title: Phylogenomic grouping of Listeria monocytogenes.
abstract: The precise delineation of lineages and clonal groups are a prerequisite to examine within-species genetic variations, particularly with respect to pathogenic potential. A whole-genome-based approach was used to subtype and subgroup isolates of Listeria monocytogenes. Core-genome typing was performed, employing 3 different approaches: total core genes (CG), high-scoring segment pairs (HSPs), and average nucleotide identity (ANI). Examination of 113 L. monocytogenes genomes available in-house and in public domains revealed 33 phylogenomic groups (PGs). Each PG could be differentiated into a number of genomic types (GTs), depending on the approach used: HSPs (n = 57 GTs), CG (n = 71 GTs), and ANI (n = 83 GTs). Demarcation of the PGs was concordant with the 4 known lineages and led to the identification of sublineages in the lineage groups I, II, and III. In addition, PG assignments had discriminatory power similar to multi-virulence-locus sequence typing types and clonal complexes of multilocus sequence typing. Clustering of genomically highly similar isolates from different countries, sources, and isolation dates using whole-genome-based PG suggested that dispersion of phylogenomic clones of L. monocytogenes preceded their subsequent evolution. Classification according to PG may act as a guideline for future epidemiological studies.
authors.affiliation: a Institute of Medical Microbiology, Justus Liebig University and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany 35392.
authors.forename: Swapnil
authors.initials: S
authors.lastname: Doijad
authors.affiliation: a Institute of Medical Microbiology, Justus Liebig University and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany 35392.
authors.forename: Markus
authors.initials: M
authors.lastname: Weigel
authors.affiliation: b National Institute of Biotic Stress Management, Raipur, Chhattisgarh, India.
authors.forename: Sukhadeo
authors.initials: S
authors.lastname: Barbuddhe
authors.affiliation: c Bioinformatics and Systems Biology, Justus Liebig University, Giessen, Germany 35392.
authors.forename: Jochen
authors.initials: J
authors.lastname: Blom
authors.affiliation: c Bioinformatics and Systems Biology, Justus Liebig University, Giessen, Germany 35392.
authors.forename: Alexander
authors.initials: A
authors.lastname: Goesmann
authors.affiliation: a Institute of Medical Microbiology, Justus Liebig University and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany 35392.
authors.forename: Torsten
authors.initials: T
authors.lastname: Hain
authors.affiliation: a Institute of Medical Microbiology, Justus Liebig University and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany 35392.
authors.forename: Trinad
authors.initials: T
authors.lastname: Chakraborty
mesh_terms: D014644:Genetic Variation; D023281:Genomics; D006801:Humans; D008089:Listeria monocytogenes / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D008088:Listeriosis; D058885:Multilocus Sequence Typing; D010802:Phylogeny
keywords: L. monocytogenes; SGE; WGS; core-genome typing; typage du génome central