DecodingKlebsiella pneumoniaein Poultry Chain: Unveiling Genetic Landscape, Antibiotic Resistance, and Biocide Tolerance in Non-Clinical Reservoirs

Abstract

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)Klebsiella pneumoniae. However, limited knowledge exists about the population structure and genomic diversity ofK. pneumoniaecirculating in conventional poultry production. We conducted a comprehensive characterization ofK. pneumoniaeacross 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 ofK. pneumoniaewere characterized through cultural, molecular (FT-IR), and whole-genome-sequencing (WGS) approaches. All except one flock were positive forK. pneumoniaewith a significant increase (p < 0.05) from early to pre-slaughter stages, most persisting in chicken meat batches. Colistin-resistantK. pneumoniaerates were low (4%), while most samples carried MDR strains (67%) and copper-tolerant isolates (63%;sil+pcoclusters; MICCuSO4≥16mM), particularly at pre-slaughter. Benzalkonium chloride consistently exhibited activity inK. pneumoniae(MIC/MBC range=4-64mg/L) from diverse and representative strains independently of the presence/absence of genes linked to QACs tolerance. A polyclonalK. pneumoniaepopulation, 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 carryingsil+pco(copper) co-located withqacEΔ1±qacF(QACs) and antibiotic resistance genes like those disseminated in humans. In conclusion, chicken farms and their derived meat are significant reservoirs for diverseK. pneumoniaeclones enriched in antibiotic resistance and metal tolerance genes, some exhibiting genetic similarities with human clinical strains. Further research is imperative to unravel the factors influencingK. pneumoniaepersistence 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.