Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene-based approaches.

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Abstract

Whole genome sequence (WGS)-based strain typing finds increasing use in the epidemiologic analysis of bacterial pathogens in both public health as well as more localized infection control settings.

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Journal

Journal ID (iso-abbrev): Clin. Microbiol. Infect.

Title: Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases

Publisher: Elsevier BV

ISSN (Electronic): 1469-0691

ISSN (Print): 1198-743X

Publication date (Electronic): Apr 2018

Volume: 24

Issue: 4

Affiliations

[1 ] Department of Medical Microbiology, University Medical Center, Utrecht, The Netherlands.

[2 ] Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE, USA. Electronic address: richardgoering@creighton.edu.

Article

Publisher Item ID: S1198-743X(17)30710-3

DOI: 10.1016/j.cmi.2017.12.016

PubMed ID: 29309930

SO-VID: 3dea850a-1eb0-42ab-9bcb-0c71d3252422

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Keywords: SNP,cgMLST,Whole genome sequencing,Relatedness threshold,Pan-genome,Core genome,Accessory genome

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Keywords: SNP, cgMLST, Whole genome sequencing, Relatedness threshold, Pan-genome, Core genome, Accessory genome

Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene-based approaches.

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