Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei.
case_report · Level V
Where this comes from
- Record sourced from PubMed, PMID 31980604.
- Also identified by DOI 10.1038/s41467-019-14139-5 and PMC identifier 6981164.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) represent an urgent threat to human health. Here we report the application of several complementary whole-genome sequencing (WGS) technologies to characterise a hospital outbreak of bla<sub>IMP-4</sub> carbapenemase-producing E. hormaechei. Using Illumina sequencing, we determined that all outbreak strains were sequence type 90 (ST90) and near-identical. Comparison to publicly available data linked all outbreak isolates to a 2013 isolate from the same ward, suggesting an environmental source in the hospital. Using Pacific Biosciences sequencing, we resolved the complete context of the bla<sub>IMP-4</sub> gene on a large IncHI2 plasmid carried by all IMP-4-producing strains across different hospitals. Shotgun metagenomic sequencing of environmental samples also found evidence of ST90 E. hormaechei and the IncHI2 plasmid within the hospital plumbing. Finally, Oxford Nanopore sequencing rapidly resolved the true relationship of subsequent isolates to the initial outbreak. Overall, our strategic application of three WGS technologies provided an in-depth analysis of the outbreak.
Medical subject headings
- Bacterial Proteins
- Carbapenem-Resistant Enterobacteriaceae
- Disease Outbreaks
- Enterobacter
- Enterobacteriaceae Infections
- beta-Lactamases