C. coli and C. jejuni isolates and macrolide resistance for US C. coli isolates. In contrast, UK C. coli and C. jejuni isolates showed a significantly higher prevalence of quinolone resistance. Specific multilocus sequence type (MLST) clonal complexes (e.g., ST-353/464) showed >95% quinolone resistance. This large-scale comparison of AMR prevalence has shown that the prevalence of AMR remains stable for Campylobacter in the UK and the US. This suggests that antimicrobial stewardship and restricted antibiotic usage may help contain further expansion of AMR prevalence in Campylobacter but are unlikely to reduce it in the short term.}, journal={ANTIMICROBIAL AGENTS AND CHEMOTHERAPY}, author={Vliet, Arnoud H. M. and Thakur, Siddhartha and Prada, Joaquin M. and Mehat, Jai W. and La Ragione, Roberto M.}, year={2022}, month={Apr} }
 @article{dieye_hull_wane_harden_fall_sambe-ba_seck_fedorka-cray_thakur_2022, title={Genomics of human and chicken Salmonella isolates in Senegal: Broilers as a source of antimicrobial resistance and potentially invasive nontyphoidal salmonellosis infections}, volume={17}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0266025}, abstractNote={Salmonella enterica is the most common foodborne pathogen worldwide. It causes two types of diseases, a self-limiting gastroenteritis and an invasive, more threatening, infection. Salmonella gastroenteritis is caused by several serotypes and is common worldwide. In contrast, invasive salmonellosis is rare in high-income countries (HIC) while frequent in low- and middle-income countries (LMIC), especially in sub-Saharan Africa (sSA). Invasive Nontyphoidal Salmonella (iNTS), corresponding to serotypes other than Typhi and Paratyphi, have emerged in sSA and pose a significant risk to public health. We conducted a whole-genome sequence (WGS) analysis of 72 strains of Salmonella isolated from diarrheic human patients and chicken meat sold in multipurpose markets in Dakar, Senegal. Antimicrobial susceptibility testing combined with WGS data analysis revealed frequent resistance to fluoroquinolones and the sulfamethoxazole-trimethoprim combination that are among the most used treatments for invasive Salmonella. In contrast, resistance to the historical first-line drugs chloramphenicol and ampicillin, and to cephalosporins was rare. Antimicrobial resistance (AMR) was lower in clinical isolates compared to chicken strains pointing to the concern posed by the excessive use of antimicrobials in farming. Phylogenetic analysis suggested possible transmission of the emerging multidrug resistant (MDR) Kentucky ST198 and serotype Schwarzengrund from chicken to human. These results stress the need for active surveillance of Salmonella and AMR in order to address invasive salmonellosis caused by nontyphoidal Salmonella strains and other important bacterial diseases in sSA.}, number={3}, journal={PLOS ONE}, author={Dieye, Yakhya and Hull, Dawn M. and Wane, Abdoul Aziz and Harden, Lyndy and Fall, Cheikh and Sambe-Ba, Bissoume and Seck, Abdoulaye and Fedorka-Cray, Paula J. and Thakur, Siddhartha}, year={2022}, month={Mar} }
 @article{medugu_aworh_iregbu_nwajiobi-princewill_abdulraheem_hull_harden_singh_obaro_egwuenu_et al._2022, title={Molecular characterization of multi drug resistant Escherichia coli isolates at a tertiary hospital in Abuja, Nigeria}, volume={12}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/s41598-022-19289-z}, DOI={10.1038/s41598-022-19289-z}, abstractNote={Abstract Infections caused by multi-drug resistant Escherichia coli cause significant morbidity and mortality especially in developing countries. In this study, we describe the molecular characteristics of E. coli isolated from clinical specimens and the patients’ outcomes. Phenotypic methods were used in the identification and antimicrobial susceptibility testing of E. coli from clinical specimens from a tertiary hospital in Abuja, Nigeria. Whole genome sequencing was used to describe the antimicrobial resistance genes, serotypes, sequence types/clonal complexes, and mobile genetic elements. The mean age of the patients was 20.3 years with 70.1% females and majority of isolates 75% from urine, 21% from blood cultures, and 3% each from cerebrospinal fluid and endo-cervical swabs. Of the 107 non-duplicate E. coli isolates, 101 (94.3%) were resistant to ampicillin, 95 (88.8%) to trimethoprim/sulfamethoxazole, 86 (80.4%) to ceftriaxone, 60 (56.1%) to gentamicin, and eight (7.5%) to meropenem. There were 102 (95.3%) isolates that were multi-drug resistant (MDR). Expression of Extended Spectrum Beta Lactamase (ESBL) phenotype was detected in 54 (50%) and bla CTX-M-15 genes detected in 75 (70.1%) isolates. The carbapenemase genes bla NDM-1 and bla NDM-5 were detected in six (5.6%), while the AmpC gene- bla CMY-2 , was detected in seven (6.5%) isolates. Two (1.9%) isolates simultaneously harboured the bla OXA-1 , bla CMY-2 , bla CTX-M-15 , and bla NDM-5 genes. In total, 35 sequence types (STs) were found with the majority being ST131 (n = 23; 21.5%). The most common serotype was O25:H4 associated with all 23 strains of ST131, followed by O1:H6/ST648 (n = 6). The ST410, ST671, and ST101 strains displayed phenotypic resistance to wide array of antibiotic classes and harbored high numbers of antibiotic resistance genes via in-silico analysis. The ST410 strain in particular harbored a higher number of antibiotic resistance genes and was phenotypically resistant to a wider array of antibiotics. Four pairs of isolates were closely related with three isolates (ST131, ST38, ST652) having a pairwise SNP difference of zero. 71/72 75/76 52/14. The MDR E. coli lineages circulating in this setting pose a clinical and public health threat as they can hinder effective prevention and management of infections. The genetic diversity and MDR E. coli with the emergence of ST410 and ST101 clones is concerning because of the potential for rapid dissemination in hospitals and communities- further increasing the problems of antibiotic resistance. Continuous routine surveillance of E. coli infections for AMR in hospitals becomes imperative, aimed at development of effective antimicrobial stewardship programs, facilitating prudent use of antimicrobial agents, and limiting dissemination of resistant strains.}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Medugu, Nubwa and Aworh, Mabel Kamweli and Iregbu, Kenneth and Nwajiobi-Princewill, Philip and Abdulraheem, Khadija and Hull, Dawn M. and Harden, Lyndy and Singh, Pallavi and Obaro, Stephen and Egwuenu, Abiodun and et al.}, year={2022}, month={Sep} }
 @article{hull_harrell_harden_thakur_2022, title={Multidrug resistance and virulence genes carried by mobile genomic elements in Salmonella enterica isolated from live food animals, processed, and retail meat in North Carolina, 2018-2019}, volume={378}, ISSN={["1879-3460"]}, DOI={10.1016/j.ijfoodmicro.2022.109821}, abstractNote={An estimated 1000,000 domestic salmonellosis cases are attributed to food as a vehicle of exposure. Among Food Safety and Inspection Service (FSIS)-regulated products, approximately 360,000 salmonellosis cases are associated with consumption of meat, poultry, and egg products. Salmonella vaccination programs instituted in U.S. poultry, cattle, and swine production have effectively reduced the prevalence of common Salmonella enterica serotypes Typhimurium, Enteritidis, Choleraesuis (swine), and Dublin (cattle) in the past several years, with some evidence of cross-immunity to other serovars. This study investigated S. enterica (n = 741) from live food animals, meat carcasses at production, and retail meat in North Carolina collected January 2018 to December 2019. Whole-genome sequencing (WGS) and bioinformatics were used to molecularly characterize and compare AMR profiles, virulence, and phylogeny of Salmonella at three stages of food processing. Multidrug-resistant (MDR) plasmids identified also contained the integrase recombinase virulence factor int associated with mobile integrons, qacE conferred quaternary ammonia resistance, and diverse AMR profiles. MDR Plasmid IncFIB(K)_1_Kpn3_JN233704, with virulence factor int had 51 different AMR profiles within poultry S. enterica Infantis isolates. Plasmid-mediated virulence factors also appear to provide a fitness advantage, as the dominant S. enterica serotype Kentucky in chicken retail meat held the greatest diversity of plasmid-mediated colicin virulence genes which are often upregulated by environmental stressors and confer a competitive advantage. Mobile genetic element recombination is increasing pathogen fitness in the food chain through the dissemination of virulence factors and resistance genes to clinically important antibiotics, posing a significant threat to human health.}, journal={INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY}, author={Hull, Dawn M. and Harrell, Erin and Harden, Lyndy and Thakur, Siddhartha}, year={2022}, month={Oct} }
 @article{young_domesle_mcdonald_lozinak_laksanalamai_harrell_thakur_kabera_strain_mcdermott_et al._2022, title={Toward the Adoption of Loop-Mediated Isothermal Amplification for Salmonella Screening at the National Antimicrobial Resistance Monitoring System's Retail Meat Sites}, volume={19}, ISSN={["1556-7125"]}, DOI={10.1089/fpd.2022.0047}, abstractNote={The National Antimicrobial Resistance Monitoring System (NARMS) is a One Health program in the United States that collects data on antimicrobial resistance in enteric bacteria from humans, animals, and the environment. Salmonella is a major pathogen tracked by the NARMS retail meat arm but currently lacks a uniform screening method. We evaluated a loop-mediated isothermal amplification (LAMP) assay for the rapid screening of Salmonella from 69 NARMS retail meat and poultry samples. All samples were processed side by side for culture isolation using two protocols, one from NARMS and the other one described in the U.S. Food and Drug Administration's Bacteriological Analytical Manual (BAM). Overall, 10 (14.5%) samples screened positive by the Salmonella LAMP assay. Of those, six were culture-confirmed by the NARMS protocol and six by the BAM method with overlap on four samples. No Salmonella isolates were recovered from samples that screened negative with LAMP. These results suggested 100% sensitivity for LAMP in reference to culture. Antimicrobial susceptibility testing and whole-genome sequencing analysis confirmed identities of these isolates. Using the BAM protocol, all Salmonella isolates were recovered from samples undergoing Rappaport-Vassiliadis medium selective enrichment and presumptive colonies (n = 130) were dominated by Hafnia alvei (44.6%), Proteus mirabilis (22.3%), and Morganella morganii (9.9%) based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. This method comparison study clearly demonstrated the benefit of a rapid, robust, and highly sensitive molecular screening method in streamlining the laboratory workflow. Fourteen NARMS retail meat sites further verified the performance of this assay using a portion of their routine samples, reporting an overall specificity of 98.8% and sensitivity of 90%. As of July 2022, the vast majority of NARMS retail meat sites have adopted the Salmonella LAMP assay for rapid screening of Salmonella in all samples.}, number={11}, journal={FOODBORNE PATHOGENS AND DISEASE}, author={Young, Shenia R. and Domesle, Kelly J. and McDonald, Ryan C. and Lozinak, Kristen A. and Laksanalamai, Pongpan and Harrell, Erin and Thakur, Siddhartha and Kabera, Claudine and Strain, Errol A. and McDermott, Patrick F. and et al.}, year={2022}, month={Nov}, pages={758–766} }
 @article{glaize_hull_raymond_vliet_gutierrez-rodriguez_thakur_2022, title={Tracking the Transmission of Antimicrobial-Resistant Non-O157 Escherichia coli and Salmonella Isolates at the Interface of Food Animals and Fresh Produce from Agriculture Operations Using Whole-Genome Sequencing}, volume={8}, ISSN={["1556-7125"]}, DOI={10.1089/fpd.2022.0016}, abstractNote={An increasing number of outbreaks are caused by foodborne pathogens such as Escherichia coli and Salmonella, which often harbor antimicrobial resistance (AMR) genes. We previously demonstrated the transmission of pathogens from animal operations to produce fields on sustainable farms, which illustrated an urgent need to develop and implement novel prevention methods and remediation practices such as the vegetative buffer zone (VBZ) to prevent this movement. The focus of this study was to use whole-genome sequencing (WGS) to characterize the AMR, virulence, and single-nucleotide polymorphism profile of 15 Salmonella and 128 E. coli isolates collected from small-scale dairy and poultry farms on a research station in North Carolina. Phenotypically, seven E. coli and three Salmonella isolates displayed resistance to antibiotics such as tetracycline (n = 4), ampicillin (n = 4), nalidixic acid (n = 3), chloramphenicol (n = 2), sulfisoxazole (n = 1), and streptomycin (n = 1). A single E. coli isolate was found to be resistant to five different antibiotic class types and possessed the blaTEM-150 resistance gene. Virulence genes that facilitate toxin production and cell invasion were identified. Mauve analysis of the E. coli isolates identified seven clusters (dairy-six and poultry-one) indicating that transmission is occurring from animal operations to fresh produce fields and the surrounding environment when the VBZ is denudated. This suggests that the VBZ is a useful barrier to reducing the transmission of enteric pathogens in agricultural systems. Our study demonstrates the prevalence of AMR and virulence genes on small-scale sustainable farms and highlights the advantage of using WGS to assess the impact of the VBZ to reduce the transmission of E. coli and Salmonella.}, journal={FOODBORNE PATHOGENS AND DISEASE}, author={Glaize, Ayanna and Hull, Dawn and Raymond, Luke and Vliet, Arnoud H. M. and Gutierrez-Rodriguez, Eduardo and Thakur, Siddhartha}, year={2022}, month={Aug} }
 @article{hull_harrell_vliet_correa_thakur_2021, title={Antimicrobial resistance and interspecies gene transfer in Campylobacter coli and Campylobacter jejuni isolated from food animals, poultry processing, and retail meat in North Carolina, 2018-2019}, volume={16}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0246571}, abstractNote={The Center for Disease Control and Prevention identifies antimicrobial resistant (AMR) Campylobacter as a serious threat to U.S. public health due to high community burden, increased transmissibility, and limited treatability. The National Antimicrobial Resistance Monitoring System (NARMS) plays an important role in surveillance of AMR bacterial pathogens in humans, food animals and retail meats. This study investigated C. coli and C. jejuni from live food animals, poultry carcasses at production, and retail meat in North Carolina between January 2018-December 2019. Whole genome sequencing and bioinformatics were used for phenotypic and genotypic characterization to compare AMR profiles, virulence factors associated with Guillain-Barré Syndrome (GBS) (neuABC and cst-II or cst-III), and phylogenic linkage between 541 Campylobacter isolates (C. coli n = 343, C. jejuni n = 198). Overall, 90.4% (489/541) Campylobacter isolates tested positive for AMR genes, while 43% (233/541) carried resistance genes for three or more antibiotic classes and were classified molecularly multidrug resistant. AMR gene frequencies were highest against tetracyclines (64.3%), beta-lactams (63.6%), aminoglycosides (38.6%), macrolides (34.8%), quinolones (24.4%), lincosamides (13.5%), and streptothricins (5%). A total of 57.6% (114/198) C. jejuni carried GBS virulence factors, while three C. coli carried the C. jejuni-like lipooligosaccharide locus, neuABC and cst-II. Further evidence of C. coli and C. jejuni interspecies genomic exchange was observed in identical multilocus sequence typing, shared sequence type (ST) 7818 clonal complex 828, and identical species-indicator genes mapA, ceuE, and hipO. There was a significant increase in novel STs from 2018 to 2019 (2 in 2018 and 21 in 2019, p<0.002), illustrating variable Campylobacter genomes within food animal production. Introgression between C. coli and C. jejuni may aid pathogen adaption, lead to higher AMR and increase Campylobacter persistence in food processing. Future studies should further characterize interspecies gene transfer and evolutionary trends in food animal production to track evolving risks to public health.}, number={2}, journal={PLOS ONE}, author={Hull, Dawn M. and Harrell, Erin and Vliet, Arnoud H. M. and Correa, Maria and Thakur, Siddhartha}, year={2021}, month={Feb} }
 @article{vearing_wilson-barnes_charlton_probst_ribeiro_thakur_mendes_lanham-new_hart_2021, title={Association between dietary vitamin D and calcium intakes and bone health outcomes in UK African-Caribbean women}, volume={80}, ISSN={["1475-2719"]}, DOI={10.1017/S0029665121000331}, abstractNote={An abstract is not available for this content. As you have access to this content, full HTML content is provided on this page. A PDF of this content is also available in through the ‘Save PDF’ action button.}, number={OCE1}, journal={PROCEEDINGS OF THE NUTRITION SOCIETY}, author={Vearing, R. M. and Wilson-Barnes, S. and Charlton, K. and Probst, Y. and Ribeiro, H. and Thakur, S. and Mendes, M. and Lanham-New, S. A. and Hart, K. H.}, year={2021} }
 @article{meredith_kularatna_nagaro_nagahawatte_bodinayake_kurukulasooriya_wijesingha_harden_piyasiri_hammouda_et al._2021, title={Colonization with multidrug-resistant Enterobacteriaceae among infants: an observational study in southern Sri Lanka}, volume={10}, ISSN={["2047-2994"]}, DOI={10.1186/s13756-021-00938-3}, abstractNote={The timing of and risk factors for intestinal colonization with multidrug-resistant Enterobacteriaceae (MDRE) are still poorly understood in areas with high MDRE carriage. We determined the prevalence, timing, and risk factors associated with MDRE intestinal colonization among infants in southern Sri Lanka.Women and their newborn children were enrolled within 48 h after delivery in southern Sri Lanka. Rectal swabs were collected from women and infants at enrollment and 4-6 weeks later. Enterobacteriaceae were isolated and identified as MDRE (positive for extended-spectrum β-lactamases or carbapenem resistant) using standard microbiologic procedures. We used exact methods (Fisher's exact and Kruskal-Wallis tests) and multivariable logistic regression to identify sociodemographic and clinical features associated with MDRE intestinal colonization. Whole-genome sequencing was performed on selected MDRE isolates to identify phylogroups and antibiotic resistance-encoding genes were identified with NCBI's AMRfinder tool.Overall, 199 post-partum women and 199 infants were enrolled; 148/199 (74.4%) women and 151/199 (75.9%) infants were reassessed later in the community. Twenty-four/199 (12.1%) women and 3/199 (1.5%) infants displayed intestinal colonization with MDRE at enrollment, while 26/148 (17.6%) women and 24/151 (15.9%) infants displayed intestinal colonization with MDRE at the reassessment. While there were no risk factors associated with infant colonization at enrollment, multivariable analysis indicated that risk factors for infant colonization at reassessment included mother colonized at enrollment (aOR = 3.62) or reassessment (aOR = 4.44), delivery by Cesarean section (aOR = 2.91), and low birth weight (aOR = 5.39). Of the 20 MDRE isolates from infants that were sequenced, multilocus sequence typing revealed that 6/20 (30%) were clustered on the same branch as MDRE isolates found in the respective mothers. All sequenced isolates for mothers (47) and infants (20) had at least one ESBL-producing gene. Genes encoding fosfomycin resistance were found in 33/47 (70%) of mothers' isolates and 16/20 (80%) of infants' isolates and genes encoding resistance to colistin were found in one (2%) mother's isolate.Our results suggest that a substantial proportion of infants undergo MDRE intestinal colonization within 6 weeks of birth, potentially due to postnatal rather than intranatal transmission.}, number={1}, journal={ANTIMICROBIAL RESISTANCE AND INFECTION CONTROL}, author={Meredith, Hannah R. and Kularatna, Sarath and Nagaro, Kristin and Nagahawatte, Ajith and Bodinayake, Champica and Kurukulasooriya, Ruvini and Wijesingha, Nishadhi and Harden, Lyndy B. and Piyasiri, Bhagya and Hammouda, Amr and et al.}, year={2021}, month={Apr} }
