Background: Multiple incompatibility (Inc) groups of plasmids have been identified in Enterobacteriaceae  species, but there are still quite a few sequenced plasmids that could not be assigned to any known Inc groups.
Methods: One IncFII_pKF727591β plasmid p205880-qnrS and two Inc_pKPHS1 plasmids p11219-CTXM and p205880-NR1 were fully sequenced in this work. Detailed genomic comparison was applied to all available sequenced plasmids of IncFII_pKF727591 or Inc_pKPHS1 group.
Results: p205880-qnrS carried a novel transposon Tn6396 , which was an ISKpn19 -compsite transposon and represented a prototype transposable element carrying a minimum core qnrS1  module. p11219-CTXM harbored a novel transposon Tn6559 , which was generated from integration of a truncated IS903D–bla _CTX-M-14–ISEcp1  unit into the Tn3 -family cryptic unit transposon Tn1722 . Two Inc groups, IncFII_pKF727591 and Inc_pKPHS1, of plasmids from Enterobacteriaceae  species were proposed, and IncFII_pKF727591 was further grouped into two subgroups IncFII_pKF727591α and IncFII_pKF727591β. Each of the 11 IncFII_pKF727591 plasmids carried multiple accessory modules including at least one resistance module, and the relatively small IncFII_pKF727591 backbones could acquire a wealth of foreign genetic contents. The modular structures of plasmid backbones were conserved within each of IncFII_pKF727591α and IncFII_pKF727591β subgroups but dramatically different, although with similar gene organizations, between these two subgroups. The Inc_pKPHS1 backbones were conserved with respect to modular structures, and only four of the 14 Inc_pKPHS1 plasmids carried accessory modules, two of which contained resistance genes.
Conclusion: A genomic comparison of sequenced Inc_pKPHS1 or IncFII_pKF727591 plasmids provides insights into modular differences and genetic diversification of these plasmids, some of which carries antimicrobial resistance genes.
Keywords: plasmids, IncFII_pKF727591, Inc_pKPHS1, Tn6396 , Tn6559