Changes detected in the genome sequences ofEscherichia coli,Listeria monocytogenes,Vibrio parahaemolyticus, andSalmonella entericaafter serial subculturing

Abstract

Whole genome sequencing (WGS) is rapidly replacing other molecular techniques for identifying and subtyping bacterial isolates. The resolution or discrimination offered by WGS is significantly higher than that offered by other molecular techniques, and WGS readily allows infrequent differences that occur between 2 closely related strains to be found. In this investigation, WGS was used to identify the changes that occurred in the genomes of 13 strains of bacterial foodborne pathogens after 100 serial subcultures. Pure cultures of Shiga-toxin-producing Escherichia coli, Salmonella enterica, Listeria monocytogenes, and Vibrio parahaemolyticus were subcultured daily for 100 successive days. The 1st and 100th subcultures were whole-genome sequenced using short-read sequencing. Single nucleotide polymorphisms (SNPs) were identified between the 1st and final culture using 2 different approaches, and multilocus sequence typing of the whole genome was also performed to detect any changes at the allelic level. The number of observed genomic changes varied by strain, species, and the SNP caller used. This study provides insight into the genomic variation that can be detected using next-generation sequencing and analysis methods after repeated subculturing of 4 important bacterial pathogens.

Contribution of Antibiotic Susceptibility Testing and CH Typing Compared to Next-Generation Sequencing for the Diagnosis of Recurrent Urinary Tract Infections Due to Genetically Identical Escherichia coli Isolates: a Prospective Cohort Study of Cystitis in Women

“…A divergence rate (number of SNPs per day) was determined using the dates of isolate collection. Isolates with a divergence rate inferior to 3.5 SNPs/day were classified as identical according to the work of Petronella et al ( 34 ) and considered responsible for a relapse.…”

Advance typing of Vibrio parahaemolyticus through the mtlA and aer gene: A high-resolution, cost-effective approach

“…Moreover, recombination in recA affected the topology of the MLST phylogenetic tree, which might bury true evolution [ 11 ]. Whole genome sequencing (WGS) analysis has the potential to identify subtle nucleotide changes among isolates [ 12 ]. Based on WGS, both core-genome MLST (cgMLST) and whole-genome MLST (wgMLST) were developed for precise typing [ 13 ].…”