 @article{slobodiuk_niven_arthur_thakur_ercumen_2021, title={Does Irrigation with Treated and Untreated Wastewater Increase Antimicrobial Resistance in Soil and Water: A Systematic Review}, DOI={10.3390/ijerph182111046}, abstractNote={Population growth and water scarcity necessitate alternative agriculture practices, such as reusing wastewater for irrigation. Domestic wastewater has been used for irrigation for centuries in many historically low-income and arid countries and is becoming more widely used by high-income countries to augment water resources in an increasingly dry climate. Wastewater treatment processes are not fully effective in removing all contaminants, such as antimicrobial resistant bacteria (ARB) and antimicrobial resistance genes (ARGs). Literature reviews on the impact of wastewater irrigation on antimicrobial resistance (AMR) in the environment have been inconclusive and mostly focused on treated wastewater. We conducted the first systematic review to assess the impact of irrigation with both treated or untreated domestic wastewater on ARB and ARGs in soil and adjacent water bodies. We screened titles/abstracts of 3002 articles, out of which 41 were screened in full text and 26 were included in this review. Of these, thirteen investigated irrigation with untreated wastewater, and nine found a positive association with ARB/ARGs in soil. Out of thirteen studies focused on treated wastewater, six found a positive association with ARB/ARGs while six found mixed/negative associations. Our findings demonstrate that irrigation with untreated wastewater increases AMR in soil and call for precautionary action by field workers, their families, and consumers when untreated wastewater is used to irrigate crops. The effect of irrigation with treated wastewater was more variable among the studies included in our review, highlighting the need to better understand to what extent AMR is disseminated through this practice. Future research should assess factors that modify the effect of wastewater irrigation on AMR in soil, such as the degree and type of wastewater treatment, and the duration and intensity of irrigation, to inform guidelines on the reuse of wastewater for irrigation.}, journal={INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH}, author={Slobodiuk, Stacy and Niven, Caitlin and Arthur, Greer and Thakur, Siddhartha and Ercumen, Ayse}, year={2021}, month={Nov} }
 @article{aworh_kwaga_hendriksen_okolocha_thakur_2021, title={Genetic relatedness of multidrug resistant Escherichia coli isolated from humans, chickens and poultry environments}, volume={10}, ISSN={2047-2994}, url={http://dx.doi.org/10.1186/s13756-021-00930-x}, DOI={10.1186/s13756-021-00930-x}, abstractNote={Inappropriate use of antimicrobial agents in animal production has led to the development of antimicrobial resistance (AMR) in foodborne pathogens. Transmission of AMR foodborne pathogens from reservoirs, particularly chickens to the human population does occur. Recently, we reported that occupational exposure was a risk factor for multidrug-resistant (MDR) Escherichia coli (E. coli) among poultry-workers. Here we determined the prevalence and genetic relatedness among MDR E. coli isolated from poultry-workers, chickens, and poultry environments in Abuja, Nigeria. This study was conducted to address the gaps identified by the Nigerian AMR situation analysis.We conducted a cross-sectional study among poultry-workers, chickens, and poultry farm/live bird market (LBM) environments. The isolates were tested phenotypically for their antimicrobial susceptibility profiles, genotypically characterized using whole-genome sequencing (WGS) and in silico multilocus sequence types (MLST). We conducted a phylogenetic single nucleotide polymorphism (SNPs) analysis to determine relatedness and clonality among the isolates.A total of 115 (26.8%) out of 429 samples were positive for E. coli. Of these, 110 isolates were viable for phenotypic and genotypic characterization. The selection comprised 47 (42.7%) isolates from poultry-workers, 36 (32.7%) from chickens, and 27 (24.5%) from poultry-farm or LBM environments. Overall, 101 (91.8%) of the isolates were MDR conferring resistance to at least three drug classes. High frequency of resistance was observed for tetracycline (n = 102; 92.7%), trimethoprim/sulfamethoxazole (n = 93; 84.5%), streptomycin (n = 87; 79.1%) and ampicillin (n = 88; 80%). Two plasmid-mediated colistin genes-mcr-1.1 harboured on IncX4 plasmids were detected in environmental isolates. The most prevalent sequence types (ST) were ST-155 (n = 8), ST-48 (n = 8) and ST-10 (n = 6). Two isolates of human and environmental sources with a SNPs difference of 6161 originating from the same farm shared a novel ST. The isolates had similar AMR genes and plasmid replicons.MDR E.coli isolates were prevalent amongst poultry-workers, poultry, and the poultry farm/LBM environment. The emergence of MDR E. coli with novel ST in two isolates may be plasmid-mediated. Competent authorities should enforce AMR regulations to ensure prudent use of antimicrobials to limit the risk of transmission along the food chain.}, number={1}, journal={Antimicrobial Resistance & Infection Control}, publisher={Springer Science and Business Media LLC}, author={Aworh, Mabel Kamweli and Kwaga, Jacob K. P. and Hendriksen, Rene S. and Okolocha, Emmanuel C. and Thakur, Siddhartha}, year={2021}, month={Mar} }
 @article{walker_suyemoto_hull_gall_jimenez_chen_thakur_crespo_borst_2021, title={Genomic Characterization of a Nalidixic Acid-Resistant Salmonella Enteritidis Strain Causing Persistent Infections in Broiler Chickens}, volume={8}, ISSN={["2297-1769"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85115006803&partnerID=MN8TOARS}, DOI={10.3389/fvets.2021.725737}, abstractNote={Virulent strains of Salmonella enterica subsp. enterica serovar Enteritidis (SE) harbored by poultry can cause disease in poultry flocks and potentially result in human foodborne illness. Two broiler flocks grown a year apart on the same premises experienced mortality throughout the growing period due to septicemic disease caused by SE. Gross lesions predominantly consisted of polyserositis followed by yolk sacculitis, arthritis, osteomyelitis, and spondylitis. Tissues with lesions were cultured yielding 59 SE isolates. These were genotyped by Rep-PCR followed by whole-genome sequencing (WGS) of 15 isolates which were clonal. The strain, SE_TAU19, was further characterized for antimicrobial susceptibility and virulence in a broiler embryo lethality assay. SE_TAU19 was resistant to nalidixic acid and sulfadimethoxine and was virulent to embryos with 100% mortality of all challenged broiler embryos within 3.5 days. Screening the SE_TAU19 whole-genome sequence revealed seven antimicrobial resistance (AMR) genes, 120 virulence genes, and two IncF plasmid replicons corresponding to a single, serovar-specific pSEV virulence plasmid. The pef, spv, and rck virulence genes localized to the plasmid sequence assembly. We report phenotypic and genomic features of a virulent SE strain from persistently infected broiler flocks and present a workflow for SE characterization from isolate collection to genome assembly and sequence analysis. Further SE surveillance and investigation of SE virulence in broiler chickens is warranted.}, journal={FRONTIERS IN VETERINARY SCIENCE}, author={Walker, Grayson K. K. and Suyemoto, M. Mitsu and Hull, Dawn M. M. and Gall, Sesny and Jimenez, Fernando and Chen, Laura R. R. and Thakur, Siddhartha and Crespo, Rocio and Borst, Luke B. B.}, year={2021}, month={Sep} }
 @article{vearing_hart_darling_probst_olayinka_mendis_ribeiro_thakur_mendes_charlton_et al._2021, title={Global Perspective of the Vitamin D Status of African-Caribbean Populations: A Systematic Review and Meta-analysis}, volume={7}, ISSN={["1476-5640"]}, DOI={10.1038/s41430-021-00980-9}, abstractNote={Vitamin D deficiency remains a global public health issue, particularly in minority ethnic groups. This review investigates the vitamin D status (as measured by 25(OH)D and dietary intake) of the African-Caribbean population globally.A systematic review was conducted by searching key databases (PUBMED, Web of Science, Scopus) from inception until October 2019. Search terms included 'Vitamin D status' and 'African-Caribbean'. A random effects and fixed effects meta-analysis was performed by combining means and standard error of the mean.The search yielded 19 papers that included n = 5670 African-Caribbean participants from six countries. A meta-analysis found this population to have sufficient (>50 nmol/L) 25(OH)D levels at 67.8 nmol/L, 95% CI (57.9, 7.6) but poor dietary intake of vitamin D at only 3.0 µg/day, 95% CI (1.67,4.31). For those living at low latitudes 'insufficient' (as defined by study authors) 25(OH)D levels were found only in participants with type 2 diabetes and in those undergoing haemodialysis. Suboptimal dietary vitamin D intake (according to the UK recommended nutrient intake of 10 µg/day) was reported in all studies at high latitudes. Studies at lower latitudes, with lower recommended dietary intakes (Caribbean recommended dietary intake: 2.5 µg/day) found 'sufficient' intake in two out of three studies.25(OH)D sufficiency was found in African-Caribbean populations at lower latitudes. However, at higher latitudes, 25(OH)D deficiency and low dietary vitamin D intake was prevalent.}, journal={EUROPEAN JOURNAL OF CLINICAL NUTRITION}, author={Vearing, Rebecca M. and Hart, Kathryn H. and Darling, Andrea L. and Probst, Yasmine and Olayinka, Aminat S. and Mendis, Jeewaka and Ribeiro, Helena and Thakur, Siddhartha and Mendes, Marcela and Charlton, Karen and et al.}, year={2021}, month={Jul} }
 @article{atlaw_keelara_correa_foster_gebreyes_aidara-kane_harden_thakur_fedorka-cray_2021, title={Identification of CTX-M type ESBL E. coli from sheep and their abattoir environment using whole-genome sequencing}, volume={10}, ISSN={["2076-0817"]}, url={https://www.mdpi.com/2076-0817/10/11/1480}, DOI={10.3390/pathogens10111480}, abstractNote={Widespread dissemination of extended-spectrum beta-lactamase (ESBL) Escherichia coli (E. coli) in animals, retail meats, and patients has been reported worldwide except for limited information on small ruminants. Our study focused on the genotypic characterization of ESBL E. coli from healthy sheep and their abattoir environment in North Carolina, USA. A total of 113 ESBL E. coli isolates from sheep (n = 65) and their abattoir environment (n = 48) were subjected to whole-genome sequencing (WGS). Bioinformatics tools were used to analyze the WGS data. Multiple CTX-M-type beta-lactamase genes were detected, namely blaCTX-M-1, blaCTX-M-14, blaCTX-M-15, blaCTX-M-27, blaCTX-M-32, blaCTX-M-55, and blaCTX-M-65. Other beta-lactamase genes detected included blaCMY-2, blaTEM-1A/B/C, and blaCARB-2. In addition, antimicrobial resistance (AMR) genes and/or point mutations that confer resistance to quinolones, aminoglycosides, phenicols, tetracyclines, macrolides, lincosamides, and folate-pathway antagonists were identified. The majority of the detected plasmids were shared between isolates from sheep and the abattoir environment. Sequence types were more clustered around seasonal sampling but dispersed across sample types. In conclusion, our study reported wide dissemination of ESBL E. coli in sheep and the abattoir environment and associated AMR genes, point mutations, and plasmids. This is the first comprehensive AMR and WGS report on ESBL E. coli from sheep and abattoir environments in the United States.}, number={11}, journal={Pathogens}, publisher={MDPI AG}, author={Atlaw, N.A. and Keelara, S. and Correa, M. and Foster, D. and Gebreyes, W. and Aidara-Kane, A. and Harden, L. and Thakur, S. and Fedorka-Cray, P.J.}, year={2021}, pages={1480} }
 @article{tomczyk_taylor_brown_kraker_el-saed_alshamrani_hendriksen_jacob_lofmark_perovic_et al._2021, title={Impact of the COVID-19 pandemic on the surveillance, prevention and control of antimicrobial resistance: a global survey}, volume={76}, ISSN={["1460-2091"]}, DOI={10.1093/jac/dkab300}, abstractNote={Abstract Objectives The COVID-19 pandemic has had a substantial impact on health systems. The WHO Antimicrobial Resistance (AMR) Surveillance and Quality Assessment Collaborating Centres Network conducted a survey to assess the effects of COVID-19 on AMR surveillance, prevention and control. Methods From October to December 2020, WHO Global Antimicrobial Resistance and Use Surveillance System (GLASS) national focal points completed a questionnaire, including Likert scales and open-ended questions. Data were descriptively analysed, income/regional differences were assessed and free-text questions were thematically analysed. Results Seventy-three countries across income levels participated. During the COVID-19 pandemic, 67% reported limited ability to work with AMR partnerships; decreases in funding were frequently reported by low- and middle-income countries (LMICs; P < 0.01). Reduced availability of nursing, medical and public health staff for AMR was reported by 71%, 69% and 64%, respectively, whereas 67% reported stable cleaning staff availability. The majority (58%) reported reduced reagents/consumables, particularly LMICs (P < 0.01). Decreased numbers of cultures, elective procedures, chronically ill admissions and outpatients and increased ICU admissions reported could bias AMR data. Reported overall infection prevention and control (IPC) improvement could decrease AMR rates, whereas increases in selected inappropriate IPC practices and antimicrobial prescribing could increase rates. Most did not yet have complete data on changing AMR rates due to COVID-19. Conclusions This was the first survey to explore the global impact of COVID-19 on AMR among GLASS countries. Responses highlight important actions to help ensure that AMR remains a global health priority, including engaging with GLASS to facilitate reliable AMR surveillance data, seizing the opportunity to develop more sustainable IPC programmes, promoting integrated antibiotic stewardship guidance, leveraging increased laboratory capabilities and other system-strengthening efforts.}, number={11}, journal={JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY}, author={Tomczyk, Sara and Taylor, Angelina and Brown, Allison and Kraker, Marlieke E. A. and El-Saed, Aiman and Alshamrani, Majid and Hendriksen, Rene S. and Jacob, Megan and Lofmark, Sonja and Perovic, Olga and et al.}, year={2021}, month={Nov}, pages={3045–3058} }
 @article{king_schmidt_thakur_fedorka-cray_keelara_harden_essack_2021, title={Resistome of a carbapenemase-producing novel ST232 Klebsiella michiganensis isolate from urban hospital effluent in South Africa}, volume={24}, ISSN={["2213-7173"]}, DOI={10.1016/j.jgar.2021.01.004}, abstractNote={Klebsiella michiganensis is an emerging pathogen implicated in nosocomial infections. Here we report on the resistome, virulome and mobilome of a carbapenemase-producing K. michiganensis isolate from urban hospital effluent in Pietermaritzburg, KwaZulu-Natal, South Africa. Klebsiella sp. isolate KP124 was originally isolated from the final effluent of an urban tertiary hospital in Pietermaritzburg, KwaZulu-Natal.Following phenotypic characterisation and antibiotic susceptibility testing, the genome of carbapenemase-producing isolate KP124 was sequenced using an Illumina MiSeq platform, de novo assembled and analysed using established bioinformatics tools.The draft genome of strain KP124 was 6 544 586 bp in length, comprising 203 contigs >200 bp. Following confirmation of isolate KP124 as K. michiganensis using reference genomes, the blaOXA-181 carbapenemase gene as well as 11 additional genes encoding resistance against β-lactams, aminoglycosides, fluoroquinolones and sulfonamides were detected. Virulence factors enabling iron acquisition and cell adherence, capsule locus type and plasmid replicon types were identified.This study represents the first report of an OXA-181 carbapenemase-producing K. michiganensis isolate from hospital effluent in South Africa. The presence of such a strain in the environment owing to the absence of hospital effluent treatment presents a potential risk to informal communities that may use contaminated surface water domestically.}, journal={JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE}, author={King, T. L. and Schmidt, S. and Thakur, S. and Fedorka-Cray, P. and Keelara, S. and Harden, L. and Essack, S. Y.}, year={2021}, month={Mar}, pages={321–324} }
 @article{glaize_young_harden_gutierrez-rodriguez_thakur_2021, title={The effect of vegetation barriers at reducing the transmission of Salmonella and Escherichia coli from animal operations to fresh produce}, volume={347}, ISSN={["1879-3460"]}, DOI={10.1016/j.ijfoodmicro.2021.109196}, abstractNote={Due to the recent outbreaks of Salmonella and Escherichia coli in fresh produce in the United States, the transfer of foodborne pathogens between animal feeding operations and fresh produce continues to be a considerable risk. The purpose of this study was to determine if the establishment of a vegetation barrier (VB) on small-scale sustainable farms could prevent the transmission of Salmonella and E. coli to nearby fresh produce fields. A 5-layer VB (31 × 49 m) was constructed between a dairy farm, a poultry farm, and a nearby produce field. Fresh produce (i.e., romaine lettuce and tomato), animal feces, and environmental (i.e., air, soil, and barrier) samples were collected for 15 months from 2018 to 2019. Four replicates of soil and fresh produce samples were taken from three plots located 10 m, 61 m, and 122 m away from the respective animal locations and processed for Salmonella and E. coli. Air and vegetative strip samples were sampled at 15-day intervals. Multiple colonies were processed from each positive sample, and a total of 143 positive Salmonella (n = 15) and E. coli (n = 128) isolates were retrieved from the soil, produce, air, and fecal samples. Interestingly, 18.2% of the Salmonella and E. coli isolates (n = 26) were recovered from fresh produce (n = 9) samples. Surprisingly, Salmonella isolates (n = 9) were only found in fecal (n = 3) samples collected from the dairy pasture. Data analysis suggests that the VB is an effective tool at reducing the transmission of E. coli and Salmonella from animal farms to fresh produce fields. However, based on phenotypic and genotypic testing, it is clear that fecal samples from animal farms are not the only source of pathogen contamination. This indicates that the environment (e.g., soil and wind), as well as the initial setup of the farm (e.g., proximity to service roads and produce plot placement), can contribute to the contamination of fresh produce. Our study recommends the need for more effective bioremediation and prevention control measures to use in conjunction with VBs to reduce pathogen transmission.}, journal={INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY}, author={Glaize, Ayanna and Young, Morgan and Harden, Lyndy and Gutierrez-Rodriguez, Eduardo and Thakur, Siddhartha}, year={2021}, month={Jun} }
