Kaptive Web: user-friendly capsule and lipopolysaccharide serotype prediction forKlebsiellagenomes

Abstract

As whole genome sequencing becomes an established component of the microbiologist's toolbox, it is imperative that researchers, clinical microbiologists and public health professionals have access to genomic analysis tools for rapid extraction of epidemiologically and clinically relevant information. For the gram-negative hospital pathogens such as Klebsiella pneumoniae, initial efforts have focused on detection and surveillance of antimicrobial resistance genes and clones. However, with the resurgence of interest in alternative infection control strategies targeting Klebsiella surface polysaccharides, the ability to extract information about these antigens is increasingly important.Here we present Kaptive Web, an online tool for rapid typing of Klebsiella K and O loci, which encode the polysaccharide capsule and lipopolysaccharide O antigen, respectively. Kaptive Web enables users to upload and analyse genome assemblies in a web browser. Results can be downloaded in tabular format or explored in detail via the graphical interface, making it accessible for users at all levels of computational expertise.We demonstrate Kaptive Web's utility by analysis of >500 K. pneumoniae genomes. We identify extensive K and O locus diversity among 201 genomes belonging to the carbapenemaseassociated clonal group 258 (25 K and six O loci). Characterisation of a further 309 genomes indicates that such diversity is common among the multi-drug resistant clones and that these loci represent useful epidemiological markers for strain subtyping. These findings reinforce the need for rapid, reliable and accessible typing methods such as Kaptive Web.Kaptive Web is available for use at kaptive.holtlab.net and source code is available at github.com/kelwyres/Kaptive-Web.

Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from south and southeast Asia

“…The most common K--loci were KL1 (n=31; including 28 ST23), KL2 (n=27; numerous STs including ST14, ST25, ST65 and ST86), KL51 (n=23; including 17 ST231) and KL24 (n=20; including 17 ST15), together accounting for 28% of K. pneumoniae BSI (Figure 2). Saliently, while ST23 and ST231 were each associated with only a single K--locus (KL1 and KL51, respectively), the two other most common STs were each associated with multiple K--loci (ST15: KL24=17, KL112=9, KL10=3, KL62=2, KL19=2; ST14: KL64=7, KL2=6, KL157=1), as has been previously observed for ST258 23 . Ten of the 12 previously described O--antigen encoding loci were also detected (Simpson's diversity index=0.80).…”

“…Chromosomal multi--locus sequence typing (MLST), virulence locus and acquired resistance genes (excluding the core ampicillin resistance gene bla SHV and oqxAB efflux genes) were typed using Kleborate v0.3.0 (https://github.com/katholt/Kleborate). Surface capsule (K) and lipopolysaccharide (O) loci were identified using Kaptive 22,23 . Novel K--loci were manually extracted using Bandage 24 , annotated using Prokka v1.13.3 25 before manual curation, and deposit in GenBank (accessions TBD).…”

K-PAM: A unified platform to distinguishKlebsiellaspecies K- and O-antigen types, model antigen structures and identify hypervirulent strains

“…This is due to the fact that the sequence identities between wza, wzb, wzc, wzi, wzx, wzy and wcaJ genes of KN3 (Genbank ID: LC189075.1) and K35 (Genbank ID: AB924573.1) are 87%, 91%, 87%, 91%, 85%, 86% and 88% respectively. Subsequently, a more rigorous testing has been carried out by considering 162 dataset from the published literature [20]. The results clearly show that K-PAM accurately predicts the serotype (Table S4).…”

“…To effectively use the eight K-locus genes of Klebsiella spp in K-type prediction, wzi, wza, wzb, wzc, wzx, wzy, wbaP and wcaJ gene and their protein sequences (http://iith.ac.in/K-PAM/doc.php) are collected from the NCBI or from the Kaptive web [20] and classified according to 141 K-types. These K-types include 77 K-antigens (viz., K1-K81, excluding K75-K78) of Klebsiella spp whose capsule types are defined serologically [21]( as well as additional K-types that have been identified based on the cps locus or K-locus (KL) arrangement.…”

“…A local database comprising Klebsiella spp wza, wzb, wzc, wzi, wzx, wzy, wbaP and wcaJ gene as well as their protein sequences (whose K-types are already known) has been constructed by fetching the FASTA format sequences from the NCBI (except for KL104, KL107, KL128, KL145, KL147, KL151, KL152, KL155, KL157, KL158 and KL160-KL165, for which, the sequences are taken from the published literature [20]) and are grouped according to 141 distinct K-serotypes. The database consists of 1345 and 1095 nonredundant gene and protein sequences respectively corresponding to 8 genes in the cps locus.…”