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SG-APSIC1123: Diagnostic and infection prevention and control (IPC) performance of rapid polymerase chain reaction (PCR) compared to conventional culture PCR methods for detecting carbapenemase-producing organisms (CPOs)

Published online by Cambridge University Press:  16 March 2023

Xiaowei Huan
Affiliation:
National Centre for Infectious Diseases, Singapore
Kyaw Zaw Linn
Affiliation:
National Public Health & Epidemiology Unit, National Centre for Infectious Diseases, Singapore
Sharifah Farhanah
Affiliation:
Infectious Disease Research and Training Office, National Centre for Infectious Diseases, Singapore
Clara Chong Hui Ong
Affiliation:
Infectious Disease Research and Training Office, National Centre for Infectious Diseases, Singapore
Pei Yun Hon
Affiliation:
Infectious Disease Research Laboratory, National Centre for Infectious Diseases, Singapore
Yan Sun
Affiliation:
Health Service and Outcomes Research, National Healthcare Group Pte Ltd, Singapore
Weixiang Lian
Affiliation:
Clinical Epidemiology, National Centre for Infectious Diseases, Singapore
Janis Wanning Loh
Affiliation:
Clinical Epidemiology, National Centre for Infectious Diseases, Singapore
Angela Chow
Affiliation:
Clinical Epidemiology, National Centre for Infectious Diseases, Singapore
Benda Sze Peng Ang
Affiliation:
Infectious Diseases, Tan Tock Seng Hospital, Singapore
Janice Wai Yeng Leong
Affiliation:
Department of Laboratory Medicine, Tan Tock Seng Hospital, Singapore
Partha P De
Affiliation:
Department of Laboratory Medicine, Tan Tock Seng Hospital, Singapore
Oon Tek Ng
Affiliation:
Infectious Diseases, Tan Tock Seng Hospital, Singapore
Marimuthu Kalisvar
Affiliation:
Infectious Diseases, Tan Tock Seng Hospital, Singapore
Shawn Vasoo
Affiliation:
Infectious Diseases, Tan Tock Seng Hospital, Singapore

Abstract

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Objectives: In this study, we compared the performance of a rapid polymerase chain reaction (PCR) method in detecting carbapenemase-producing organisms (CPOs) and its impact on infection prevention and control (IPC) measures compared with a culture PCR method. Methods: All patients requiring CPO screening were included. Rectal swabs were collected with double rayon swabs (Copan 139C). They were simultaneously analyzed for the presence of CPOs using rapid PCR assay (Xpert Carba-R assay, Cepheid, Sunnyvale, CA) and a culture–PCR method (ChromID CARBA-SMART, bioMerieux, Marcy-l’Etoile, France). For CARBA-SMART, only colored colonies (ie, Enterobacterales) were evaluated for CPOs according to the prevailing institutional protocol. We tracked time to CPO detection. Using CPO positivity from either the rapid PCR or the culture PCR method as the gold standard, we calculated the sensitivity and specificity of both tests. We calculated the number of epidemiologically linked contacts generated when the first test results were known. We prospectively followed the ward census to identify the putative additional number of contacts generated by the later known result. Contacts were patients who shared the same ward (with overlapping time) as the CPO patients. Results: Between April 2019 and June 2020, culture PCR method detected CPOs in 316 (1.3%) of 24,514 samples (blaOXA48, N = 211; blaNDM, N = 51; blaIMI, N = 21; blaIMP, N = 10; blaKPC, N = 9; mixed genotypes, N = 14). The rapid PCR test detected CPOs in 605(2.5%) of 24,514 samples (blaOXA48, N = 266; blaNDM, N = 161; blaIMP, N = 99; blaVIM, N = 29; blaKPC, N = 15; mixed genotypes, N = 35). The sensitivity of direct PCR and culture PCR methods were 94.2% (95% CI, 92.1%–95.8%) and 43.5% (95% CI, 39.6%–47.4%), respectively. Both tests had 100% specificity. The median times to detection for the rapid PCR and culture PCR methods were 3–4 hours and 4 days, respectively. Compared with rapid PCR, the culture PCR method generated additional 7,415 contacts when it also tested positive for CPOs and an additional 23,135 contacts when it tested negative for CPOs. Conclusions: In our study, the rapid PCR test was more sensitive, identified CPO faster, and generated fewer epidemiologically linked contacts than the culture PCR method.

Type
Multidrug-Resistant (MDR) Organisms
Creative Commons
Creative Common License - CCCreative Common License - BY
This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
Copyright
© The Author(s), 2023. Published by Cambridge University Press on behalf of The Society for Healthcare Epidemiology of America