 @article{callahan_grinevich_thakur_balamotis_ben yehezkel_2021, title={Ultra-accurate microbial amplicon sequencing with synthetic long reads}, volume={9}, ISSN={["2049-2618"]}, url={https://doi.org/10.1186/s40168-021-01072-3}, DOI={10.1186/s40168-021-01072-3}, abstractNote={Out of the many pathogenic bacterial species that are known, only a fraction are readily identifiable directly from a complex microbial community using standard next generation DNA sequencing. Long-read sequencing offers the potential to identify a wider range of species and to differentiate between strains within a species, but attaining sufficient accuracy in complex metagenomes remains a challenge.Here, we describe and analytically validate LoopSeq, a commercially available synthetic long-read (SLR) sequencing technology that generates highly accurate long reads from standard short reads.LoopSeq reads are sufficiently long and accurate to identify microbial genes and species directly from complex samples. LoopSeq perfectly recovered the full diversity of 16S rRNA genes from known strains in a synthetic microbial community. Full-length LoopSeq reads had a per-base error rate of 0.005%, which exceeds the accuracy reported for other long-read sequencing technologies. 18S-ITS and genomic sequencing of fungal and bacterial isolates confirmed that LoopSeq sequencing maintains that accuracy for reads up to 6 kb in length. LoopSeq full-length 16S rRNA reads could accurately classify organisms down to the species level in rinsate from retail meat samples, and could differentiate strains within species identified by the CDC as potential foodborne pathogens.The order-of-magnitude improvement in length and accuracy over standard Illumina amplicon sequencing achieved with LoopSeq enables accurate species-level and strain identification from complex- to low-biomass microbiome samples. The ability to generate accurate and long microbiome sequencing reads using standard short read sequencers will accelerate the building of quality microbial sequence databases and removes a significant hurdle on the path to precision microbial genomics. Video abstract.}, number={1}, journal={MICROBIOME}, author={Callahan, Benjamin J. and Grinevich, Dmitry and Thakur, Siddhartha and Balamotis, Michael A. and Ben Yehezkel, Tuval}, year={2021}, month={Jun} }
 @article{balbin_hull_guest_nichols_dunn_thakur_2020, title={Antimicrobial resistance and virulence factors profile of Salmonella spp. and Escherichia coli isolated from different environments exposed to anthropogenic activity}, volume={22}, ISSN={["2213-7173"]}, url={http://dx.doi.org/10.1016/j.jgar.2020.05.016}, DOI={10.1016/j.jgar.2020.05.016}, abstractNote={The study aimed to identify the antimicrobial resistance (AMR) determinants and virulence factors in Salmonella spp. and Escherichia coli recovered from different anthropogenic areas in North Carolina. Soil samples were collected from different anthropogenic areas, urban and natural. The minimum inhibitory concentration (MIC) was determined by using the broth microdilution method. Whole-genome sequencing (WGS) and analysis were done to identify the AMR determinants and virulence factors. A higher prevalence of Salmonella spp. and E. coli was detected in the urban environment. The Salmonella spp. isolates showed resistance to sulfisoxazole and streptomycin, whereas E. coli was resistant to sulfisoxazole, cefoxitin and ampicillin. Salmonella serotypes Schwarzengrund and Mississippi were identified based on WGS analysis. Aminoglycoside resistance genes and IncFIB and IncFIC(FII) plasmids were detected among Salmonella spp. In general, E. coli was predominated by isolates from phylogroups B1, B2 and D. The multidrug transporter mdfA gene was detected in most of the E. coli from both the urban (100%) and natural (84.5%) environments. The FosA7 gene was detected in an isolate from a residential yard. The pCoo and pB171 plasmids were detected in an urban environment; col(156) and pHN7A8 plasmids were detected in natural environments. The detection of AMR determinants and virulence factors in these bacteria is significant in understanding the occurrence and even the development of AMR. The presence of these determinants in different anthropogenic areas suggests the need to conduct longitudinal studies for comparing the profile of pathogens across different environments.}, journal={JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE}, author={Balbin, Michelle M. and Hull, Dawn and Guest, Chloe and Nichols, Lauren and Dunn, Robert and Thakur, Siddhartha}, year={2020}, month={Sep}, pages={578–583} }
 @article{monte_sellera_lopes_keelara_landgraf_greene_fedorka-cray_thakur_2020, title={Class 1 integron-borne cassettes harboring blaCARB-2 gene in multidrug-resistant and virulent Salmonella Typhimurium ST19 strains recovered from clinical human stool samples, United States}, volume={15}, url={http://dx.doi.org/10.1371/journal.pone.0240978}, DOI={10.1371/journal.pone.0240978}, abstractNote={International lineages, such as Salmonella Typhimurium sequence type (ST) 19, are most often associated with foodborne diseases and deaths in humans. In this study, we compared the whole-genome sequences of five S. Typhimurium strains belonging to ST19 recovered from clinical human stool samples in North Carolina, United States. Overall, S. Typhimurium strains displayed multidrug-resistant profile, being resistance to critically and highly important antimicrobials including ampicillin, ticarcillin/clavulanic acid, streptomycin and sulfisoxazole, chloramphenicol, tetracycline, respectively. Interestingly, all S. Typhimurium strains carried class 1 integron (intl1) and we were able to describe two genomic regions surrounding blaCARB-2 gene, size 4,062 bp and 4,422 bp for S. Typhimurium strains (HS5344, HS5437, and HS5478) and (HS5302 and HS5368), respectively. Genomic analysis for antimicrobial resistome confirmed the presence of clinically important genes, including blaCARB-2, aac(6’)-Iaa, aadA2b, sul1, tetG, floR, and biocide resistance genes (qacEΔ1). S. Typhimurium strains harbored IncFIB plasmid containing spvRABCD operon, as well as rck and pef virulence genes, which constitute an important apparatus for spreading the virulence plasmid. In addition, we identified several virulence genes, chromosomally located, while the phylogenetic analysis revealed clonal relatedness among these strains with S. enterica isolated from human and non-human sources obtained in European and Asian countries. Our results provide new insights into this unusual class 1 integron in virulent S. Typhimurium strains that harbors a pool of genes acting as potential hotspots for horizontal gene transfer providing readily adaptation to new surrounds, as well as being crucially required for virulence in vivo. Therefore, continuous genomic surveillance is an important tool for safeguarding human health.}, number={10}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Monte, Daniel F. M. and Sellera, Fábio P. and Lopes, Ralf and Keelara, Shivaramu and Landgraf, Mariza and Greene, Shermalyn and Fedorka-Cray, Paula J. and Thakur, Siddhartha}, editor={Karunasagar, IddyaEditor}, year={2020}, month={Oct}, pages={e0240978} }
 @article{mendes_charlton_thakur_ribeiro_lanham-new_2020, title={Future perspectives in addressing the global issue of vitamin D deficiency}, volume={79}, ISSN={["1475-2719"]}, DOI={10.1017/S0029665119001538}, abstractNote={Vitamin D is a fundamentally critical nutrient that the human body requires to function properly. It plays an important role in musculoskeletal health due to its involvement in the regulation of calcium and phosphorus. Having a low level of vitamin D in the body may be detrimental for a wide range of health outcomes, including risk of osteoporotic and stress fractures, risk of CVD and some cancers, and lowering of the capability of the immune system. Vitamin D is an unusual nutrient; it is not a vitamin, in the true sense of the word but a pro-hormone. The main source of vitamin D is UV exposure, not dietary intake. Interestingly, there are two forms of vitamin D, vitamin D2and vitamin D3, both of which are metabolised into 25-hydroxyvitamin D (25(OH)D) in the liver, the biomarker of vitamin D status. Vitamin D deficiency is a global public health problem, especially amongst older people and ethnic minority groups. The newest publication from the UK Government's Public Health England Department recommends that vitamin D intake should be 10 μg daily and this recommendation compares well (albeit lower) with other guidelines such as the Institute of Medicine recommendation of 15 μg for those aged 1–70 years and 20 μg for those 70 years or over. Few countries, however, have a specific vitamin D policy to prevent deficiency in populations. Finland leads the way, demonstrating impressive results in reducing population-level vitamin D deficiency through mandatory food fortification programmes. Collaboration between academia, government and industry, including countries from varying latitudes, is essential to identify long-term solutions to the global issue of vitamin D deficiency. This paper provides a narrative review of the evidence related to the role of vitamin D deficiency in health outcomes, outlines controversies regarding setting levels of adequacy, identifies the prevalence of vitamin D deficiency across the globe, and identifies population-level strategies adopted by countries to prevent vitamin D deficiency.}, number={2}, journal={PROCEEDINGS OF THE NUTRITION SOCIETY}, author={Mendes, M. M. and Charlton, K. and Thakur, S. and Ribeiro, H. and Lanham-New, S. A.}, year={2020}, month={May}, pages={246–251} }
 @article{ball_monte_aidara-kane_matheu_ru_thakur_ejobi_fedorka-cray_2020, title={International lineages of Salmonella enterica serovars isolated from chicken farms, Wakiso District, Uganda}, volume={15}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0220484}, abstractNote={The growing occurrence of multidrug-resistant (MDR) Salmonella enterica in poultry has been reported with public health concern worldwide. We reported, recently, the occurrence of Escherichia coli and Salmonella enterica serovars carrying clinically relevant resistance genes in dairy cattle farms in the Wakiso District, Uganda, highlighting an urgent need to monitor food-producing animal environments. Here, we present the prevalence, antimicrobial resistance, and sequence type of 51 Salmonella isolates recovered from 400 environmental samples from chicken farms in Uganda. Among the Salmonella isolates, 32/51 (62.7%) were resistant to at least one antimicrobial, and 10/51 (19.6%) displayed multiple drug resistance. Through PCR, five replicon plasmids were identified among all chicken Salmonella including IncFIIS 17/51 (33.3%), IncI1α 12/51 (23.5%), IncP 8/51 (15.7%), IncX1 8/51 (15.7%), and IncX2 1/51 (2.0%). In addition, we identified replicons through WGS (ColpVC and IncFIB). A significant seasonal difference between chicken sampling periods was observed (p= 0.0017). We conclude that MDR Salmonella highlights the risks posed to the animals, environment, and humans for infection. Implementing a robust integrated surveillance system in Uganda will help monitor MDR to help control infectious threats.}, number={1}, journal={PLOS ONE}, author={Ball, Takiyah and Monte, Daniel and Aidara-Kane, Awa and Matheu, Jorge and Ru, Hongyu and Thakur, Siddhartha and Ejobi, Francis and Fedorka-Cray, Paula}, year={2020}, month={Jan} }
 @article{gebreyes_jackwood_bruno de oliveira_lee_hoet_thakur_2020, title={Molecular Epidemiology of Infectious Zoonotic and Livestock Diseases}, volume={8}, ISSN={["2165-0497"]}, DOI={10.1128/microbiolspec.AME-0011-2019}, abstractNote={ABSTRACT}, number={2}, journal={MICROBIOLOGY SPECTRUM}, author={Gebreyes, Wondwossen A. and Jackwood, Daral and Bruno De Oliveira, Celso Jose and Lee, Chang-Won and Hoet, Armando E. and Thakur, Siddhartha}, year={2020}, month={Mar} }
 @article{walker_suyemoto_gall_chen_thakur_borst_2020, title={The role ofEnterococcus faecalisduring co-infection with avian pathogenicEscherichia coliin avian colibacillosis}, volume={49}, ISSN={["1465-3338"]}, url={http://dx.doi.org/10.1080/03079457.2020.1796926}, DOI={10.1080/03079457.2020.1796926}, abstractNote={ABSTRACT Enterococcus spp. (ENT) are frequently co-isolated with avian pathogenic E. coli (APEC) from poultry with colibacillosis, a leading cause of flock mortality. Although largely overlooked, ENT may play an active role in these infections. To assess the frequency of ENT co-isolation in colibacillosis, cultures were collected from birds with gross lesions of omphalitis, polyserositis, and septicaemia over a 3-year period from three turkey flocks and three broiler flocks. In birds diagnosed with colibacillosis based on gross findings and isolation of E. coli, ENT were co-isolated with APEC in 35.7% (n = 41/115) of colibacillosis mortality and 3.7% of total mortality (n = 41/1122). Co-isolated APEC and ENT pairs (n = 41) were further characterized using antimicrobial resistance phenotyping and in vitro co-culture assays. E. faecalis (EF) was the most commonly co-isolated species (68% n = 28/41) and tetracycline resistance was the resistance phenotype most commonly found among APEC (51% n = 21/41) and ENT (93% n = 38/41). Under iron-restricted conditions, EF enhanced APEC growth in a proximity-dependent manner and APEC grown in mixed culture with EF exhibited a significant growth and survival advantage (P ≤ 0.01). In an embryo lethality assay, APEC co-infection with EF resulted in decreased survival of broiler embryos compared to mono-infections (P ≤ 0.05). These data demonstrate that EF augmented APEC survival and growth under iron limiting conditions, possibly translating to the increased virulence of APEC in broiler embryos. Thus, ENT co-infections may be a previously unrecognized contributor to colibacillosis-related mortality. Further investigations into the mechanism of this interaction are warranted. RESEARCH HIGHLIGHTS Enterococcus is frequently co-isolated with avian pathogenic E. coli (APEC). Enterococcus faecalis (EF) enhances survival of APEC in iron restricted conditions. EF co-infection increases APEC virulence in broiler embryos.}, number={6}, journal={AVIAN PATHOLOGY}, publisher={Informa UK Limited}, author={Walker, Grayson K. and Suyemoto, M. Mitsu and Gall, Sesny and Chen, Laura and Thakur, Siddhartha and Borst, Luke B.}, year={2020}, month={Nov}, pages={589–599} }
 @article{glaize_gutierrez-rodriguez_hanning_díaz-sánchez_gunter_van vliet_watson_thakur_2020, title={Transmission of antimicrobial resistant non-O157 Escherichia coli at the interface of animal-fresh produce in sustainable farming environments}, volume={319}, ISSN={0168-1605}, url={http://dx.doi.org/10.1016/j.ijfoodmicro.2019.108472}, DOI={10.1016/j.ijfoodmicro.2019.108472}, abstractNote={The interaction of typical host adapted enteric bacterial pathogens with fresh produce grown in fields is complex. These interactions can be more pronounced in co-managed or sustainable farms where animal operations are, by design, close to fresh produce, and growers frequently move between the two production environments. The primary objectives of this study were to 1) determine the transmission of STEC or enteric pathogens from small and large animal herds or operations to fresh produce on sustainable farms in TN and NC, 2) identify the possible sources that impact transmission of AMR E. coli, specifically STEC on these systems, and 3) WGS to characterize recovered E. coli from these sources. Samples were collected from raw and composted manure, environment, and produce sources. The serotype, virulence, and genotypic resistance profile were determined using the assembled genome sequences sequenced by Illumina technology. Broth microdilution was used to determine the antimicrobial susceptibility of each isolate against a panel of fourteen antimicrobials. The prevalence of E. coli increased during the summer season for all sources tested. ParSNP trees generated demonstrated that the transmission of AMR E. coli is occurring between animal feeding operations and fresh produce. Ten isolates were identified as serotype O45, a serotype that is associated with the "Big Six" group that is frequently linked with foodborne outbreaks caused by non-O157 E. coli. However, these isolates did not possess the stx gene. The highest frequency of resistance was detected against streptomycin (n = 225), ampicillin (n = 190) and sulfisoxazole FIS (n = 140). A total of 35 (13.7%) isolates from two TN farms were positive for the blaCMY (n = 5) and blaTEM (n = 32) genes. The results of this study show the potential of AMR E. coli transmission between animal feeding operations and fresh produce, and more studies are recommended to study this interaction and prevent dissemination in sustainable farming systems.}, journal={International Journal of Food Microbiology}, publisher={Elsevier BV}, author={Glaize, Ayanna and Gutierrez-Rodriguez, Eduardo and Hanning, Irene and Díaz-Sánchez, Sandra and Gunter, Chris and van Vliet, Arnoud H.M. and Watson, Wes and Thakur, Siddhartha}, year={2020}, month={Apr}, pages={108472} }
 @article{mahindroo_thanh_nguyen_mohan_thakur_baker_taneja_2019, title={Endemic fluoroquinolone-resistant Salmonella enterica serovar Kentucky ST198 in northern India}, volume={5}, ISSN={["2057-5858"]}, DOI={10.1099/mgen.0.000275}, abstractNote={
                  
                     
                        Salmonella
                     
                  
                  e
                  nterica serovar Kentucky is an emergent human pathogen. Human infection with ciprofloxacin-resistant 
                     S. enterica
                   Kentucky ST198 has been reported in Europe and North America as a consequence of travel to Asia/the Middle East. This is, to the best of our knowledge, the first study reporting the identification of this epidemic clone in India and South Asia.}, number={7}, journal={MICROBIAL GENOMICS}, author={Mahindroo, Jaspreet and Thanh, Duy Pham and Nguyen, To Nguyen Thi and Mohan, Balvinder and Thakur, Siddhartha and Baker, Stephen and Taneja, Neelam}, year={2019}, month={Jul} }
 @article{islam_el zowalaty_vliet_thakur_khatun_saha_rahman_noreddin_islam_2019, title={First Genome Sequence of Brucella abortus Biovar 3 Strain BAU21/S4023, Isolated from a Dairy Cow in Bangladesh}, volume={8}, ISSN={["2576-098X"]}, DOI={10.1128/MRA.00446-19}, abstractNote={
            We report the genome sequence of
            Brucella abortus
            biovar 3 strain BAU21/S4023, isolated from a dairy cow that suffered an abortion in Savar, Dhaka, Bangladesh. The genome sequence length is 3,244,234 bp with a 57.2% GC content, 3,147 coding DNA sequences (CDSs), 51 tRNAs, 1 transfer messenger RNA (tmRNA), and 3 rRNA genes.
