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

Abstract

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/bla_OXA-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.

Fig. 1.

Hospital wards, patient movement and timeline of the K. pneumoniae outbreaks. (a) Map of the AICU and patient movement during outbreak one. The coloured arrows show the movement of the three patients. The circled numbers indicate the movement of patient one; bed numbers are shown in the map (i.e. 15A, 25A, 4A, 1A, 18B). (b) Map of the VA ward and circulation of patients during outbreak two. The coloured arrows show the movement of patients. (c) Timeline showing duration of hospital stay, diagnosis and outcome for the patients during the outbreaks in the AICU and VA ward. The dashed line separates patients from the two outbreaks [outbreak one (O1), bottom; outbreak two (O2), top].

Fig. 2.

AMR phenotype and phylogeny of ST16 K. pneumoniae from the outbreaks and environmental samples. (a) Antimicrobial susceptibility of outbreak isolates (O1, outbreak one; O2, outbreak two) and environmental isolates (ENVI). Red, orange and light orange colours correspond to full resistance, intermediate resistance and sensitivity, respectively. AMP, Ampicillin; CIP, ciprofloxacin; IMP, imipenem; LEV, levofloxacin; MEM, meropenem; CRO, ceftriaxone; CN, gentamicin; CAZ, ceftazidime; CTX, cefoxitin; AMK, amikacin; CT, colistin. (b) ML phylogeny reconstructed from 826 non-recombinant SNPs identified in 9 ST16 outbreak strains and 36 global ST16 K. pneumoniae . An ST412 isolate was used as an outgroup to root the tree. The coloured circles at terminal leaves highlight the outbreak isolates (red) and environmental isolates (cyan). The tip labels highlighted with grey backgrounds indicate ST16 isolates from Vietnam. The stars show bootstrap support values ≥80 % on internal nodes, with larger stars showing higher bootstrap values. Bar, the number of nucleotide substitutions per site. The heat map shows the presence (blue colour) or absence (grey colour) of resistance genes.