Dhiviya Prabaa MS, Naveen Kumar DR, Yesurajan IF, Anandan S, Kamini W, Balaji V. Identification of nonserotypeable
Shigella spp. using genome sequencing: a step forward.
Future Sci OA 2017;
3:FSO229. [PMID:
29134117 PMCID:
PMC5674244 DOI:
10.4155/fsoa-2017-0063]
[Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 05/30/2017] [Indexed: 12/04/2022] Open
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.
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