A review of methods for subtyping Yersinia pestis: From phenotypes to whole genome sequencing

Amy J. Vogler; Paul Keim; David M. Wagner

doi:10.1016/j.meegid.2015.10.024

A review of methods for subtyping Yersinia pestis: From phenotypes to whole genome sequencing

Amy J. Vogler, Paul Keim, David M. Wagner

Biological Sciences

Research output: Contribution to journal › Review article › peer-review

16 Scopus citations

Abstract

Numerous subtyping methods have been applied to Yersinia pestis with varying success. Here, we review the various subtyping methods that have been applied to Y. pestis and their capacity for answering questions regarding the population genetics, phylogeography, and molecular epidemiology of this important human pathogen. Methods are evaluated in terms of expense, difficulty, transferability among laboratories, discriminatory power, usefulness for different study questions, and current applicability in light of the advent of whole genome sequencing.

Original language	English (US)
Pages (from-to)	21-36
Number of pages	16
Journal	Infection, Genetics and Evolution
Volume	37
DOIs	https://doi.org/10.1016/j.meegid.2015.10.024
State	Published - Jan 1 2016

Keywords

CRISPR
DFR
Genotyping
IS element
LCB linking modes
MLVA
RFLP
SNP
Subtyping
VNTR
Yersinia pestis

ASJC Scopus subject areas

Microbiology
Ecology, Evolution, Behavior and Systematics
Molecular Biology
Genetics
Microbiology (medical)
Infectious Diseases

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10.1016/j.meegid.2015.10.024

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title = "A review of methods for subtyping Yersinia pestis: From phenotypes to whole genome sequencing",

abstract = "Numerous subtyping methods have been applied to Yersinia pestis with varying success. Here, we review the various subtyping methods that have been applied to Y. pestis and their capacity for answering questions regarding the population genetics, phylogeography, and molecular epidemiology of this important human pathogen. Methods are evaluated in terms of expense, difficulty, transferability among laboratories, discriminatory power, usefulness for different study questions, and current applicability in light of the advent of whole genome sequencing.",

keywords = "CRISPR, DFR, Genotyping, IS element, LCB linking modes, MLVA, RFLP, SNP, Subtyping, VNTR, Yersinia pestis",

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T2 - From phenotypes to whole genome sequencing

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AU - Keim, Paul

AU - Wagner, David M.

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N2 - Numerous subtyping methods have been applied to Yersinia pestis with varying success. Here, we review the various subtyping methods that have been applied to Y. pestis and their capacity for answering questions regarding the population genetics, phylogeography, and molecular epidemiology of this important human pathogen. Methods are evaluated in terms of expense, difficulty, transferability among laboratories, discriminatory power, usefulness for different study questions, and current applicability in light of the advent of whole genome sequencing.

AB - Numerous subtyping methods have been applied to Yersinia pestis with varying success. Here, we review the various subtyping methods that have been applied to Y. pestis and their capacity for answering questions regarding the population genetics, phylogeography, and molecular epidemiology of this important human pathogen. Methods are evaluated in terms of expense, difficulty, transferability among laboratories, discriminatory power, usefulness for different study questions, and current applicability in light of the advent of whole genome sequencing.

KW - CRISPR

KW - DFR

KW - Genotyping

KW - IS element

KW - LCB linking modes

KW - MLVA

KW - RFLP

KW - SNP

KW - Subtyping

KW - VNTR

KW - Yersinia pestis

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JO - Infection, Genetics and Evolution

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ER -

A review of methods for subtyping Yersinia pestis: From phenotypes to whole genome sequencing

Abstract

Keywords

ASJC Scopus subject areas

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