Abstract
Shigella flexneri is a major etiological agent of shigellosis in developing countries, primarily occurring in children under 5 years of age. We have sequenced, for the first time, the complete genome of S. flexneri serotype 3b (strain SFL1520). We used a hybrid sequencing method––both long-read MinION Flow (Oxford Nanopore Technologies) and short-read MiSeq (Illumina) sequencing to generate a high-quality reference genome. The SFL1520 chromosome was found to be ∼4.58 Mb long, with 4,729 coding sequences. Despite sharing a substantial number of genes with other publicly available S. flexneri genomes (2,803), the SFL1520 strain contains 1,926 accessory genes. The phage-related genes accounted for 8% of the SFL1520 genome, including remnants of the Sf6 bacteriophage with an intact O-acetyltransferase gene specific to serotype 3b. The SFL1520 chromosome was also found to contain a multiple-antibiotic resistance cassette conferring resistance to ampicillin, chloramphenicol, streptomycin, and tetracycline, which was potentially acquired from a plasmid via transposases. The phylogenetic analysis based on core genes showed a high level of similarity of SFL1520 with other S. flexneri serotypes; however, there were marked differences in the accessory genes of SFL1520. In particular, a large number of unique genes were identified in SFL1520 suggesting significant horizontal gene acquisition in a relatively short time period. The major virulence traits of SFL1520 (such as serotype conversion and antimicrobial resistance) were associated with horizontal gene acquisitions highlighting the role of horizontal gene transfer in S. flexneri diversity and evolution.
Highlights
Shigella species are the Gram-negative facultative anaerobic bacteria that cause shigellosis, characterized by acute colonic and rectal mucosal inflammation leading to fever, abdominal cramps, and bloody mucoid stools (Jennison and Verma 2004)
The phage genes were clustered in 15 regions across the bacterial chromosome and collectively account for 8% of the SFL1520 bacterial chromosome
The upstream of Sf6 phage region in SFL1520 possesses several transposases and mobile genetic elements making this area a recombination hotspot. These findings suggest that the Sf6 phage had undergone several recombination events resulting in gene deletions leading to a defective or cryptic prophage as seen in many other bacterial pathogens (Campbell 1998; Canchaya et al 2003)
Summary
Shigella species are the Gram-negative facultative anaerobic bacteria that cause shigellosis, characterized by acute colonic and rectal mucosal inflammation leading to fever, abdominal cramps, and bloody mucoid stools (Jennison and Verma 2004). No individual is immune to shigellosis, the morbidity and mortality are highest among children
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