Genomically-suported redefinition of an outbreak in a pediatric unit caused by blaVIM-harboring Klebsiella michiganensis

Klebsiella michiganensis, a member of the Klebsiella oxytoca complex, is an emerging nosocomial pathogen known to frequently carry plasmids with antibiotic resistance genes, including carbapenemases. This study employed Illumina and Nanopore whole genome sequencing technologies to redefine an outbreak alert caused by K. michiganensis carrying a blaVIM carbapenemase in a pediatric ward of a Spanish hospital in 2021. All but one of the isolates (one isolate per patient) corresponded to rectal swabs; in one of the case, we obtained an additional isolate from blood. One environmental K.oxytoca-VIM isolate was also included. Twelve out of the 14 K. michiganensis-VIM cases identified in 2021 showed pairwise SNP distances ranging from 0 to 16 SNPs, confirming the outbreak. Examination of isolates before and after the study period revealed additional seven cases, two in 2020 and five in 2022, prior to the presumed start of the outbreak. The outbreak comprised 19 K. michiganensis-VIM isolates from 17 patients and four different pediatric wards, along with one environmental sample. The blaVIM-1 gene was located within a gene cassette in a type 1 integron inserted into an IncFIB(pQil) plasmid in all outbreak isolates. A genomic network was constructed by utilizing phylogenetic relationships based on single-nucleotide polymorphisms (SNPs). The genomic network revealed five unsampled nodes, and no correlation was found between time of sample collection and genetic distance. This suggests the simultaneous existence of different subclones. Unsampled nodes could include healthcare staff, patients' relatives, or environmental reservoirs. Blood and rectal isolates obtained from the same patient were positioned in separate branches of the network, thereby eliminating any direct evolutionary route from one to the other. Our genomic study has redefined the full scale of this K.michiganensis-VIM outbreak, establishing the true duration and scope. The outbreak persisted between 2020 and mid-2022 and spread across three additional hospital wards beyond the initially suspected one. Additionally, the chronological redefinition of the outbreak allowed us to reassign the potential index case, revealing that the outbreak isolate infiltrated the hospital and disseminated among patients and units. These results highlight the critical relevance of genomic analyses in accurately understanding and investigating outbreaks within healthcare settings.