Whole genome sequencing reveals hidden transmission of carbapenemase-producing Enterobacterales

Kalisvar Marimuthu (), Indumathi Venkatachalam, Vanessa Koh, Stephan Harbarth, Eli Perencevich, Benjamin Pei Zhi Cherng, Raymond Kok Choon Fong, Surinder Kaur Pada, Say Tat Ooi, Nares Smitasin, Koh Cheng Thoon, Paul Anantharajah Tambyah, Li Yang Hsu, Tse Hsien Koh, Partha Pratim De, Thean Yen Tan, Douglas Chan, Rama Narayana Deepak, Nancy Wen Sim Tee, Andrea Kwa, Yiying Cai, Yik-Ying Teo, Natascha May Thevasagayam, Sai Rama Sridatta Prakki, Weizhen Xu, Wei Xin Khong, David Henderson, Nicole Stoesser, David W. Eyre, Derrick Crook, Michelle Ang, Raymond Tzer Pin Lin, Angela Chow, Alex R. Cook, Jeanette Teo and Oon Tek Ng ()
Additional contact information
Kalisvar Marimuthu: National Centre for Infectious Diseases
Indumathi Venkatachalam: Singapore General Hospital
Vanessa Koh: National Centre for Infectious Diseases
Stephan Harbarth: Infection Control Program, WHO Collaborating Center, Geneva University Hospitals and Faculty of Medicine
Eli Perencevich: University of Iowa Carver College of Medicine
Benjamin Pei Zhi Cherng: Yong Loo Lin School of Medicine, National University of Singapore and National University Health System
Raymond Kok Choon Fong: Changi General Hospital
Surinder Kaur Pada: Ng Teng Fong General Hospital
Say Tat Ooi: Khoo Teck Puat Hospital
Nares Smitasin: Yong Loo Lin School of Medicine, National University of Singapore and National University Health System
Koh Cheng Thoon: KK Women’s and Children’s Hospital
Paul Anantharajah Tambyah: National University Hospital and National University Health System
Li Yang Hsu: Yong Loo Lin School of Medicine, National University of Singapore and National University Health System
Tse Hsien Koh: Singapore General Hospital
Partha Pratim De: Tan Tock Seng Hospital
Thean Yen Tan: Changi General Hospital
Douglas Chan: Ng Teng Fong General Hospital
Rama Narayana Deepak: Khoo Teck Puat Hospital
Nancy Wen Sim Tee: National University Hospital and National University Health System
Andrea Kwa: Singapore General Hospital
Yiying Cai: Singapore General Hospital
Yik-Ying Teo: Saw Swee Hock School of Public Health, National University of Singapore and National University Health System
Natascha May Thevasagayam: National Centre for Infectious Diseases
Sai Rama Sridatta Prakki: National Centre for Infectious Diseases
Weizhen Xu: National Centre for Infectious Diseases
Wei Xin Khong: Tan Tock Seng Hospital
David Henderson: Clinical Centre, National Institutes of Health
Nicole Stoesser: Nuffield Department of Medicine, University of Oxford
David W. Eyre: Nuffield Department of Population Health, University of Oxford
Derrick Crook: Nuffield Department of Medicine, University of Oxford
Michelle Ang: National Centre for Infectious Diseases
Raymond Tzer Pin Lin: National Centre for Infectious Diseases
Angela Chow: Tan Tock Seng Hospital
Alex R. Cook: Saw Swee Hock School of Public Health, National University of Singapore and National University Health System
Jeanette Teo: National University Hospital and National University Health System
Oon Tek Ng: National Centre for Infectious Diseases

Nature Communications, 2022, vol. 13, issue 1, 1-11

Abstract: Abstract Carbapenemase-producing Enterobacterales (CPE) infection control practices are based on the paradigm that detected carriers in the hospital transmit to other patients who stay in the same ward. The role of plasmid-mediated transmission at population level remains largely unknown. In this retrospective cohort study over 4.7 years involving all multi-disciplinary public hospitals in Singapore, we analysed 779 patients who acquired CPE (1215 CPE isolates) detected by clinical or surveillance cultures. 42.0% met putative clonal transmission criteria, 44.8% met putative plasmid-mediated transmission criteria and 13.2% were unlinked. Only putative clonal transmissions associated with direct ward contact decreased in the second half of the study. Both putative clonal and plasmid-mediated transmission associated with indirect (no temporal overlap in patients’ admission period) ward and hospital contact did not decrease during the study period. Indirect ward and hospital contact were identified as independent risk factors associated with clonal transmission. In conclusion, undetected CPE reservoirs continue to evade hospital infection prevention measures. New measures are needed to address plasmid-mediated transmission, which accounted for 50% of CPE dissemination.

Date: 2022
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DOI: 10.1038/s41467-022-30637-5

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