In silico typing and comparative genomic analysis of IncFIIK plasmids: insights into the evolution of replicons, plasmid backbones and resistance determinant profiles [PublishAheadOfPrint]

IncFII_K plasmids are associated with the acquisition and dissemination of multiple antimicrobial resistance in Klebsiella pneumoniae and often encountered in clinical isolates of this species. Since the phylogeny and evolution of IncFII_K plasmids remain unclear, herein we performed large-scale in silico typing and comparative analysis of these plasmids in publicly available bacterial/plasmid genomes. IncFII_K plasmids are prevalent in K. pneumoniae, as found in 69% sequenced genomes, covering 66% sequenced STs (sequence types), but sparse in other Enterobacteriaceae. IncFII_K replicons have three lineages. One IncFII_K allele could be found in distinct K. pneumoniae STs, highlighting the lateral genetic flow of IncFII_K plasmids. A set of 77 IncFII_K plasmids with full sequences were further analysed. A pool of 327 antibiotic resistance genes or remnants were annotated in 75.3% of these plasmids. Plasmid genome comparison reiterated that they often contain other replicons belonging to IncFIA, IncFIB, IncFII_Yp, IncFII_pCRY, IncR, IncL and IncN groups and that they share a conserved backbone featuring an F-like conjugation module that has divergent components responsible for regulation and mating pair stabilization. Further epidemiological studies of IncFII_K plasmids are required due to sample bias of K. pneumoniae genomes in public database. This study provides insights into the evolution and structures of IncFII_K plasmids.

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