Identification of further variation at the lipooligosaccharide outer core locus in Acinetobacter baumannii genomes and extension of the OCL reference sequence database for Kaptive

Abstract

The outer core locus (OCL) that includes genes for the synthesis of the variable outer core region of the lipooligosaccharide (LOS) is one of the key epidemiological markers used for tracing the spread of <i>Acinetobacter baumannii</i>, a bacterial pathogen of global concern. In this study, we screened 12 476 publicly available <i>A. baumannii</i> genome assemblies for novel OCL sequences, detecting six new OCL types that were designated OCL17-OCL22. These were compiled with previously characterized OCL sequences to create an updated version of the <i>A. baumannii</i> OCL reference database, providing a total of 22 OCL reference sequences for use with the bioinformatics tool <i>Kaptive</i>. Use of this database against the 12 476 downloaded assemblies found OCL1 to be the most common locus, present in 73.6 % of sequenced genomes assigned by <i>Kaptive</i> with a match confidence score of good or above. OCL1 was most common amongst isolates belonging to sequence types (STs) ST1, ST2, ST3 and ST78, all of which are over-represented clonal lineages. The highest level of diversity in OCL types was found in ST2, with eight different OCLs identified. The updated OCL reference database is available for download from GitHub (https://github.com/klebgenomics/Kaptive; under version <i>v. 2.0.5</i>), and has been integrated for use on <i>Kaptive-</i>Web (https://kaptive-web.erc.monash.edu/) and PathogenWatch (https://pathogen.watch/), enhancing current methods for <i>A. baumannii</i> strain identification, classification and surveillance.