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Background   Shigella flexneri  has an extremely complex genome with a significant number of virulence traits acquired by mobile genetic elements including bacteriophages and plasmids.  S. flexneri  serotype 1c is an emerging etiological agent of bacillary dysentery in developing countries. In this study, the complete nucleotide sequence of two plasmids of  S. flexneri  serotype 1c strain Y394 was determined and analysed.    Results  The plasmid pINV-Y394 is an invasive or virulence plasmid of size 221,293 bp composed of a large number of insertion sequences (IS), virulence genes, regulatory and maintenance genes. Three hundred and twenty-eight open reading frames (ORFs) were identified in pINV-Y394, of which about a half (159 ORFs) were identified as IS elements. Ninety-seven ORFs were related to characterized genes (majority of which are associated with virulence and their regulons), and 72 ORFs were uncharacterized or hypothetical genes. The second plasmid pNV-Y394 is of size 10,866 bp and encodes genes conferring resistance against multiple antibiotics of clinical importance. The multidrug resistance gene cassette consists of tetracycline resistance gene  tetA , streptomycin resistance gene  strA-strB  and sulfonamide-resistant dihydropteroate synthase gene  sul2 .    Conclusions  These two plasmids together play a key role in the fitness of Y394 in the host environment. The findings from this study indicate that the pathogenic  S. flexneri  is a highly niche adaptive pathogen which is able to co-evolve with its host and respond to the selection pressure in its environment.    Electronic supplementary material  The online version of this article (10.1186/s12866-019-1455-1) contains supplementary material, which is available to authorized users.

Plasmids of Shigella flexneri serotype 1c strain Y394 provide advantages to bacteria in the host