K-PAM: a unified platform to distinguish Klebsiella species K- and O-antigen types, model antigen structures and identify hypervirulent strains

L. Ponoop Prasad Patro,Karpagam Uma Sudhakar,Thenmalarchelvi Rathinavelan

doi:10.1038/s41598-020-73360-1

L. Ponoop Prasad Patro, Karpagam Uma Sudhakar + Show 1 more

Open Access

https://doi.org/10.1038/s41598-020-73360-1

Copy DOI

Journal: Scientific Reports	Publication Date: Oct 7, 2020
Citations: 16	License type: open-access

Affiliation: Indian Institute of Technology Hyderabad

Abstract

A computational method has been developed to distinguish the Klebsiella species serotypes to aid in outbreak surveillance. A reliability score (estimated based on the accuracy of a specific K-type prediction against the dataset of 141 distinct K-types) average (ARS) that reflects the specificity between the Klebsiella species capsular polysaccharide biosynthesis and surface expression proteins, and their K-types has been established. ARS indicates the following order of potency in accurate serotyping: Wzx (ARS = 98.5%),Wzy (ARS = 97.5%),WbaP (ARS = 97.2%),Wzc (ARS = 96.4%),Wzb (ARS = 94.3%),WcaJ (ARS = 93.8%),Wza (ARS = 79.9%) and Wzi (ARS = 37.1%). Thus, Wzx, Wzy and WbaP can give more reliable K-typing compared with other proteins. A fragment-based approach has further increased the Wzi ARS from 37.1% to 80.8%. The efficacy of these 8 proteins in accurate K-typing has been confirmed by a rigorous testing and the method has been automated as K-PAM (www.iith.ac.in/K-PAM/). Testing also indicates that the use of multiple genes/proteins helps in reducing the K-type multiplicity, distinguishing the K-types that have identical K-locus (like KN3 and K35) and identifying the ancestral serotypes of Klebsiella spp. K-PAM has the facilities to O-type using Wzm (ARS = 85.7%) and Wzt (ARS = 85.7%) and identifies the hypervirulent Klebsiella species by the use of rmpA, rmpA2, iucA, iroB and peg-344 marker genes. Yet another highlight of the server is the repository of the modeled 11 O- and 79 K- antigen 3D structures.

Highlights

Abbreviations capsular polysaccharides (CPS) Capsular polysaccharide LPS Lipopolysaccharides RS Reliability score average reliability score (ARS) Average reliability score relative sequence identity factor (RSF) Relative sequence identity factor relative reliability factor (RRF) Relative reliability factor glycosyl transferases (GTs) Glycosyl transferase hypervirulent Klebsiella pneumoniae (hvKp) Hypervirulent Klebsiella species classical Klebsiella pneumoniae (cKp) Classical Klebsiella species NN Nucleotide sequence searched against nucleotide sequence in the reference database PP Protein sequence searched against protein sequence reference database NP Nucleotide sequence searched against protein sequence in the reference database CFG Consortium for functional glycomics rigid multimer modeling (RMM) Rigid multimer modeling flexible multimer modeling (FMM) Flexible multimer modelling CHARMM Chemistry at HARvard macromolecular mechanics
The protein sequence logo corresponding to the dataset indicates that significant variation in Wzi and Wzc are confined to a particular region (Figure S1), whereas no such distinct region specific diversity is seen in the cases of Wza, Wzb, WbaP, WcaJ, Wzx and Wzy
The precision in the K-typing efficacy of each protein has been tested through the K-PAM web server and the results are used in the estimation of ARS (Eqs. 1 and 2)

Summary

Introduction

Abbreviations CPS Capsular polysaccharide LPS Lipopolysaccharides RS Reliability score ARS Average reliability score RSF Relative sequence identity factor RRF Relative reliability factor GT Glycosyl transferase hvKp Hypervirulent Klebsiella species cKp Classical Klebsiella species NN Nucleotide sequence searched against nucleotide sequence in the reference database PP Protein sequence searched against protein sequence reference database NP Nucleotide sequence searched against protein sequence in the reference database CFG Consortium for functional glycomics RMM Rigid multimer modeling FMM Flexible multimer modelling CHARMM Chemistry at HARvard macromolecular mechanics. WbaP, wcaJ, wzx, wzy, wzc, wzb, wza and wzi are common among all the K-types 22 as these genes are essential for the assembly, transport and surface anchorage of the K-antigen. K-typing with the use of these eight genes may be a reliable and time saving option, instead of considering all the cps locus genes (there are 508 unique protein-encoding genes) 22 for K-typing In this context, we have classified the gene and protein sequences of wzi, wza, wzb, wzc, wzx, wzy, wbaP and wcaJ according to different Klebsiella spp K-types and demonstrated their importance in K-typing. Aforementioned approach has been implemented as an automated Klebsiella species K-/O-typing web server, namely, K-PAM (Klebsiella species serotype predictor and surface antigens modeler) (www.iith.ac.in/K-PAM/) The server accepts both the amino acid and nucleotide sequences corresponding to a single gene or multiple genes or the entire cps locus or the whole genome. The modeled K- and O- antigen repository may be useful in the perspective of designing polyvalent anti-Klebsiella vaccines [24,25,26,27] against a greater number of Klebsiella spp

Methods

Results

Conclusion