Genomic characterisation of multidrug-resistant Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii in two intensive care units in Hanoi, Viet Nam: a prospective observational cohort study.

Background: Viet Nam has high rates of antimicrobial resistance (AMR) but little capacity for genomic surveillance. This study used whole genome sequencing to examine the prevalence and transmission of three key AMR pathogens in two intensive care units (ICUs) in Hanoi, Viet Nam.
Methods: A prospective surveillance study of all adults admitted to ICUs at the National Hospital for Tropical Diseases and Bach Mai Hospital was done between June 19, 2017, and Jan 16, 2018. Clinical and environmental samples were cultured on selective media, characterised with MALDI TOF mass spectrometry, and sequenced with Illumina. Phylogenies based on the de-novo assemblies (SPAdes) were constructed with MAFFT (PARsnp), Gubbins, and RAxML. Resistance genes were detected with Abricate against the US National Center for Biotechnology Information database.
Findings: 3153 Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii isolates from 369 patients were analysed. Phylogenetic analysis revealed predominant lineages within A baumannii (global clone 2, sequence types ST2 and ST571) and K pneumoniae (ST15, ST16, ST656, ST11, and ST147) isolates. Isolation from stool was most common with E coli (87·0%) followed by K pneumoniae (62·5%). Of the E coli, 85·0% carried a bla _CTX-M variant, while 81·8% of K pneumoniae isolates carried bla _NDM (54·4%), or bla _KPC (45·1%), or both. Transmission analysis with single nucleotide polymorphisms identified 167 clusters involving 251 (68%) of 369 patients, in some cases involving patients from both ICUs. There were no clear differences between the lineages or AMR genes recovered between the two ICUs.
Interpretation: This study represents the largest prospective surveillance study of key AMR pathogens in Vietnamese ICUs. Clusters of closely related isolates in patients across both ICUs suggests recent transmission before ICU admission in other health-care settings or in the community.
Funding: UK Medical Research Council Newton Fund, Viet Nam Ministry of Science and Technology, Wellcome Trust, Academy of Medical Sciences, Health Foundation, and UK National Institute for Health and Care Research Cambridge Biomedical Research Centre.
Competing Interests: Declaration of interests LWR reports travel fees from European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), and is on the Microbial Genomics Early Career Microbiologists board of reviewers, outside of the submitted work. HRvD is a board member of the Surveillance and Epidemiology of Drug Resistant Infections Consortium, outside of the submitted work. JP reports grants from the National Institute for Health and Care Research and Wellcome Trust and consulting fees and stock options from Next Gen Diagnostics, outside of the submitted work. ZI reports grants from Global Challenges Research Fund, UK Research and Innovation, and National Institute for Health and Care Research Health Protection Research Unit, travel fees from the US Centers for Disease Control and Prevention, and is part of the advisory board for Laboratory of Molecular Infection Medicine Sweden and CLIMB-BIG-DATA, outside of the submitted work. MET reports book royalties from Oxford University Press and teaching honoraria from Wellcome Sanger Institute, outside of the submitted work. All other authors declare no competing interests.
(Copyright © 2022 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license. Published by Elsevier Ltd.. All rights reserved.)