Decoding Klebsiella pneumoniae in Poultry Chain: Unveiling Genetic Landscape, Antibiotic Resistance, and Biocide Tolerance in Non-Clinical Reservoirs

Abstract

<jats:title>Abstract</jats:title><jats: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)<jats:italic>Klebsiella pneumoniae</jats:italic>. However, limited knowledge exists about the population structure and genomic diversity of<jats:italic>K. pneumoniae</jats:italic>circulating in conventional poultry production. We conducted a comprehensive characterization of<jats:italic>K. pneumoniae</jats:italic>across the whole chicken production chain (flocks/environment/meat, 2019-2022), exploring factors beyond antibiotics, like copper and quaternary ammonium compounds (QACs). Clonal diversity and adaptive features of<jats:italic>K. pneumoniae</jats:italic>were characterized through cultural, molecular (FT-IR), and whole-genome-sequencing (WGS) approaches. All except one flock were positive for<jats:italic>K. pneumoniae</jats:italic>with a significant increase (p < 0.05) from early to pre-slaughter stages, most persisting in chicken meat batches. Colistin-resistant<jats:italic>K. pneumoniae</jats:italic>rates were low (4%), while most samples carried MDR strains (67%) and copper-tolerant isolates (63%;<jats:italic>sil</jats:italic>+<jats:italic>pco</jats:italic>clusters; MIC<jats:sub>CuSO4</jats:sub>16mM), particularly at pre-slaughter. Benzalkonium chloride consistently exhibited activity in<jats:italic>K. pneumoniae</jats:italic>(MIC/MBC range=4-64mg/L) from diverse and representative strains independently of the presence/absence of genes linked to QACs tolerance. A polyclonal<jats:italic>K. pneumoniae</jats:italic>population, discriminated by FT-IR and WGS, included various lineages dispersed throughout the chickens 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<jats:italic>sil</jats:italic>+<jats:italic>pco</jats:italic>(copper) co-located with<jats:italic>qacE</jats:italic>1±<jats:italic>qacF</jats:italic>(QACs) and antibiotic resistance genes like those disseminated in humans. In conclusion, chicken farms and their derived meat are significant reservoirs for diverse<jats:italic>K. pneumoniae</jats: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<jats:italic>K. pneumoniae</jats: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.</jats:p>