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. The proposed scheme is publicly available at: https://github.com/BioinformaticsHIAEMolecularMicrobiology/cgMLST-Pseudomonas-aeruginosa.
Highlights
Pseudomonas aeruginosa is an opportunistic human pathogen responsible for nosocomial infections worldwide, such as ventilator-associated pneumonia and burn wound infections, mainly in immunosuppressed patients (De Bentzmann and Plesiat, 2011; Gellatly and Hancock, 2013; Cabot et al, 2016; Sousa et al, 2018; Yin et al, 2018)
A total of 518 different sequence types (STs) characterized the available population: 402 STs previously reported in the pubMLST database and 116 new STs determined for the purpose of this study (Supplementary Table S1)
Recent technical advances in whole genome sequencing (WGS) and lower costs have brought new possibilities for both global surveillance and local clinical investigations. Both wgMLST and core genome multilocus sequence typing (cgMLST) solutions are being implemented for a diverse set of microorganisms, such as those contemplated within the Global Platform for Pathogen Surveillance6. cgMLST is being considered the method of choice for typing pathogens for epidemiological surveillance of infectious diseases in the European Union and European Economic Area countries, overcoming SNP-based typing (Revez et al, 2017)
Summary
Pseudomonas aeruginosa is an opportunistic human pathogen responsible for nosocomial infections worldwide, such as ventilator-associated pneumonia and burn wound infections, mainly in immunosuppressed patients (De Bentzmann and Plesiat, 2011; Gellatly and Hancock, 2013; Cabot et al, 2016; Sousa et al, 2018; Yin et al, 2018). Both PFGE and MLST methods are often simultaneously required (Li et al, 2009; Kidd et al, 2011; Sabat et al, 2013)
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