Extending RAD tag analysis to microbial ecology: a comparison between MultiLocus Sequence Typing and 2b‐RAD to investigate Listeria monocytogenes genetic structure
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E-Artikel
Titel:
Extending RAD tag analysis to microbial ecology: a comparison between MultiLocus Sequence Typing and 2b‐RAD to investigate Listeria monocytogenes genetic structure
Beschreibung:
<jats:title>Abstract</jats:title><jats:p>The advent of next‐generation sequencing (<jats:styled-content style="fixed-case">NGS</jats:styled-content>) has dramatically changed bacterial typing technologies, increasing our ability to differentiate bacterial isolates. Despite it is now possible to sequence a bacterial genome in a few days and at reasonable costs, most genetic analyses do not require whole‐genome sequencing, which also remains impractical for large population samples due to the cost of individual library preparation and bioinformatics. More traditional sequencing approaches, however, such as MultiLocus Sequence Typing (<jats:sc>mlst</jats:sc>) are quite laborious and time‐consuming, especially for large‐scale analyses. In this study, a genotyping approach based on restriction site‐associated (<jats:styled-content style="fixed-case">RAD</jats:styled-content>) tag sequencing, 2b‐<jats:styled-content style="fixed-case">RAD</jats:styled-content>, was applied to characterize <jats:italic>Listeria monocytogenes</jats:italic> strains. To verify the feasibility of the method, an in silico analysis was performed on 30 available complete genomes. For the same set of strains, in silico <jats:sc>mlst</jats:sc> analysis was conducted as well. Subsequently, 2b‐<jats:styled-content style="fixed-case">RAD</jats:styled-content> and <jats:sc>mlst</jats:sc> analyses were experimentally carried out on 58 isolates collected from food samples or food‐processing sites. The obtained results demonstrate that 2b‐<jats:styled-content style="fixed-case">RAD</jats:styled-content> predicts <jats:sc>mlst</jats:sc> types and often provides more detailed information on population structure than <jats:sc>mlst</jats:sc>. Moreover, the majority of variants differentiating identical sequence type isolates mapped against accessory fragments, thus providing additional information to characterize strains. Although <jats:sc>mlst</jats:sc> still represents a reliable typing method, large‐scale studies on molecular epidemiology and public health, as well as bacterial phylogenetics, population genetics and biosafety could benefit of a low cost and fast turnaround time approach such as the 2b‐<jats:styled-content style="fixed-case">RAD</jats:styled-content> analysis proposed here.</jats:p>