@article{aworh_thakur_gensler_harrell_harden_fedorka-cray_jacob_2024, title={Characteristics of antimicrobial resistance in Escherichia coli 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).
Materials and 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 was 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 multidrug resistant (MDR: being resistant to ≥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{parzygnat_dunn_koci_crespo_harden_thakur_2024, title={Fluoroquinolone-resistant Campylobacter in backyard and commercial broiler production systems in the United States}, volume={6}, ISSN={["2632-1823"]}, DOI={10.1093/jacamr/dlae102}, abstractNote={Abstract Objectives Campylobacter spp. are one of the leading foodborne pathogens in the world, and chickens are a known reservoir. This is significant considering broiler chicken is the top consumed meat worldwide. In the USA, backyard poultry production is increasing, but little research has been done to investigate prevalence and antimicrobial resistance associated with Campylobacter in these environments. Methods Our study encompasses a farm-to-genome approach to identify Campylobacter and investigate its antimicrobial resistance phenotypically and genotypically. We travelled to 10 backyard and 10 integrated commercial broiler farms to follow a flock throughout production. We sampled at days 10, 31 and 52 for backyard and 10, 24 and 38 for commercial farms. Bird faecal (n = 10) and various environmental samples (soil n = 5, litter/compost n = 5, and feeder and waterer swabs n = 6) were collected at each visit and processed for Campylobacter. Results Our results show a higher prevalence of Campylobacter in samples from backyard farms (21.9%) compared to commercial (12.2%). Most of our isolates were identified as C. jejuni (70.8%) and the remainder as C. coli (29.2%). Antimicrobial susceptibility testing reveals phenotypic resistance to ciprofloxacin (40.2%), an important treatment drug for Campylobacter infection, and tetracycline (46.6%). A higher proportion of resistance was found in C. jejuni isolates and commercial farms. Whole-genome sequencing revealed resistance genes, such as tet(O) and gyrA_T86I point mutation, that may confer resistance. Conclusion Overall, our research emphasizes the need for interventions to curb prevalence of resistant Campylobacter spp. on broiler production systems.}, number={4}, journal={JAC-ANTIMICROBIAL RESISTANCE}, author={Parzygnat, Jessica L. and Dunn, Robert R. and Koci, Matthew D. and Crespo, Rocio and Harden, Lyndy and Thakur, Siddhartha}, year={2024}, month={Jul} }
@article{parzygnat_crespo_fosnaught_muyyarrikkandy_hull_harden_thakur_2024, title={Megaplasmid Dissemination in Multidrug-Resistant Salmonella Serotypes from Backyard and Commercial Broiler Production Systems in the Southeastern United States}, volume={4}, ISSN={["1556-7125"]}, DOI={10.1089/fpd.2023.0181}, abstractNote={Over the past decade, there has been a rise in U.S. backyard poultry ownership, raising concern for residential area antimicrobial-resistant (AMR) Salmonella contamination. This study aims to lay the groundwork to better understand the persistence of AMR Salmonella in residential broiler production systems and make comparisons with commercial systems. Ten backyard and 10 commercial farms were sampled at three time points across bird production. Both fecal (n = 10) and environmental (soil, n = 5, litter/compost, n = 5, feeder, and waterer swabs, n = 6) samples were collected at each visit on days 10, 31, and 52 of production for backyard farms and days 10, 24, and 38 of production for commercial farms. AMR Salmonella was characterized phenotypically by broth microdilution and genotypically by whole-genome sequencing. Overall, Salmonella was more prevalent in commercial farm samples (52.31%) over backyard farms (19.10%). Kentucky (sequence type (ST) 152) was the most common serotype found in both backyard and commercial farms. Multidrug-resistant (MDR, resistance to ≥3 or more antimicrobial classes) isolates were found in both production systems, while ciprofloxacin- and nalidixic acid-resistant and intermediate isolates were more prevalent in commercial (33%) than backyard samples (1%). Plasmids that have been associated with MDR were found in Kentucky and Infantis isolates, particularly IncFIB(K)_1_Kpn3 megaplasmid (Infantis). Our study emphasizes the need to understand the selection pressures in disseminating megaplasmids in MDR Salmonella in distinct broiler production systems.}, journal={FOODBORNE PATHOGENS AND DISEASE}, author={Parzygnat, Jessica L. and Crespo, Rocio and Fosnaught, Mary and Muyyarrikkandy, Muhammed and Hull, Dawn and Harden, Lyndy and Thakur, Siddhartha}, year={2024}, month={Apr} }
@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{parzygnat_crespo_koci_dunn_harden_fosnaught_thakur_2024, title={Widespread prevalence of plasmid-mediated blaCTX-M type extended-spectrum beta-lactamase Escherichia coli in backyard broiler production systems in the United States}, volume={19}, ISSN={["1932-6203"]}, url={https://doi.org/10.1371/journal.pone.0304599}, DOI={10.1371/journal.pone.0304599}, abstractNote={Extended-spectrum beta-lactamase (ESBL) Escherichia coli ( E . coli ) is an emerging pathogen of high concern given its resistance to extended-spectrum cephalosporins. Broiler chicken, which is the number one consumed meat in the United States and worldwide, can be a reservoir of ESBL E . coli . Backyard poultry ownership is on the rise in the United States, yet there is little research investigating prevalence of ESBL E . coli in this setting. This study aims to identify the prevalence and antimicrobial resistance profiles (phenotypically and genotypically) of ESBL E . coli in some backyard and commercial broiler farms in