A high-resolution genomic analysis of multidrug-resistant hospital outbreaks of Klebsiella pneumoniae

作者：Hao Chung The; Karkey Abhilasha; Duy Pham Thanh; Boinett Christine J; Cain Amy K; Ellington Matthew; Baker Kate S; Dongol Sabina; Thompson Corinne; Harris Simon R; Jombart Thibaut; Tu Le Thi Phuong; Nhu Tran Do Hoang; Tuyen Ha Thanh; Shretha Shrijana; Joshi Suchita; Basnyat Buddha; Thwaites Guy; Thomson Nicholas R; Rabaa Maia A; Baker Stephen

来源：EMBO Molecular Medicine, 2015, 7(3): 227-239.

DOI：10.15252/emmm.201404767

• antimicrobial resistance
• bloodstream infections
• carbapenemases
• Klebsiella pneumoniae
• nosocomial infections

Multidrug-resistant (MDR) Klebsiella pneumoniae has become a leading cause of nosocomial infections worldwide. Despite itsprominence, little is known about the genetic diversity of K.pneumoniae in resource-poor hospital settings. Through whole-genome sequencing (WGS), we reconstructed an outbreak of MDR K.pneumoniae occurring on high-dependency wards in a hospital in Kathmandu during 2012 with a case-fatality rate of 75%. The WGS analysis permitted the identification of two MDR K.pneumoniae lineages causing distinct outbreaks within the complex endemic K.pneumoniae. Using phylogenetic reconstruction and lineage-specific PCR, our data predicted a scenario in which K.pneumoniae, circulating for 6months before the outbreak, underwent a series of ward-specific clonal expansions after the acquisition of genes facilitating virulence and MDR. We suggest that the early detection of a specific NDM-1 containing lineage in 2011 would have alerted the high-dependency ward staff to intervene. We argue that some form of real-time genetic characterisation, alongside clade-specific PCR during an outbreak, should be factored into future healthcare infection control practices in both high- and low-income settings.

• 出版日期2015-3