In Silico Typing and Comparative Genomic Analysis of IncFIIK Plasmids and Insights into the Evolution of Replicons, Plasmid Backbones, and Resistance Determinant Profiles

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, here 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, being found in 69% of sequenced genomes, covering 66% of 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 analyzed. 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 the sample bias of K. pneumoniae genomes in public databases. This study provides insights into the evolution and structures of IncFII(K) plasmids.