          }, number={24}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Islam, M. Sadequl and El Zowalaty, Mohamed E. and Vliet, Arnoud H. M. and Thakur, Siddhartha and Khatun, M. Minara and Saha, Sukumar and Rahman, M. Tanvir and Noreddin, Ayman and Islam, M. Ariful}, year={2019}, month={Jun} }
 @article{islam_el zowalaty_vliet_thakur_khatun_saha_rahman_noreddin_islam_2019, title={First Genome Sequence of Brucella abortus Biovar 3 Strain BAU21/S4023, Isolated from a Dairy Cow in Bangladesh (vol 8, e00446-19, 2019)}, volume={8}, ISSN={["2576-098X"]}, DOI={10.1128/MRA.00779-19}, abstractNote={Volume 8, no. 24, e00446-19, 2019, [https://doi.org/10.1128/MRA.00446-19][1]. Page 3: The following should be added to Acknowledgments. “M.E.E.Z., M.A.I., S.T., and A.H.M.V.V. contributed to writing the initial draft, M.A.I. submitted the strain for sequencing, and M.E.E.Z. analyzed the sequences}, number={29}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Islam, M. Sadequl and El Zowalaty, Mohamed E. and Vliet, Arnoud H. M. and Thakur, Siddhartha and Khatun, M. Minara and Saha, Sukumar and Rahman, M. Tanvir and Noreddin, Ayman and Islam, M. Ariful}, year={2019}, month={Jul} }
 @book{venkitanarayanan_thakur_ricke_2019, edition={1}, title={Food safety in Poultry meat production}, publisher={Springer US}, author={Venkitanarayanan, Kumar and Thakur, Siddhartha and Ricke, Steven}, year={2019} }
 @article{monte_lincopan_berman_cerdeira_keelara_thakur_fedorka-cray_landgraf_2019, title={Genomic Features of High-Priority Salmonella enterica Serovars Circulating in the Food Production Chain, Brazil, 2000-2016}, volume={9}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-019-45838-0}, abstractNote={Abstract}, journal={SCIENTIFIC REPORTS}, author={Monte, Daniel F. . and Lincopan, Nilton and Berman, Hanna and Cerdeira, Louise and Keelara, Shivaramu and Thakur, Siddhartha and Fedorka-Cray, Paula J. and Landgraf, Mariza}, year={2019}, month={Jul} }
 @article{monte_nelson_cerdeira_keelara_greene_griffin_rath_hall_page_fedorka-cray_et al._2019, title={Multidrug- and colistin-resistant Salmonella enterica 4,[5],12:i:- sequence type 34 carrying the mcr-3.1 gene on the IncHI2 plasmid recovered from a human}, volume={68}, ISSN={0022-2615 1473-5644}, url={http://dx.doi.org/10.1099/jmm.0.001012}, DOI={10.1099/jmm.0.001012}, abstractNote={A colistin-resistant Salmonella enterica 4, [5],12:i:- sequence type (ST) 34 harbouring mcr-3.1 was recovered from a patient who travelled to China 2 weeks prior to diarrhoea onset. Genomic analysis revealed the presence of the mcr-3.1 gene located in the globally disseminated IncHI2 plasmid, highlighting the intercontinental dissemination of the colistin-resistant S. enterica 4, [5],12:i:- ST34 pandemic clone.}, number={7}, journal={Journal of Medical Microbiology}, publisher={Microbiology Society}, author={Monte, Daniel F. and Nelson, Valerie and Cerdeira, Louise and Keelara, Shivaramu and Greene, Shermalyn and Griffin, Denise and Rath, Shadia and Hall, Robbie and Page, Nichole and Fedorka-Cray, Paula J. and et al.}, year={2019}, month={Jul}, pages={986–990} }
 @article{monte_nelson_cerdeira_keelara_greene_griffin_rath_hall_page_lawson_et al._2019, title={Multidrug- and colistin-resistant Salmonella enterica 4,[5],12:i:- sequence type 34 carrying the mcr-3.1 gene on the IncHI2 plasmid recovered from a human (vol 68, pg 986, 2019)}, volume={68}, ISSN={["1473-5644"]}, DOI={10.1099/jmm.0.001057}, abstractNote={Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.}, number={11}, journal={JOURNAL OF MEDICAL MICROBIOLOGY}, author={Monte, Daniel F. and Nelson, Valerie and Cerdeira, Louise and Keelara, Shivaramu and Greene, Shermalyn and Griffin, Denise and Rath, Shadia and Hall, Robbie and Page, Nichole and Lawson, Thomas and et al.}, year={2019}, month={Nov}, pages={1694–1694} }
 @article{ball_monte_aidara-kane_matheu-alvarez_ru_thakur_horovitz_ejobi_lacher_fedorka-cray_et al._2019, title={Phenotypic and Genotypic Characterization of Escherichia coli and Salmonella enterica from Dairy Cattle Farms in the Wakiso District, Uganda: A Cross-Sectional Study}, volume={16}, ISSN={1535-3141 1556-7125}, url={http://dx.doi.org/10.1089/fpd.2018.2528}, DOI={10.1089/fpd.2018.2528}, abstractNote={Enterobacteriaceae producing β-lactamases have spread rapidly worldwide and pose a serious threat to human-animal-environment interface. In this study, we present the presence of Salmonella enterica (1.3%) and commensal Escherichia coli (96.3%) isolated from 400 environmental fecal dairy cattle samples over 20 farms in Uganda. Among E. coli isolates, 21% were resistant to at least one antimicrobial tested and 7% exhibited multidrug resistance. Four E. coli isolates displayed extended-spectrum beta-lactamase (ESBL)-producing genes, including blaCTX-M-15 (n = 2/4), blaCTX-M-27 (n = 1/4), blaSHV-12 (n = 1/4), and blaTEM-1B (n = 2/4). Whole genome sequencing confirmed the presence of the plasmid-mediated quinolone resistance qnrS1 gene among three ESBL isolates. No statistically significant differences in seasonal prevalence for E. coli and S. enterica among dairy cattle sampling periods were observed. Furthermore, to our knowledge, this is the first report of E. coli carrying blaCTX-M-15, blaCTX-M-27, blaSHV-12, or qnrS1 isolated from dairy cattle in Uganda. We conclude that the presence of globally disseminated blaCTX-M-15 and blaCTX-M-27 warrants further study to prevent further spread. In addition, the presence of fluoroquinolone resistant ESBL-producing E. coli on dairy farms highlights the potential risk among the human-livestock-environment interaction. This study can be used as a baseline for implementation of a more robust national integrated surveillance system throughout Uganda.}, number={1}, journal={Foodborne Pathogens and Disease}, publisher={Mary Ann Liebert Inc}, author={Ball, Takiyah A. and Monte, Daniel F. and Aidara-Kane, Awa and Matheu-Alvarez, Jorge and Ru, Hongyu and Thakur, Siddhartha and Horovitz, Joy and Ejobi, Francis and Lacher, David W. and Fedorka-Cray, Paula J. and et al.}, year={2019}, month={Jan}, pages={54–59} }
 @article{aworh_kwaga_okolocha_mba_thakur_2019, title={Prevalence and risk factors for multi-drug resistant Escherichia coli among poultry workers in the Federal Capital Territory, Abuja, Nigeria}, volume={14}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0225379}, DOI={10.1371/journal.pone.0225379}, abstractNote={Background Antimicrobial resistance has emerged as a global health threat. Antimicrobial resistant Escherichia coli infections are associated with high morbidity and expenditure when compared with infections caused by susceptible strains. In Nigeria, antimicrobial drugs are readily available over-the-counter with potential for indiscriminate use by poultry farmers and eventual development of drug resistance. The objective of this study was to investigate prevalence and risk factors for multi-drug resistant E. coli among poultry workers (PW) in Abuja, Nigeria. Materials and methods A cross-sectional study was conducted among 122 randomly selected apparently healthy poultry workers (poultry-farmers/ sellers) in Municipal and Kuje Area Councils from December 2018 to April 2019. Data was collected on socio-demographics and exposure factors using a structured interviewer-administered questionnaire. E. coli was isolated and identified from stool samples of poultry workers. Antibiotic susceptibility testing was done using Kirby-Bauer disk diffusion method. Multidrug resistance (MDR) was defined as resistance to three or more classes of antimicrobials. Data was analyzed by computing proportions, prevalence odds-ratios (POR) and logistic regression at 5% significance level. Results Among PW, there were 121 males (99.2%). Mean age of the male workers was 30.6 ± 9.7years, 54.6% (n = 66) married, 57.9% (n = 70) had secondary education and 62.0% (n = 75) were farm-workers. Prevalence of E. coli was 39.7% (n = 48), highest among farm-workers (POR = 2.7, 95% Confidence Interval [CI] = 1.3–5.7; p = 0.01) compared to poultry-sellers. Of the 48 E. coli isolates, 16.7% (n = 8) were extended spectrum beta lactamase (ESBL) producers and 79.2% (n = 38) were MDR. We detected resistance against Tetracycline: (83.3%, n = 40), Sulfamethoxazole-Trimethoprim: (79.2%, n = 38), Ampicillin: (77.1%, n = 37), Streptomycin: (72.9%, n = 35), Nalidixic acid: (50%, n = 24), Gentamicin: (41.7%, n = 20), Chloramphenicol: (31.3%, n = 15), Cephalothin: (27.1%, n = 13), Nitrofurantoin: (10.4%, n = 5) and Imipenem: (6.3%, n = 3). Absence of lavatory (POR = 2.7, 95% CI = 1.1–6.7); existence of farm/market for >10years (POR = 2.5, 95% CI = 1.1–5.4) and PW’s history of diarrhea in last three months (POR = 2.8, CI = 1.2–6.3) were associated with MDR. Controlling for age, absence of lavatory (adjusted OR [aOR] = 4.31, 95% CI = 1.6–11.9); PW’s history of diarrhea in last three months (aOR = 3.3,95%CI = 1.3–8.5) and work exposure >10years (aOR = 0.3, 95%CI = 0.1–0.9) remained independent risk factors for MDR. Conclusion Prevalence of resistant E. coli was highest among farm-workers and associated with older farms/markets, occupational exposure of over 10 years and poor hygienic measures. The management of Municipal and Kuje Area Councils were recommended to provide lavatories for public use in farm-settlements/markets. The importance of hand-hygiene and responsible use of antimicrobials in poultry production was emphasized.}, number={11}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Aworh, Mabel Kamweli and Kwaga, Jacob and Okolocha, Emmanuel and Mba, Nwando and Thakur, Siddhartha}, editor={Woźniakowski, GrzegorzEditor}, year={2019}, month={Nov}, pages={e0225379} }
 @article{thakur_gray_2019, title={The Mandate for a Global “One Health” Approach to Antimicrobial Resistance Surveillance}, volume={1}, ISSN={0002-9637 1476-1645}, url={http://dx.doi.org/10.4269/ajtmh.18-0973}, DOI={10.4269/ajtmh.18-0973}, abstractNote={In 1940, one year before the first administration of penicillin in man, two members of the team who discovered the drug revealed that resistance to penicillin already existed. Since then, as antimicrobial resistance (AMR) has progressed in the wake of exponential antimicrobial use, scientists have raced against extraordinarily efficient microbial gene dissemination and evolution to provide effective antimicrobial therapeutics. Today, with the existence of genes resistant to every natural and synthetic antimicrobial compound, national surveillance systems track AMR in human and animal populations to deepen our understanding of resistance and find ways to circumvent it. Although we have established surveillance systems across North America and Europe, pathogens do not respect international boundaries, and the emergence of resistance in any country poses a worldwide threat. In this issue of the AJTMH, Hedman et al. report spillover of AMR to developing world settings with no prior history of agricultural antimicrobial use. We are reminded that surveillance must become a global “One Health” effort if we are to solve one of today’s most significant threats to human, animal, and environmental health. Antimicrobial resistance has reached its tipping point, and some are saying we are now in the post-antibiotic era. Recent reports have highlighted this trend, including the emergence of multiple plasmid-mediated colistin resistance genes in human and animal pathogens, spread of metallobeta-lactamase-1 in India, and the emergence of plasmidmediated carbapenem-resistant Enterobacteriaceae in swine for the first time in the United States. Leading world health agencies consider the threat of AMR as paramount and recognize its complex causation: expanding human and domestic animal populations; increased globalization, international trade, and demand for animal source foods; and all-too-easy access to antimicrobials in both developed and developing countries. The proficiency of genome evolution via horizontal gene transfer and the emergence of new forms of resistance have compounded the lack of new antibiotic discovery and development, while intensifying the threat posed by drug-resistant pathogens. By 2050, an estimated 10million human lives per year will be at risk if we fail to attenuate the rise of drug resistance, and critical medical procedures such as administration of cancer chemotherapy, joint replacement, and gastrointestinal surgery may be associatedwith increasingmorbidity. The increase inAMRburden correlates with a 65% increase in antimicrobial consumption in humans between 2000 and 2015 in 76 countries and administration of 63,000 tons in animals in 2010,with a projected 67% increase in consumption by 2030. Antimicrobial resistance poses a particularly significant threat to lowand middle-income countries. This is due not only to the health-care challenges these countries face, but also to an increase in small-scale intensive animal production, exacerbated by poor sanitation infrastructure. The findings reported by Hedman et al. in this issue exemplify this problem and the difficulty of understanding the complicated dynamics of AMR transmission between humans and animals sharing the same environment. The researchers investigated the prevalence of CTX-M extended-spectrum beta-lactamases in chickens from small-scale poultry farms and in children living on the farms in rural Ecuador. CTX-M-mediated cephalosporin resistance was seen in bacteria both in commercially bred “broiler” chickens treated with high levels of antibiotics and in free-grazing animals that had no direct exposure to antibiotics. Resistance was also detected in bacteria from children in the community. After phylogenetic analysis, the authors reported a shared evolutionary history between chicken and human samples. Hedman et al., thus, provide valuable insight into the rise of phenotypic resistance and avian-to-human spillover in areas that have previously reported low AMR levels in both poultry and humans. Altogether, the data provided by Hedman et al. support a familiar narrative: gene exchange is a property of bacteria that efficiently enables the transmission of resistance between animals and humans. Of particular importance to surveillance systems, the study also highlights the pivotal role of the environment in AMR transmission. The ability of the environment to act as a reservoir for resistance is not a new concept and may have promoted the potential spillover event described by Hedman et al. in Ecuador. Indeed, the environmental AMR resistome consists of more than one million distinct bacterial species, which markedly exceeds the number of species that infect human and animal populations. Despite the knowledge of environmental influences on AMR, current surveillance systems often neglect environmental sampling. It is now crucial that we re-emphasize the role that the environment plays as a reservoir and in maintaining AMR genes as we establish surveillance systems to combat AMR. We know that many of the resistance mechanisms we see in veterinary clinics and animal production systems likely have environmental origins. Recently, we have reported horizontal dissemination of resistance determinants in multiple Salmonella serotypes across commercial swine farms following manure application. In addition, numerous studies have reported very little difference in the shedding of drug-resistant bacterial strains between animals raised under organic or antimicrobial-free production systems. Combined with studies such as that conducted by Hedman et al., these findings demonstrate the need to apply a One Health approach and study environmental reservoirs more closely, rather than focusing only on the resistance that arises following antimicrobial administration. * Address correspondence to Siddhartha Thakur, College of VeterinaryMedicine, NC State, 1060WilliamMoore Dr., Raleigh, NC 27606. E-mail: sthakur@ncsu.edu}, journal={The American Journal of Tropical Medicine and Hygiene}, publisher={American Society of Tropical Medicine and Hygiene}, author={Thakur, Siddhartha and Gray, Gregory C.}, year={2019}, month={Jan} }
 @inbook{kumar_pornsukarom_thakur_2018, place={Publisher}, series={Food Microbiology and Food Safety}, title={Antibiotic Usage in Poultry Production and Antimicrobial Resistant Salmonella in Poultry}, booktitle={Food safety in Poultry meat production}, publisher={Springer US}, author={Kumar, Deepak and Pornsukarom, Suchawan and Thakur, Siddhartha}, editor={Venkitanarayanan, Kumar and Thakur, Siddhartha and Ricke, Steven C.Editors}, year={2018}, pages={301}, collection={Food Microbiology and Food Safety} }
