Identification ofAcinetobacter baumanniiloci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive
Authors: Wyres Kelly L. , Cahill Sarah M. , Holt Kathryn E. , Hall Ruth M. , Kenyon Johanna J. 
Published: December 2019

AbstractMultiply antibiotic resistantAcinetobacter baumanniiinfections are a global public health concern and accurate tracking of the spread of specific lineages is needed. Variation in the composition and structure of capsular polysaccharide (CPS), a critical determinant of virulence and phage susceptibility, makes it an attractive epidemiological marker. The outer core (OC) of lipooligosaccharide also exhibits variation. To take better advantage of the untapped information available in whole genome sequences, we have created a curated reference database of the 92 publicly available gene clusters at the locus encoding proteins responsible for biosynthesis and export of CPS (K locus), and a second database for the 12 gene clusters at the locus for outer core biosynthesis (OC locus). Each entry has been assigned a unique KL or OCL number, and is fully annotated using a simple, transparent and standardised nomenclature. These databases are compatible withKaptive, a tool forin silicotyping of bacterial surface polysaccharide loci, and their utility was validated using a) >630 assembledA. baumanniidraft genomes for which the KL and OCL regions had been previously typed manually, and b) 3386A. baumanniigenome assemblies downloaded from NCBI. Among the previously typed genomes,Kaptivewas able to confidently assign KL and OCL types with 100% accuracy. Among the genomes retrieved from NCBI,Kaptivedetected known KL and OCL in 87% and 90% of genomes, respectively indicating that the majority of common KL and OCL types are captured within the databases; 13 KL were not detected in any public genome assembly. The failure to assign a KL or OCL type may indicate incomplete or poor-quality genomes. However, further novel variants may remain to be documented. Combining outputs with multi-locus sequence typing (Institut Pasteur scheme) revealed multiple KL and OCL types in collections of a single sequence type (ST) representing each of the two predominant globally-distributed clones, ST1 of GC1 and ST2 of GC2, and in collections of other clones comprising >20 isolates each (ST10, ST25, and ST140), indicating extensive within-clone replacement of these loci. The databases are available athttps://github.com/katholt/Kaptiveand will be updated as further locus types become available.Data Summary1. Databases including fully annotated gene cluster sequences forA. baumanniiK loci and OC loci are available for download athttps://github.com/katholt/Kaptive2. TheKaptivesoftware, which can be used to screen new genomes against the K and O locus database is available athttps://github.com/katholt/Kaptive(command-line code) andhttp://kaptive.holtlab.net/(interactive web service).3. Details of theKaptivesearch results validatingin silicoserotyping of K and O loci using our approach are provided as supplementary files, Dataset 1 (92 KL reference sequences and 12 OCL reference sequences), Dataset 2 (642 genomes assembled from reads available in NCBI SRA) and Dataset 3 (3415 genome assemblies downloaded from NCBI GenBank).Impact statementThe ability to identify and track closely related isolates is key to understanding, and ultimately controlling, the spread of multiply antibiotic resistantA. baumanniicausing difficult to treat infections, which are an urgent public health threat. Extensive variation in the KL and OCL gene clusters responsible for biosynthesis of capsule and the outer core of lipooligosaccharide, respectively, are potentially highly informative epidemiological markers. However, clear, well-documented identification of each variant and simple-to-use tools and procedures are needed to reliably identify them in genome sequence data. Here, we present curated databases compatible with the available web-based and command-lineKaptivetool to make KL and OCL typing readily accessible to assist epidemiological surveillance of this species. As many bacteriophage recognise specific properties of the capsule and attach to it, capsule typing is also important in assessing the potential of specific phage for therapy on a case by case basis.