Cookies on this website

We use cookies to ensure that we give you the best experience on our website. If you click 'Accept all cookies' we'll assume that you are happy to receive all cookies and you won't see this message again. If you click 'Reject all non-essential cookies' only necessary cookies providing core functionality such as security, network management, and accessibility will be enabled. Click 'Find out more' for information on how to change your cookie settings.

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.

Original publication




Journal article


EMBO Mol Med

Publication Date





227 - 239


Klebsiella pneumoniae, antimicrobial resistance, bloodstream infections, carbapenemases, nosocomial infections, Animals, Cluster Analysis, Cross Infection, Disease Outbreaks, Drug Resistance, Multiple, Bacterial, Evolution, Molecular, Genes, Bacterial, Genome, Bacterial, Genomics, Genotype, Humans, Infection Control, Klebsiella Infections, Klebsiella pneumoniae, Mice, Molecular Sequence Data, Nepal, Phylogeny, Polymerase Chain Reaction, Sequence Analysis, DNA, Sequence Homology, Virulence Factors