A capsule polysaccharide synthesis locus database for the Klebsiella oxytoca Species Complex

Abstract

The Klebsiella oxytoca Species Complex (SC) represents an emerging healthcare-associated group of opportunistic pathogens. The capsular polysaccharide is a virulence determinant and target for novel vaccines, monoclonal antibodies and phage therapy. In the absence of broadly accessible phenotyping techniques, prediction of capsule types from whole-genome sequence data is critical for understanding capsule diversity and epidemiology, and to prioritise capsule types as targets for novel anti-K. oxytoca SC interventions. Here we present the first comprehensive capsule synthesis locus (K locus) database targeted for the K. oxytoca SC, comprising 88 distinct loci defined by gene content and which is compatible with the rapid genome typing tool Kaptive. The database provides high coverage of publicly available K. oxytoca SC genomes (97.6% of 2,244 genomes, dereplicated from a total of 4,055), and the typing rate is significantly higher than that achieved with the pre-existing Klebsiella K locus database (97.6% vs 50.3%, p <0.0001), which primarily targets the Klebsiella pneumoniae SC. We demonstrate the utility of the novel K. oxytoca SC database by application to three diverse clinical K. oxytoca SC isolate collections (n=61 to 102 genomes each), suggesting a high diversity of K types. The novel K. oxytoca SC K locus database (github.com/klebgenomics/KoSC-surface-antigen-loci) will provide a key resource to support larger systematic studies and ongoing genomics surveillance efforts for the K. oxytoca SC. IMPACT STATEMENTMembers of the Klebsiella oxytoca Species Complex (SC) are an emerging cause of infections in humans and are frequently associated with antimicrobial resistance. Klebsiella species produce two key surface antigen sugars (capsular polysaccharide and lipopolysaccharide) that are immunogenic and are targets for novel control strategies such as vaccines and phage therapy. Phenotypic typing of these surface antigen sugars (serotyping) is costly and laborious, with genotyping (predicting the serotype from whole-genome sequence data) a useful alternative. Here, we present a curated capsule (K) locus reference database for the K. oxytoca SC, which represents a useful tool to assist in the epidemiological surveillance of this emerging pathogen. DATA SUMMARYAll Klebsiella oxytoca Species Complex genomes used in this work were publicly available, with accession details listed in Supplementary Tables 1, 2 and 3. The K. oxytoca Species Complex K locus reference database is available under GNU public license at github.com/klebgenomics/KoSC-surface-antigen-loci.