Dissemination of Pseudomonas aeruginosa blaNDM-1-Positive ST308 Clone in Singapore

Abstract

Pseudomonas aeruginosa ST308 clone has been reported to carry carbapenemase genes such as bla_IMP and bla_VIM but has been rarely associated with bla_NDM-1. A total of 199 P. aeruginosa ST308 clinical and environmental isolates obtained between April 2019 and November 2020 from a tertiary-care hospital in Singapore were characterized using whole-genome sequencing. In addition, 71 bla_NDM-1-positive ST308 whole-genome sequences from two other local tertiary-care hospitals in Singapore and 83 global bla_NDM-1-negative ST308 whole-genome sequences in public databases were included to assess phylogenetic relationships and perform genome analyses. Phylogenetic analysis and divergent time estimation revealed that bla_NDM-1-positive P. aeruginosa ST308 was introduced into Singapore in 2005 (95 % highest posterior density: 2001 to 2008). Core genome, resistome, and analyses of all local bla_NDM-1-positive ST308 isolates showed chromosomal integration of multiple antibiotic resistance genes (ARGs) [aac(3)-Id, aac(6')-Il, aadA6, aadA11, dfrB5, msr(E), floR, sul2, and qnrVC1], which was absent in global bla_NDM-1-negative ST308 sequences. Most ARGs and virulence genes were conserved across isolates originating from the three different local hospitals. Close genetic relatedness of the bla_NDM-1-positive ST308 clinical and environmental isolates suggests cocirculation between the hospital environment and human hosts with the hospital environment as a potential reservoir. Core genome single nucleotide polymorphism analyses revealed possible clonal transmission of bla_NDM-1-positive ST308 isolates between the three hospitals over 7 years. Bloodstream isolates accounted for six of 95 (6.3%) clinical isolates. This study reports the introduction of a pathogenic bla_NDM-1-positive P. aeruginosa ST308 more than a decade ago in Singapore and warrants surveillance for wider dissemination. IMPORTANCE P. aeruginosa is a Gram-negative opportunistic pathogen ubiquitously found in the environment and a major cause of nosocomial infections. While the P. aeruginosa ST308 clone has been known to bear bla_IMP and bla_VIM among global isolates, reports of bla_NDM-1-positive P. aeruginosa ST308 are rare. The local bla_NDM-1-positive P. aeruginosa ST308 isolates detected in this study appear to be unique to this region, with evidence of chromosomal acquisition of multiple ARGs compared to global bla_NDM-1-negative P. aeruginosa ST308 isolates. Surveillance in Singapore and beyond for dissemination is essential to determine whether existing measures are sufficient to control the spread of this ST308 clone.

Keywords: Pseudomonas aeruginosa; ST308; carbapenemase; chromosomal integration; region-specific; whole-genome sequencing.

FIG 1

Maximum-likelihood phylogenetic tree with local and global P. aeruginosa ST308 genomes.

FIG 2

Bayesian maximum clade credibility tree with 261 patient and environmental isolates from local hospitals A, B, and C. Horizontal bars (light blue) on nodes represent posterior probability values and 95% credibility intervals. The color of the tree tip indicates the cluster number the isolate belongs to. Information on the corresponding sample type, hospital, and resistant gene presence/absence matrix are indicated on the right of the tree tip. The presence or absence of ARGs is represented as a heatmap, with green indicating the presence of the corresponding genes, respectively. For completeness, the single bla_NDM-1-negative ST308 P. aeruginosa isolate was included in the phylogenetic tree. The scale represents the number of years.

FIG 3

Linear comparison of genomic assemblies of P. aeruginosa involving local bla_NDM-1-positive ST308 environmental isolates (cyan) and clinical isolates (yellow-green) from hospital C with global bla_NDM-1-negative ST308 isolates (pink) and PAO1 reference genome (brown). ARGs (labeled in red) and virulence genes (labeled in purple) are indicated at their respective genomic locations. Cassettes 1, 3, and 4 represent ARG regions, cassette 2 indicates WYL domain containing protein region, and cassette 5 represents Dobby phage integration in local ST308 genomes. To demonstrate the missing cassettes in global samples with higher confidence, two additional global bla_NDM-1-negative ST308 isolates (SCAID PLC1-2021 and SCAID TST-2021) that were not part of the phylogenetic tree analysis have also been included in the visualization.

FIG 4

Linear comparison of bla_NDM-1 gene region in local ST308 isolate with global ST308 isolates.