Genomic Surveillance of Carbapenem-Resistant Klebsiella pneumoniae from a Major Public Health Hospital in Singapore
ABSTRACT Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a global public health threat. In this study, we employed whole-genome sequencing (WGS) to determine the genomic epidemiology of a longitudinal collection of clinical CRKP isolates recovered from a large public acute care hospital in Sing...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2022-10-01
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| Series: | Microbiology Spectrum |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.00957-22 |
| _version_ | 1811198168428183552 |
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| author | Jocelyn Qi-Min Teo Cheng Yee Tang Si Hui Tan Hong Yi Chang Sze Min Ong Shannon Jing-Yi Lee Tse-Hsien Koh James Heng-Chiak Sim Andrea Lay-Hoon Kwa Rick Twee-Hee Ong |
| author_facet | Jocelyn Qi-Min Teo Cheng Yee Tang Si Hui Tan Hong Yi Chang Sze Min Ong Shannon Jing-Yi Lee Tse-Hsien Koh James Heng-Chiak Sim Andrea Lay-Hoon Kwa Rick Twee-Hee Ong |
| author_sort | Jocelyn Qi-Min Teo |
| collection | DOAJ |
| description | ABSTRACT Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a global public health threat. In this study, we employed whole-genome sequencing (WGS) to determine the genomic epidemiology of a longitudinal collection of clinical CRKP isolates recovered from a large public acute care hospital in Singapore. Phylogenetic analyses, a characterization of resistance and virulence determinants, and plasmid profiling were performed for 575 unique CRKP isolates collected between 2009 and 2020. The phylogenetic analyses identified the presence of global high-risk clones among the CRKP population (clonal group [CG] 14/15, CG17/20, CG147, CG258, and sequence type [ST] 231), and these clones constituted 50% of the isolates. Carbapenemase production was common (n = 497, 86.4%), and KPC was the predominant carbapenemase (n = 235, 40.9%), followed by OXA-48-like (n = 128, 22.3%) and NDM (n = 93, 16.2%). Hypervirulence was detected in 59 (10.3%) isolates and was most common in the ST231 carbapenemase-producing isolates (21/59, 35.6%). Carbapenemase genes were associated with diverse plasmid replicons; however, there was an association of blaOXA-181/232 with ColKP3 plasmids. This study presents the complex and diverse epidemiology of the CRKP strains circulating in Singapore. Our study highlights the utility of WGS-based genomic surveillance in tracking the population dynamics of CRKP. IMPORTANCE In this study, we characterized carbapenem-resistant Klebsiella pneumoniae clinical isolates collected over a 12-year period in the largest public acute-care hospital in Singapore using whole-genome sequencing. The results of this study demonstrate significant genomic diversity with the presence of well-known epidemic, multidrug-resistant clones amid a diverse pool of nonepidemic lineages. Genomic surveillance involving comprehensive resistance, virulence, and plasmid gene content profiling provided critical information for antimicrobial resistance monitoring and highlighted future surveillance priorities, such as the emergence of ST231 K. pneumoniae strains bearing multidrug resistance, virulence elements, and the potential plasmid-mediated transmission of the blaOXA-48-like gene. The findings here also reinforce the necessity of unique infection control and prevention strategies that take the genomic diversity of local circulating strains into consideration. |
| first_indexed | 2024-04-12T01:26:17Z |
| format | Article |
| id | doaj.art-53a0fae1adb540489d0eeb021e4d269b |
| institution | Directory Open Access Journal |
| issn | 2165-0497 |
| language | English |
| last_indexed | 2024-04-12T01:26:17Z |
| publishDate | 2022-10-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | Microbiology Spectrum |
| spelling | doaj.art-53a0fae1adb540489d0eeb021e4d269b2022-12-22T03:53:38ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972022-10-0110510.1128/spectrum.00957-22Genomic Surveillance of Carbapenem-Resistant Klebsiella pneumoniae from a Major Public Health Hospital in SingaporeJocelyn Qi-Min Teo0Cheng Yee Tang1Si Hui Tan2Hong Yi Chang3Sze Min Ong4Shannon Jing-Yi Lee5Tse-Hsien Koh6James Heng-Chiak Sim7Andrea Lay-Hoon Kwa8Rick Twee-Hee Ong9Department of Pharmacy, Singapore General Hospital, Singapore, SingaporeSaw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, SingaporeDepartment of Pharmacy, Singapore General Hospital, Singapore, SingaporeDepartment of Pharmacy, Singapore General