Whole genome sequencing reveals hidden transmission of carbapenemase-producing Enterobacterales

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.

Genomic Surveillance of Carbapenem-Resistant Klebsiella pneumoniae from a Major Public Health Hospital in Singapore

“…Nevertheless, the acquisition of carbapenem resistance could have also occurred through indirect ward/hospital contact, which was not as easily detected. This hypothesis is supported by the findings from another local paper, which identified an independent association of indirect contact with putative clonal transmissions ( 33 ). Furthermore, the larger contribution of plasmid transmission toward carbapenem resistance dissemination may be related to non-human reservoirs, such as the hospital environment, which has been identified in previous studies as an important source of MDR organisms.…”

Estimating the economic cost of carbapenem resistant Enterobacterales healthcare associated infections in Singapore acute-care hospitals

“…The cost of a CRE HAI represented the amount incurred by the hospital if a CRE HAI had developed in an uninfected patient (e.g. via patient-to-patient or environment-topatient transmission) [21]. In patients that developed a CRE HAI after a CSE HAI (e.g.…”

Genomic Characterization of Carbapenem-Resistant Acinetobacter baumannii (CRAB) in Mechanically Ventilated COVID-19 Patients and Impact of Infection Control Measures on Reducing CRAB Circulation during the Second Wave of the SARS-CoV-2 Pandemic in Milan, Italy

“…Furthermore, to better characterize CRAB transmission chains, the core genomes of CRAB strains (i) clustering together in a number ≥3 in the ML phylogenetic tree with a bootstrap value higher than 90% and (ii) characterized by a pairwise intracluster SNP distance of <10 compared to the other strains in the same ML cluster were incorporated in a Bayesian tree inference together with information about the date of first positivity. The Bayesian coalescent tree analysis was undertaken with BEAST (v.1.10.4) ( 30 , 47 – 50 ) as detailed in the supplemental material.…”