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

Autor:	Dhiviya Prabaa MS; Department of Clinical Microbiology, Christian Medical College, Vellore - 632 004, India.; Department of Clinical Microbiology, Christian Medical College, Vellore - 632 004, India., Naveen Kumar DR; Department of Clinical Microbiology, Christian Medical College, Vellore - 632 004, India.; Department of Clinical Microbiology, Christian Medical College, Vellore - 632 004, India., Yesurajan IF; Department of Clinical Microbiology, Christian Medical College, Vellore - 632 004, India.; Department of Clinical Microbiology, Christian Medical College, Vellore - 632 004, India., Anandan S; Department of Clinical Microbiology, Christian Medical College, Vellore - 632 004, India.; Department of Clinical Microbiology, Christian Medical College, Vellore - 632 004, India., Kamini W; Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi - 110 029, India.; Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi - 110 029, India., Balaji V; Department of Clinical Microbiology, Christian Medical College, Vellore - 632 004, India.; Department of Clinical Microbiology, Christian Medical College, Vellore - 632 004, India.
Jazyk:	angličtina
Zdroj:	Future science OA [Future Sci OA] 2017 Jul 07; Vol. 3 (4), pp. FSO229. Date of Electronic Publication: 2017 Jul 07 (Print Publication: 2017).
DOI:	10.4155/fsoa-2017-0063
Abstrakt:	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 . Competing Interests: Financial & competing interests disclosure The study was funded by the Indian Council of Medical Research (ICMR), New Delhi (Ref. no: AMR/TF/55/13ECDII dated 23 October 2013). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.
Databáze:	MEDLINE
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