Limited evidence of spill over of antimicrobial resistant Klebsiella pneumoniae from animal/environmental reservoirs to humans in India

Background: Klebsiella pneumoniae is a common opportunistic pathogen known for having virulent and antimicrobial resistance (AMR) phenotypes. In addition to accumulating AMR and virulence genes, K. pneumoniae serves 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. Methods: We sequenced representative genomes of Klebsiella pneumoniae isolated 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 of K. pneumoniae, the abundance of AMR, virulence genes, and mobile genetic elements between isolates from three sources. Results: Klebsiella spp. was the second most commonly isolated species (n=2,569). The clonal distribution of K. pneumoniae suggested 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 of K. pneumoniae clones, AMR genes, virulence determinants, and plasmids between the different settings. Conclusion: Currently, the spread of XDR or hypervirulent clones of K. pneumoniae appears to be confined to humans with no clear linkage with non-clinical sources. Moreover, emerging convergent clones of K. pneumoniae carrying 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 in K. pneumoniae in a One-Health context. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was funded by grants from Indian Council of Medical Research, New Delhi, India (AMR/Adhoc/232/2020/ECD-II) for the Project Integrated genomic and epidemiological surveillance of multi-drug resistant, extensively drug resistant and hypervirulent Klebsiella pneumoniae in India ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: No human subjects were directly involved in the study. The data of clinical isolates was obtained from the electronic laboratory register of the Department of Clinical Microbiology, Christian Medical College, Vellore. All the patient-identifying variables in the data were removed before the analysis. Institutional Review Board (IRB) of Christian Medical College (CMC), Vellore, India gave ethical approval for this work vide IRB Min no. 12626 dated 26.02.2020. As the required data had been collected as part of the standard of care for diagnosis, an informed consent waiver was granted by the IRB committee CMC, Vellore. The Declaration of Helsinki norms were adhered to while conducting the study. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Raw read data were deposited in the European Nucleotide Archive (ENA) under project accession number: PRJEB58136. The individual sample accession numbers are listed in Supplementary Table