Additional file 2: of NGS-based phylogeny of diphtheria-related pathogenicity factors in different Corynebacterium spp. implies species-specific virulence transmission

Detected tox, dtxR, prophage and PAI coordinates, annotations and GC content (Table S3): For each of the 137 isolates, coordinates of tox and dtxR genes are given along with their species affiliation and their tox status analysed by qPCR and modified Elek test. All detected prophage sequences and PAIs are shown one line per region. For prophages and PAIs, information about region type and their overlapping or non-overlapping behavior in regard to the tox gene is indicated. For detected prophages, results from the prophage annotation software PHASTER [31] are given. For the alternative PAI, genomic start coordinates of the individual CDS sequences and structural annotations are indicated as well. Average GC content of the draft genome and the specific prophage/PAI regions is given. (XLSX 88 kb

Additional file 3: of NGS-based phylogeny of diphtheria-related pathogenicity factors in different Corynebacterium spp. implies species-specific virulence transmission

Tax IDs used for the generation of the Corynebacterium spp. annotation database in prokka [29]. (DOCX 21 kb

Additional file 1: of NGS-based phylogeny of diphtheria-related pathogenicity factors in different Corynebacterium spp. implies species-specific virulence transmission

NCBI accession numbers of downloaded DT sequences (Table S1) and SRA accession numbers of analysed WGS data (Table S2). (DOCX 28 kb

Prevalence of <i>S</i>. <i>aureus</i> in nursing home residents by socio-demographic factors.

Prevalence of S. aureus in nursing home residents by socio-demographic factors.</p

Prevalence of <i>S</i>. <i>aureus</i> in nursing home residents and health and lifestyle factors.

Prevalence of S. aureus in nursing home residents and health and lifestyle factors.</p

Prevalence of <i>S</i>. <i>aureus</i> in elderly community-dwellers and health and lifestyle factors.

Prevalence of S. aureus in elderly community-dwellers and health and lifestyle factors.</p

Prevalence of <i>S</i>. <i>aureus</i> in elderly community-dwellers by socio-demographic factors.

Prevalence of S. aureus in elderly community-dwellers by socio-demographic factors.</p

Prevalence of <i>S</i>. <i>aureus</i> and MRSA.

Prevalence of S. aureus and MRSA.</p

Multivariable logistic regression models: Risk factors associated with carriage of <i>S</i>. <i>aureus</i>.

Multivariable logistic regression models: Risk factors associated with carriage of S. aureus.</p

Additional file 1: of Recurrent evolution of host and vector association in bacteria of the Borrelia burgdorferi sensu lato species complex

S1. Strains included in this study, date of isolation, biological source, MLST sequence type (ST), geographic origin and previously determined species designation. S2. Phylogenetic inference including outgroup B. duttonii. S3. Estimates of divergence in generations for Borrelia genospecies. S4. Genes showing nucleotide diversity (π) (Nei 1987) or Tajima’s D (Tajima 1989) values exceeding two standard deviations in each species with respect to the 114 genes under study. S5. Additional material and methods: Phylogeny reconstruction and recombination estimation for three genes in 12 reference Borrelia species. S6. Four-Gamete analysis of loci used by Morlon et al. [18]. S7. Phylogenies reconstructed with BEAST v1.7.5 of a) three genes studied by Morlon et al. [18] combined, b) fla, c) groEL and d) rrs. (PDF 460 kb