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Muhle, E.

Publications and source records attributed to Muhle, E..

2 recordsLinked to original sources

Neisseria leonis sp. nov. isolated from rabbits, reclassification of Uruburuella suis, Uruburuella testudinis, Kingella potus, Bergeriella denitrificans and Morococcus cerebrosus into Neisseria genus and reclassification of Neisseria shayeganii into Eikenella genus

Genome sequence-based identification of two strains (3986T and 51.81) isolated from rabbits in France in 1972 and 1981 and deposited in the Collection of Institut Pasteur (CIP) has led to the description of a novel species in the genus Neisseria. The cells of both strains were non-motile, Gram-stain-negative and diplococcobacilli. Optimal growth on trypticase soy agar was recorded at 37{degrees}C and pH 8.5 in aerobic conditions. Phylogeny based on 16S rRNA gene placed the strains close to Neisseria bacilliformis ATCC BAA-1200T (96.38%) nesting with the members of Neisseriaceae family. Furthermore, the phylogenetic analysis based on bac120 gene set from the Genome Taxonomy Database (GTDB) placed both strains within the monophyletic Neisseria clade, which also included type strains of Morococcus cerebrosus, Bergeriella denitrificans, Kingella potus, Uruburuella suis and Uruburuella testudinis. However, Neisseria shayeganii strain 871T was placed outside Neisseria clade and close to the members of Eikenella genus. Strains 3986T and 51.81 were placed in a branch distinct from all species of the genus Neisseria and exhibited the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values below the species demarcation values. In contrast, ANI value within the two strains was 96.9% confirming that they represent same species. The genomic DNA G+C content of strain 3986T was 56.92%. Based on the phylogenetic and phenotypic data, the strains 3986T and 51.81 represent a novel species of the genus Neisseria, for which the name Neisseria leonis sp. nov. is proposed (type strain 3986T = CIP 109994T = LMG 32907T). Additionally, based on phylogenetic analysis, DUS dialect and average amino acid identity (AAI) values, we also proposed the reclassification of Morococcus cerebrosus, Bergeriella denitrificans, Kingella potus, Uruburuella suis and Uruburuella testudinis into Neisseria genus and Neisseria shayeganii into Eikenella genus. Author NotesThe GenBank accession numbers for the 16S rRNA gene sequence of strains 3986T and 51.81 are respectively OQ121838.1 and OQ428162.1. The draft genome sequences have been deposited in GenBank under the accession numbers JAPQFK000000000 (strain 3986T) and JAPQFL000000000 (strain 51.81). Further explanations mentioned in the article as well as 7 supplementary tables and 7 supplementary figures are available with the online version of this article.

evolutionary biology↗

Genomic library of Bordetella

BackgroundThe re-emergence of whooping cough and geographic disparities in vaccine escape or antimicrobial resistance dynamics, underline the importance of a unified definition of Bordetella pertussis strains. Understanding of the evolutionary adaptations of Bordetella pathogens to humans and animals requires comparative studies with environmental bordetellae. MethodsWe have set-up a unified library of Bordetella genomes by merging previously existing Oxford and Pasteur databases, importing genomes from public repositories, and developing harmonized genotyping schemes. We developed a genus-wide cgMLST genotyping scheme and incorporated a previous B. pertussis cgMLST scheme. Specific schemes were developed to define antigenic, virulence and macrolide resistance profiles. Genomic sequencing of 83 French B. bronchiseptica isolates and of B. tumulicola, B. muralis and B. tumbae type strains was performed. ResultsThe public library currently includes 2,581 Bordetella isolates and their provenance data, and 2,084 genomes. The "classical Bordetella" (B. bronchiseptica, B. parapertussis and B. pertussis), which form a single genomic species (B. bronchiseptica genomic species, BbGS), were overrepresented (n=2,382). The phylogenetic analysis of Bordetella genomes associated the three novel species B. tumulicola, B. muralis and B. tumbae in a clade with B. petrii and revealed 18 yet undescribed species. A sister lineage of the classical bordetellae, provisionally named Bbs lineage II, was uncovered and may represent a novel species (average nucleotide identity with BbGS strains: [~]95%). It comprised strain HT200 from India, two strains of genogroup 6 from the USA and six clinical isolates from France; this lineage lacked ptxP and its fim2 gene was divergent. Within B. pertussis, vaccine antigen sequence types marked important phylogenetic subdivisions, and macrolide resistance markers (23S_rRNA allele 13 and fhaB3) confirmed the current restriction of this phenotype in China with few exceptions. ConclusionsThe genomic platform provides an expandable resource for unified genotyping of Bordetella strains and will facilitate collective evolutionary and epidemiological understanding of the re-emergence of whooping cough and other Bordetella infections. Data summaryBordetella genomes list and accession numbers: Supplementary Table S4 Bordetella genus phylogeny dataset (92 isolates): https://bigsdb.pasteur.fr/cgi-bin/bigsdb/bigsdb.pl?db=pubmlst_bordetella_isolates&page=query&project_list=23&submit=1 B. bronchiseptica phylogeny dataset (213 isolates): https://bigsdb.pasteur.fr/cgi-bin/bigsdb/bigsdb.pl?db=pubmlst_bordetella_isolates&page=query&project_list=24&submit=1 B. pertussis phylogeny (124 isolates): https://bigsdb.pasteur.fr/cgi-bin/bigsdb/bigsdb.pl?db=pubmlst_bordetella_isolates&page=query&project_list=25&submit=1 iTOL interactive trees: https://itol.embl.de/shared/1l7Fw0AvKOoCF

microbiology↗