Comparative genomics of clinical strains of Pseudomonas aeruginosa strains isolated from different geographic sites

Abstract

The large and complex genome of Pseudomonas aeruginosa, which consists of significant portions (up to 20%) of transferable genetic elements contributes to the rapid development of antibiotic resistance. The whole genome sequences of 22 strains isolated from eye and cystic fibrosis patients in Australia and India between 1992 and 2007 were used to compare genomic divergence and phylogenetic relationships as well as genes for antibiotic resistance and virulence factors. Analysis of the pangenome indicated a large variation in the size of accessory genome amongst 22 stains and the size of the accessory genome correlated with number of genomic islands, insertion sequences and prophages. The strains were diverse in terms of sequence type and dissimilar to that of global epidemic P. aeruginosa clones. Of the eye isolates, 62% clustered together within a single lineage. Indian eye isolates possessed genes associated with resistance to aminoglycoside, beta-lactams, sulphonamide, quaternary ammonium compounds, tetracycline, trimethoprims and chloramphenicols. These genes were, however, absent in Australian isolates regardless of source. Overall, our results provide valuable information for understanding the genomic diversity of P. aeruginosa isolated from two different infection types and countries.

Accessory genome contributes to the virulence and resistance of the ocular isolate of Pseudomonas aeruginosa: A complete genome analysis

“…These components are important for interaction of a bacterium with external environments including other species or hosts and hence are under continuous selection pressure (58-61). The pvdE and fliC orthologs have been shown to vary greatly between different strains of P. aeruginosa (62). The replacement islands may contribute to higher virulence in PA34 although this needs to be tested.…”

“…P. aeruginosa strain PA34 (referred to as PA34 hereafter) is a multi-drug resistant microbial keratitis isolate which is resistant to gentamicin, imipenem, ciprofloxacin and moxifloxacin. Analysis of its draft genome revealed that PA34 belongs to sequence type 1284 based on multi-locus sequence typing and carried at least 12 acquired resistance genes and possessed the exoU gene (11), an important effector gene in the pathogenesis of microbial keratitis (12). A class I integron (In 1427 ) that carries two antibiotic resistance genes has been shown to be integrated into a Tn3-like transposon carried by PA34 (13).…”

Changes to the resistome ofPseudomonas aeruginosaclone ST308 associated with corneal infection over time

“…Integrons were located using Integron finder v1.5.1. The genes possessed by strains 198 and 219 were then compared to those from other ST308 isolates that had been previously examined [6].…”

“…For example, P. aeruginosa isolated from water sources can also be isolated from cystic fibrosis patients [4]. Only a few studies have identified clones of ocular isolates of P. aeruginosa [5, 6]. Five multi-drug resistant P. aeruginosa isolates from corneal infections have been reported to be clonal and of sequence type 308.…”

“…Five multi-drug resistant P. aeruginosa isolates from corneal infections have been reported to be clonal and of sequence type 308. [6] The isolates were collected in 1997 from microbial keratitis cases in India. The current study investigated the genomes of more recently collected MDR P. aeruginosa corneal isolates recovered from the same location in India to investigate whether this clonal variant had persisted and whether it had acquired or lost antibiotic resistance genes.…”