Identification of further variation at the lipooligosaccharide outer core locus inAcinetobacter baumanniigenomes and extension of the OCL reference sequence database forKaptive

Abstract

ABSTRACTThe 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 ofAcinetobacter baumannii, a bacterial pathogen of global concern. In this study, we screened 12476 publicly availableA. baumanniigenome assemblies for novel OCL sequences, detecting six new OCL types that were designated OCL17-OCL22. These were compiled with previously characterised OCL to create an updated version of theA. baumanniiOCL reference database, providing a total of 22 OCL reference sequences for use with the bioinformatics tool,Kaptive. Use of this database against the 12476 downloaded assemblies found OCL1 to be the most common locus, present in 73.6% of sequenced genomes assigned byKaptivewith a match confidence score of ‘Good’ or above. OCL1 was most common amongst isolates belonging to sequence types, ST1, ST2, ST3 and ST78, all of which are over-represented clonal lineages associated with extensive antibiotic resistance. The highest level of diversity in OCL types was found in ST2, with eight different OCL identified. The updated OCL reference database is available for download from GitHub (https://github.com/katholt/Kaptive; under versionv 2.0.5), and has been integrated for use onKaptive-Web (https://kaptive-web.erc.monash.edu/) and PathogenWatch (https://pathogen.watch/), enhancing current methods forA. baumanniistrain identification, classification and surveillance.IMPACT STATEMENTIn the absence of effective treatment options for multi-drug resistantAcinetobacter baumannii, the highest-ranking critical priority bacterial pathogen of global concern, national and global surveillance is necessary to detect, track and subsequently curb the spread of isolates that resist current therapies. Several epidemiological markers are used to characteriseA. baumanniistrains by detecting genetic differences in specific regions of the genome. One of these is the chromosomal OC locus (OCL) responsible for the synthesis of the outer core (OC) component of the lipooligosaccharide (LOS). Here, we provide an update to the internationalA. baumanniiOCL reference sequence database, extending the number of known OCL types to assist with clinical surveillance of important strains or clonal lineages.Data summaryThe updatedA. baumanniiOCL reference sequence database including 22 annotated OCL sequences is available for download underKaptive v. 2.0.5athttps://github.com/katholt/Kaptive.Genome assemblies or GenBank records used as representative reference sequences are listed in Table 1 and acknowledged in each record in the database.