Tracking the Outbreak of Carbapenem-Resistant Klebsiella pneumoniae in an Emergency Intensive Care Unit by Whole Genome Sequencing.

Abstract

The spread of carbapenem-resistant Klebsiella pneumoniae (CRKP) has become a great threat to human health, especially in the intensive care unit. The aim of this study was to identify the origin and transmission route of a CRKP outbreak in an emergency intensive care unit (EICU), so as to provide prevention and control strategies for CRKP outbreak. Between Mar and Jun 2018, 10 CRKP isolates from 5 patients in the EICU ward of Shanghai Ruijin hospital north were collected. Modified carbapenem inactivation method (mCIM) and whole-genome sequencing (WGS) were performed on all 10 CRKP isolates. By integrating the genomic and epidemiological data of our isolates and 9 CRKP isolates from an outbreak in another hospital, a putative transmission map was constructed. All 10 outbreak strains were carbapenemase positive in mCIM and belonged to the sequence type 11 (ST11) clone, harbored a set of resistance genes and virulence genes. The phylogenetic tree of CRKP isolates based on two outbreaks revealed that the initial isolate A1 in our EICU ward belonged to one branch of isolates in another hospital, this introductive isolate evolved and caused a subsequent outbreak in our EICU. Integration of genomic and epidemiological data can yield a clear transmission map of CRKP outbreak. Monitoring the rapid evolution of CRKP at the early stage of outbreak, CRKP monitoring after patients are discharged, active surveillance of newly admitted patients, environmental hygiene and efficient antibiotic treatment may be the key to prevent and control of CRKP outbreak.