Objectives Shigella is a human pathogen that causes shigellosis, an acute invasive intestinal infection. Recent studies in the model bacterium Escherichia coli ( E. coli ) provided evidence that small regulatory RNAs (sRNAs) can contribute to antimicrobial resistance or susceptibility. One of the sRNAs is SdsR, which increases sensitivity of E. coli against fluoroquinolone by repressing the drug efflux pump, TolC. However, no reports exist about the effect of SdsR on fluoroquinolone resistance in Shigella sonnei ( S. sonnei ). In this study, we established the effect of SdsR on the sensitivity of S. sonnei to norfloxacin. Data description We tested the effects of SdsR and SdsRv2 on fluoroquinolone resistance in S. sonnei in vivo. SdsRv2 is a synthetic version which promotes higher binding stability to tolC mRNA. Overexpression of either SdsR or SdsRv2 lowers the expression of tolC mRNA. Interestingly, SdsR and SdsRv2 promote the growth of S. sonnei in the presence of a sub-inhibitory concentration of norfloxacin. Mutant carrying SdsRv2 showed the highest growth advantage. This phenotype is opposite to the effect of SdsR reported in E. coli . This study is an example that demonstrates the difference in the phenotypic effect of a highly conserved sRNA in two closely related bacteria.

Shigella spp. commonly causes gastroenteritis known as shigellosis, and severe cases require antibiotic treatments. However, the increased presence of antibiotics in the environment in recent years can lead to antibiotic resistance. Sub-lethal antibiotic concentrations can promote resistance, but its effect on sensitive bacteria prior to resistance development is unknown. In this study, the complete genome of Shigella sonnei UKMCC1015, a sensitive strain from Malaysia is presented. Subsequently, the transcriptomic response of this strain towards sub-MIC levels of norfloxacin, a commonly used fluoroquinolone is investigated. This study reveals that the expressions of the antimicrobial resistance genes and antibiotic targets (DNA gyrase and topoisomerase IV) are not affected. Interestingly, multiple ribosomal protein operons were downregulated while a small regulatory RNA (sRNA), GcvB was upregulated in response to constant exposure to sub-MIC norfloxacin.. To our knowledge, association between sub-lethal fluoroquinolone and expression of ribosomal protein operons as well as GcvB sRNA have never been reported. Collectively, these findings suggest that there are novel pathways possibly related to ppGpp levels that are involved in the adaptive response of S. sonnei towards fluoroquinolones.Impact StatementIn this study, the genome of a sensitive Shigella sonnei UKMCC1015 and the transcriptomic analysis of its response towards sub-lethal norfloxacin is presented. This study brings new information towards the multitudes of responses S. sonnei can have against a low concentration of antibiotics, including the involvement of the stringent response and a small non-coding RNA called GcvB. This study also highlights the idea that the response of a sensitive strain towards antibiotics are different compared to a resistant strain. Future studies elucidating the exact pathways involving the stringent response and GcvB can lead to the discovery of potential targets as antibiotics or as anti-resistance agents.Data SummaryThe complete genome of Shigella sonnei UKMCC1015 and its plasmids has been deposited at GenBank under accession numbers CP060117, CP060118 and CP060119. RNA-seq data are accessible through BioSample accession number SAMN16871737.