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

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 specif...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	L. Ponoop Prasad Patro, Karpagam Uma Sudhakar, Thenmalarchelvi Rathinavelan
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2020
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/87d2a2b15fd84ba5a7f384554e1ce81c
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:87d2a2b15fd84ba5a7f384554e1ce81c
record_format	dspace
spelling	oai:doaj.org-article:87d2a2b15fd84ba5a7f384554e1ce81c2021-12-02T18:37:07ZK-PAM: a unified platform to distinguish Klebsiella species K- and O-antigen types, model antigen structures and identify hypervirulent strains10.1038/s41598-020-73360-12045-2322https://doaj.org/article/87d2a2b15fd84ba5a7f384554e1ce81c2020-10-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-73360-1https://doaj.org/toc/2045-2322Abstract 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.L. Ponoop Prasad PatroKarpagam Uma SudhakarThenmalarchelvi RathinavelanNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 10, Iss 1, Pp 1-14 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q L. Ponoop Prasad Patro Karpagam Uma Sudhakar Thenmalarchelvi Rathinavelan K-PAM: a unified platform to distinguish Klebsiella species K- and O-antigen types, model antigen structures and identify hypervirulent strains
description	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.
format	article
author	L. Ponoop Prasad Patro Karpagam Uma Sudhakar Thenmalarchelvi Rathinavelan
author_facet	L. Ponoop Prasad Patro Karpagam Uma Sudhakar Thenmalarchelvi Rathinavelan
author_sort	L. Ponoop Prasad Patro
title	K-PAM: a unified platform to distinguish Klebsiella species K- and O-antigen types, model antigen structures and identify hypervirulent strains
title_short	K-PAM: a unified platform to distinguish Klebsiella species K- and O-antigen types, model antigen structures and identify hypervirulent strains
title_full	K-PAM: a unified platform to distinguish Klebsiella species K- and O-antigen types, model antigen structures and identify hypervirulent strains
title_fullStr	K-PAM: a unified platform to distinguish Klebsiella species K- and O-antigen types, model antigen structures and identify hypervirulent strains
title_full_unstemmed	K-PAM: a unified platform to distinguish Klebsiella species K- and O-antigen types, model antigen structures and identify hypervirulent strains
title_sort	k-pam: a unified platform to distinguish klebsiella species k- and o-antigen types, model antigen structures and identify hypervirulent strains
publisher	Nature Portfolio
publishDate	2020
url	https://doaj.org/article/87d2a2b15fd84ba5a7f384554e1ce81c
work_keys_str_mv	AT lponoopprasadpatro kpamaunifiedplatformtodistinguishklebsiellaspecieskandoantigentypesmodelantigenstructuresandidentifyhypervirulentstrains AT karpagamumasudhakar kpamaunifiedplatformtodistinguishklebsiellaspecieskandoantigentypesmodelantigenstructuresandidentifyhypervirulentstrains AT thenmalarchelvirathinavelan kpamaunifiedplatformtodistinguishklebsiellaspecieskandoantigentypesmodelantigenstructuresandidentifyhypervirulentstrains
_version_	1718377809227808768

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

Ejemplares similares