A Core Genome Multilocus Sequence Typing Scheme for Pseudomonas aeruginosa

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 analysis for the characterization of the population structure of the epidemic clone ST235 and results were highly similar. In order to evaluate the typing resolution of the proposed scheme, collections of isolates belonging to two important STs associated with cystic fibrosis, ST146 and ST274, were typed using this scheme, and ST235 isolates associated with an outbreak were evaluated. Besides confirming the relatedness of all the isolates, earlier determined by MLST, the higher resolution of cgMLST denotes that it may be suitable for surveillance programs, overcoming possible shortcomings of classical MLST.

Comparison of Whole Genome (wg-) and Core Genome (cg-) MLST (BioNumericsTM) Versus SNP Variant Calling for Epidemiological Investigation of Pseudomonas aeruginosa

“…These results show the importance of using a cgMLST scheme to evaluate the effect of recombination on the genetic similarity between isolates. Such schemes have been proposed, but none of the studies addressed a comparison with a SNP calling approach or the effect of recombination ( Mellmann et al, 2016 ; de Sales et al, 2020 ; Perez-Vazquez et al, 2020 ; Royer et al, 2020 ; Stanton et al, 2020 ).…”

Diversity and Distribution of Resistance Markers in Pseudomonas aeruginosa International High-Risk Clones

“…According to STs, high-risk clones are identified and their disseminations can be tracked. Additionally, core genome MLST has a higher resolution capacity that can be also applied in surveillance programs [ 36 ]. MDR clones are present worldwide and they evolve usually in hospital environments, as these clones are generally selected out in hospitals, due to antibiotic selection pressure and they can survive long-lasting in favorable conditions in hospital environments.…”

Molecular epidemiology in current times

“…For example, within 1 month in 2020 cgMLST schemes have been published for Campylobacter jejuni (Hsu et al ., 2020), Leptospira spp. (Grillová and Picardeau, 2020), Pseudomonas aeruginosa (De Sales et al ., 2020; Martak et al ., 2020; Stanton et al ., 2020), Streptococcus mutans (Liu et al ., 2020) and Vibrio cholera (Liang et al ., 2020). cgMLST schemes consist of a fixed set of conserved genome‐wide genes.…”

“…cgMLST schemes consist of a fixed set of conserved genome‐wide genes. The three cgMLST schemes for P. aeruginosa consist of 3831 (Martak et al ., 2020); 2653 (De Sales et al ., 2020) or 4400 core genes (Stanton et al ., 2020) which probably will give rise to confusion in the next years when P. aeruginosa genotypes will be published that are based on different typing schemes. A cgMLST scheme is fixed and agreed upon number of genes for each species or group of closely related species.…”