ena-STUDY-ANSES-03-10-2016-10:03:58:864-652
Listeria monocytogenes (L. monocytogenes) is the foodborne pathogen responsible for listeriosis consequently it is of importance to use a rapid, standardized and accurate typing tool for its surveillance. WGS (Whole genome sequencing) has been demonstrated useful to characterize L. monocytogenes for its rapidity and high resolution. The offer of genomic data analysis is diverse, here we propose to assess and compare a number of phylogenic methods using a panel of L. monocytogenes strains of food origin.
Listeria monocytogenes (L. monocytogenes) is the foodborne pathogen responsible for listeriosis consequently it is of importance to use a rapid, standardized and accurate typing tool for its surveillance. WGS (Whole genome sequencing) has been demonstrated useful to characterize L. monocytogenes for its rapidity and high resolution. The offer of genomic data analysis is diverse, here we propose to assess and compare a number of phylogenic methods using a panel of L. monocytogenes strains of food origin.We used a representative subset of 208 L. monocytogenes from the LNR database (French National laboratory for L. monocytogenes). These strains were characterized using PCR serotyping, PFGE (Pulse Field Gel Electrophoresis) and seven genes MLST (Multi Loci Sequence Type). We analysis our panel using genome MLST (core and whole), SNP (Single Nucleotide Polymorphism) analysis with two different references for SNP calling (EGDe and EGD), and eventually we performed pan genome and core genes trees based on our strains subset. Backward comparisons were done between those genomic methods and the standard typing tools. Finally, trees were compared two by two using original indexes for distances and topology variation of trees.
Listeria monocytogenes (L. monocytogenes) is the foodborne pathogen responsible for listeriosis consequently it is of importance to use a rapid, standardized and accurate typing tool for its surveillance. WGS (Whole genome sequencing) has been demonstrated useful to characterize L. monocytogenes for its rapidity and high resolution. The offer of genomic data analysis is diverse, here we propose to assess and compare a number of phylogenic methods using a panel of L. monocytogenes strains of food origin.We used a representative subset of 208 L. monocytogenes from the LNR database (French National laboratory for L. monocytogenes). These strains were characterized using PCR serotyping, PFGE (Pulse Field Gel Electrophoresis) and seven genes MLST (Multi Loci Sequence Type). We analysis our panel using genome MLST (core and whole), SNP (Single Nucleotide Polymorphism) analysis with two different references for SNP calling (EGDe and EGD), and eventually we performed pan genome and core genes trees based on our strains subset. Backward comparisons were done between those genomic methods and the standard typing tools. Finally, trees were compared two by two using original indexes for distances and topology variation of trees.