Development and Application of a Core Genome Multilocus Sequence Typing Scheme for the Health Care-Associated Pathogen Pseudomonas aeruginosa

Abstract

Pseudomonas aeruginosa is an opportunistic human pathogen that frequently causes health care-associated infections (HAIs). Due to its metabolic diversity and ability to form biofilms, this Gram-negative nonfermenting bacterium can persist in the health care environment, which can lead to prolonged HAI outbreaks. We describe the creation of a core genome multilocus sequence typing (cgMLST) scheme to provide a stable platform for the rapid comparison of P. aeruginosa isolates using whole-genome sequencing (WGS) data. We used a diverse set of 58 complete P. aeruginosa genomes to curate a set of 4,440 core genes found in each isolate, representing ∼64% of the average genome size. We then expanded the alleles for each gene using 1,991 contig-level genome sequences. The scheme was used to analyze genomes from four historical HAI outbreaks to compare the phylogenies generated using cgMLST to those of other means (traditional MLST, pulsed-field gel electrophoresis [PFGE], and single-nucleotide variant [SNV] analysis). The cgMLST scheme provides sufficient resolution for analyzing individual outbreaks, as well as the stability for comparisons across a variety of isolates encountered in surveillance studies, making it a valuable tool for the rapid analysis of P. aeruginosa genomes.

Keywords: HAI; Pseudomonas aeruginosa; antibiotic resistance; cgMLST.

FIG 1

Creation of P. aeruginosa cgMLST gene set.

FIG 2

Dendrogram from cgMLST scheme of 2,049 P. aeruginosa genomes. Stars indicate entries used to construct the core gene list. The most common MLST types are highlighted on the dendrogram.

FIG 3

PFGE and cgMLST trees of isolates from three P. aeruginosa HAI outbreaks. Isolates from outbreaks 1 and 3 are colored by MLST sequence types (ST), while those from outbreak 2 (which were all from the same ST) are colored by the facility they were recovered from.

FIG 4

Trees generated by cgMLST scheme and hqSNV pipeline (SNVPhyl) for outbreak 4 isolates. Both techniques revealed two clusters of the same genomes (outlined in red and blue) distinct from the larger set. Support values for 1,000 bootstraps are labeled on the cgMLST tree.