Introduction: Various Shigella species are the causative agent of the food-borne illness, shigellosis, which is an acute invasive enteric infection. Shigella can be differentiated into four serogroups, which are then each... [ view full abstract ]
Introduction: Various Shigella species are the causative agent of the food-borne illness, shigellosis, which is an acute invasive enteric infection. Shigella can be differentiated into four serogroups, which are then each further differentiated into serotypes. Serotypes are based on their individual biochemical properties and group-specific O-antigens. These serogroups are: S. dysenteriae, S. flexneri, S. boydii, and S. sonnei. The majority of sporadic cases, as well as outbreaks of bloody diarrheal diseases, are usually caused by S. flexneri or S. sonnei in Georgia. In 2014, an outbreak of shigellosis occurred in western Georgia. At the time pulse-field gel electrophoresis (PFGE) revealed that all seven strains were identical yet distinct from previously isolated strains; seven strains from this outbreak were isolated and characterized by bacteriological and biochemical methods. Serotypes of isolates could not be identified by classical serotyping methods, yet they matched the profile of serologically-atypical Shigella spp. In this study, one of these strains were genetically characterized.
Methods: Draft whole-genome sequencing (WGS) reads were generated for the Shigella isolates (2106/15-G) using next-generation sequencing (NGS) technologies (Illumina MiSeq platform). Reads were further analyzed by the CLC Genomics Workbench 8.5.1 (CLC Bio) software. Comparative sequence analysis was performed using Multi BLAST tool and single nucleotide polymorphism (SNP) WGS-based phylogenetic analysis using the EDGE bioinformatics software.
Results: SNP-WGS-based phylogenetic analysis showed more genetic similarity with S. boydii (CDC 3083-94). Preliminary results of the reference-based analysis showed the high sequence similarity with S. flexneri (2002017 plasmid pSFxv_3) and S. boydii (CDC 2083-94 plasmid pBS512_2). The Specialty Genes Profiling Tool revealed both class C and D beta-lactamase genes.
Conclusion: This study is the first attempt for genetic characterization of a Shigella strain in Georgia, which was difficult to identify by traditional serotyping or other methods. Whole genome sequences based analysis of a non-typable Shigella strain, will provide valuable information for epidemiologists regarding species identification and serve in the enhancement of the epi-surveillance system in the country. Also, application of WGS technology in routine surveillance of bloody diarrheal diseases caused by atypical Shigella isolates in Georgia will help us to build a database of genetic variants of circulating organisms. A study of virulence factors with EDGE bioinformatics software is in progress.
