Correction: Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica

Abstract

Brisse, the S. enterica MLST study group Some URLs within the article are now inactive. The MLST website at University College Cork moved to University of Warwick in 2013 and was subsequently superseded by EnteroBase, which can be accessed at http://enterobase. warwick.ac.uk [2]. EnteroBase offers MLST genotyping on the basis of genomic short reads for all levels of MLST from 7-gene legacy MLST through core genome cgMLST to whole genome wgMLST. However, it no longer accepts new alleles based on ABI sequences as explained due to their excessive error rate. Allelic designations for sequences of 7-gene legacy MLST loci for Salmonella enterica, Escherichia coli, Yersinia pseudotuberculosis and Moraxella catarrhalis can be obtained from EnteroBase at http:// enterobase.warwick.ac.uk/warwick_mlst_legacy. The authors, however, now recommend using short read sequencing which is handled at http://enterobase.warwick.ac.uk [2].

The Spatiotemporal Dynamics and Microevolution Events That Favored the Success of the Highly Clonal Multidrug-Resistant Monophasic Salmonella Typhimurium Circulating in Europe

“…All genomes were characterized by in silico MLST using seven housekeeping genes aroC, dnaN, hemD, hisD, purE, sucA, and thrA (Achtman et al, 2012). The seven housekeeping gene sequences for each strain were uploaded to the MLST service of the Center for Genomic Epidemiology (CGE) 1 , which allowed us to determine the sequence type (ST) directly from the read files.…”

Bayesian Source Attribution of Salmonella Typhimurium Isolates From Human Patients and Farm Animals in England and Wales

“…Hierarchical grouping of isolates into clusters based on increasing levels of similarity is performed by calculating the pairwise SNP distance for each pair of isolates in the analysis set and performing a single linkage clustering at 250, 100, 50, 25, 10, 5, and 0 SNPs from the deduced distance matrix (SNP address). The resultant “SNP address” provides an isolate level nomenclature where two isolates with the same SNP addresses have 0 SNP differences ( Achtman et al, 2012 ). The range of SNP/CgMLST differences considered for the subsequent source attribution analysis was restricted to those ranges between 10 and 100, as it was considered that differences of 5 or less would be too discriminatory and ranges over 100 would link together a high proportion of isolates that were not genuinely epidemiologically linked.…”

Phylogenomic Analysis of Salmonella enterica subsp. enterica Serovar Bovismorbificans from Clinical and Food Samples Using Whole Genome Wide Core Genes and kmer Binning Methods to Identify Two Distinct Polyphyletic Genome Pathotypes

“…Sequence types of all S. Bovismorbificans genomes used in this study were determined using the MLST schema [17,38] mplemented on the Center for Genomic Epidemiology (CGE) web servers (http://cge.cbs.dtu.dk/services/MLST, accessed on 6 August 2021). For serological confirmation and antimicrobial resistance gene analyses, genome assemblies (FASTA files) were uploaded to the CFSAN's GalaxyTrakr SeqSero and AMRFinderPlus tool, respectively (https://galaxytrakr.org/root/login?redirect=%2F, accessed on 6 August 2021).…”

“…When the digital profiles of representative strains from different STs originally reported [8] and included in this study were queried against this database, they sorted between these two clusters (Supplemental Figure S1B), as expected. Previous reports [17,35] had pointed to significant sequence variations within STs using techniques ranging from PFGE to WGS to a limited number of genes used for clustering. As foodborne outbreaks of minor, zoonotic serovars such as S. Bovismorbificans are being reported to cause illness in humans [8,9] by entering the food-supply chain, a detailed understanding of the genomic differences between the lineages that constitute S. Bovismorbificans and other serovars not currently on the top list of public health agencies becomes important for risk assessment, import control, and the development of prevention measures for efficient food safety and public health outbreak management.…”

“…Genome-wide variations of different groups within the serovars of S. enterica have been extensively studied using whole genome sequencing (WGS) datasets. A high number of polyphyletic lineages in many serovars have been predicted using MLST and genome-wide SNP profiling methods [17][18][19][20][21][22]. For example, phylogenetic analysis of 156 WGS datasets from 78 serovars using about 120,000 whole genome SNPs present in at least 95% of the strains identified the presence of polyphyletic lineages in a handful of serovars [19].…”