Emergence and Spread of Epidemic Multidrug-Resistant Pseudomonas aeruginosa

Abstract

Pseudomonas aeruginosa (P. aeruginosa) is one of the most common nosocomial pathogens worldwide. Although the emergence of multidrug-resistant (MDR) P. aeruginosa is a critical problem in medical practice, the key features involved in the emergence and spread of MDR P. aeruginosa remain unknown. This study utilized whole genome sequence (WGS) analyses to define the population structure of 185 P. aeruginosa clinical isolates from several countries. Of these 185 isolates, 136 were categorized into sequence type (ST) 235, one of the most common types worldwide. Phylogenetic analysis showed that these isolates fell within seven subclades. Each subclade harbors characteristic drug resistance genes and a characteristic genetic background confined to a geographic location, suggesting that clonal expansion following antibiotic exposure is the driving force in generating the population structure of MDR P. aeruginosa. WGS analyses also showed that the substitution rate was markedly higher in ST235 MDR P. aeruginosa than in other strains. Notably, almost all ST235 isolates harbor the specific type IV secretion system and very few or none harbor the CRISPR/CAS system. These findings may help explain the mechanism underlying the emergence and spread of ST235 P. aeruginosa as the predominant MDR lineage.

Keywords: Pseudomonas aeruginosa; multidrug-resistance; population structure; whole genome sequence.

Fig. 1.

—Phylogenic tree of the 185 Pseudomonas aeruginosa strains. The unrooted phylogeny of all P. aeruginosa strains was based on the maximum-likelihood method using PhyML 3.0 (Guindon et al. 2010). Each sequence type with more than one isolate [i.e. ST27 (n = 2), ST111 (n = 3), ST235 (n = 136), ST244 (n = 3), ST274 (n = 2), ST277 (n = 5), ST357 (n = 11), ST966 (n = 4), ST1284 (n = 2), and ST1342 (n = 4)] is indicated in color. Scale bar: 0.04 substitutions per variable site. Each main branch had >99% bootstrap support.

Fig. 2.

—Phylogenic tree of the 136 ST235 Pseudomonas aeruginosa strains. The phylogeny of ST235 MDR P. aeruginosa strains was evaluated using the BEAST program (Drummond and Rambaut 2007). The seven subclades are shown in color. The estimated ages of the branches are shown as median values with 95% highest posterior density (HPD). The proportion of isolates from each location carrying conserved antibiotic resistance genes (>50% per subclade) and their oprD disruption status are also indicated. The posterior probability value for each main branch was >0.99. More detailed results are shown in supplementary figure 2 and supplementary data 1, Supplementary Material online. The posterior probability of each subclade designated was > 0.95.

Fig. 3.

—Substitution rate of various bacteria, including ST235 Pseudomonas aeruginosa. Comparison of reported substitution rates of MRSA (Harris et al. 2010), Streptococcus pneumonia (Croucher et al. 2011), Salmonella typhimurium (Okoro et al. 2012), Clostridium difficile (He et al. 2013), ST235 MDR P. aeruginosa, and P. aeruginosa (supplementary 4, Supplementary Material online). The substitution rates of P. aeruginosa were estimated using the BEAST program (Drummond and Rambaut 2007).