Genomic characterization of carbapenem-non-susceptible Pseudomonas aeruginosa in Singapore

• Published in: Emerging microbes & infections Vol. 10; no. 1; pp. 1706 - 1716
• Main Authors: Teo, Jocelyn Qi-Min, Tang, Cheng Yee, Lim, Jie Chong, Lee, Shannon Jing-Yi, Tan, Si Hui, Koh, Tse-Hsien, Sim, James Heng-Chiak, Tan, Thuan-Tong, Kwa, Andrea Lay-Hoon, Ong, Rick Twee-Hee
• Format: Journal Article
• Language: English
• Published: United States Taylor & Francis 01.01.2021; Taylor & Francis Group
• Subjects: Anti-Bacterial Agents - pharmacology; Bacterial Typing Techniques; Carbapenems - pharmacology; clones; Drug Resistance, Bacterial; Genome, Bacterial; genomic surveillance; Genomics - methods; Humans; Microbial Sensitivity Tests; multi-drug resistant; Multilocus Sequence Typing; Prospective Studies; Pseudomonas aeruginosa; Pseudomonas aeruginosa - classification; Pseudomonas aeruginosa - drug effects; Pseudomonas aeruginosa - genetics; resistome; Singapore; Whole Genome Sequencing; Singapore; Pseudomonas aeruginosa; resistome; multi-drug resistant; clones; whole-genome sequencing; genomic surveillance
• DOI: 10.1080/22221751.2021.1968318
• ISSN: 2222-1751

Pseudomonas aeruginosa is a clinically important pathogen implicated in many hospital-acquired infections. Its propensity to acquire broad-spectrum resistance has earned the organism its status as a severe public health threat requiring urgent control measures. While whole-genome sequencing-based genomic surveillance provides a means to track antimicrobial resistance, its use in molecular epidemiological surveys of P. aeruginosa remains limited, especially in the Southeast Asian region. We sequenced the whole genomes of 222 carbapenem-non-susceptible P. aeruginosa (CNPA) isolates collected in 2006-2020 at the largest public acute care hospital in Singapore. Antimicrobial susceptibilities were determined using broth microdilution. Clonal relatedness, multi-locus sequence types, and antimicrobial resistance determinants (acquired and chromosomal) were determined. In this study, CNPA exhibited broad-spectrum resistance (87.8% multi-drug resistance), retaining susceptibility only to polymyxin B (95.0%) and amikacin (55.0%). Carbapenemases were detected in 51.4% of the isolates, where IMP and NDM metallo-β-lactamases were the most frequent. Carbapenem resistance was also likely associated with OprD alterations or efflux mechanisms (ArmZ/NalD mutations), which occurred in strains with or without carbapenemases. The population of CNPA in the hospital was diverse; the 222 isolates grouped into 68 sequence types (ST), which included various high-risk clones. We detected an emerging clone, the NDM-1-producing ST308, in addition to the global high-risk ST235 clone which was the predominant clone in our population. Our results thus provide a "snapshot" of the circulating lineages of CNPA locally and the prevailing genetic mechanisms contributing to carbapenem resistance. This database also serves as the baseline for future prospective surveillance studies.