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bioRxiv · 10.1101/2023.02.23.529771

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

Sorbello, B.·Cahill, S. M.·Kenyon, J. J.
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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 Acinetobacter baumannii, a bacterial pathogen of global concern. In this study, we screened 12476 publicly available A. baumannii genome 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 the A. baumannii OCL 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 by Kaptive with 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 version v 2.0.5), and has been integrated for use on Kaptive-Web (https://kaptive-web.erc.monash.edu/) and PathogenWatch (https://pathogen.watch/), enhancing current methods for A. baumannii strain identification, classification and surveillance. IMPACT STATEMENTIn the absence of effective treatment options for multi-drug resistant Acinetobacter 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 characterise A. baumannii strains 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 international A. baumannii OCL reference sequence database, extending the number of known OCL types to assist with clinical surveillance of important strains or clonal lineages. Data summaryO_LIThe updated A. baumannii OCL reference sequence database including 22 annotated OCL sequences is available for download under Kaptive v. 2.0.5 at https://github.com/katholt/Kaptive. C_LIO_LIGenome assemblies or GenBank records used as representative reference sequences are listed in Table 1 and acknowledged in each record in the database. C_LI O_TBL View this table: org.highwire.dtl.DTLVardef@1d32ff1org.highwire.dtl.DTLVardef@1f0af8borg.highwire.dtl.DTLVardef@94f185org.highwire.dtl.DTLVardef@7c8b7aorg.highwire.dtl.DTLVardef@a93255_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 1.C_FLOATNO O_TABLECAPTIONInformation on A. baumannii OCL reference sequences used to populate the updated OCL database for Kaptive v 2.0.5 C_TABLECAPTION C_TBL

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Sorbello, B., Cahill, S. M., Kenyon, J. J.. 2023-02-24. Identification of further variation at the lipooligosaccharide outer core locus in Acinetobacter baumannii genomes and extension of the OCL reference sequence database for Kaptive. https://doi.org/10.1101/2023.02.23.529771

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