@article{parzygnat_crespo_fosnaught_muyyarrikkandy_hull_harden_thakur_2024, title={Megaplasmid Dissemination in Multidrug-Resistant <i>Salmonella</i> 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{parzygnat_crespo_koci_dunn_harden_fosnaught_thakur_2024, title={Widespread prevalence of plasmid-mediated <i>bla</i><sub>CTX-M</sub> type extended-spectrum beta-lactamase <i>Escherichia coli</i> 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{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}, number={5}, journal={MICROBIOLOGY SPECTRUM}, author={Muyyarikkandy, Muhammed Shafeekh and Parzygnat, Jessica and Thakur, Siddhartha}, editor={Steven, BlaireEditor}, year={2023} }