Identification of nonserotypeable Shigella spp. using genome sequencing: a step forward

Aim: Sequencing technology has replaced conventional methods in identifying and characterizing bacterial pathogens. We characterized 23 nonserotypeable Shigella that biochemically resembled Shigella spp. using whole genome sequencing. Materials & methods: Genome sequences were analyzed using online tools based on 16S rRNA, k-mer, gyrB sequences and analysis of O-antigen arrangement was done using PATRIC database for species identification. Sequence types, plasmid types, antimicrobial resistance and virulence genes were also investigated. Results: The SpeciesFinder using 16S rRNA sequences identified only 74% of the isolates, whereas KmerFinder and gyrB sequence analysis identified 100% of the isolates to its species level. Antimicrobial resistance, virulence and plasmid incompatibility groups were identified in all the isolates. Sequence types were determined. Conclusion: This study shows that whole genome sequencing approach for Shigella O-antigen analysis has greater discriminative power than other methods using different bioinformatics pipeline for identification of nonserotypeable Shigella.
Lay abstract Shigellosis is one of the major health concerns in developing countries. Shigella spp. that is not serotypeable with available antisera is a hurdle in laboratory diagnosis. Sequencing technology has replaced conventional methods in identifying nonserotypeable Shigella. In this study, we characterized 23 nonserotypeable Shigella using whole genome sequences. Manual comparison of O-antigen gene arrangement provided definitive results compared with other methods. Development of a database including whole genome sequencing of all known serotypes will help in easy identification of Shigella serotypes in the future.