Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei.
Leah W RobertsPatrick N A HarrisBrian M FordeNouri L Ben ZakourElizabeth CatchpooleMitchell Stanton-CookMinh Duy PhanHanna Evelina SidjabatHaakon BerghClaire HeneyJayde A GawthorneJeffrey LipmanAnthony AllworthKok Gan ChanTeik Min ChongWai-Fong YinMark A SchembriDavid L PatersonScott A BeatsonPublished in: Nature communications (2020)
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 blaIMP-4 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 blaIMP-4 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.
Keyphrases
- human health
- escherichia coli
- single cell
- healthcare
- risk assessment
- klebsiella pneumoniae
- climate change
- adverse drug
- pseudomonas aeruginosa
- crispr cas
- emergency department
- acute care
- gram negative
- electronic health record
- copy number
- genome wide
- dna methylation
- gene expression
- cystic fibrosis
- transcription factor
- machine learning
- deep learning
- artificial intelligence