 @article{kumar_pornsukarom_sivaraman_thakur_2018, title={Environmental Dissemination of Multidrug Methicillin-Resistant Staphylococcus sciuri After Application of Manure from Commercial Swine Production Systems}, volume={15}, ISSN={["1556-7125"]}, DOI={10.1089/fpd.2017.2354}, abstractNote={The deposition of manure originating from food animal farms in the environment can lead to the dissemination of antimicrobial-resistant (AMR) bacterial foodborne pathogens, thereby potentially impacting human health. The objective of our study was to determine the dissemination of multidrug methicillin-resistant Staphylococcus sciuri (MDR-MRSS) in the environment after land application of manure on commercial swine farms. A total of 400 environmental samples (40 manure and 360 soil) were collected after repeated sampling from four commercial swine farms located in North Carolina (n = 1) and Iowa (n = 3) in the United States. At each farm, we collected 10 manure and 40 soil samples (20 samples before and after 2 h of manure application) from four plots (five soil samples/plot) on day 0. Subsequently, 20 soil samples were collected on day 7, 14, and 21 from the same plots. A total of 67 (16.75%) MRSS were isolated from the 400 samples. The prevalence in soil and manure was 13.33% (48/360) and 47.5% (19/40), respectively. Prevalence was highest in the soil samples collected after 2 h of manure application on day 0 and decreased subsequently on 7, 14, and 21 days. Antimicrobial susceptibility testing was done against a panel of 12 antibiotics. A majority of S. sciuri isolates exhibited resistance against ampicillin (AMP; 95.5%), penicillin (PEN; 95.5%), clindamycin (CLI; 95.5%), cefoxitin (FOX; 92.5%), ceftiofur (XNL; 92.5%), tetracycline (TET; 86.56%), and erythromycin (ERY; 50.74%). The MDR pattern AMP FOX CLI PEN TET XNL (n = 24; 35.8%) was the most commonly observed. We detected multiple AMR genes, including mecA, aac(6'), Ie-aph(2″)Ia, tetM, tetK, mphC, ermA, ermB, and ermC. Pulsed-field gel electrophoresis clustered isolates from different sample collection days from the same farm into one group. Overall, our study identifies swine manure as an important reservoir of MDR-MRSS and highlights its dissemination in the environment upon spreading of manure.}, number={4}, journal={FOODBORNE PATHOGENS AND DISEASE}, author={Kumar, Deepak and Pornsukarom, Suchawan and Sivaraman, G. K. and Thakur, Siddhartha}, year={2018}, month={Apr}, pages={210–217} }
 @article{moreno_gomes_moreira_de oliveira_peres_silva_thakur_la ragione_moreno_2018, title={First report of mcr-1-harboring Salmonella enterica serovar Schwarzengrund isolated from poultry meat in Brazil}, volume={11}, ISSN={0732-8893}, url={http://dx.doi.org/10.1016/j.diagmicrobio.2018.10.016}, DOI={10.1016/j.diagmicrobio.2018.10.016}, abstractNote={Brazilian poultry meat samples were screened for colistin-resistant Salmonella enterica. Sixty Salmonella isolates were tested for in vitro colistin resistance and mcr-1, mcr-2, mcr-3 and mcr-4 genes. Two isolates harbored the mcr-1 gene and whole-genome analysis determined the serovar to be Schwarzengrund, ST96, harboring the IncX4 plasmid. This is the first report of mcr-1-harboring Salmonella enterica serovar Schwarzengrund in Brazil.}, journal={Diagnostic Microbiology and Infectious Disease}, publisher={Elsevier BV}, author={Moreno, Luisa Z. and Gomes, Vasco T.M. and Moreira, Jéssica and de Oliveira, Carolina H. and Peres, Bárbara P. and Silva, Ana Paula S. and Thakur, Siddhartha and La Ragione, Roberto M. and Moreno, Andrea M.}, year={2018}, month={Nov} }
 @article{ball_cray_horovitz_thakur_2018, title={Molecular Characterization of Salmonella spp. from Cattle and Chicken Farms in Uganda}, volume={10}, number={1}, journal={Online Journal of Public Health Informatics}, author={Ball, T.A. and Cray, P.J. and Horovitz, J. and Thakur, S.}, year={2018}, pages={148} }
 @article{kumar_thakur_2018, title={Molecular Tools To Study Preharvest Food Safety Challenges}, volume={6}, ISBN={978-1-55581-707-7 978-1-55581-964-4}, ISSN={2165-0497}, url={http://dx.doi.org/10.1128/microbiolspec.PFS-0019-2017}, DOI={10.1128/microbiolspec.PFS-0019-2017}, abstractNote={ABSTRACT}, number={1}, journal={Microbiology Spectrum}, publisher={American Society for Microbiology}, author={Kumar, Deepak and Thakur, Siddhartha}, editor={Thakur, S. and Kniel, K.Editors}, year={2018}, month={Feb}, pages={361–382} }
 @article{kumar_thakur_2018, title={Molecular tools to study preharvest food safety challenges}, volume={6}, number={1}, journal={Microbiology Spectrum}, author={Kumar, D. and Thakur, S.}, year={2018} }
 @book{libraries_2018, title={Preharvest Food Safety}, ISBN={9781555817077 9781555819644}, url={http://dx.doi.org/10.1128/9781555819644}, DOI={10.1128/9781555819644}, publisher={American Society of Microbiology}, author={Libraries, NC State University}, editor={Thakur and KnielEditors}, year={2018}, month={Jul} }
 @book{thakur_kniel_2018, title={Preharvest Food Safety}, publisher={American Society for Microbiology}, author={Thakur, Siddhartha and Kniel, Kalmia}, year={2018} }
 @book{thakur_kniel_2018, place={Washington, DC}, title={Preharvest food safety}, publisher={ASM Press}, year={2018} }
 @article{ryan_adamson_aktipis_andersen_austin_barnes_beasley_bedell_briggs_chapman_et al._2018, title={The role of citizen science in addressing grand challenges in food and agriculture research}, volume={285}, ISSN={0962-8452 1471-2954}, url={http://dx.doi.org/10.1098/rspb.2018.1977}, DOI={10.1098/rspb.2018.1977}, abstractNote={The power of citizen science to contribute to both science and society is gaining increased recognition, particularly in physics and biology. Although there is a long history of public engagement in agriculture and food science, the term ‘citizen science’ has rarely been applied to these efforts. Similarly, in the emerging field of citizen science, most new citizen science projects do not focus on food or agriculture. Here, we convened thought leaders from a broad range of fields related to citizen science, agriculture, and food science to highlight key opportunities for bridging these overlapping yet disconnected communities/fields and identify ways to leverage their respective strengths. Specifically, we show that (i) citizen science projects are addressing many grand challenges facing our food systems, as outlined by the United States National Institute of Food and Agriculture, as well as broader Sustainable Development Goals set by the United Nations Development Programme, (ii) there exist emerging opportunities and unique challenges for citizen science in agriculture/food research, and (iii) the greatest opportunities for the development of citizen science projects in agriculture and food science will be gained by using the existing infrastructure and tools of Extension programmes and through the engagement of urban communities. Further, we argue there is no better time to foster greater collaboration between these fields given the trend of shrinking Extension programmes, the increasing need to apply innovative solutions to address rising demands on agricultural systems, and the exponential growth of the field of citizen science.}, number={1891}, journal={Proceedings of the Royal Society B: Biological Sciences}, publisher={The Royal Society}, author={Ryan, S. F. and Adamson, N. L. and Aktipis, A. and Andersen, L. K. and Austin, R. and Barnes, L. and Beasley, M. R. and Bedell, K. D. and Briggs, S. and Chapman, B. and et al.}, year={2018}, month={Nov}, pages={20181977} }
 @article{kniel_kumar_thakur_2018, title={Understanding the Complexities of Food Safety Using a “One Health” Approach}, volume={6}, ISSN={2165-0497}, url={http://dx.doi.org/10.1128/microbiolspec.PFS-0021-2017}, DOI={10.1128/microbiolspec.pfs-0021-2017}, abstractNote={ABSTRACT}, number={1}, journal={Microbiology Spectrum}, publisher={American Society for Microbiology}, author={Kniel, Kalmia E. and Kumar, Deepak and Thakur, Siddhartha}, year={2018}, month={Feb} }
 @article{pornsukarom_vliet_thakur_2018, title={Whole genome sequencing analysis of multiple Salmonella serovars provides insights into phylogenetic relatedness, antimicrobial resistance, and virulence markers across humans, food animals and agriculture environmental sources}, volume={19}, ISSN={["1471-2164"]}, DOI={10.1186/s12864-018-5137-4}, abstractNote={Salmonella enterica is a significant foodborne pathogen, which can be transmitted via several distinct routes, and reports on acquisition of antimicrobial resistance (AMR) are increasing. To better understand the association between human Salmonella clinical isolates and the potential environmental/animal reservoirs, whole genome sequencing (WGS) was used to investigate the epidemiology and AMR patterns within Salmonella isolates from two adjacent US states.WGS data of 200 S. enterica isolates recovered from human (n = 44), swine (n = 32), poultry (n = 22), and farm environment (n = 102) were used for in silico prediction of serovar, distribution of virulence genes, and phylogenetically clustered using core genome single nucleotide polymorphism (SNP) and feature frequency profiling (FFP). Furthermore, AMR was studied both by genotypic prediction using five curated AMR databases, and compared to phenotypic AMR using broth microdilution. Core genome SNP-based and FFP-based phylogenetic trees showed consistent clustering of isolates into the respective serovars, and suggested clustering of isolates based on the source of isolation. The overall correlation of phenotypic and genotypic AMR was 87.61% and 97.13% for sensitivity and specificity, respectively. AMR and virulence genes clustered with the Salmonella serovars, while there were also associations between the presence of virulence genes in both animal/environmental isolates and human clinical samples.WGS is a helpful tool for Salmonella phylogenetic analysis, AMR and virulence gene predictions. The clinical isolates clustered closely with animal and environmental isolates, suggesting that animals and environment are potential sources for dissemination of AMR and virulence genes between Salmonella serovars.}, journal={BMC GENOMICS}, author={Pornsukarom, Suchawan and Vliet, Arnoud H. M. and Thakur, Siddhartha}, year={2018}, month={Nov} }
 @article{pornsukarom_thakur_2017, title={Horizontal Dissemination of Antimicrobial Resistance Determinants in Multiple Salmonella Serotypes following Isolation from the Commercial Swine Operation Environment after Manure Application}, volume={83}, ISSN={["1098-5336"]}, DOI={10.1128/aem.01503-17}, abstractNote={ABSTRACT}, number={20}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Pornsukarom, Suchawan and Thakur, Siddhartha}, year={2017}, month={Oct} }
 @inbook{gebreyes_jackwood_lee_hoet_thakur_riley_2017, edition={2nd}, title={Molecular epidemiology of zoonotic and livestock diseases}, booktitle={Molecular Epidemiology of Infectious Diseases, Principles and Practices}, publisher={ASM Publications}, author={Gebreyes, Wondwossen and Jackwood, Daral and Lee, Chang-Won and Hoet, Armando and Thakur, Siddhartha and Riley, Lee W.}, editor={Riley, Lee W.Editor}, year={2017} }
 @article{reimschuessel_grabenstein_guag_nemser_song_qiu_clothier_byrne_marks_cadmus_et al._2017, title={Multilaboratory Survey To Evaluate Salmonella Prevalence in Diarrheic and Nondiarrheic Dogs and Cats in the United States between 2012 and 2014}, volume={55}, ISSN={0095-1137 1098-660X}, url={http://dx.doi.org/10.1128/JCM.02137-16}, DOI={10.1128/jcm.02137-16}, abstractNote={ABSTRACT}, number={5}, journal={Journal of Clinical Microbiology}, publisher={American Society for Microbiology}, author={Reimschuessel, Renate and Grabenstein, Michael and Guag, Jake and Nemser, Sarah M. and Song, Kyunghee and Qiu, Junshan and Clothier, Kristin A. and Byrne, Barbara A. and Marks, Stanley L. and Cadmus, Kyran and et al.}, editor={Fenwick, BradEditor}, year={2017}, month={Feb}, pages={1350–1368} }
 @article{pornsukarom_thakur_2016, title={Assessing the Impact of Manure Application in Commercial Swine Farms on the Transmission of Antimicrobial Resistant Salmonella in the Environment}, volume={11}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0164621}, abstractNote={Land application of swine manure in commercial hog farms is an integral part of their waste management system which recycles the nutrients back to the soil. However, manure application can lead to the dissemination of bacterial pathogens in the environment and pose a serious public health threat. The aim of this study was to determine the dissemination of antimicrobial resistant Salmonella in the environment due to manure application in commercial swine farms in North Carolina (n = 6) and Iowa (n = 7), two leading pork producing states in the US. We collected manure and soil samples twice on day 0 (before and after manure application) from four distinct plots of lands (5 soil samples/plot) located at 20 feet away from each other in the field. Subsequent soil samples were collected again on days 7, 14, 21 from the same plots. A total of 1,300 soil samples (NC = 600; IA = 700) and 130 manure samples (NC = 60; IA = 70) were collected and analyzed in this study. The overall Salmonella prevalence was 13.22% (189/1,430), represented by 10.69% and 38.46% prevalence in soil and manure, respectively. The prevalence in NC (25.45%) was significantly higher than in IA (2.73%) (P<0.001) and a consistent decrease in Salmonella prevalence was detected from Day 0-Day 21 in all the farms that tested positive. Salmonella serotypes detected in NC were not detected in IA, thereby highlighting serotype association based on manure storage and soil application method used in the two regions. Antimicrobial susceptibility testing was done by the broth microdilution method to a panel of 15 antimicrobial drugs. A high frequency of isolates (58.73%) were multidrug resistant (resistance to three or more class of antimicrobials) and the most frequent resistance was detected against streptomycin (88.36%), sulfisoxazole (67.2%), and tetracycline (57.67%). Genotypic characterization by pulse field gel electrophoresis revealed clonally related Salmonella in both manure and soil at multiple time points in the positive farms. Our study highlights the potential role of swine manure application in the dissemination and persistence of antimicrobial resistant Salmonella in the environment.}, number={10}, journal={PLOS ONE}, author={Pornsukarom, Suchawan and Thakur, Siddhartha}, year={2016}, month={Oct} }
 @article{keelara_thakur_patel_2016, title={Biofilm Formation by Environmental Isolates of Salmonella and Their Sensitivity to Natural Antimicrobials}, volume={13}, ISSN={["1556-7125"]}, DOI={10.1089/fpd.2016.2145}, abstractNote={The objective of this study was to determine reduction of Salmonella in biofilms by essential oils. Biofilm formation of 15 Salmonella isolates from conventional swine farm environment was evaluated by 96-well microtiter plate crystal violet and minimum biofilm eradication concentration (MBEC) assays. Only one of the 15 isolates was a strong biofilm producer as classified by crystal violet assay. All Salmonella isolates formed biofilm on MBEC assay. The curli expression was robust among strains S322 and S435 (Salmonella Infantis), S644, S777, S931, S953, and S977 (Salmonella Typhimurium) as observed by Congo red dye binding assay. The cell hydrophobicity varied with strains and growth phase of the strain; however, there was no significant difference in hydrophobicity of these strains. Natural antimicrobials were evaluated with MBEC assay for their bactericidal efficacy in reducing Salmonella in biofilms. Cinnamaldehyde and sporran at 1000 ppm significantly reduced Salmonella in biofilms. The bactericidal effect of these antimicrobials increased with their concentrations. Salmonella were reduced by 6 log CFU from their initial populations of 7-7.5 log CFU/cm(2) when 2000 ppm concentration of these antimicrobials were used. Salmonella were undetectable when 3000 ppm of cinnamaldehyde or sporran was used. Natural antimicrobials such as cinnamaldehyde and sporran can be used to reduce Salmonella in biofilms.}, number={9}, journal={FOODBORNE PATHOGENS AND DISEASE}, author={Keelara, Shivaramu and Thakur, Siddhartha and Patel, Jitendra}, year={2016}, month={Sep}, pages={509–516} }
 @article{mahindroo_shyam_mohan_thakur_taneja_2016, title={Cronobacter sakazakii - An unrecognised food borne pathogen, India}, volume={45}, ISSN={1201-9712}, url={http://dx.doi.org/10.1016/j.ijid.2016.02.426}, DOI={10.1016/j.ijid.2016.02.426}, abstractNote={Background: Cronobacter sakazakii (formerly Enterobacter sakazakii) causes serious infections in infants with high mortality. Though contaminated powdered infant formula is the most common implicated vehicle, the organism has been isolated from other foods and environmental sources and infections have occurred among persons who did not consume or handle formula milk. There is significant underreporting of C. sakazakii infections in most countries and very little data is available from India. There is no information on human carriage, environmental sources and potential transmission routes of this pathogen from India. The aim of this study was to study the prevalence of this organism in North India (Haryana, Punjab and Chandigarh) and study the antibiotic resistance. Methods & Materials: A wide range of samples (n = 887) were collected from poultry farms, meat abattoirs (pork and mutton), dairy farms (pig stool, goat stool), human diarrhea stool samples and domestic environmental samples (water and soil) and processed for Cronobacter sakazakii. Presumptive C. sakazakii colonies were confirmed by MALDI-TOF. Antibiotic sensitivity was performed. Results: Incidence of Cronobacter sakazakii was found to be 7.1% with individual incidence of 3.37% in humans, 9.4% in goat meat, 11.1% goat feces, 5.9% in pork, 7% pig stool, 6.7% in chicken stool, 11.5% environment. Of the 63 isolates, maximum resistance was observed against ampicillin (50.8%), followed by ciprofloxacin (20.6%) and them meropenem (17.2%). Carbapenem resistance was found in both animal food source and human strains. Conclusion: Cronobacter sakazakii is part of fecal flora of humans as well as is carried by food production animals and is also present in domestic environment with potential risk of cross-contamination. The overall antibiotic resistance in human isolates was low in comparison to food animals and their fecal samples. A higher resistance in animal isolates could be due to rampant use of antibiotics as growth promoters in animals.}, journal={International Journal of Infectious Diseases}, publisher={Elsevier BV}, author={Mahindroo, J. and Shyam, I. and Mohan, B. and Thakur, S. and Taneja, N.}, year={2016}, month={Apr}, pages={182} }
