Whole genome sequencing revealed high occurrence of antimicrobial resistance genes in bacteria isolated from poultry manure

Tripathi, A; Jaiswal, A; Kumar, D; Pandit, R; Blake, D; Tomley, F; Joshi, M; Joshi, CG; Dubey, SK

Abstract

Background: Global demand for food has driven expansion and intensification of livestock production, particularly in developing nations where antibiotic use is often routine. Waste from poultry production, including manure, is commonly utilized as fertilizers in agroecosystems, risking environmental contamination with potentially zoonotic bacteria and antimicrobial resistance genes (ARGs). Methods: Here, 33 bacterial isolates were recovered from broiler ( n = 17) and layer ( n = 16) chicken manure by aerobic culture using Luria Bertani agar. Antimicrobial susceptibility testing (AST) was performed using disc diffusion method. MALDI-ToF and 16S rRNA sequencing were used to identify and compare a subset of antibiotic-resistant isolates ( n = 13). Comparison of whole genome sequence assemblies and phenotypic assays were used to assess capacity for biofilm formation, heavy metal tolerance and virulence. Results: AST by disc diffusion revealed all isolates were resistant to a minimum of three antibiotics, with resistance to ampicillin, co-trimoxazole, fluoroquinolones, tetracyclines, streptomycin, rifampicin and/or chloramphenicol detected. Stutzerimonas sp. and Acinetobacter sp. were the common genera observed in this study. Genome sequencing of each selected isolate revealed carriage of multiple ARGs capable of conferring resistance to many antimicrobials commonly employed in poultry production and human medicine, including tetracyclines, quinolones, macrolides, sulfonamide and cephalosporins. Conclusions: The high occurrence of ARGs in studied bacterial isolates confirms that poultry manure could act as a source of genetic material that could be transferred to commensal microbiota and opportunistic pathogens of humans. Understanding the complex resistome interplay between humans, animals, and the environment requires a One Health approach, with implications for agricultural settings and public health. (c) 2025 Elsevier Ltd and International Society of Antimicrobial Chemotherapy. All rights are reserved, including those for text and data mining, AI training, and similar technologies.

Citation

Tripathi, A., Jaiswal, A., Kumar, D., Pandit, R., Blake, D., Tomley, F., Joshi, M., Joshi, C., & Dubey, S. (2025). Whole genome sequencing revealed high occurrence of antimicrobial resistance genes in bacteria isolated from poultry manure. International Journal of Antimicrobial Agents, 65(3), https://doi.org/10.1016/j.ijantimicag.2025.107452

• Journal Article Type: Article
• Acceptance Date: Jan 22, 2025
• Online Publication Date: Jan 27, 2025
• Publication Date: 2025
• Deposit Date: Apr 8, 2025
• Publicly Available Date: Jan 28, 2026
• Print ISSN: 0924-8579
• Publisher: Elsevier
• Peer Reviewed: Peer Reviewed
• Volume: 65
• Issue: 3
• DOI: https://doi.org/10.1016/j.ijantimicag.2025.107452
• Keywords: Agriculture; Poultry litter; One Health; Antimicrobial resistance; Heavy metals; Resistome; ANTIBIOTIC-RESISTANCE; HEAVY-METALS; ESCHERICHIA-COLI; SWINE MANURE; QUALITY; ACCUMULATION; PREVALENCE; ADHERENCE; DYNAMICS; SAMPLES