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ON-rep-seq as a rapid and cost-effective alternative to whole-genome sequencing for species-level identification and strain-level discrimination of Listeria monocytogenes contamination in a salmon processing plant
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  • Gunn Merethe Thomassen,
  • Lukasz Krych,
  • Susanne Knøchel,
  • Lisbeth Mehli
Gunn Merethe Thomassen
Norwegian University of Science and Technology
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Lukasz Krych
University of Copenhagen
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Susanne Knøchel
University of Copenhagen
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Lisbeth Mehli
NTNU Faculty of Natural Sciences
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Abstract

Identification, source tracking, and surveillance of food pathogens is a crucial factor for the food-producing industry. Over the last decade, the techniques used for this have moved from conventional enrichment methods, through species-specific detection by PCR to sequencing-based methods, whole-genome sequencing (WGS) being the ultimate method. However, using WGS requires the right infrastructure, high computational power, and bioinformatics expertise. Therefore, there is a need for faster, more cost-effective, and more user-friendly methods. A newly developed method, ON-rep-seq, combines the classical rep-PCR method with nanopore sequencing, resulting in a highly discriminating set of sequences that can be used for species identification and also strain discrimination. This study is essentially a real industry case from a salmon processing plant. Twenty Listeria monocytogenes isolates were analyzed both by ON-rep-seq and WGS to identify and differentiate putative L. monocytogenes from a routine sampling of processing equipment and products, and finally, compare the strain-level discriminatory power of ON-rep-seq to different analyzing levels delivered from the WGS data. The analyses revealed that among the isolates tested there were three different strains. The isolates of the most frequently detected strain (n=15) were all detected in the problematic area in the processing plant. The strain level discrimination done by ON-rep-seq was in full accordance with the interpretation of WGS data. Our findings also demonstrate that ON-rep-seq may serve as a primary screening method alternative to WGS for identification and strain-level differentiation for surveillance of potential pathogens in a food-producing environment.

Peer review status:Published

17 Aug 2021Submitted to MicrobiologyOpen
18 Aug 2021Submission Checks Completed
18 Aug 2021Assigned to Editor
19 Aug 2021Reviewer(s) Assigned
09 Sep 2021Review(s) Completed, Editorial Evaluation Pending
13 Sep 2021Editorial Decision: Revise Major
08 Oct 20211st Revision Received
08 Oct 2021Submission Checks Completed
08 Oct 2021Assigned to Editor
08 Oct 2021Review(s) Completed, Editorial Evaluation Pending
08 Oct 2021Reviewer(s) Assigned
19 Oct 2021Editorial Decision: Accept
Nov 2021Published in MicrobiologyOpen volume 10 issue 6. 10.1002/mbo3.1246