Limited evidence of spill over of antimicrobial resistantKlebsiella pneumoniaefrom animal/environmental reservoirs to humans in India

Abstract

BackgroundKlebsiella pneumoniaeis a common opportunistic pathogen known for having virulent and antimicrobial resistance (AMR) phenotypes. In addition to accumulating AMR and virulence genes,K. pneumoniaeserves as a vehicle for broadly disseminating these elements into other species. Here, we applied genomic surveillance in a one-health framework to assess the impact of the human-animal-environment interface on AMR transmission.MethodsWe sequenced representative genomes ofKlebsiella pneumoniaeisolated from clinical specimens (n=59), livestock samples (n=71), and hospital sewage samples (n=16) from a two-year surveillance study. We compared the taxonomic and genomic distribution ofK. pneumoniae, the abundance of AMR, virulence genes, and mobile genetic elements between isolates from three sources.ResultsKlebsiellaspp. was the second most commonly isolated species (n=2,569). The clonal distribution ofK. pneumoniaesuggested isolates originating from livestock were clonally distinct from those derived from clinical/hospital effluent isolates. Clinical and hospital sewage isolates typically carried a higher number of resistance/virulence genes. There was limited overlap ofK. pneumoniaeclones, AMR genes, virulence determinants, and plasmids between the different settings.ConclusionCurrently, the spread of XDR or hypervirulent clones ofK. pneumoniaeappears to be confined to humans with no clear linkage with non-clinical sources. Moreover, emerging convergent clones ofK. pneumoniaecarrying both resistance and virulence determinants (ST231, ST2096) are likely to have emerged in hospital settings rather than in animal or natural environments. These data challenge the current view of AMR transmission inK. pneumoniaein a One-Health context.