Hybrid genome assembly of Shigella sonnei reveals the novel finding of chromosomal integration of an IncFII plasmid carrying a mphA gene.

Azithromycin is increasingly being used for the treatment of shigellosis despite a lack of interpretative guidelines and with limited clinical evidence. The present study determined azithromycin susceptibility and correlated this with macrolide-resistance genes in spp. isolated from stool specimens in Vellore, India. The susceptibility of 332 isolates to azithromycin was determined using the disc diffusion method. Of these, 31 isolates were found to be azithromycin resistant. The azithromycin minimum inhibitory concentration (MIC) was determined using the broth microdilution method. In addition, isolates were screened for and genes using conventional PCR. Furthermore, an isolate that was positive for resistance genes was subjected to complete genome analysis, and was analysed for mobile genetic elements. The azithromycin MIC for the 31 resistant isolates ranged between 2 and 16 mg l. PCR results showed that a single isolate of carried a gene. Complete genome analysis revealed integration of an IncFII plasmid into the chromosome of , which was also found to carry the following resistance genes: 1, , B4, A, . Mutations in the quinolone-resistance-determining region (QRDR) were also observed. Additionally, prophages, insertion sequences and integrons were identified. The novel finding of IncFII plasmid integration into the chromosome of highlights the potential risk of spp. becoming resistance to azithromycin in the future. These suggests that it is imperative to monitor susceptibility and to study the resistance mechanism of to azithromycin considering the limited treatment choices for shigellosis.