Genomic surveillance, characterization and intervention of a polymicrobial multidrug-resistant outbreak in critical care

Microb Genom. 2021 Mar;7(3):mgen000530. doi: 10.1099/mgen.0.000530. Epub 2021 Feb 18.


Background. Infections caused by carbapenem-resistant Acinetobacter baumannii (CR-Ab) have become increasingly prevalent in clinical settings and often result in significant morbidity and mortality due to their multidrug resistance (MDR). Here we present an integrated whole-genome sequencing (WGS) response to a persistent CR-Ab outbreak in a Brisbane hospital between 2016-2018.Methods. A. baumannii, Klebsiella pneumoniae, Serratia marcescens and Pseudomonas aeruginosa isolates were sequenced using the Illumina platform primarily to establish isolate relationships based on core-genome SNPs, MLST and antimicrobial resistance gene profiles. Representative isolates were selected for PacBio sequencing. Environmental metagenomic sequencing with Illumina was used to detect persistence of the outbreak strain in the hospital.Results. In response to a suspected polymicrobial outbreak between May to August of 2016, 28 CR-Ab (and 21 other MDR Gram-negative bacilli) were collected from Intensive Care Unit and Burns Unit patients and sent for WGS with a 7 day turn-around time in clinical reporting. All CR-Ab were sequence type (ST)1050 (Pasteur ST2) and within 10 SNPs apart, indicative of an ongoing outbreak, and distinct from historical CR-Ab isolates from the same hospital. Possible transmission routes between patients were identified on the basis of CR-Ab and K. pneumoniae SNP profiles. Continued WGS surveillance between 2016 to 2018 enabled suspected outbreak cases to be refuted, but a resurgence of the outbreak CR-Ab mid-2018 in the Burns Unit prompted additional screening. Environmental metagenomic sequencing identified the hospital plumbing as a potential source. Replacement of the plumbing and routine drain maintenance resulted in rapid resolution of the secondary outbreak and significant risk reduction with no discernable transmission in the Burns Unit since.Conclusion. We implemented a comprehensive WGS and metagenomics investigation that resolved a persistent CR-Ab outbreak in a critical care setting.

Keywords: Acinetobacter baumannii; CR-Ab; WGS; burns ward; carbapenem resistance; genomics; intensive care unit; metagenomics; surveillance; whole-genome sequencing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acinetobacter baumannii / classification
  • Acinetobacter baumannii / drug effects
  • Acinetobacter baumannii / genetics*
  • Acinetobacter baumannii / isolation & purification
  • Adult
  • Aged
  • Anti-Bacterial Agents / pharmacology
  • Critical Care / statistics & numerical data
  • Cross Infection / microbiology*
  • Disease Outbreaks
  • Drug Resistance, Multiple, Bacterial*
  • Female
  • Genome, Bacterial
  • Genomics
  • Gram-Negative Bacterial Infections / microbiology*
  • Humans
  • Klebsiella pneumoniae / classification
  • Klebsiella pneumoniae / drug effects
  • Klebsiella pneumoniae / genetics*
  • Klebsiella pneumoniae / isolation & purification
  • Male
  • Middle Aged
  • Phylogeny
  • Pseudomonas aeruginosa / classification
  • Pseudomonas aeruginosa / drug effects
  • Pseudomonas aeruginosa / genetics*
  • Pseudomonas aeruginosa / isolation & purification
  • Serratia marcescens / classification
  • Serratia marcescens / drug effects
  • Serratia marcescens / genetics*
  • Serratia marcescens / isolation & purification
  • Whole Genome Sequencing


  • Anti-Bacterial Agents