Emerging carbapenem-resistant Klebsiella pneumoniae sequence type 16 causing multiple outbreaks in a tertiary hospital in southern Vietnam

Microb Genom. 2021 Mar;7(3):mgen000519. doi: 10.1099/mgen.0.000519. Epub 2021 Feb 10.


The emergence of carbapenem resistance in Klebsiella pneumoniae represents a major global public health concern. Nosocomial outbreaks caused by multidrug-resistant K. pneumoniae are commonly reported to result in high morbidity and mortality due to limited treatment options. Between October 2019 and January 2020, two concurrent high-mortality nosocomial outbreaks occurred in a referral hospital in Ho Chi Minh City, Vietnam. We performed genome sequencing and phylogenetic analysis of eight K. pneumoniae isolates from infected patients and two environmental isolates for outbreak investigation. We identified two outbreaks caused by two distinct lineages of the international sequence type (ST) 16 clone, which displayed extensive drug resistance, including resistance to carbapenem and colistin. Carbapenem-resistant ST16 outbreak strains clustered tightly with previously described ST16 K. pneumoniae from other hospitals in Vietnam, suggesting local persistence and transmission of this particular clone in this setting. We found environmental isolates from a hospital bed and blood pressure cuff that were genetically linked to an outbreak case cluster, confirming the potential of high-touch surfaces as sources for nosocomial spread of K. pneumoniae. Further, we found colistin resistance caused by disruption of the mgrB gene by an ISL3-like element, and carbapenem resistance mediated by a transferable IncF/blaOXA-181 plasmid carrying the ISL3-like element. Our study highlights the importance of coordinated efforts between clinical and molecular microbiologists and infection control teams to rapidly identify, investigate and contain nosocomial outbreaks. Routine surveillance with advanced sequencing technology should be implemented to strengthen hospital infection control and prevention measures.

Keywords: Klebsiella pneumoniae; ST16; carbapenem resistance; colistin resistance; extensive drug resistance; nosocomial outbreaks.

MeSH terms

  • Adult
  • Anti-Bacterial Agents / pharmacology*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Carbapenems / pharmacology*
  • Cross Infection / epidemiology
  • Cross Infection / microbiology*
  • Drug Resistance, Multiple, Bacterial*
  • Female
  • Humans
  • Klebsiella Infections / epidemiology
  • Klebsiella Infections / microbiology*
  • Klebsiella pneumoniae / classification
  • Klebsiella pneumoniae / drug effects
  • Klebsiella pneumoniae / genetics
  • Klebsiella pneumoniae / isolation & purification*
  • Male
  • Microbial Sensitivity Tests
  • Middle Aged
  • Molecular Epidemiology
  • Multilocus Sequence Typing
  • Phylogeny
  • Tertiary Care Centers / statistics & numerical data
  • Vietnam / epidemiology


  • Anti-Bacterial Agents
  • Bacterial Proteins
  • Carbapenems

Associated data

  • figshare/10.6084/m9.figshare.13378745