Abstract
BackgroundIn 2017, a food-borne Salmonella Agona outbreak caused by infant milk products from a French supplier occurred in Europe. Simultaneously, S. Agona was detected in animal feed samples in Bavaria.AimUsing next generation sequencing (NGS) and three data analysis methods, this study’s objectives were to verify clonality of the Bavarian feed strains, rule out their connection to the outbreak, explore the genetic diversity of Bavarian S. Agona isolates from 1993 to 2018 and compare the analysis approaches employed, for practicality and ability to delineate outbreaks caused by the genetically monomorphic Agona serovar.MethodsIn this observational retrospective study, three 2017 Bavarian feed isolates were compared to a French outbreak isolate and 48 S. Agona isolates from our strain collections. The later included human, food, feed, veterinary and environmental isolates, of which 28 were epidemiologically outbreak related. All isolates were subjected to NGS and analysed by: (i) a publicly available species-specific core genome multilocus sequence typing (cgMLST) scheme, (ii) single nucleotide polymorphism phylogeny and (iii) an in-house serovar-specific cgMLST scheme. Using additional international S. Agona outbreak NGS data, the cluster resolution capacity of the two cgMLST schemes was assessed.ResultsWe could prove clonality of the feed isolates and exclude their relation to the French outbreak. All approaches confirmed former Bavarian epidemiological clusters.ConclusionEven for S. Agona, species-level cgMLST can produce reasonable resolution, being standardisable by public health laboratories. For single samples or homogeneous sample sets, higher resolution by serovar-specific cgMLST or SNP genotyping can facilitate outbreak investigations.
Highlights
Salmonellosis is one of the most common food-borne human diseases
In our bioinformatics data analyses, we included the published next generation sequencing (NGS) raw data (ENA accession: ERR2219379) of an isolate from a case of the infant-milk-caused outbreak originating from a France-based manufacturer [24]
The isolates were typed with Ridom SeqSphere + software with the public S. enterica core genome multilocus sequence typing (cgMLST) scheme, consisting of Enterobasedeveloped 3,002 target loci (Figure 1)
Summary
Salmonellosis is one of the most common food-borne human diseases. It is often transmitted via contaminated meat, eggs or seafood products. Enterica, these serovars include for example Enteridis, Typhimurium and Agona. Agona is a common pathogen and food-borne outbreaks connected to it have been consistently reported in several countries. In 2017, a food-borne Salmonella Agona outbreak caused by infant milk products from a French supplier occurred in Europe. Aim: Using generation sequencing (NGS) and three data analysis methods, this study’s objectives were to verify clonality of the Bavarian feed strains, rule out their connection to the outbreak, explore the genetic diversity of Bavarian S. The later included human, food, feed, veterinary and environmental isolates, of which 28 were epidemiologically outbreak related. Agona outbreak NGS data, the cluster resolution capacity of the two cgMLST schemes was assessed. For single samples or homogeneous sample sets, higher resolution by serovar-specific cgMLST or SNP genotyping can facilitate outbreak investigations
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