Multi-species blaNDM outbreak in multiple tertiary and a primary healthcare facility in Merseyside, UK, driven by a combination of multi-species plasmids and small clonal outbreaks

BackgroundThe blaNDM carbapenemase gene provides Gram-negative bacteria the ability to hydrolyse almost all {beta}-lactam antibiotics. A 90% year on year increase from 2022 to 2023 in prevalence of blaNDM in clinical isolates was identified in a clinical microbiology laboratory serving Merseyside, UK hospitals and GP practices in 2023. We analysed isolates identified to disclose the species and plasmid diversity and to understand the mechanism of dissemination of blaNDM across Merseyside hospitals. MethodsData regarding the sample type, the isolation date and location of samples was collected and analysed to establish initial transmission hypotheses; 64 Gram-negative bacterial isolates which tested positive for blaNDM using routine diagnostics underwent short read whole-genome sequencing. The samples were derived from seven Merseyside hospitals and a Merseyside GP practice, of these, 24 were also long-read sequenced to produce local reference assemblies and enable us to confidently resolve resistance gene locations and plasmids. ResultsOverall, six species were identified, including Enterobacter hormaechei (n=22) Klebsiella pneumoniae (n=21), Escherichia coli (n=15) Citrobacter freundii (n=3), Citrobacter brakii (n=1) and Enterobacter kobei (n=1). Most multi-isolate species belonged to a number of sequence types (IQR, 1-10), apart from K. pneumoniae where 18/21 were ST101. Four variants of blaNDM were identified: blaNDM-1 (n=43), blaNDM-5 (n=12), blaNDM-6 (n=1), blaNDM-14 (n=1), and in six isolates blaNDM was not identified by sequencing. Long-read sequencing of 24 representative isolates found that blaNDM-1 was commonly encoded by a IncHI2/IncHI2A plasmid (82.4%, n=14) whereas blaNDM-5, (n=4) was encoded on different plasmids in each isolate but had the same conserved gene cassette including blaNDM-5 in all instances. Potential evidence of transposition events was noted in two isolates, where blaNDM-1 was found on a small (8.5kbp) untypable plasmid. ConclusionsThis study captures an outbreak of blaNDM positive Enterobacterales in Merseyside hospitals and highlights the complex epidemiology of spread mediated both by expansion of successful lineages (K. pneumoniae ST101) and plasmids. A dominant IncHI2/IncHI2A plasmid that has disseminated blaNDM-1 across different species and subsequently led to small clonal outbreaks within-hospitals. This highlights the cross-species movement of AMR elements as an important factor in AMR dissemination, and the importance of both species-specific surveillance to monitor local outbreaks, but also species-agnostic surveillance to include plasmids spreading across species.