Cowboy song

Seemann, Charlie

doi:10.1093/gmo/9781561592630.article.a2240569

Cited by 1 publication

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“…MLST was determined using the hybrid assemblies and the tool mlst (v2.19.0) [28] with the following profiles: ( Acinetobacter baumannii Pasteur , Citrobacter freundii, Enterobacter, Escherichia coli Achtman , Klebsiella pneumoniae, Pseudomonas aeruginosa ) [29]. Resistance genes and plasmid profiles were detected using the complete assemblies and Abricate (v1.0.1) [30] against the CARD (date: 27 March 2021) [31] and Plasmidfinder (date: 24 october 2020) [32] databases using a minimum coverage of 90 % and minimum nucleotide identity of 90 %.…”

Section: Methodsmentioning

confidence: 99%

Long-read sequencing reveals genomic diversity and associated plasmid movement of carbapenemase-producing bacteria in a UK hospital over 6 years

Roberts

Enoch²,

Khokhar

et al. 2023

Microbial Genomics

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Healthcare-associated infections (HCAIs) affect the most vulnerable people in society and are increasingly difficult to treat in the face of mounting antimicrobial resistance (AMR). Routine surveillance represents an effective way of understanding the circulation and burden of bacterial resistance and transmission in hospital settings. Here, we used whole-genome sequencing (WGS) to retrospectively analyse carbapenemase-producing Gram-negative bacteria from a single hospital in the UK over 6 years (n=165). We found that the vast majority of isolates were either hospital-onset (HAI) or HCAI. Most carbapenemase-producing organisms were carriage isolates, with 71 % isolated from screening (rectal) swabs. Using WGS, we identified 15 species, the most common being Escherichia coli and Klebsiella pneumoniae . Only one significant clonal outbreak occurred during the study period and involved a sequence type (ST)78 K . pneumoniae carrying bla NDM-1 on an IncFIB/IncHI1B plasmid. Contextualization with public data revealed little evidence of this ST outside of the study hospital, warranting ongoing surveillance. Carbapenemase genes were found on plasmids in 86 % of isolates, the most common types being bla NDM- and bla OXA-type alleles. Using long-read sequencing, we determined that approximately 30 % of isolates with carbapenemase genes on plasmids had acquired them via horizontal transmission. Overall, a national framework to collate more contextual genomic data, particularly for plasmids and resistant bacteria in the community, is needed to better understand how carbapenemase genes are transmitted in the UK.

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