@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{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={Abstract}, 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{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)Campylobacteras 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 investigatedC.coliandC.jejunifrom 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) (neuABCandcst-IIorcst-III), and phylogenic linkage between 541Campylobacterisolates (C.colin = 343,C.jejunin = 198). Overall, 90.4% (489/541)Campylobacterisolates 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.jejunicarried GBS virulence factors, while threeC.colicarried theC.jejuni-like lipooligosaccharide locus,neuABCand cst-II. Further evidence ofC.coliandC.jejuniinterspecies genomic exchange was observed in identical multilocus sequence typing, shared sequence type (ST) 7818 clonal complex 828, and identical species-indicator genesmapA,ceuE, andhipO. There was a significant increase in novel STs from 2018 to 2019 (2 in 2018 and 21 in 2019, p<0.002), illustrating variableCampylobactergenomes within food animal production. Introgression betweenC.coliandC.jejunimay aid pathogen adaption, lead to higher AMR and increaseCampylobacterpersistence 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{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{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{aworh_kwaga_okolocha_harden_hull_hendriksen_thakur_2020, title={Extended-spectrum ß-lactamase-producing Escherichia coli among humans, chickens and poultry environments in Abuja, Nigeria}, volume={2}, ISSN={2524-4655}, url={http://dx.doi.org/10.1186/s42522-020-00014-7}, DOI={10.1186/s42522-020-00014-7}, abstractNote={Abstract}, number={1}, journal={One Health Outlook}, publisher={Springer Science and Business Media LLC}, author={Aworh, Mabel Kamweli and Kwaga, Jacob and Okolocha, Emmanuel and Harden, Lyndy and Hull, Dawn and Hendriksen, Rene S. and Thakur, Siddhartha}, year={2020}, month={May} }