Anatomy of an Extensively Drug Resistant Klebsiella pneumoniae Outbreak in Tuscany, Italy [article]

Melissa J Martin, Brendan W Corey, Filomena Sannio, Lindsey R Hall, Ulrike MacDonald, Brendan T Jones, Emma G Mills, Jason Stam, Rosslyn Maybank, Yoon Kwak, Katharina Schaufler, Karsten Becker (+10 others)
2021 bioRxiv   pre-print
A protracted outbreak of New Delhi metallo–β–lactamase (NDM)–producing carbapenem–resistant Klebsiella pneumoniae, started in Tuscany, Italy, in November 2018 and has continued in 2020 and through 2021. To understand the regional emergence and transmission dynamics over time, we collected and sequenced the genomes of 117 extensively drug–resistant, NDM–producing K. pneumoniae isolates cultured over a 20–month period from 76 patients at several health care facilities in South–East Tuscany. All
more » ... olates belonged to high–risk clone ST–147 and were typically non–susceptible to all first line antibiotics. Albeit sporadic, resistances to colistin, tigecycline and fosfomycin were also observed as a result of repeated, independent mutations. Genomic analysis revealed that ST–147 isolates circulating in Tuscany were monophyletic, highly genetically related (including a network of 42 patients from the same hospital and sharing nearly identical isolates) and shared a recent ancestor with isolates collected from the Middle East. While the blaNDM–1 gene was carried by an IncFIB–type plasmid, our investigations revealed that the ST–147 lineage from Italy also acquired a hybrid IncH–type plasmid carrying the 16S methyltransferase armA gene as well as key virulence biomarkers often found in hypervirulent isolates. This plasmid shared extensive homologies with mosaic plasmids circulating globally including from ST–11 and ST–307 convergent lineages. Phenotypically, the carriage of this hybrid plasmid resulted in increased siderophore production but did not confer virulence to the level of archetypical, hypervirulent K. pneumoniae in a subcutaneous model of infection with immunocompetent CD1 mice. Our findings highlight the importance of performing genomic surveillance to identify emerging threats.
doi:10.1101/2021.06.02.446696 fatcat:rle7j6lzfbd7pksg5ejl5dhmkq