Background: The Klebsiella oxytoca Species Complex (KoSC) is an emerging pathogen associated with pneumonia, and urinary tract and systemic infections. In Klebsiella spp., the capsular polysaccharide is a critical virulence determinant, representing a useful epidemiological marker and is considered a target for the development of vaccines and phage therapy. Prediction of capsule types from whole genome sequence (WGS) data and understanding their distribution across the population is critical for the development of these therapies. However, despite the increasing global prevalence of the KoSC, little is known about the sero-epidemiology within this group.
Methods: We obtained publicly available WGS data for 3,288 KoSC isolates, which were screened using Kleborate and Kaptive. We extracted, clustered, annotated, and visualised full-length capsule synthesis (K)-loci to characterise and compare K-locus structures. Multi-locus sequence typing was performed in silico.
Results: A total of 45 distinct K-loci were identified from 1,077 genome assemblies which had contiguous capsule loci, including 10 K-loci that were found in only a single genome and 12 that have previously been defined in the Klebsiella pneumoniae Species Complex. Six K-loci (KL4, KL5, KL6, KL8, KL10 and KL28) were overrepresented (≥5%), collectively representing 52.56% of the 1,077 genomes. The population structure of these 1,077 genomes was distributed across 114 Multi-locus Sequence Types (STs). Nine STs across three species (K. grimontii, K. oxytoca and K. michiganensis) were comprised of ≥20 isolates, of which ST50 (n=67, 6.2%), ST180 (n=60, 5.6%) and ST177 (n=34, 3.2%) were the most prevalent. Major STs were primarily associated with 1-2 distinct K-loci, with ST50, ST180 and ST177 associated with the K-loci KL12 and KL28, KL5, and KL28 respectively. Notably, KL5 was the most common capsule type overall and the dominant type across four of the top nine STs (n=186/1,077, 17.27%).
Conclusions: These results highlight the considerable diversity of the KoSC population and indicate the presence of both dominant and lineage-specific capsule serotypes. Ongoing work will see the generation of a curated K-locus reference database, which we will use to estimate the protection coverage that can be achieved via alternate therapies targeting the KoSC capsule.