AUTHOR=Mourão Joana , Magalhães Mafalda , Ribeiro-Almeida Marisa , Rebelo Andreia , Novais Carla , Peixe Luísa , Novais Ângela , Antunes Patrícia 

TITLE=Decoding Klebsiella pneumoniae in poultry chain: unveiling genetic landscape, antibiotic resistance, and biocide tolerance in non-clinical reservoirs

JOURNAL=Frontiers in Microbiology

VOLUME=15

YEAR=2024

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2024.1365011

DOI=10.3389/fmicb.2024.1365011

ISSN=1664-302X

ABSTRACT=<p>The rise of antibiotic resistance in the food chain is influenced by the use of antimicrobial agents, such as antibiotics, metals, and biocides, throughout the entire farm-to-fork continuum. Besides, non-clinical reservoirs potentially contribute to the transmission of critical pathogens such as multidrug-resistant (MDR) <italic>Klebsiella pneumoniae</italic>. However, limited knowledge exists about the population structure and genomic diversity of <italic>K. pneumoniae</italic> circulating in conventional poultry production. We conducted a comprehensive characterization of <italic>K. pneumoniae</italic> across the whole chicken production chain (7 farms; 14 flocks + environment + meat, 56 samples; 2019–2022), exploring factors beyond antibiotics, like copper and quaternary ammonium compounds (QACs). Clonal diversity and adaptive features of <italic>K. pneumoniae</italic> were characterized through cultural, molecular (FT-IR), and whole-genome-sequencing (WGS) approaches. All except one flock were positive for <italic>K. pneumoniae</italic> with a significant increase (<italic>p</italic> &lt; 0.05) from early (<italic>n</italic> = 1/14) to pre-slaughter (<italic>n</italic> = 11/14) stages, most (<italic>n</italic> = 6/7) persisting in chicken meat batches. Colistin-resistant <italic>K. pneumoniae</italic> rates were low (4%-<italic>n</italic> = 1/24 positive samples), while most samples carried MDR strains (67%-<italic>n</italic> = 16/24) and copper-tolerant isolates (63%-<italic>n</italic> = 15/24, with <italic>sil</italic> and <italic>pco</italic> gene clusters; MIC<sub>CuSO4</sub> ≥ 16 mM), particularly at pre-slaughter. Benzalkonium chloride consistently exhibited activity against <italic>K. pneumoniae</italic> (MIC/MBC range = 4–64 mg/L) from representative strains independently of the presence or absence of genes linked to QACs tolerance. A polyclonal <italic>K. pneumoniae</italic> population, discriminated by FT-IR and WGS, included various lineages dispersed throughout the chicken’s lifecycle at the farm (ST29-KL124, ST11-KL106, ST15-KL19, ST1228-KL38), until the meat (ST1-KL19, ST11-KL111, ST6405-KL109, and ST6406-CG147-KL111), or over years (ST631-49 KL109, ST6651-KL107, ST6406-CG147-KL111). Notably, some lineages were identical to those from human clinical isolates. WGS also revealed F-type multireplicon plasmids carrying <italic>sil</italic> + <italic>pco</italic> (copper) co-located with <italic>qacE</italic>Δ1 ± <italic>qacF</italic> (QACs) and antibiotic resistance genes like those disseminated in humans. In conclusion, chicken farms and their derived meat are significant reservoirs for diverse <italic>K. pneumoniae</italic> clones enriched in antibiotic resistance and metal tolerance genes, some exhibiting genetic similarities with human clinical strains. Further research is imperative to unravel the factors influencing <italic>K. pneumoniae</italic> persistence and dissemination within poultry production, contributing to improved food safety risk management. This study underscores the significance of understanding the interplay between antimicrobial control strategies and non-clinical sources to effectively address the spread of antimicrobial resistance.</p>