 @inbook{gebereys_thakur_2016, title={Phenotypic Sub typing of Foodborne Pathogens}, booktitle={Tracking Pathogens in the Food Chain}, publisher={Woodhead Publishing Limited}, author={Gebereys, Wondwossen and Thakur, Siddhartha}, editor={Brul, S. and Fratamico, P.M. and McMeekin, T.A.Editors}, year={2016} }
 @article{boyer_s. d'costa_edwards_milloway_susick_borst_thakur_campbell_crenshaw_polo_et al._2015, title={Early-life dietary spray-dried plasma influences immunological and intestinal injury responses to later-life Salmonella typhimurium challenge}, volume={113}, ISSN={["1475-2662"]}, DOI={10.1017/s000711451400422x}, abstractNote={Increasing evidence supports the concept that early-life environmental influences, including nutrition and stress, have an impact on long-term health outcomes and disease susceptibility. The objective of the present study was to determine whether dietary spray-dried plasma (SDP), fed during the first 2 weeks post-weaning (PW), influences subsequent immunological and intestinal injury responses toSalmonellatyphimuriumchallenge. A total of thirty-two piglets (age 16–17 d) were weaned onto nursery diets containing 0, 2·5 % SDP (fed for 7 d PW) or 5 % SDP (fed for 14 d PW), and were then fed control diets (without SDP), for the remainder of the experiment. At 34 d PW (age 50 d), pigs were challenged with 3 × 109colony-forming units ofS. typhimurium. A control group (non-challenged) that was fed 0 % SDP in the nursery was included. At 2 d post-challenge, the distal ileum was harvested for the measurement of inflammatory, histological and intestinal physiological parameters.S.typhimuriumchallenge induced elevated ileal histological scores, myeloperoxidase (MPO), IL-8 and TNF, and increased intestinal permeability (indicated by reduced transepithelial voltage (potential difference) and elevated 4 kDa fluorescein isothiocyanate dextran (FD4) flux rates). Compared withS.typhimurium-challenged controls (0 % SDP), pigs fed the 5 % SDP-14 d diet exhibited reduced ileal histological scores, MPO levels, IL-8 levels and FD4 flux rates. Pigs fed the 5 % SDP-14 d nursery diet exhibited increased levels of plasma and ileal TNF-α in response to the challenge, compared with the other treatments. These results indicate that inclusion of SDP in PW diets can have an influence on subsequent immunological and intestinal injury responses induced by later-lifeS.typhimuriumchallenge.}, number={5}, journal={BRITISH JOURNAL OF NUTRITION}, author={Boyer, P. E. and S. D'Costa and Edwards, L. L. and Milloway, M. and Susick, E. and Borst, L. B. and Thakur, S. and Campbell, J. M. and Crenshaw, J. D. and Polo, J. and et al.}, year={2015}, month={Mar}, pages={783–793} }
 @article{keelara_scott_morrow_hartley_griffin_gebreyes_thakur_2014, title={Comparative phenotypic and genotypic characterization of temporally related nontyphoidal salmonella isolated from human clinical cases, pigs, and the environment in North Carolina}, volume={11}, DOI={10.1089/fpd.2013.1630}, abstractNote={Nontyphoidal Salmonella infections caused by antimicrobial-resistant (AMR) strains are of great public health concern. We compared the phenotypic and genotypic relationships among temporally and spatially related AMR Salmonella isolates (n=1058) representing several predominant serovars, including Salmonella Typhimurium, Salmonella Typhimurium var. 5-, Salmonella Derby, Salmonella Heidelberg, Salmonella Muenchen, Salmonella Schwarzengrund, and Salmonella Rissen of human clinical cases (n=572), pig (n=212), and farm environment (n=274) origin in North Carolina. Antimicrobial susceptibility testing was performed using the broth microdilution method, and genotypic resistance determinants, including class I and II integrons, were identified. Overall, Salmonella isolates exhibited the highest frequency of resistance to tetracycline (50%), followed by sulfisoxazole (36%) and streptomycin (27%). We identified 16 different antimicrobial resistance genes, including extended spectrum and AmpC β-lactamases-producing genes (bla(TEM), bla(PSE), and bla(CMY-2)), in all the β-lactam- and cephalosporin-resistant Salmonella isolates from humans, pigs, and the environment. Class I integrons of 1-kb and 1.2-kb size were identified from all the three sources (humans, 66%; pigs, 85%; environment, 58%), while Class II integrons of 2-kb size were identified only in pig (10%) and environmental (19%) isolates. We detected genotypic similarity between Salmonella Typhimurium isolated from humans, pigs, and the environment while serovars Derby, Heidelberg, and Muenchen exhibited genotypic diversity. Detection of AMR Salmonella isolates from humans, pigs, and the environment is a concern for clinicians and veterinarians to mitigate the dissemination of AMR Salmonella strains.}, number={2}, journal={Foodborne Pathogens and Disease}, author={Keelara, S. and Scott, H. M. and Morrow, W. M. and Hartley, C. S. and Griffin, D. L. and Gebreyes, W. A. and Thakur, Siddhartha}, year={2014}, pages={156–164} }
 @article{keelara_thakur_2014, title={Dissemination of plasmid-encoded AmpC beta-lactamases in antimicrobial resistant Salmonella serotypes originating from humans, pigs and the swine environment}, volume={173}, ISSN={["1873-2542"]}, DOI={10.1016/j.vetmic.2014.07.018}, abstractNote={The aim of this study was to characterize and determine the inter-serovar exchange of AmpC β-lactamase conferring plasmids isolated from humans, pigs and the swine environment. Plasmids isolated from a total of 21 antimicrobial resistant (AMR) Salmonella isolates representing human clinical cases (n = 6), pigs (n = 6) and the swine farm environment (n = 9) were characterized by replicon typing and restriction digestion, inter-serovar transferability by conjugation, and presence of AmpC β-lactamase enzyme encoding gene blaCMY-2 by southern hybridization. Based on replicon typing, the majority (17/21, 81%) of the plasmids belonged to the I1-Iγ Inc group and were between 70 and 103 kb. The potential for inter-serovar plasmid transfer was further confirmed by the PCR detection of AMR genes on the plasmids isolated from trans-conjugants. Plasmids from Salmonella serovars Anatum, Ouakam, Johannesburg and Typhimurium isolated from the same cohort of pigs and their environment and S. Heidelberg from a single human clinical isolate had identical plasmids based on digestion with multiple restriction enzymes (EcoRI, HindIII and PstI) and southern blotting. We demonstrated likely horizontal inter-serovar exchange of plasmid-encoding AmpC β-lactamases resistance among MDR Salmonella serotypes isolated from pigs, swine farm environment and clinical human cases. This study provides valuable information on the role of the swine farm environment and by extension other livestock farm environments, as a potential reservoir of resistant bacterial strains that potentially transmit resistance determinants to livestock, in this case, swine, humans and possibly other hosts by horizontal exchange of plasmids.}, number={1-2}, journal={VETERINARY MICROBIOLOGY}, author={Keelara, Shivaramu and Thakur, Siddhartha}, year={2014}, month={Sep}, pages={76–83} }
 @article{thakur_brake_keelara_zou_susick_2013, title={Co-occurrence and Environmental Distribution of Campylobacter and Salmonella in Broiler Flocks}, volume={94}, journal={Research in Veterinary Science}, author={Thakur, S. and Brake, J. and Keelara, S. and Zou, M. and Susick, E.}, year={2013}, pages={33–42} }
 @article{thakur_brake_keelara_zou_susick_2013, title={Farm and environmental distribution of Campylobacter and Salmonella in broiler flocks}, volume={94}, ISSN={["1532-2661"]}, DOI={10.1016/j.rvsc.2012.07.014}, abstractNote={The objective of this study was to determine the prevalence of Campylobacter and Salmonella in broilers and their distribution in the indoor and outdoor farm environment. Nine hundred samples (400 faecal; 300 indoor environment; 200 outdoor environment), were collected from 10 individual broiler houses on 10 farms. Campylobacter jejuni prevalence was significantly higher (P = 0.003) in faeces (29.5%; 118/400) than the environment (0.8%; 4/500) in contrast to Salmonella Typhimurium from faecal (8.8%; 35/400) and environmental (8.4%; n = 42/500) sources (P = 0.217). S. Typhimurium predominantly exhibited antimicrobial resistance (AR) to streptomycin (46%) and tetracycline (31.5%). C. jejuni isolates exhibited AR only to tetracycline (55.5%). The PFGE profile revealed 100% similarity between S. Typhimurium isolates from faecal and environmental sources. No relationship was detected between C. jejuni isolates. The low prevalence of Campylobacter and Salmonella in the outdoor environment indicates that it may not be a significant reservoir for transmission of these pathogens on broiler farms.}, number={1}, journal={RESEARCH IN VETERINARY SCIENCE}, author={Thakur, S. and Brake, J. and Keelara, S. and Zou, M. and Susick, E.}, year={2013}, month={Feb}, pages={33–42} }
 @article{keelara_scott_morrow_gebreyes_correa_nayak_stefanova_thakur_2013, title={Longitudinal Study of Distributions of Similar Antimicrobial-Resistant Salmonella Serovars in Pigs and Their Environment in Two Distinct Swine Production Systems}, volume={79}, ISSN={0099-2240 1098-5336}, url={http://dx.doi.org/10.1128/AEM.01419-13}, DOI={10.1128/aem.01419-13}, abstractNote={ABSTRACT}, number={17}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={Keelara, Shivaramu and Scott, H. Morgan and Morrow, William M. and Gebreyes, Wondwossen A. and Correa, Maria and Nayak, Rajesh and Stefanova, Rossina and Thakur, Siddhartha}, year={2013}, month={Jun}, pages={5167–5178} }
 @article{smith_gebreyes_abley_harper_forshey_male_martin_molla_sreevatsan_thakur_et al._2013, title={Methicillin-Resistant Staphylococcus aureus in Pigs and Farm Workers on Conventional and Antibiotic-Free Swine Farms in the USA}, volume={8}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0063704}, abstractNote={Much uncertainty remains about the origin and public health implications of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA). This study aimed to investigate the occurrence and prevalence of MRSA in general and LA-MRSA in particular in pigs and farm workers in five states. We collected nasal swabs from pigs and farm workers at 45 swine herds (21 antibiotic-free herds; 24 conventional herds) in Illinois, Iowa, Minnesota, North Carolina and Ohio. MRSA was isolated from 50 of 1085 pigs (4.6%) and 31 of 148 (20.9%) of farm workers. MRSA-positive pigs and people were clustered in four conventional swine farms in Iowa and Illinois. Based on genotyping, spa type t034, a common livestock associated variant, was predominant among both human and swine isolates. These results confirm the presence of LA-MRSA in pigs and swine farm workers in the USA, but the prevalence found is relatively low compared with European studies.}, number={5}, journal={PLOS ONE}, author={Smith, Tara C. and Gebreyes, Wondwossen A. and Abley, Melanie J. and Harper, Abby L. and Forshey, Brett M. and Male, Michael J. and Martin, H. Wayne and Molla, Bayleyegn Z. and Sreevatsan, Srinand and Thakur, Siddhartha and et al.}, year={2013}, month={May} }
 @article{tadesse_bahnson_funk_morrow_abley_ponte_thakur_wittum_degraves_rajala-schultz_et al._2013, title={Yersinia enterocolitica of Porcine Origin: Carriage of Virulence Genes and Genotypic Diversity}, volume={10}, ISSN={["1556-7125"]}, DOI={10.1089/fpd.2011.1120}, abstractNote={Yersinia enterocolitica is an important foodborne pathogen, and pigs are recognized as a major reservoir and potential source of pathogenic strains to humans. A total of 172 Y. enterocolitica recovered from conventional and antimicrobial-free pig production systems from different geographic regions (North Carolina, Ohio, Michigan, Wisconsin, and Iowa) were investigated to determine their pathogenic significance to humans. Phenotypic and genotypic diversity of the isolates was assessed using antibiogram, serogrouping, and amplified fragment length polymorphism (AFLP). Carriage of chromosomal and plasmid-borne virulence genes were investigated using polymerase chain reaction. A total of 12 antimicrobial resistance patterns were identified. More than two-thirds (67.4%) of Y. enterocolitica were pan-susceptible, and 27.9% were resistant against β-lactams. The most predominant serogroup was O:3 (43%), followed by O:5 (25.6%) and O:9 (4.1%). Twenty-two of 172 (12.8%) isolates were found to carry Yersinia adhesion A (yadA), a virulence gene encoded on the Yersinia virulence plasmid. Sixty-nine (40.1%) isolates were found to carry ail gene. The ystA and ystB genes were detected in 77% and 26.2% of the strains, respectively. AFLP genotyping of isolates showed wide genotypic diversity and were grouped into nine clades with an overall genotypic similarity of 66.8-99.3%. AFLP analysis revealed that isolates from the same production system showed clonal relatedness, while more than one genotype of Y. enterocolitica circulates within a farm.}, number={1}, journal={FOODBORNE PATHOGENS AND DISEASE}, author={Tadesse, Daniel A. and Bahnson, Peter B. and Funk, Julie A. and Morrow, W. E. Morgan and Abley, Melanie J. and Ponte, Valeria A. and Thakur, Siddhartha and Wittum, Thomas and DeGraves, Fred J. and Rajala-Schultz, Paivi J. and et al.}, year={2013}, month={Jan}, pages={80–86} }
 @article{fry_thakur_abley_gebreyes_2012, title={Antimicrobial resistance, toxinotype, and genotypic profiling of clostridium difficile isolates of swine origin}, volume={50}, DOI={10.1128/jcm.06581-11}, abstractNote={ABSTRACT}, number={7}, journal={Journal of Clinical Microbiology}, author={Fry, P. R. and Thakur, Siddhartha and Abley, M. and Gebreyes, W. A.}, year={2012}, pages={2366–2372} }
 @article{quintana-hayashi_thakur_2012, title={Longitudinal Study of the Persistence of Antimicrobial-Resistant Campylobacter Strains in Distinct Swine Production Systems on Farms, at Slaughter, and in the Environment}, volume={78}, ISSN={["0099-2240"]}, DOI={10.1128/aem.07723-11}, abstractNote={ABSTRACT}, number={8}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Quintana-Hayashi, Macarena P. and Thakur, Siddhartha}, year={2012}, month={Apr}, pages={2698–2705} }
 @article{susick_putnam_bermudez_thakur_2012, title={Longitudinal study comparing the dynamics of Clostridium difficile in conventional and antimicrobial free pigs at farm and slaughter}, volume={157}, ISSN={["0378-1135"]}, DOI={10.1016/j.vetmic.2011.12.017}, abstractNote={Clostridium difficile is the leading cause of nosocomial diarrhea in humans and a major cause of enteritis in neonatal piglets, foals and calves. The aim of this longitudinal study was to determine and compare the prevalence, antimicrobial susceptibility, and toxinotype profiles of C. difficile isolated from pigs and their environment in the indoor conventional and outdoor antimicrobial free (ABF) production systems. Ten conventional and eight ABF cohorts of 35 pigs each and their environment were sampled at different stages of production at farm and slaughter. C. difficile prevalence in pigs was highest at the farrowing stage in both conventional (34%, 120/350) and ABF (23%, 56/244) systems, and decreased with age. This reduction in C. difficile prevalence in pigs at later stages of production mirrored the decreased prevalence in the farm environment. At slaughter, C. difficile was isolated at a low frequency from the carcasses and processing environment in both production systems. All but three isolates were resistant to ciprofloxacin (99%, 505/508), while 1.0% (5/508) and 6.0% (23/508) of isolates exhibited resistance to tetracycline and erythromycin, respectively. Toxinotype V (tcdA(+)tcdB(+)) was the predominant strain identified in both systems (conventional: 94%, 376/401; ABF: 82%, 88/107), while the rest were toxinotype XIII (tcdA(+)tcdB(+)). To conclude, we isolated antimicrobial resistant C. difficile regardless of antimicrobial use on the farm. Based on the phenotypic and genotypic similarity of C. difficile isolated in this study, we conclude that the unique production practices employed in conventional and ABF production systems have no impact on the pathogen population.}, number={1-2}, journal={VETERINARY MICROBIOLOGY}, author={Susick, E. K. and Putnam, M. and Bermudez, D. M. and Thakur, S.}, year={2012}, month={May}, pages={172–178} }
