Phenotypic and genotypic description of the carbapenemase-producing or ertapenem non-susceptible isolates from dairy cattle faeces that were subjected to WGS.

<p>Phenotypic and genotypic description of the carbapenemase-producing or ertapenem non-susceptible isolates from dairy cattle faeces that were subjected to WGS.</p

MBLFP_MRE

Nexus file of MBLFP gene sequences from MRE

16S_rRNA_MRE

Nexus file of 16S rRNA gene sequences from MRE

Identification and Characterization of Novel <em>Salmonella</em> Mobile Elements Involved in the Dissemination of Genes Linked to Virulence and Transmission

<div><p>The genetic diversity represented by >2,500 different <em>Salmonella</em> serovars provides a yet largely uncharacterized reservoir of mobile elements that can contribute to the frequent emergence of new pathogenic strains of this important zoonotic pathogen. Currently, our understanding of <em>Salmonella</em> mobile elements is skewed by the fact that most studies have focused on highly virulent or common serovars. To gain a more global picture of mobile elements in <em>Salmonella</em>, we used prediction algorithms to screen for mobile elements in 16 sequenced <em>Salmonella</em> genomes representing serovars for which no prior genome scale mobile element data were available. From these results, selected mobile elements underwent further analyses in the form of validation studies, comparative analyses, and PCR-based population screens. Through this analysis we identified a novel plasmid that has two cointegrated replicons (IncI1-IncFIB); this plasmid type was found in four genomes representing different <em>Salmonella</em> serovars and contained a virulence gene array that had not been previously identified. A <em>Salmonella</em> Montevideo isolate contained an IncHI and an IncN2 plasmid, which both encoded antimicrobial resistance genes. We also identified two novel genomic islands (SGI2 and SGI3), and 42 prophages with mosaic architecture, seven of them harboring known virulence genes. Finally, we identified a novel integrative conjugative element (ICE) encoding a type IVb pilus operon in three non-typhoidal <em>Salmonella</em> serovars. Our analyses not only identified a considerable number of mobile elements that have not been previously reported in <em>Salmonella</em>, but also found evidence that these elements facilitate transfer of genes that were previously thought to be limited in their distribution among <em>Salmonella</em> serovars. The abundance of mobile elements encoding pathogenic properties may facilitate the emergence of strains with novel combinations of pathogenic traits.</p> </div

Clade membership plot of individual genes plotted against the genome of <i>L. monocytogenes</i> F2365.

<p>The order of genome rings is listed in the circle center, with F2365 being the outermost ring. The 7 outermost rings represent lineage I (serotype 4b and 1/2b), the next three rings represent lineage III and lineage IV strains (serotype 4a and 4c), and the last 11 rings represent lineage II strains (serotype 1/2a, 1/2c, and 3a). Clade membership of the individual genes is indicated by color; blue indicates lineage II, red indicates lineage I, and gray is unresolved membership. The two O-antigen gene clusters are highlighted in green and yellow. Genes in these clusters found in serotype 1/2b lineage I cluster phylogenetically with orthologs found in lineage II clade.</p

Top 25 most abundant Gene Ontology (GO) terms which are significantly enriched in the accessory genome versus the core genome of <i>Listeria monocytogenes</i>.

<p>P values were calculated using Fisher’s exact test and Bonferroni corrected.</p

Synteny and gene-specific phylogenetic history of the two O-antigen specific gene clusters.

<p>The organismal phylogeny of the genus <i>Listeria</i> is shown in the upper panel (A), while the syntenic relationships of the two O-antigen gene clusters between the two major serotype divisions and the phylogenetic tree based on a representative serotype specific gene are shown in the two lower panels (B and C). Genes are colored by their phylogenetic histories: Serotype-specific genes (i.e., genes found only in specific serotypes) are colored green, while genes displaying an organismal phylogeny across the <i>Listera</i> genus are colored blue. Genes which follow a serotype-related phylogeny across <i>Listeria</i> are shown in orange. Values on the branches represent bootstrap values based on 100 bootstrap replicates. The organismal tree is based on a 10 locus multi-locus sequence analysis as described in Den Bakker et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067511#pone.0067511-Bakkerden2" target="_blank">[52]</a>. The topology of this tree is congruent with a tree based on the MLST scheme used in Ragon et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067511#pone.0067511-Ragon1" target="_blank">[6]</a>.</p

Genome statistics of <i>L. monocytogenes</i> genome sequences used in this study.

<p>Contig N50 values are given for draft (unfinished) genomes assembled here, while the percent Q40 bases is given for all genomes assembled here.</p>1<p>N/A = not available, because the genome sequence is closed.</p>2<p>Percentage Q40 bases is only given for genome sequences newly presented in this publication.</p

Accessory genome loci that distinguish lineages I and II.

1<p>+ = present, – = absent, +/− = present in some strains.</p>2<p>The putative function is inferred from the initial gene annotation.</p><p>Presence/absence of orthologs in each of the four lineages is listed, as well as putative function and the locus identifier(s) in the reference genome, either F2365 (lineage I) or EGDe (lineage II).</p

Phylogenetic reconstruction of serotype evolution in <i>Listeria</i>. Serotype 4 is shown in red while serotype 1/2 is shown in green.

<p>This construction suggests that serotype 1/2 genes were horizontally transferred from <i>L. seeligeri</i> to an ancestor of <i>L. monocytogenes</i> lineages I and II. The origin of the serotype 1/2 cluster is unclear, we hypothesize that this cluster putatively originated in the most recent common ancestor of the <i>L. seeligeri</i> and <i>L. ivanovii</i> clade (as indicated by the dashed line). Serotype 4 genes appear to be largely inherited by vertical descent, except for a lateral transfer of genes from <i>L. welshimeri</i> into some strains of <i>L. monocytogenes</i> lineage III (dotted red line).</p