International journal of systematic and evolutionary microbiology 20140305 Pt 6
Sampling of agricultural and natural environments in two US states (Colorado and Florida) yielded 18 Listeria-like isolates that could not be assigned to previously described species using traditional methods. Using whole-genome sequencing and traditional phenotypic methods, we identified five novel species, each with a genome-wide average BLAST nucleotide identity (ANIb) of less than 85% to currently described species. Phylogenetic analysis based on 16S rRNA gene sequences and amino acid sequen ...[more]
Project description:<i>Listeria monocytogenes</i> serotype 7 lacks glycosidic constituents in wall teichoic acids. Here, we present the complete genome sequence of <i>L. monocytogenes</i> serotype 7 strain FSL R9-0915 and an analysis of genes known to affect <i>L. monocytogenes</i> antigenicity. This strain is used as a control strain in <i>Listeria</i> phage host range analyses.
Project description:The bacterial genus Listeria contains both saprotrophic and facultative pathogenic species. A small genome size has been suggested to be associated with the loss of pathogenic potential of L. welshimeri and L. seeligeri. In this paper we present data on the genome of L. monocytogenes strain FSL J1-208, a representative of phylogenetic lineage IV. Although this strain was isolated from a clinical case in a caprine host and has no decreased invasiveness in human intestinal epithelial cells, our analyses show that this strain has one of the smallest Listeria chromosomes reported to date (2.78 Mb). The chromosome contains 2,772 protein-coding genes, including well-characterized virulence-associated genes, such as inlA, inlB, and inlC and the full prfA gene cluster. The small genome size is mainly caused by the absence of prophages in the genome of L. monocytogenes FSL J1-208, and further analyses showed that the total size of prophage-related regions is highly correlated to chromosome size in the genus Listeria. L. monocytogenes FSL J1-208 carries a unique type of plasmid of approximately 80 kbp that does not carry genes annotated as being involved in resistance to antibiotics or heavy metals. The accessory genes in this plasmid belong to the internalin family, a family of virulence-associated proteins, and therefore this is the first report of a potential virulence plasmid in the genus Listeria.
Project description:A total of 27 <i>Listeria</i> isolates that could not be classified to the species level were obtained from soil samples from different locations in the contiguous United States and an agricultural water sample from New York. Whole-genome sequence-based average nucleotide identity blast (ANIb) showed that the 27 isolates form five distinct clusters; for each cluster, all draft genomes showed ANI values of <95 % similarity to each other and any currently described <i>Listeria</i> species, indicating that each cluster represents a novel species. Of the five novel species, three cluster with the <i>Listeria sensu stricto</i> clade and two cluster with <i>sensu lato</i>. One of the novel <i>sensu stricto</i> species, designated <i>L. cossartiae</i> sp. nov., contains two subclusters with an average ANI similarity of 94.9%, which were designated as subspecies. The proposed three novel <i>sensu stricto</i> species (including two subspecies) are <i>Listeria farberi</i> sp. nov. (type strain FSL L7-0091<sup>T</sup>=CCUG 74668<sup>T</sup>=LMG 31917<sup>T</sup>; maximum ANI 91.9 % to <i>L. innocua</i>), <i>Listeria immobilis</i> sp. nov. (type strain FSL L7-1519<sup>T</sup>=CCUG 74666<sup>T</sup>=LMG 31920<sup>T</sup>; maximum ANI 87.4 % to <i>L. ivanovii</i> subsp. <i>londoniensis</i>) and <i>Listeria cossartiae</i> sp. nov. [subsp. <i>cossartiae</i> (type strain FSL L7-1447<sup>T</sup>=CCUG 74667<sup>T</sup>=LMG 31919<sup>T</sup>; maximum ANI 93.4 % to <i>L. marthii</i>) and subsp. <i>cayugensis</i> (type strain FSL L7-0993<sup>T</sup>=CCUG 74670<sup>T</sup>=LMG 31918<sup>T</sup>; maximum ANI 94.7 % to <i>L. marthii</i>). The two proposed novel <i>sensu lato</i> species are <i>Listeria portnoyi</i> sp. nov. (type strain FSL L7-1582<sup>T</sup>=CCUG 74671<sup>T</sup>=LMG 31921<sup>T</sup>; maximum ANI value of 88.9 % to <i>L. cornellensis</i> and 89.2 % to <i>L. newyorkensis</i>) and <i>Listeria rustica</i> sp. nov. (type strain FSL W9-0585<sup>T</sup>=CCUG 74665<sup>T</sup>=LMG 31922<sup>T</sup>; maximum ANI value of 88.7 % to <i>L. cornellensis</i> and 88.9 % to <i>L</i>. <i>newyorkensis</i>). <i>L. immobilis</i> is the first <i>sensu stricto</i> species isolated to date that is non-motile. All five of the novel species are non-haemolytic and negative for phosphatidylinositol-specific phospholipase C activity; the draft genomes lack the virulence genes found in <i>Listeria</i> pathogenicity island 1 (LIPI-1), and the internalin genes <i>inlA</i> and <i>inlB</i>, indicating that they are non-pathogenic.
Project description:The genetic lineages of Listeria monocytogenes and other species of the genus Listeria are correlated with pathogenesis in humans. Although matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has become a prevailing tool for rapid and reliable microbial identification, the precise discrimination of Listeria species and lineages remains a crucial issue in clinical settings and for food safety. In this study, we constructed an accurate and reliable MS database to discriminate the lineages of L. monocytogenes and the species of Listeria (L. monocytogenes, L. innocua, L. welshimeri, L. seeligeri, L. ivanovii, L. grayi, and L. rocourtiae) based on the S10-spc-alpha operon gene encoded ribosomal protein mass spectrum (S10-GERMS) proteotyping method, which relies on both genetic information (genomics) and observed MS peaks in MALDI-TOF MS (proteomics). The specific set of eight biomarkers (ribosomal proteins L24, L6, L18, L15, S11, S9, L31 type B, and S16) yielded characteristic MS patterns for the lineages of L. monocytogenes and the different species of Listeria, and led to the construction of a MS database that was successful in discriminating between these organisms in MALDI-TOF MS fingerprinting analysis followed by advanced proteotyping software Strain Solution analysis. We also confirmed the constructed database on the proteotyping software Strain Solution by using 23 Listeria strains collected from natural sources.