Pankaj Gaonkar

Antimicrobial resistance (AMR) is a threat to the poultry industry, resulting in significant economic losses due to reduced effectiveness of therapeutic antimicrobials. AMR transmission can occur between animals, humans, and the environment, yet environmental AMR remains understudied. This study investigated i) AMR and antimicrobial residue levels in the farm environment, and ii) their association across different stages of vertically integrated poultry production systems. Litter and soil samples were collected from pullet, breeder, and broiler farms from a vertically integrated commercial broiler production complexes practicing restricted antimicrobial use. Broiler flocks were followed to the processing plant, where carcass rinses were collected at post-pick and post-chill stages. Quantitative PCR was used to detect 3 mobile genetic elements (MGEs) and 14 antimicrobial resistance genes (ARGs). High performance liquid chromatography-tandem mass spectrometry was used to detect antimicrobial residues in the litter and soil. Generalized linear models evaluated the effects of farm and sample type on ARGs and MGEs quantification and association with antimicrobial residue levels. ARGs and MGEs quantification was higher in litter than soil in breeder and broiler farms, but comparable in pullet farms. ARGs quantification in litter was higher in broiler than pullet stages, while in soil it remained comparable. In processing plant samples, ARGs quantification did not differ between post-pick and post-chill stages. Sulfamethoxazole, tetracycline, and oxytetracycline residues were higher in the early stages of production and positively associated with the MGEs levels in litter. Litter is a hotspot for AMR and antimicrobial residues may enhance MGE quantification, facilitating ARGs dissemination. Comprehensive AMR surveillance should include environmental monitoring to address the multifactorial drivers of AMR in poultry production system.

Avian pathogenic Escherichia coli (APEC) poses a threat to poultry and public health due to its ability to cause avian disease, potentially contribute to foodborne illness, and carry antimicrobial resistance genes (ARGs). Given its ubiquitous nature and capacity to persist in diverse environments, APEC has potential as a marker organism for tracking antimicrobial resistance (AMR) in poultry production systems and surrounding environments. This study investigated the prevalence, genotypic diversity, AMR profile, and potential transmission of APEC across different production stages in commercial, vertically integrated broiler operations. APEC isolates were recovered from environmental samples across the production chain, including pullet, breeder, and broiler farms as well as processing plants. E. coli isolates were classified as APEC if carrying three or more out of five virulence genes. Whole genome sequencing was conducted on 42 APECs. We determined their serotypes, phylogroups, sequence types (ST), and AMR profiles and constructed a single-nucleotide polymorphism (SNP)-based phylogenetic tree. High-risk APEC strains were detected, with ST131 recovered at the post-chill stage, raising food safety concerns. All isolates shared a core resistome, while several ARGs were differently distributed across sample types. SNP analysis revealed genetically closely related APEC strains inside the poultry house and the adjacent outside environment, and critically, between broiler litter and carcass rinses collected at the processing plant that processed the same flock. We demonstrate APEC carrying clinically relevant ARGs spread within farm environment and along the production chain, supporting its utility for AMR surveillance. IMPORTANCE: Avian pathogenic Escherichia coli (APEC) is a threat to poultry production and public health due to its ability to cause avian disease, economic losses, potential foodborne implications, and ability to carry antimicrobial resistance genes (ARGs) relevant to human health. In this study, we proposed APEC as a potential marker organism of antimicrobial resistance (AMR) due to its capacity to persist in diverse environments. Our findings show that APEC, across the vertically integrated poultry production chain, harbored clinically important ARGs and exhibited resistance to antimicrobials of human health importance. We also identified evidence of APEC transmission within the farm environment and into the processing plant, with the potential to reach consumers. By examining multiple stages of production and diverse environmental samples, our study provides a more comprehensive understanding of APEC ecology, its resistome, and dissemination. These insights highlight APEC’s utility as a marker organism for AMR surveillance in poultry production.

Antimicrobial residues excreted in the environment following antimicrobial treatment enhance resistant microbial communities in the environment and have long-term effects on the selection and maintenance of antimicrobial resistance genes (AMRGs). In this study, we focused on understanding the impact of antimicrobial use on antimicrobial residue pollution and antimicrobial resistance (AMR) in the environment of horse-breeding farms. Rhodococcus equi is an ideal microbe to study these associations because it lives naturally in the soil, exchanges AMRGs with other bacteria in the environment, and can cause disease in animals and humans. The environment is the main source of R. equi infections in foals; therefore, higher levels of multidrug-resistant (MDR) R. equi in the environment contribute to clinical infections with MDR R. equi. We found that macrolide residues in the environment of horse-breeding farms and the use of thoracic ultrasonographic screening (TUS) for early detection of subclinically affected foals with R. equi infections were strongly associated with the presence of R. equi carrying AMRGs in the soil. Our findings indicate that the use of TUS contributed to historically higher antimicrobial use in foals, leading to the accumulation of antimicrobial residues in the environment and enhancing MDR R. equi.

International Journal of Current Microbiology and Applied Sciences ISSN:2319-7692(Print), ISSN:2319-7706(Online) is a multidisciplinary peer-reviewed journal with reputable academics and experts as members of its Editorial Board. The Current Microbiology aims to publish all the latest and outstanding research articles. Review and letters in all areas of major importance to techniques of microbiology and applied research with publishes high quality of review and research articles on novel aspects of Microbiology including Environmental, Food, Agricultural, Medical, Pharmaceutical, Veterinary, Soil, Water and Biodeterioration.