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

Abstract

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.

Acquisition and loss of CTX-M plasmids in Shigella species associated with MSM transmission in the UK

“…This element recently drove a prolonged S. sonnei outbreak among MSM in Victoria, Australia [17] but few CTX-M Shigella plasmids have been characterised [18]; seemingly only one other has been described in detail, in a Swiss S. sonnei isolate [19].…”

“…However, in 2015 Public Health England (PHE) described an ESBL-producing S. sonnei MSM cluster [ 16 ] conferred by a pKSR100-like plasmid (p183660), which had acquired bla CTX-M-27 . This element recently drove a prolonged S. sonnei outbreak among MSM in Victoria, Australia [ 17 ] but few CTX-M Shigella plasmids have been characterised [ 18 ]; seemingly only one other has been described in detail, in a Swiss S. sonnei isolate [ 19 ].…”

First Comparative Analysis of Clostridium septicum Genomes Provides Insights Into the Taxonomy, Species Genetic Diversity, and Virulence Related to Gas Gangrene

“…Prophage 1 and 3 matched to phiCD38-2/phiCD111/phiCD146 and phiCD6356 phages respectively, reported earlier from C. difficle ( Fortier and Moineau, 2007 ; Sekulovic et al, 2014 ). On the other hand, prophages (Geobac_E2/Bacill_phIS3501/Coryne_StAB) identical to prophage 4 are also reported in the genus Clostridium ( Smith et al, 2021 ) as well as in other species such as Shigella ( Muthuirulandi Sethuvel et al, 2019 ) and Corynebacterium (NC_048780). Phage vB_CpeS-CP51 (prophage 2), has been initially recognized as a temperate bacteriophage of C. perfringens ( Gervasi et al, 2013 ) and was later reported also in C. chauvoei ( Frey and Falquet, 2015 ).…”

Complete Genome Analysis of Campylobacter jejuni subsp. jejuni Isolated from Bloodstream Infection

“…The quality of the MinION reads was assessed using MinIONQC ( https://github.com/roblanf/minion_qc ). The hybrid assembly was performed using the resulting Ion Torrent reads (1,571,892) and MinION reads (1,745,808) using Unicycler (v.0.4.7) as described earlier ( 7 – 9 ). Unicycler utilizes SPAdes v.3.12 by default to assemble the short reads along with error correction and quality checks.…”