Salmonella enterica Serovar Abony Outbreak Caused by Clone of Reference Strain WDCM 00029, Chile, 2024

Abstract

A Salmonella enterica serovar Abony outbreak occurred during January-April 2024 in Chile. Genomic evidence indicated that the outbreak strain was a clone of reference strain WDCM 00029, which is routinely used in microbiological quality control tests. When rare or unreported serovars cause human infections, clinicians and health authorities should request strain characterization.

Keywords: Chile; Salmonella enterica; WDCM 00029; bacteria; enteric infections; food safety; outbreak; serovar Abony.

Figure 1

Phylogenetic analysis of Salmonella enterica serovar Abony from an outbreak caused by a WDCM 00029 Clone, Chile, 2024. A core SNP maximum-likelihood phylogenetic tree was constructed by using RAxML version 8 (https://github.com/stamatak/standard-RAxML) and genomes of Salmonella Abony isolates from the HC50_20673 cluster with the ATCC 6017 genome as the reference (Enterobase Barcode SAL_BA5138AA; Sequence Read Archive accession no. SRR1786283). The tree was constructed by using the Enterobase pipelines refMasker, refMapper, refMapperMatrix, and matrix_phylogeny, which together masked repeated regions, tandem repeats, and CRISPR regions in the reference genome, aligned genomes to reference, called nonrepetitive core SNPs, and built the maximum likelihood tree. Metadata regarding HC10 clusters (<10 allele differences) include isolation source, collection year, country of origin, antibiotic drug resistance genes (AMRFinderPlus version 3.12.8; database version 2024-05-02.2; https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder), and plasmid replicons (ABRicate version 1.0.1, https://github.com/tseemann/abricate; PlasmidFinder database, updated June 4, 2024). Red arrows indicate the WDCM 00029 genomes found in the public databases (Enterobase, https://enterobase.warwick.ac.uk/species/index/senterica; National Center for Biotechnology Information Sequence Read Archive, https://www.ncbi.nlm.nih.gov/sra) that were made public in 2013 (accession no. SRR955283), 2016 (accession no. SRR1815498), 2019 (accession no. SRR8599079), and 2021 (accession no. SRR15145673). Asterisks (*) in the collection year column indicate that information was missing. The figure was made by using iTOL version 6.9 (https://itol.embl.de). ATCC, American Type Culture Collection; cgMLST, core genome multilocus sequence typing; CRISPR, clustered regularly interspaced short palindromic repeats; SNP, single-nucleotide polymorphism.

Figure 2

Whole-genome comparisons of Salmonella enterica serovar Abony from an outbreak caused by a WDCM 00029 clone, Chile, 2024. A) Example whole-genome comparison between Salmonella Abony WDCM 00029 (genome provided by ATCC; strain BAA-2162) and an isolate from the HC10_20673 cluster (strain SAbH24_18) from Chile, or the most closely related isolate (strain 201808966) outside the HC10_20673 cluster (mean difference to HC10_20673 isolates: 73 SNPs). Red lines connect regions of genome identity between each pair of compared genomes, with color indicating the percent identity. The red vertical arrow points to a region of difference between the compared genomes. B, C) Truncated violin plots of AF (B) and ANI (C) to the WDCM 00029 genome of the Salmonella Abony isolates (n = 18 genomes) from Chile and other isolates from the same HC50 cluster (HC10_142933 and HC10_165393; n = 12 genomes). In the violin plots, black horizontal lines represent medians and dotted lines represent 25% and 75% quartiles. Differences between the median values were assessed by using Mann-Whitney tests. AF and ANI calculations were made with FastANI version 1.34 (https://github.com/ParBliSS/FastANI). AF, alignment fraction; ANI, average nucleotide identity; ATCC, American Type Culture Collection; SNP, single-nucleotide polymorphism.