Identification of nonserotypeable Shigella spp. using genome sequencing: a step forward. (7th July 2017)

• Record Type: Journal Article
• Authors: Dhiviya Prabaa, Muthuirulandi Sethuvel; Naveen Kumar, Devanga Ragupathi; Yesurajan, Inbanathan Francis; Anandan, Shalini; Kamini, Walia; Balaji, Veeraraghavan
• Is Part Of: Future science OA. Volume 3:Number 4(2017)
• Publication Date: 2017-07-07
• Subjects: IncF plasmid -- k-mer -- nonserotypeable Shigella -- O-antigen gene cluster -- whole genome sequencing; Medicine -- Periodicals; Biotechnology -- Periodicals; 610
• DOI: 10.4155/fsoa-2017-0063
• Languages: English
• ISSNs: 2056-5623

Abstract

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, gyr B 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 gyr B 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.