Open AccessA high‐resolution genomic analysis of multidrug‐resistant hospital outbreaks of Klebsiella pneumoniae
Author(s) -
Chung The Hao,
Karkey Abhilasha,
Pham Thanh Duy,
Boinett Christine J,
Cain Amy K,
Ellington Matthew,
Baker Kate S,
Dongol Sabina,
Thompson Corinne,
Harris Simon R,
Jombart Thibaut,
Le Thi Phuong Tu,
Tran Do Hoang Nhu,
Ha Thanh Tuyen,
Shretha Shrijana,
Joshi Suchita,
Basnyat Buddha,
Thwaites Guy,
Thomson Nicholas R,
Rabaa Maia A,
Baker Stephen
Publication year - 2015
Publication title -
embo molecular medicine
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 4.923
H-Index - 107
eISSN - 1757-4684
pISSN - 1757-4676
DOI - 10.15252/emmm.201404767
Subject(s) - klebsiella pneumoniae , multiple drug resistance , outbreak , microbiology and biotechnology , klebsiella , biology , virology , medicine , genetics , drug resistance , escherichia coli , gene
Multidrug‐resistant ( MDR ) Klebsiella pneumoniae has become a leading cause of nosocomial infections worldwide. Despite its prominence, 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 6 months 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.