 @article{zou_keelara_thakur_2012, title={Molecular Characterization of Salmonella enterica Serotype Enteritidis Isolates from Humans by Antimicrobial Resistance, Virulence Genes, and Pulsed-Field Gel Electrophoresis}, volume={9}, ISSN={["1556-7125"]}, DOI={10.1089/fpd.2011.1012}, abstractNote={Salmonella enterica serovar Enteritidis (S. Enteritidis) is a major serovar associated with human salmonellosis. A total of 425 clinical S. Enteritidis isolates of human origin were collected between June 2009 and September 2010 from North Carolina. The isolates were further characterized for antimicrobial susceptibility, antimicrobial resistance coding determinants, virulence genes, and fingerprint profiles to determine whether they were similar or different to the S. Enteritidis strain responsible for the human outbreak due to consumption of contaminated eggs. Ten different antimicrobial resistance phenotypes were observed with the highest frequency of resistance exhibited to ampicillin (n=10; 2.35%). The isolates were predominantly pansusceptible (n=409; 96.23%); however, seven isolates were multidrug resistant (MDR; i.e., resistant to three or more antimicrobials). Extended spectrum β-lactamase (ESBL) coding genes (bla(TEM) and bla(PSE)) were detected in the ampicillin-resistant isolates, whereas a single MDR isolate tested positive for class 1 integron (1 kb). The majority of the isolates (n=422; 99.3%) carried the invA, mgtC, stn, sopB, sopE1, and sefA virulence genes. However, 37 (8.7%) and 46 (10.82%) S. Enteritidis isolates tested negative for the plasmid encoded genes spvC and rck, respectively. Pulsed-field gel electrophoresis (PFGE) typing of 118 S. Enteritidis isolates by restriction enzymes XbaI and BlnI resulted in seven clusters, each with a discriminatory index (DI) of 0.715 and 0.785, respectively. The combination of XbaI-BlnI patterns generated a dendrogram with 14 clusters and a higher DI of 0.914. The PFGE profile of 80 isolates matched 100% with the S. Enteritidis strain that has been cited for the recent outbreak in the United States due to consumption of contaminated eggs. In conclusion, we identified a genotypic similar S. Enteritidis population in our study based on antimicrobial susceptibility, virulence gene, and PFGE fingerprint profiles.}, number={3}, journal={FOODBORNE PATHOGENS AND DISEASE}, author={Zou, Ming and Keelara, Shivaramu and Thakur, Siddhartha}, year={2012}, month={Mar}, pages={232–238} }
 @article{quintana-hayashi_thakur_2012, title={Phylogenetic Analysis Reveals Common Antimicrobial Resistant Campylobacter coli Population in Antimicrobial-Free (ABF) and Commercial Swine Systems}, volume={7}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0044662}, abstractNote={The objective of this study was to compare the population biology of antimicrobial resistant (AR) Campylobacter coli isolated from swine reared in the conventional and antimicrobial-free (ABF) swine production systems at farm, slaughter and environment. A total of 200 C. coli isolates selected from fecal, environmental, and carcass samples of ABF (n = 100) and conventional (n = 100) swine production systems were typed by multilocus sequence typing (MLST). Sequence data from seven housekeeping genes was analyzed for the identification of allelic profiles, sequence types (STs) and clonal complex determination. Phylogenetic trees were generated to establish the relationships between the genotyped isolates. A total of 51 STs were detected including two novel alleles (glnA 424 and glyA 464) and 14 novel STs reported for the first time. The majority of the C. coli isolates belonged to ST-854 (ABF: 31, conventional: 17), and were grouped in clonal complex ST-828 (ABF: 68%, conventional: 66%). The mean genetic diversity (H) for the ABF (0.3963+/−0.0806) and conventional (0.4655+/−0.0714) systems were similar. The index of association () for the ABF ( = 0.1513) and conventional ( = 0.0991) C. coli populations were close to linkage equilibrium, indicative of a freely recombining population. Identical STs were detected between the pigs and their environment both at farm and slaughter. A minimum spanning tree revealed the close clustering of C. coli STs that originated from swine and carcass with those from the environment. In conclusion, our study reveals a genotypic diverse C. coli population that shares a common ancestry in the conventional and ABF swine production systems. This could potentially explain the high prevalence of antimicrobial resistant C. coli in the ABF system in the absence of antimicrobial selection pressure.}, number={9}, journal={PLOS ONE}, author={Quintana-Hayashi, Macarena P. and Thakur, Siddhartha}, year={2012}, month={Sep} }
 @article{perez_whitacre_thakur_keelara_fauls_breitschwerdt_2012, title={Unilateral Epididymitis Associated with Salmonella Bacteremia in a Dog}, volume={4}, number={1}, journal={Clinical Theriogenology}, author={Perez, C. and Whitacre, M.D. and Thakur, S. and Keelara, S. and Fauls, M. and Breitschwerdt, E.B.}, year={2012}, pages={61–65} }
 @inbook{gebreyes_thakur_2011, series={Woodhead Publishing Series in Food Science, Technology and Nutrition}, title={7 - Phenotypic subtyping of foodborne pathogens}, ISBN={978-1-84569-496-8}, url={http://www.sciencedirect.com/science/article/pii/B9781845694968500077}, booktitle={Tracing Pathogens in the Food Chain}, publisher={Woodhead Publishing}, author={Gebreyes, W. A. and Thakur, S.}, editor={Brul, Stanley and Fratamico, Pina M. and McMeekin, Tom A.Editors}, year={2011}, month={Jan}, pages={141–156}, collection={Woodhead Publishing Series in Food Science, Technology and Nutrition} }
 @article{thakur_sandfoss_kennedy-stoskopf_deperno_2011, title={Detection of Clostridium difficile and Salmonella in Feral Swine Population in North Carolina}, volume={47}, ISSN={["0090-3558"]}, DOI={10.7589/0090-3558-47.3.774}, abstractNote={We sampled 161 feral pigs in eastern North Carolina, USA, to determine the prevalence and antimicrobial resistance profile of Clostridium difficile and Salmonella. Seven (4.4%) and eight (5.0%) pigs tested positive for C. difficile and Salmonella, respectively, highlighting the importance of determining the epidemiology of these pathogens in feral pigs.}, number={3}, journal={JOURNAL OF WILDLIFE DISEASES}, author={Thakur, Siddhartha and Sandfoss, Mark and Kennedy-Stoskopf, Suzanne and DePerno, Christopher S.}, year={2011}, month={Jul}, pages={774–776} }
 @article{tadesse_bahnson_funk_thakur_morrow_wittum_degraves_rajala-schultz_gebreyes_2011, title={Prevalence and Antimicrobial Resistance Profile of Campylobacter Spp. Isolated from Conventional and Antimicrobial-Free Swine Production Systems from Different U.S. Regions}, volume={8}, ISSN={["1556-7125"]}, DOI={10.1089/fpd.2010.0665}, abstractNote={We conducted a study to compare the prevalence and antimicrobial resistance profile of Campylobacter isolated from 34 farm-slaughter pair cohorts of pigs raised in conventional and antimicrobial-free (ABF) production systems. Isolates originated from four different states of two geographic regions (region 1--Ohio and Michigan; region 2--Wisconsin and Iowa). A total of 838 fecal and 1173 carcass samples were examined. Campylobacter isolates were speciated using multiplex polymerase chain reaction targeting ceuE and hipO genes. The minimum inhibitory concentration was determined using agar dilution to a panel of six antimicrobials: chloramphenicol, erythromycin, gentamicin, ciprofloxacin, nalidixic acid, and tetracycline. Campylobacter spp. was isolated from 472 of 838 pigs (56.3%). Campylobacter prevalence did not vary significantly based on production system (conventional [58.9%] and ABF [53.7%], odds ratio [OR] 1.4, 95% confidence interval [CI] 0.8-2.6, p = 0.24) or geographic region (region 1 [54.1%] and region 2 [58.2%], OR 1.02, 95% CI 0.6-1.9, p = 0.92). At slaughter plant, Campylobacter prevalence varied based on processing stages (19.4% at pre-evisceration, 25.3% at postevisceration, and 3.2% at postchill). Resistance was common to tetracycline (64.5%), erythromycin (47.9%), and nalidixic acid (23.5%). Campylobacter isolates from conventional production systems were more likely to be erythromycin resistant than from ABF (OR 3.2, 95% CI 1.4-7.2, p = 0.01). The proportion of ciprofloxacin-resistant Campylobacter coli isolates were 3.7% and 1.2% from ABF and conventional production systems, respectively. Thirty-seven out of 1257 C. coli (2.9%) were resistant to both erythromycin and ciprofloxacin, drugs of choice for treatment of invasive human campylobacteriosis. The finding of ciprofloxacin resistance, particularly from ABF herds, has significant implications on the potential role of risk factors other than mere antimicrobial use for production purposes.}, number={3}, journal={FOODBORNE PATHOGENS AND DISEASE}, author={Tadesse, Daniel A. and Bahnson, Peter B. and Funk, Julie A. and Thakur, Siddhartha and Morrow, William E. Morgan and Wittum, Thomas and DeGraves, Fred and Rajala-Schultz, Paivi and Gebreyes, Wondwossen A.}, year={2011}, month={Mar}, pages={367–374} }
 @article{thakur_zhao_mcdermott_harbottle_abbott_english_gebreyes_white_2010, title={Antimicrobial Resistance, Virulence, and Genotypic Profile Comparison of Campylobacter jejuni and Campylobacter coli Isolated from Humans and Retail Meats}, volume={7}, ISSN={["1556-7125"]}, DOI={10.1089/fpd.2009.0487}, abstractNote={A total of 360 spatially and temporally related Campylobacter isolates, including 168 from clinical human cases (Campylobacter jejuni n = 148; Campylobacter coli n = 20) and 192 from retail meats (C. jejuni n = 114; C. coli n = 78), were analyzed for antimicrobial susceptibilities, virulence, and genotypic profiles. Ciprofloxacin-resistant C. jejuni was observed in 13.5% and 19% of the isolates from humans and retail chicken breasts, respectively. Antimicrobial resistance to ciprofloxacin and erythromycin was detected in C. coli isolates recovered from 29% and 16.6% of retail meats and 15% and 5% humans, respectively. Overall, virulence determinants were more prevalent in Campylobacter isolates recovered from retail meats than from humans. C. jejuni isolates from humans were significantly associated with the rakR, dnaJ, and pld genes, whereas C. coli isolates from retail meats were associated with the dnaJ, pld, and virB11 virulence genes. Genotyping of 262 C. jejuni isolates using pulsed-field gel electrophoresis revealed a total of 186 unique SmaI patterns, with 14% of patterns composed of isolates recovered from retail meats and ill humans. All unique groups with indistinguishable SmaI patterns were further analyzed by a second restriction enzyme (KpnI), which revealed limited overlap between isolates from different sources. Significant association between doxycycline-resistant C. jejuni strains recovered from humans and different virulence genes (e.g., cdtB) was identified at the statistical level but not at the genotypic level. In conclusion, significant differences observed in the distribution of antimicrobial resistance profiles, virulence determinants, and genotypic diversity among C. jejuni and C. coli isolates indicate that there are sources other than retail meats that may also contribute to human Campylobacter infections.}, number={7}, journal={FOODBORNE PATHOGENS AND DISEASE}, author={Thakur, Siddhartha and Zhao, Shaohua and McDermott, Patrick F. and Harbottle, Heather and Abbott, Jason and English, Linda and Gebreyes, Wondwossen A. and White, David G.}, year={2010}, month={Jul}, pages={835–844} }
 @article{thakur_gebreyes_2010, title={Phenotypic and Genotypic Heterogeneity of Campylobacter coli Within Individual Pigs at Farm and Slaughter in the US}, volume={57}, ISSN={["1863-2378"]}, DOI={10.1111/j.1863-2378.2010.01363.x}, abstractNote={Summary}, journal={ZOONOSES AND PUBLIC HEALTH}, author={Thakur, S. and Gebreyes, W. A.}, year={2010}, month={Nov}, pages={100–106} }
 @article{alali_thakur_berghaus_martin_gebreyes_2010, title={Prevalence and Distribution of Salmonella in Organic and Conventional Broiler Poultry Farms}, volume={7}, ISSN={["1556-7125"]}, DOI={10.1089/fpd.2010.0566}, abstractNote={The objective of this cross-sectional study was to compare the prevalence of Salmonella and antimicrobial-resistant Salmonella, as well as investigate the distribution of this pathogen in organic and conventional broiler poultry farms. Fecal (n = 420), feed (n = 140), and drinking water (n = 140) samples were collected from birds at 3 and 8 weeks of age for 2-flock cycles. One house was sampled per farm at three organic and four conventional broiler farms from the same company in North Carolina. All samples were analyzed for the presence of Salmonella using selective enrichment techniques. Further phenotypic (antimicrobial susceptibility) and genotypic (pulsed-field gel electrophoresis [PFGE]) testing were performed. Salmonella prevalences in fecal samples were 5.6% (10/180) and 38.8% (93/240) from organic and conventional farms, respectively. From feed, 5.0% (3/60) and 27.5% (22/80) of the samples were positive for Salmonella from organic and conventional farms, respectively. None of the water samples were positive for Salmonella. Seventy isolates were characterized by antimicrobial susceptibility and PFGE types. The two most common resistance phenotypes were single resistance to streptomycin (36.2% [25/58]: conventional; 25% [3/12] organic), and multidrug resistance to six antimicrobial agents: ampicillin-streptomycin-amoxicillin/clavulanic acid-cephalothin-ceftiofur-cefoxitin (AmStAxChCfFx; 39.7%: conventional only). Genotypic analysis using PFGE showed clonality among isolates within and between the two types of farms. The results of our study suggest that within this poultry company, the prevalence of fecal Salmonella was lower in certified-organic birds than in conventionally raised birds, and the prevalence of antimicrobial-resistant Salmonella was also higher in conventionally raised birds than in certified-organic birds.}, number={11}, journal={FOODBORNE PATHOGENS AND DISEASE}, author={Alali, Walid Q. and Thakur, Siddhartha and Berghaus, Roy D. and Martin, Michael P. and Gebreyes, Wondwossen A.}, year={2010}, month={Nov}, pages={1363–1371} }
 @article{thakur_putnam_fry_abley_gebreyes_2010, title={Prevalence of antimicrobial resistance and association with toxin genes in Clostridium difficile in commercial swine}, volume={71}, ISSN={["0002-9645"]}, DOI={10.2460/ajvr.71.10.1189}, abstractNote={Abstract}, number={10}, journal={AMERICAN JOURNAL OF VETERINARY RESEARCH}, author={Thakur, Siddhartha and Putnam, Michelle and Fry, Pamela R. and Abley, Melanie and Gebreyes, Wondwossen A.}, year={2010}, month={Oct}, pages={1189–1194} }
 @article{thakur_white_mcdermott_zhao_kroft_gebreyes_abbott_cullen_english_carter_et al._2009, title={Genotyping of Campylobacter coli isolated from humans and retail meats using multilocus sequence typing and pulsed-field gel electrophoresis}, volume={106}, ISSN={["1365-2672"]}, DOI={10.1111/j.1365-2672.2008.04142.x}, abstractNote={Aims:  To determine the antimicrobial resistant profiles and clonality of Campylobacter coli isolated from clinically ill humans and retail meats.}, number={5}, journal={JOURNAL OF APPLIED MICROBIOLOGY}, author={Thakur, S. and White, D. G. and McDermott, P. F. and Zhao, S. and Kroft, B. and Gebreyes, W. and Abbott, J. and Cullen, P. and English, L. and Carter, P. and et al.}, year={2009}, month={May}, pages={1722–1733} }
 @article{dorr_tadesse_zewde_fry_thakur_gebreyes_2009, title={Longitudinal Study of Salmonella Dispersion and the Role of Environmental Contamination in Commercial Swine Production Systems}, volume={75}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.01632-08}, abstractNote={ABSTRACT}, number={6}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Dorr, Paul M. and Tadesse, Daniel A. and Zewde, Bayleyegn Molla and Fry, Pamela and Thakur, Siddhartha and Gebreyes, Wondwossen A.}, year={2009}, month={Mar}, pages={1478–1486} }
 @article{gebreyes_thakur_dorr_tadesse_post_wolf_2009, title={Occurrence of spvA Virulence Gene and Clinical Significance for Multidrug-Resistant Salmonella Strains}, volume={47}, ISSN={["0095-1137"]}, DOI={10.1128/JCM.01660-08}, abstractNote={
            Nontyphoidal
            Salmonella
            strains are important reservoirs of antimicrobial resistance. An important issue that has not been investigated is whether the multiresistant
            Salmonella
            strains are more virulent than their susceptible counterparts.
            Salmonella
            isolates collected from clinical human (
            n
            = 888) and porcine (
            n
            = 2,120) cases at the same time period and geographic location were investigated. Antimicrobial susceptibility, PCR analysis for the
            spvA
            virulence gene, and pulsed-field gel electrophoresis (PFGE) genotyping were done. Carriage of
            spvA
            was associated with multidrug-resistant (MDR) type ACSSuT strains (odds ratio, 7.1;
            P
            < 0.05), a type often implicated in bacteremic human cases. PFGE revealed that clinical isolates from pigs were more clonally related to those of human origin than the nonclinical porcine isolates. The findings suggest that MDR strains that also carry specific virulence factors are more likely to be of clinical significance.