Hospital, Singapore, SingaporeDepartment of Pharmacy, National University of Singapore, Singapore, SingaporeDepartment of Pharmacy, Singapore General Hospital, Singapore, SingaporeDepartment of Microbiology, Singapore General Hospital, Singapore, SingaporeDepartment of Microbiology, Singapore General Hospital, Singapore, SingaporeDepartment of Pharmacy, Singapore General Hospital, Singapore, SingaporeSaw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, SingaporeABSTRACT Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a global public health threat. In this study, we employed whole-genome sequencing (WGS) to determine the genomic epidemiology of a longitudinal collection of clinical CRKP isolates recovered from a large public acute care hospital in Singapore. Phylogenetic analyses, a characterization of resistance and virulence determinants, and plasmid profiling were performed for 575 unique CRKP isolates collected between 2009 and 2020. The phylogenetic analyses identified the presence of global high-risk clones among the CRKP population (clonal group [CG] 14/15, CG17/20, CG147, CG258, and sequence type [ST] 231), and these clones constituted 50% of the isolates. Carbapenemase production was common (n = 497, 86.4%), and KPC was the predominant carbapenemase (n = 235, 40.9%), followed by OXA-48-like (n = 128, 22.3%) and NDM (n = 93, 16.2%). Hypervirulence was detected in 59 (10.3%) isolates and was most common in the ST231 carbapenemase-producing isolates (21/59, 35.6%). Carbapenemase genes were associated with diverse plasmid replicons; however, there was an association of blaOXA-181/232 with ColKP3 plasmids. This study presents the complex and diverse epidemiology of the CRKP strains circulating in Singapore. Our study highlights the utility of WGS-based genomic surveillance in tracking the population dynamics of CRKP. IMPORTANCE In this study, we characterized carbapenem-resistant Klebsiella pneumoniae clinical isolates collected over a 12-year period in the largest public acute-care hospital in Singapore using whole-genome sequencing. The results of this study demonstrate significant genomic diversity with the presence of well-known epidemic, multidrug-resistant clones amid a diverse pool of nonepidemic lineages. Genomic surveillance involving comprehensive resistance, virulence, and plasmid gene content profiling provided critical information for antimicrobial resistance monitoring and highlighted future surveillance priorities, such as the emergence of ST231 K. pneumoniae strains bearing multidrug resistance, virulence elements, and the potential plasmid-mediated transmission of the blaOXA-48-like gene. The findings here also reinforce the necessity of unique infection control and prevention strategies that take the genomic diversity of local circulating strains into consideration.https://journals.asm.org/doi/10.1128/spectrum.00957-22carbapenem-resistantKlebsiella pneumoniaewhole-genome sequencingdrug resistance mechanismsplasmid-mediated resistancevirulence factors |
| spellingShingle | Jocelyn Qi-Min Teo Cheng Yee Tang Si Hui Tan Hong Yi Chang Sze Min Ong Shannon Jing-Yi Lee Tse-Hsien Koh James Heng-Chiak Sim Andrea Lay-Hoon Kwa Rick Twee-Hee Ong Genomic Surveillance of Carbapenem-Resistant Klebsiella pneumoniae from a Major Public Health Hospital in Singapore Microbiology Spectrum carbapenem-resistant Klebsiella pneumoniae whole-genome sequencing drug resistance mechanisms plasmid-mediated resistance virulence factors |
| title | Genomic Surveillance of Carbapenem-Resistant Klebsiella pneumoniae from a Major Public Health Hospital in Singapore |
| title_full | Genomic Surveillance of Carbapenem-Resistant Klebsiella pneumoniae from a Major Public Health Hospital in Singapore |
| title_fullStr | Genomic Surveillance of Carbapenem-Resistant Klebsiella pneumoniae from a Major Public Health Hospital in Singapore |
| title_full_unstemmed | Genomic Surveillance of Carbapenem-Resistant Klebsiella pneumoniae from a Major Public Health Hospital in Singapore |
| title_short | Genomic Surveillance of Carbapenem-Resistant Klebsiella pneumoniae from a Major Public Health Hospital in Singapore |
| title_sort | genomic surveillance of carbapenem resistant klebsiella pneumoniae from a major public health hospital in singapore |
| topic | carbapenem-resistant Klebsiella pneumoniae whole-genome sequencing drug resistance mechanisms plasmid-mediated resistance virulence factors |
| url | https://journals.asm.org/doi/10.1128/spectrum.00957-22 |
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