Characterization of antimicrobial resistance carriage in Klebsiella pneumoniae and Enterobacter cloacae
This study highlights the importance of broadening the focus beyond Escherichia coli (E. coli) when monitoring antimicrobial resistance (AMR) in the food chain. While E. coli is commonly used as an indicator of AMR spread, it's essential not to underestimate the role of other Enterobacteriaceae, such as Klebsiella pneumoniae and Enterobacter cloacae. Our findings indicate that K. pneumoniae and E. cloacae, isolated from the same sample origin and host species, harbour more AMR genes compared to E. coli. K. pneumoniae, known for facilitating multidrug resistance (MDR), displays intrinsic resistance to ampicillin due to the presence of SHV-1 penicillinase in its chromosome. Notably, our data reveals that the sequence type influences the variant of SHV isolates harboured. Furthermore, K. pneumoniae, through the acquisition of large conjugative plasmids, demonstrates the ability to carry multiple AMR genes, with IncF plasmids being predominant, as commonly found in both human and animal sources. Two pan-resistant isolates were identified, carrying 4-6 plasmid replicons and up to 26 AMR genes, conferring resistance to 10 different classes of antimicrobials and disinfectants. In E. cloacae isolates, similar AMR genes were observed compared to K. pneumoniae, but the predominant plasmid replicon was Col, except for one isolate carrying 6 plasmid replicons and various ß-lactamase genes, including CMH-1. CMH-1, a class C ß-lactamase gene previously identified in E. cloacae from human hosts, was detected in food animals for the first time, indicating an expanding ecological niche. Additionally, our results stress the importance of considering virulence genes in E. coli from ruminants, as they may carry genes linked to human infections. This comprehensive perspective on AMR, encompassing multiple Enterobacteriaceae species and virulence genes, is crucial for a thorough understanding and effective management of antimicrobial resistance in the food chain.