          }, number={3}, journal={JOURNAL OF CLINICAL MICROBIOLOGY}, author={Gebreyes, Wondwossen A. and Thakur, Siddhartha and Dorr, Paul and Tadesse, Daniel A. and Post, Karen and Wolf, Leslie}, year={2009}, month={Mar}, pages={777–780} }
 @article{thakur_morrow_funk_bahnson_gebreyes_2008, title={Molecular epidemiologic investigation of Campylobacter coli in swine production systems, using multilocus sequence typing (vol 72, pg 5666, 2006)}, volume={74}, ISSN={["0099-2240"]}, DOI={10.1128/aem.02326-07}, abstractNote={Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough St., Raleigh, North Carolina 27606; Department of Animal Science, North Carolina State University, Raleigh, North Carolina 27606; Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio; and Department of Medical Sciences, University of Wisconsin, Madison, Wisconsin}, number={1}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Thakur, Siddhartha and Morrow, W. E. Morgan and Funk, Julie A. and Bahnson, Peter B. and Gebreyes, Wondwossen A.}, year={2008}, month={Jan}, pages={342–342} }
 @article{thakur_tadesse_morrow_gebreyes_2007, title={Occurrence of multidrug resistant Salmonella in antimicrobial-free (ABF) swine production systems}, volume={125}, ISSN={["0378-1135"]}, DOI={10.1016/j.vetmic.2007.05.025}, abstractNote={This cross-sectional study was conducted to determine the prevalence and antimicrobial resistance of Salmonella species in swine reared in the intensive (indoor) and extensive (outdoor) ABF production systems at farm and slaughter in North Carolina, U.S.A. We sampled a total of 279 pigs at farm (extensive 107; intensive 172) and collected 274 carcass swabs (extensive 124; intensive 150) at slaughter. Salmonella species were tested for their susceptibility against 12 antimicrobial agents using the Kirby-Bauer disk diffusion method. Serogrouping was done using polyvalent and group specific antisera. A total of 400 salmonellae were isolated in this study with a significantly higher Salmonella prevalence from the intensive (30%) than the extensive farms (0.9%) (P<0.001). At slaughter, significantly higher Salmonella was isolated at the pre- and post-evisceration stages from extensively (29% pre-evisceration and 33.3% post-evisceration) than the intensively (2% pre-evisceration and 6% post-evisceration) reared swine (P<0.001). The isolates were clustered in six serogroups including B, C, E1, E4, G and R. Highest frequency of antimicrobial resistance was observed against tetracycline (78.5%) and streptomycin (31.5%). A total of 13 antimicrobial resistance patterns were observed including the pentaresistant strains with ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, tetracycline resistance pattern observed only among isolates from the intensive farms (n=28) and all were serotype Salmonella typhimurium var. Copenhagen. In conclusion, this study shows that multidrug resistant Salmonella are prevalent in ABF production systems despite the absence of antimicrobial selection pressure. In addition, it also highlights the possible role played by slaughterhouse and other environmental factors in the contamination and dissemination of antimicrobial resistant Salmonella in ABF production systems.}, number={3-4}, journal={VETERINARY MICROBIOLOGY}, author={Thakur, Siddhartha and Tadesse, Daniel A. and Morrow, Morgan and Gebreyes, Wondwossen A.}, year={2007}, month={Dec}, pages={362–367} }
 @article{gebreyes_thakur_morrow_2006, title={Comparison of prevalence, antimicrobial resistance, and occurrence of multidrug-resistant Salmonella in antimicrobial-free and conventional pig production}, volume={69}, ISSN={["1944-9097"]}, DOI={10.4315/0362-028x-69.4.743}, abstractNote={Conventional swine production evolved to routinely use antimicrobials, and common occurrence of antimicrobial-resistant Salmonella has been reported. There is a paucity of information on the antimicrobial resistance of Salmonella in swine production in the absence of antimicrobial selective pressure. Therefore, we compared the prevalence and antimicrobial resistance of Salmonella isolated from antimicrobial-free and conventional production systems. A total of 889 pigs and 743 carcasses were sampled in the study. Salmonella prevalence was significantly higher among the antimicrobial-free systems (15.2%) than the conventional systems (4.2%) (odds ratio [OR] = 4.23; P < 0.05). Antimicrobial resistance was detected against 10 of the 12 antimicrobials tested. The highest frequency of resistance was found against tetracycline (80%), followed by streptomycin (43.4%) and sulfamethoxazole (36%). Frequency of resistance to most classes of antimicrobials (except tetracycline) was significantly higher among conventional farms than antimicrobial-free farms, with ORs ranging from 2.84 for chloramphenicol to 23.22 for kanamycin at the on-farm level. A total of 28 antimicrobial resistance patterns were detected. A resistance pattern with streptomycin, sulfamethoxazole, and tetracycline (n = 130) was the most common multidrug resistance pattern. There was no significant difference in the proportion of isolates with this pattern between the conventional (19.5%) and the antimicrobial-free systems (18%) (OR = 1.8; P > 0.05). A pentaresistance pattern with ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, and tetracycline was strongly associated with antimicrobial-free groups (OR = 5.4; P = 0.01). While showing the higher likelihood of finding antimicrobial resistance among conventional herds, this study also implies that specific multidrug-resistant strains may occur on antimicrobial-free farms. A longitudinal study with a representative sample size is needed to reach more conclusive results of the associations detected in this study.}, number={4}, journal={JOURNAL OF FOOD PROTECTION}, author={Gebreyes, WA and Thakur, S and Morrow, WEM}, year={2006}, month={Apr}, pages={743–748} }
 @article{harbottle_thakur_zhao_white_2006, title={Genetics of Antimicrobial Resistance}, volume={17}, ISSN={1049-5398 1532-2378}, url={http://dx.doi.org/10.1080/10495390600957092}, DOI={10.1080/10495390600957092}, abstractNote={Antimicrobial resistant strains of bacteria are an increasing threat to animal and human health. Resistance mechanisms to circumvent the toxic action of antimicrobials have been identified and described for all known antimicrobials currently available for clinical use in human and veterinary medicine. Acquired bacterial antibiotic resistance can result from the mutation of normal cellular genes, the acquisition of foreign resistance genes, or a combination of these two mechanisms. The most common resistance mechanisms employed by bacteria include enzymatic degradation or alteration of the antimicrobial, mutation in the antimicrobial target site, decreased cell wall permeability to antimicrobials, and active efflux of the antimicrobial across the cell membrane. The spread of mobile genetic elements such as plasmids, transposons, and integrons has greatly contributed to the rapid dissemination of antimicrobial resistance among several bacterial genera of human and veterinary importance. Antimicrobial resistance genes have been shown to accumulate on mobile elements, leading to a situation where multidrug resistance phenotypes can be transferred to a susceptible recipient via a single genetic event. The increasing prevalence of antimicrobial resistant bacterial pathogens has severe implications for the future treatment and prevention of infectious diseases in both animals and humans. The versatility with which bacteria adapt to their environment and exchange DNA between different genera highlights the need to implement effective antimicrobial stewardship and infection control programs in both human and veterinary medicine.}, number={2}, journal={Animal Biotechnology}, publisher={Informa UK Limited}, author={Harbottle, H. and Thakur, S. and Zhao, S. and White, D. G.}, year={2006}, month={Dec}, pages={111–124} }
 @article{thakur_morrow_funk_bahnson_gebreyes_2006, title={Molecular epidemiologic investigation of Campylobacter coli in swine production systems, using multilocus sequence typing}, volume={72}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.00658-06}, abstractNote={ABSTRACT}, number={8}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Thakur, Siddhartha and Morrow, W. E. Morgan and Funk, Julie A. and Bahnson, Peter B. and Gebreyes, Wondwossen A.}, year={2006}, month={Aug}, pages={5666–5669} }
 @article{gebreyes_altier_thakur_2006, title={Molecular epidemiology and diversity of Salmonella serovar Typhimurium in pigs using phenotypic and genotypic approaches}, volume={134}, ISSN={["1469-4409"]}, DOI={10.1017/S0950268805004723}, abstractNote={SUMMARY}, number={1}, journal={EPIDEMIOLOGY AND INFECTION}, author={Gebreyes, WA and Altier, C and Thakur, S}, year={2006}, month={Feb}, pages={187–198} }
 @article{thakur_gebreyes_2005, title={Campylobacter coli in swine production: Antimicrobial resistance mechanisms and molecular epidemiology}, volume={43}, ISSN={["1098-660X"]}, DOI={10.1128/JCM.43.11.5705-5714.2005}, abstractNote={ABSTRACT}, number={11}, journal={JOURNAL OF CLINICAL MICROBIOLOGY}, author={Thakur, S and Gebreyes, WA}, year={2005}, month={Nov}, pages={5705–5714} }
 @article{gebreyes_thakur_morrow_2005, title={Campylobacter coli: prevalence and antimicrobial resistance in antimicrobial-free (ABF) swine production systems}, volume={56}, ISSN={["1460-2091"]}, DOI={10.1093/jac/dki305}, abstractNote={OBJECTIVES
To determine the prevalence and antimicrobial resistance of Campylobacter species in swine reared in the intensive and extensive antimicrobial-free (ABF) production systems at farm and slaughter. In the ABF system, antimicrobials are neither used for growth promotion nor therapeutic purposes.


METHODS
Swine faecal and carcass swabs were collected from 10 groups of pigs (five each from intensive and extensive ABF farms) at the finishing farm and the slaughter plant. A total of 292 pigs at farm (extensive 118; intensive 174) and 254 carcass swabs (extensive 134; intensive 120) were collected during the study. Campylobacter species were isolated under microaerobic conditions and confirmed by biochemical testing. Up to three presumptive Campylobacter colonies per positive pig/carcass were further characterized. Speciation was done by PCR, targeting ceuE and hipO genes for Campylobacter coli and Campylobacter jejuni, respectively. The isolates were tested for their antimicrobial resistance profile using the agar dilution method against six antimicrobials.


RESULTS
A total of 526 Campylobacter isolates were cultured from 292 pigs and 254 carcasses sampled. All the isolates were found to be C. coli. Overall prevalence of C. coli was 55.8% on farm (55% extensive and 56.3% intensive) and 26% at slaughter (32.8% extensive and 18.3% intensive). There was no significant difference in C. coli between the intensive and extensive systems on the finishing farms (P = 0.83). At post-chill stage, C. coli were isolated only from the extensively reared ABF pigs. Antimicrobial resistance against ciprofloxacin (MIC > 4 mg/L) was found at the farm level in both the intensive- and extensive-reared groups. The erythromycin/nalidixic acid/tetracycline resistance pattern (3%) was the most common pattern in multidrug-resistant C. coli.


CONCLUSIONS
This study highlights the high prevalence of diverse and antimicrobial-resistant C. coli in the ABF production systems of swine. This is the first study reporting the isolation of ciprofloxacin-resistant strains from ABF pigs in the USA and warrants concern.}, number={4}, journal={JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY}, author={Gebreyes, WA and Thakur, S and Morrow, WEM}, year={2005}, month={Oct}, pages={765–768} }
 @article{gebreyes_thakur_2005, title={Multidrug-resistant Salmonella enterica serovar Muenchen from pigs and humans and potential interserovar transfer of antimicrobial resistance}, volume={49}, ISSN={["1098-6596"]}, DOI={10.1128/AAC.49.2.503-511.2005}, abstractNote={ABSTRACT}, number={2}, journal={ANTIMICROBIAL AGENTS AND CHEMOTHERAPY}, author={Gebreyes, WA and Thakur, S}, year={2005}, month={Feb}, pages={503–511} }
 @article{thakur_gebreyes_2005, title={Prevalence and antimicrobial resistance of Campylobacter in antimicrobial-free and conventional pig production systems}, volume={68}, ISSN={["1944-9097"]}, DOI={10.4315/0362-028X-68.11.2402}, abstractNote={The objectives of this study were to determine and compare the prevalence and antimicrobial resistance of Campylobacter species in swine reared in conventional and antimicrobial-free (ABF) production systems. Campylobacter coli was the predominant species, with 1,459 isolates (99%) in the study. We found significantly higher prevalence of C. coli on the ABF farms (77.3%) than on the conventional farms (27.6%) among pigs at the nursery stage (P < 0.001). At slaughter, we found significantly higher prevalence at the postevisceration than at the preevisceration stage (P < 0.001) in both production systems. The 1,459 C. coli isolates were tested with the agar dilution method for their susceptibility to six antimicrobials: chloramphenicol, ciprofloxacin, erythromycin, gentamicin, nalidixic acid, and tetracycline. Resistance was most prevalent against tetracycline (66.2% of isolates) followed by erythromycin (53.6% of isolates). Frequency of resistance to these two antimicrobials was significantly higher among conventional herds (83.4% for tetracycline and 77% for erythromycin) than among ABF herds (56.2% for tetracycline and 34.5% for erythromycin). Resistance to ciprofloxacin at the MIC (> 4 mg/liter) was also found on farms in both systems. Multidrug-resistant C. coli strains were detected in both the conventional (7%) and ABF (4%) herds. This is the first report of ciprofloxacin-resistant strains of C. coli in ABF pigs in the United States. These findings highlight the high prevalence of antimicrobial-resistant C. coli in both conventional and ABF pig production systems and have significant implications for the persistence of antimicrobial-resistant Campylobacter in the pig production environment regardless of levels of antimicrobial use.}, number={11}, journal={JOURNAL OF FOOD PROTECTION}, author={Thakur, S and Gebreyes, WA}, year={2005}, month={Nov}, pages={2402–2410} }
 @article{gebreyes_davies_turkson_morgan morrow_funk_altier_thakur_2004, title={Characterization of Antimicrobial-Resistant Phenotypes and Genotypes among Salmonella enterica Recovered from Pigs on Farms, from Transport Trucks, and from Pigs after Slaughter}, volume={67}, ISSN={0362-028X}, url={http://jfoodprotection.org/doi/abs/10.4315/0362-028X-67.4.698}, DOI={10.4315/0362-028X-67.4.698}, abstractNote={The main objectives of this study were to determine antimicrobial resistance patterns among Salmonella serotypes and to evaluate the role of transport trucks in dissemination of antimicrobial-resistant strains of Salmonella. Salmonella from groups of nursery and finishing pigs on farms, from trucks, and from pigs after slaughter were compared using serotyping, patterns of antimicrobial resistance, and pulsed-field gel electrophoresis patterns. The five farms included in the study yielded 858 isolates representing 27 Salmonella serovars. The most common resistance observed (80% of all isolates) was to tetracycline; resistance to ampicillin (42%), chloramphenicol (31%), amoxicillin/clavulanic acid (30%), and piperacillin (31%) also were common. We found a correlation between serovar and antimicrobial resistance. High correlation was found between Salmonella Typhimurium var. Copenhagen and chloramphenicol resistance (Spearman rank correlation, rho = 0.7). Multidrug resistance was observed primarily in Salmonella Typhimurium var. Copenhagen (94%) and Salmonella Typhimurium (93%) and was much less common in the other common serovars, including Salmonella Derby (7%) and Salmonella Heidelberg (8%). Of the 225 isolates exhibiting the most common pentaresistance pattern in this study, amoxicillin/clavulanic acid-ampicillin-chloramphenicol-piperacillin-tetracycline, 220 (98%) were Salmonella Typhimurium var. Copenhagen, and 86% of the isolates of this serovar had this pattern. Isolates from the trucks were similar, based on pulsed-field gel electrophoresis patterns, to those from the cecum and mesenteric lymph nodes of pigs on two of the farms, suggesting the probable infection of pigs during transport. Class I integrons were also common among various serovars.}, number={4}, journal={Journal of Food Protection}, author={Gebreyes, Wondwossen A. and Davies, Peter R. and Turkson, Paa-Kobina and Morgan Morrow, W. E. and Funk, Julie A. and Altier, Craig and Thakur, Siddhartha}, year={2004}, month={Apr}, pages={698–705} }
 @article{gebreyes_thakur_davies_funk_altier_2004, title={Trends in antimicrobial resistance, phage types and integrons among Salmonella serotypes from pigs, 1997-2000}, volume={53}, ISSN={["1460-2091"]}, DOI={10.1093/jac/dkh247}, abstractNote={OBJECTIVES
The objectives of this study were to determine antimicrobial resistance and to identify phage types and class 1 integrons among non-typhoidal Salmonella isolates from 24 pig farms in North Carolina collected between 1997 and 2000.


METHODS
A total of 1314 isolates of 30 serotypes from pig faecal samples were collected and analysed over a 3 year period. The isolates were characterized using antimicrobial susceptibility testing, phage typing, PCR and DNA sequencing for class 1 integrons.


RESULTS
A high frequency of resistance to antimicrobial agents including tetracycline (85%), ampicillin (47%), co-amoxiclav (23%) and chloramphenicol (21%) was detected. Two multidrug resistance patterns were common in Typhimurium (including variant Copenhagen): isolates with co-amoxiclav, ampicillin, chloramphenicol, streptomycin, sulfamethoxazole and tetracycline (R-type AxACSSuT) [36%] and isolates with ampicillin, kanamycin, streptomycin, sulfamethoxazole and tetracycline (R-type AKSSuT) [45%] resistance patterns. Definitive Type 104 (DT104) was the most common (34%) among eight phage types identified. AKSSuT was found among non-DT104 phage types, particularly DT21 and DT193. Class 1 integrons were detected among various serotypes including Typhimurium, Derby, Muenchen, Worthington, Bere and Muenster. aadA was the most common resistance gene insert, and the oxa30 beta-lactamase resistance gene was also identified among serovar Muenchen.


CONCLUSIONS
In this study, two most important multidrug resistance patterns (AxACSSuT and AKSSuT) and phage types of public health significance (DT104 and DT193) constituted two-thirds of the serotype Typhimurium isolates. The findings imply that pigs raised in the commercial production system may pose a risk in serving as reservoirs of resistant Salmonella.}, number={6}, journal={Journal of Antimicrobial Chemotherapy}, author={Gebreyes, W.A. and Thakur, S. and Davies, P.R. and Funk, J.A. and Altier, C.}, year={2004}, month={Jun}, pages={997–1003} }
 @article{gebreyes_thakur_2003, title={Molecular Epidemiology of Multi-drug resistant Salmonella enterica serovar Typhimurium isolated from Swine and Humans}, volume={2}, journal={Infection, Genetics and Evolution}, author={Gebreyes, W.A. and Thakur, S.}, year={2003}, pages={277} }