Complete genome analysis of clinical Shigella strains reveals plasmid pSS1653 with resistance determinants: a triumph of hybrid approach

Shigella is ranked as the second leading cause of diarrheal disease worldwide. Though infection occurs in people of all ages, most of the disease burden constitutes among the children less than 5 years in low and middle income countries. Recent increasing incidence of drug resistant strains make thi...

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Bibliographic Details
Published inGut pathogens Vol. 11; no. 1; pp. 1 - 8
Main Authors Muthuirulandi Sethuvel, Dhiviya Prabaa, Veeraraghavan, Balaji, Vasudevan, Karthick, Devanga Ragupathi, Naveen Kumar, Murugan, Dhivya, Walia, Kamini, Anandan, Shalini
Format Journal Article
LanguageEnglish
Published London BioMed Central Ltd 06.11.2019
BioMed Central
BMC
Subjects
Diarrhea
Drug resistance
Genes
Genetic aspects
Genome Report
Genomes
Genomics
Genotypes
Health aspects
Hybrid assembly
Identification and classification
Infection
Insertion sequences
Microbial drug resistance
Pathogenic microorganisms
Pathogenicity island
Plasmids
Properties
Prophages
Shigella
Technology
Tetracyclines
India
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Summary:Shigella is ranked as the second leading cause of diarrheal disease worldwide. Though infection occurs in people of all ages, most of the disease burden constitutes among the children less than 5 years in low and middle income countries. Recent increasing incidence of drug resistant strains make this as a priority pathogen under the antimicrobial resistance surveillance by WHO. Despite this, only limited genomic studies on drug resistant Shigella exists. Here we report the first complete genome of clinical S. flexneri serotype 2a and S. sonnei strains using a hybrid approach of both long-read MinION (Oxford Nanopore Technologies) and short-read Ion Torrent 400 bp sequencing platforms. The utilization of this novel approach in the present study helped to identify the complete plasmid sequence of pSS1653 with structural genetic information of AMR genes such as sulII, tetA, tetR, aph(6)-Id and aph(3'')-Ib. Identification of AMR genes in mobile elements in this human-restricted enteric pathogen is a potential threat for dissemination to other gut pathogens. The information on Shigella at genome level could help us to understand the genome dynamics of existing and emerging resistant clones. Keywords: Hybrid assembly, Pathogenicity island, Prophages, Insertion sequences, Plasmids
ISSN:1757-4749
1757-4749
DOI:10.1186/s13099-019-0334-5