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<p>The main goal was for FSA and Fera to contribute data to the GMI pilot study. However, there was also the opportunity to carry out bioinformatics analyses of listeria data.</p>
<p>The listeria species Fera sequenced have been selected as a wide reference set for the bioinformatics studies on genomic comparisons. Listeria innocua was the most frequently encountered non-pathogenic listeria and is sufficiently distantly related to other species including Listeria monocytogenes to be used as an out group in the later phylogenetic analysis of the sequenced genomes. Listeria seeligeri is found as a contaminant of soft cheese and processed meat and Listeria welshimeri which is a non-pathogenic listeria found in soil, water, food, and sewage was also sequenced. The non-monocytogenes were chosen to have a diverse collection of isolates to perform a comprehensive wide comparative genomic analysis.</p>
Fera used the in-house isolates for two reasons:
<ul><li>Fera has the isolates on site so could get the sequence data rapidly, in time to complete some bioinformatics analysis of the genomes for the GMI meeting in September 2013.</li>
<li>The isolates represent the diversity of listeria circulating in the retail supply chain across the UK – the sampling was extremely widespread both geographically and across different meats.</li></ul>
<p>The isolates are not the most current isolates. This helped to address the question of what temporal variability there is amongst listeria strains. </p>
<p>Background: This pilot project aimed to show that whole bacterial genome sequencing, to a draft quality using next generation DNA sequencing (NGS) platforms such as Illumina MiSeq, could be used for comparative genomics. This will help our understanding of foodborne bacterial pathogens from both a biological perspective, and to help microbial source tracking and identify relationships between strains. The aim was also to contribute sequencing data to an international initiative – the Global Microbial Identifier (GMI) – as part of a wider GMI pilot study gathering listeria data from international participants from the food safety and public health sectors.</p>
<p>Isolates originating from the FSA red meat survey were sequenced as part of Fera’s collection of Listeria monocytogenes from the red meat study strains. Other closely related listeria species, namely Listeria innocua, Listeria seeligeri and Listeria welshimeri, were also sequenced. The project involved bioinformatics comparative genomics analysis. </p>