@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{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{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.
}, number={5}, journal={MICROBIOLOGY SPECTRUM}, author={Muyyarikkandy, Muhammed Shafeekh and Parzygnat, Jessica and Thakur, Siddhartha}, editor={Steven, BlaireEditor}, year={2023} }