99. Impact of Covid-19, Divergent Genomic Modes of Transmission and Strain Replacement of Carbapenem-Resistant Organisms in a Single Hospital in Singapore over 12 years
Authors: Qin Lim Ze , Loy Dennis , sridatta Prakki Sai Rama , May Thevasagayam Natascha , Koh Vanessa , Yin Chua Jie , Yun Hon Pei , Mohamed Yazid Nurhidayah Binte , Ting Ong Jin , Huan Xiaowei , Linn Kyaw Zaw , Rao Pooja , Teo Jeanette , Venkatachalam Indumathi , De Partha P , Vasoo Shawn , Marimuthu Kalisvar , Tek Ng Oon 
Published: January 2025

Background

Much remains unknown about the different genomic characteristics of transmission comparing Carbapenem-Resistant Enterobacterales (CREs), Carbapenem-Resistant A. baumannii (CRAB) and Carbapenem-Resistant P. aeruginosa (CRPA). In this study, we examine the genomic characteristics and transmission dynamics of Carbapenemase-producing Organisms (CPOs) isolated in a single hospital from 2010 to 2022.Table 1.Genomic characterization of CPOs detected between 2010 and 2022

Methods

All Carbapenemase-Producing Enterobacterales (CPE) (n=160) identified between 2010 and 2015 and all CRE (n=2,573), carbapenem-resistant Acinetobacter spp. (n=500) and carbapenem-resistant Pseudomonas spp. (n=1,434) identified between 2019 and 2022 were whole-genome-sequenced. An outbreak was defined as monthly count greater than 2 SD above the mean. Two or more isolates of a unique species-ST combination formed an ST-cluster.Table 2.Outbreak periods among three major groups of CPOs between 2010 and 2022.

Results

Of the total 4,667 WGS isolates, 2,828 (60.6%) were surveillance and 1,839 (39.4%) were clinical cultures. The predominant species-ST and carbapenemase gene detected between 2010 and 2015 was E. coli ST131 (n=31, 19.3%) and blaNDM-1 (n=100, 62.5%), respectively, while K. pneumoniae ST76 (n=172, 6.7%) and blaOXA-48-like (n=1,577, 70.7%) was the predominant species-ST and carbapenemase gene detected among CPEs isolated between 2019 and 2022 (Table 1). The majority of CRE (87.0%), CRAB (99.4%) and CRPA (54.0%) were carbapenemase-producers. During outbreaks, ST-clusters accounted for the majority of A. baumannii (92.6% – 100%) and P. aeruginosa (87.5% – 97.1%). ST-clusters accounted for approximately half of CPE outbreaks (37.5% – 55.2%) (Table 2). CRAB and CRPA numbers declined during Covid-19 (2020 to 2021) and remained low (2022) while CRE numbers increased post-Covid-19 (2022) (Figure 1).Figure 1.Monthly incidence rates of carbapenem-resistant Enterobacterales, A. baumannii and P. aeruginosa from 2019 to 2022.

Conclusion

Clonal transmission accounted for the vast majority of CRAB and CRPA transmission while horizontal gene transfer, likely via plasmid-mediated transmission, accounted for significant CPE transmission. The varying genomic transmission modes is a possible factor for the different trends observed for CRAB, CRPA and CRE transmission pre- and post-Covid-19. Bacterial strain replacement accounted for the carbapenemase gene replacement observed over the 12-year period, possibly due to plasmid-bacterial host factors.

Disclosures

Shawn Vasoo, MBBS, MRCP, D(ABP), D(ABIM) (Inf Dis), FRCPath, bioMerieux: In-kind, for this study|Rosco Diagnostica: In-kind, for this study