One Health genomic study of human and animal Klebsiella pneumoniae isolated at diagnostic laboratories on a small Caribbean island

Klebsiella pneumoniae causes a variety of infections in both humans and animals. In order to assess the risk of zoonotic transmission, we characterised the genomes of human and animal isolates obtained from the diagnostic laboratories of a hospital and a veterinary school located on St. Kitts, a small Caribbean island inhabited by a large population of vervet monkeys. Using the Illumina platform, we sequenced 82 presumptive K. pneumoniae isolates from humans (n=51), vervets (n=21), horses (n=5), dogs (n=4) and cats (n=1). De novo assembly and multilocus sequence typing (MLST) were performed in CLC Genomics Workbench v.11.0. Single nucleotide polymorphisms were detected using NASP followed by phylogenetic analysis using IQ-TREE. Virulence and antimicrobial resistance content was analysed using the Kleborate and CGE pipelines. WGS-based analysis showed that 72 isolates were K. pneumoniae sensu stricto, five K. quasipneumoniae and five K. variicola. K. pneumoniae isolates belonged to 35 sequence types (ST), three of which were shared between humans and animals: ST23 (one human and five vervets), ST37 (one human and one vervet) and ST307 (four humans, one horse and one cat). The ST23 isolates from vervets clustered separately from the human ST23 isolate, indicating a specific vervet lineage. Animal strains harboured fewer antibiotic resistance genes and displayed distinct virulence traits that appeared to be associated to vervet isolates. Altogether, these results show that human and animal K. pneumoniae infections are usually caused by genetically distinct, host-specific lineages, though some spillover events between hosts might occur.