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Identification of nonserotypeable Shigella spp. using genome sequencing: a step forward
- Source :
- Future Science OA
- Publication Year :
- 2017
- Publisher :
- Future Science Ltd, 2017.
-
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, 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.<br />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.
- Subjects :
- 0301 basic medicine
Whole genome sequencing
Genetics
whole genome sequencing
Sequence analysis
030106 microbiology
k-mer
Virulence
Biology
medicine.disease_cause
Genome
DNA sequencing
03 medical and health sciences
Plasmid
nonserotypeable Shigella
O-antigen gene cluster
medicine
Shigella
Gene
Research Article
IncF plasmid
Biotechnology
Subjects
Details
- ISSN :
- 20565623
- Volume :
- 3
- Database :
- OpenAIRE
- Journal :
- Future Science OA
- Accession number :
- edsair.doi.dedup.....660f51488f9cf35bd56d5b04418800e4