<i>In Silico</i> Typing and Comparative Genomic Analysis of IncFII _K Plasmids and Insights into the Evolution of Replicons, Plasmid Backbones, and Resistance Determinant Profiles

Abstract

IncFII_K plasmids are associated with the acquisition and dissemination of multiple-antimicrobial resistance in <i>Klebsiella pneumoniae</i> 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 <i>in silico</i> typing and comparative analysis of these plasmids in publicly available bacterial/plasmid genomes. IncFII_K plasmids are prevalent in <i>K. pneumoniae</i>, being found in 69% of sequenced genomes, covering 66% of sequenced STs (sequence types), but sparse in other <i>Enterobacteriaceae</i> IncFII_K replicons have three lineages. One IncFII_K allele could be found in distinct <i>K. pneumoniae</i> 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 <i>K. pneumoniae</i> genomes in public databases. This study provides insights into the evolution and structures of IncFII_K plasmids.