Class 1 integron driving a blaVIM-1 interspecies outbreak in a large tertiary hospital in Italy

ObjectivesWe investigated an outbreak of VIM+ pathogens lasting over a year, affecting intensive care unit (ICU) patients in tertiary Hospital in Bergamo, Italy. To identify the routes of transmission of pathogens we combined the classical epidemiological investigation with the molecular identification of the mobile genetic elements (MGEs), including plasmids and integrons that could have played a role in the outbreak persistence.MethodsShort and long reads sequencing were performed respectively with Illumina MiniSeq platform (Illumina Inc., San Diego, CA, USA) and MinION Mk1B platform (Oxford Nanopore Technologies, Oxford, UK). Transmission, resistome and virulome analysis were conducted as well as the identification of plasmids and integrons harbouring blaVIM-1.ResultsForty four isolates, including Enterobacterales and Pseudomonaceae, were identified from patients and environmental samples. The strains exhibited diverse resistomes and virulomes, with high mortality rates among infected patients. Genomic analysis revealed a consistent presence of Class 1 integrons (IntI1) in all the analysed strains. The identified integrons harboured fused genes conferring resistance to disinfectants and sulfonamides. The identifications of the same IntI1 in environmental samples suggests a potential reservoir for resistant strains in hospital sinks and siphons.ConclusionsThese findings emphasize the need for comprehensive infection control measures addressing MGEs spreading and persistence in the healthcare setting, including genomic based surveillance.