A Core Genome Multilocus Sequence Typing Scheme for Pseudomonas aeruginosa

Frontiers in Microbiology
Romário Oliveira de SalesPatricia Severino

Abstract

Pseudomonas aeruginosa is a ubiquitous microorganism and an important opportunistic pathogen responsible for a broad spectrum of infections mainly in immunosuppressed and critically ill patients. Molecular investigations traditionally rely on pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). In this work we propose a core genome multilocus sequence typing (cgMLST) scheme for P. aeruginosa, a methodology that combines traditional MLST principles with whole genome sequencing data. All publicly available complete P. aeruginosa genomes, representing the diversity of this species, were used to establish a cgMLST scheme targeting 2,653 genes. The scheme was then tested using genomes available at contig, chromosome and scaffold levels. The proposed cgMLST scheme for P. aeruginosa typed over 99% (2,314/2,325) of the genomes available for this study considering at least 95% of the cgMLST target genes present. The absence of a certain number gene targets at the threshold considered for both the creation and validation steps due to low genome sequence quality is possibly the main reason for this result. The cgMLST scheme was compared with previously published whole genome single nucleotide polymorphism analysi...Continue Reading

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Citations

Sep 19, 2020·Environmental Microbiology·Burkhard Tümmler
May 28, 2021·Current Opinion in Infectious Diseases·Shelby R SimarCesar A Arias

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Datasets Mentioned

BETA
PRJEB6642
PRJNA282164
PRJEB32170

Methods Mentioned

BETA
Electrophoresis

Software Mentioned

GrapeTree
iToL
MSTree
SeqSphere
BioNumerics
mlst
SeqSphere +
AlleleCall
BIGSdb
Interactive Tree Of Life ( iTOL

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