the U.S. For this study ten backyard and ten commercial farms were visited at three time-points across flock production. Fecal (n = 10), litter/compost (n = 5), soil (n = 5), and swabs of feeders and waterers (n = 6) were collected at each visit and processed for E . coli . Assessment of ESBL phenotype was determined through using disk diffusion with 3 rd generation cephalosporins, cefotaxime and ceftazidime, and that with clavulanic acid. Broth microdilution and whole genome sequencing were used to investigate both phenotypic and genotypic resistance profiles, respectively. ESBL E . coli was more prevalent in backyard farms with 12.95% of samples testing positive whereas 0.77% of commercial farm samples were positive. All isolates contained a bla CTX-M gene, the dominant variant being bla CTX-M-1 , and its presence was entirely due to plasmids. Our study confirms concerns of growing resistance to fourth generation cephalosporin, cefepime, as roughly half (51.4%) of all isolates were found to be susceptible dose-dependent and few were resistant. Resistance to non-beta lactams, gentamicin and ciprofloxacin, was also detected in our samples. Our study identifies prevalence of bla CTX-M type ESBL E . coli in U.S. backyard broiler farms, emphasizing the need for interventions for food and production safety.}, number={6}, journal={PLOS ONE}, author={Parzygnat, Jessica L. and Crespo, Rocio and Koci, Matthew D. and Dunn, Robert R. and Harden, Lyndy and Fosnaught, Mary and Thakur, Siddhartha}, editor={Trueba, GabrielEditor}, year={2024}, month={Jun} }
@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.
}, 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{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 entericais the most common foodborne pathogen worldwide. It causes two types of diseases, a self-limiting gastroenteritis and an invasive, more threatening, infection.Salmonellagastroenteritis 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 NontyphoidalSalmonella(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 ofSalmonellaisolated 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 invasiveSalmonella. 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 ofSalmonellaand AMR in order to address invasive salmonellosis caused by nontyphoidalSalmonellastrains 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={AbstractInfections 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 blaCTX-M-15 genes detected in 75 (70.1%) isolates. The carbapenemase genes blaNDM-1 and blaNDM-5 were detected in six (5.6%), while the AmpC gene- blaCMY-2, was detected in seven (6.5%) isolates. Two (1.9%) isolates simultaneously harboured the blaOXA-1, blaCMY-2, blaCTX-M-15, and blaNDM-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{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={Abstract
Background
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.
Methods
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.
Results
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.
Conclusions
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{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{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://doi.org/10.3390/pathogens10111480}, 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{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{stevens_frantz_orlando_griffith_harden_gruen_sherman_2016, title={Efficacy of a single dose of trazodone hydrochloride given to cats prior to veterinary visits to reduce signs of transport- and examination-related anxiety}, volume={249}, ISSN={0003-1488}, url={http://dx.doi.org/10.2460/javma.249.2.202}, DOI={10.2460/javma.249.2.202}, abstractNote={Abstract
OBJECTIVE To evaluate the efficacy of a single dose of trazodone for reducing anxiety in cats during transport to a veterinary hospital and facilitating handling during veterinary examination.
DESIGN Double-blind, placebo-controlled, randomized crossover study.
ANIMALS 10 healthy client-owned cats (2 to 12 years of age) with a history of anxiety during transport or veterinary examination.
PROCEDURES Each cat was randomly assigned to first receive trazodone hydrochloride (50 mg) or a placebo PO. The assigned treatment was administered, and each cat was placed in a carrier and transported by car to a veterinary clinic, where it received a structured veterinary examination. Owners scored their cat's signs of anxiety before, during, and after transport and examination. The veterinarian also assessed signs of anxiety during examination. After a 1- to 3-week washout period, each cat received the opposite treatment and the protocol was repeated.
RESULTS Compared with placebo, trazodone resulted in a significant improvement in the cats’ signs of anxiety during transport. Veterinarian and owner scores for ease of handling during veterinary examination also improved with trazodone versus the placebo. No significant differences were identified between treatments in heart rate or other physiologic variables. The most common adverse event related to trazodone administration was signs of sleepiness.
CONCLUSIONS AND CLINICAL RELEVANCE Oral administration of a single dose of trazodone to cats prior to a veterinary visit resulted in fewer signs of transport- and examination-related anxiety than did a placebo and was generally well tolerated by most cats. Use of trazodone in this manner may promote veterinary visits and, consequently, enhance cat welfare.}, number={2}, journal={Journal of the American Veterinary Medical Association}, publisher={American Veterinary Medical Association (AVMA)}, author={Stevens, Brenda J. and Frantz, Eva and Orlando, Jillian M. and Griffith, Emily and Harden, Lyndy and Gruen, Margaret E. and Sherman, Barbara L.}, year={2016}, month={Jul}, pages={202–207} }