A Core Genome Multilocus Sequence Typing Scheme for Pseudomonas aeruginosa

Area of Science:

• Microbiology
• Genomics
• Epidemiology

Background:

• Pseudomonas aeruginosa is a significant opportunistic pathogen causing diverse infections, particularly in vulnerable patients.
• Traditional molecular typing methods like PFGE and MLST have limitations in high-resolution strain characterization.
• Whole genome sequencing (WGS) offers a powerful tool for microbial typing and population structure analysis.

Purpose of the Study:

• To develop and validate a core genome multilocus sequence typing (cgMLST) scheme for Pseudomonas aeruginosa.
• To assess the cgMLST scheme's performance in typing diverse P. aeruginosa genomes and comparing it with existing methods.
• To evaluate the cgMLST scheme's utility for high-resolution typing in surveillance and outbreak investigations.

Main Methods:

• Establishment of a cgMLST scheme targeting 2,653 genes using publicly available P. aeruginosa genomes.
• Validation of the scheme on genomes at various assembly levels (contig, chromosome, scaffold).
• Comparison of cgMLST results with whole genome SNP analysis for epidemic clone ST235 and typing of cystic fibrosis-associated STs (ST146, ST274).

Main Results:

• The P. aeruginosa cgMLST scheme successfully typed over 99% of the studied genomes.
• The cgMLST scheme demonstrated high concordance with whole genome SNP analysis for population structure characterization.
• cgMLST provided higher resolution typing for outbreak and cystic fibrosis-associated isolates compared to traditional MLST.

Conclusions:

• The developed cgMLST scheme is a robust and high-resolution tool for P. aeruginosa typing.
• This cgMLST approach can effectively support public health surveillance programs and outbreak investigations.
• The scheme overcomes limitations of classical MLST, offering improved discriminatory power for P. aeruginosa strains.