Corynebacterium rouxii sp. nov., a novel member of the diphtheriae species complex

Badell, Edgar; Hennart, Mélanie; Rodrigues, Carla; Passet, Virginie; Dazas, Mélody; Panunzi, Leonardo G.; Bouchez, Valérie; Carmi–Leroy, Annick; Toubiana, Julie; Brisse, Sylvain

doi:10.1016/j.resmic.2020.02.003

Cited by 50 publications

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“…Further investigation is required to verify whether this lineage could be classified as a new species. Recently, C. belfantii and C. diphtheriae lausannense were suggested as synonyms [3]. Our analysis using TYGS corroborated the suggestion and showed that other genomes of C. belfantii besides the type strain (FRC0043 T ) are C. diphtheriae (S3 File), showing the difficulty in classifying this recently described species [2].…”

Section: Discussionsupporting

confidence: 81%

“…The tox tree included all sequences in genomes of C. ulcerans and outgroups from C. silvaticum, C. pseudotuberculosis and C. belfantii. C. rouxii was not included due to all sequenced genomes being tox- [3]. All trees were visualized using iTOL [27].…”

Section: Methodsmentioning

confidence: 99%

“…In this group, three new species were recently described. C. belfantii is a reclassification of C. diphtheriae biovar Belfanti [2] and a synonym of C. diphtheriae subspecies lausannense [3], C. rouxii [3] is reclassifications of C. diphtheriae biovar Belfanti, and C. silvaticum [4] is a reclassification of atypical C. ulcerans strains. Strains of C. silvaticum were previously described as atypical non-toxigenic but tox -gene-bearing (NTTB) strains of C. ulcerans , isolated from wild boars and roe deer in Germany, which caused caseous lymphadenitis similar to C. pseudotuberculosis infections [5–7].…”

Section: Introductionmentioning

confidence: 99%

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Taxonomic classification of strain PO100/5 shows a broader geographic distribution and genetic markers of the recently describedCorynebacterium silvaticum

Viana

Profeta

Silva

et al. 2020

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The bacterial strain PO100/5 was isolated from a skin abscess of a pig (Sus scrofa domesticus) in the Alentejo region of southern Portugal. It was identified as Corynebacterium pseudotuberculosis using biochemical tests, multiplex PCR and Pulsed Field Gel Electrophoresis. After genome sequencing and rpoB phylogeny, the strain was classified as C. ulcerans. To better understand the taxonomy of this strain and improve identification methods, we compared strain PO100/5 to other publicly available genomes from the C. diphtheriae group. Taxonomic analysis reclassified it and three others strains as belonging to the recently described C. silvaticum, which have been isolated from wild boar and roe deer in Germany and Austria. The results showed that PO100/5 is the first sequenced genome of a C. silvaticum strain from a domestic animal and a different geographical region, is a putative producer of the diphtheriae toxin, and has a unique sequence type. Genomic analysis of PO100/5 showed four prophages and eight conserved genomic islands when compared to C. ulcerans. Pangenome analysis of 38 C. silvaticum and 76 C. ulcerans samples suggest that C. silvaticum is a clonal species, with 73.6% of conserved genes and a pangenome near to being closed (α > 0.952). 172 conserved genes are unique to C. silvaticum when compared to C. ulcerans, with most related to nutrient uptake and metabolism, prophages or immune evasion. These unique genes could be used as genetic markers for species identification. This information can be useful for identification and surveillance of this pathogen, especially in regard to the possibility of zoonotic transmission.

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Section: Discussionsupporting

confidence: 81%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Taxonomic classification of strain PO100/5 shows a broader geographic distribution and genetic markers of the recently describedCorynebacterium silvaticum

Viana

Profeta

Silva

et al. 2020

Preprint

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“…Isolates collected since 2014 were confirmed as C. diphtheriae by matrixassisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) using Bruker technology. In order to exclude strains initially identified as C. diphtheriae but now classified as C. belfantii [42] or C. rouxii [43], genome-wide average nucleotide identity (ANI) was used as described previously [42]. Strains were characterized biochemically for pyrazinamidase, urease, and nitrate reductase and for utilization of maltose and trehalose using API Coryne strips (BioMérieux, Marcy l'Etoile, France) and the Rosco Diagnostica reagents (Eurobio, Les Ulis, France).…”

Section: Bacterial Cultures Identification and Biovarmentioning

confidence: 99%

Population genomics and antimicrobial resistance in Corynebacterium diphtheriae

et al. 2020

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Background Corynebacterium diphtheriae, the agent of diphtheria, is a genetically diverse bacterial species. Although antimicrobial resistance has emerged against several drugs including first-line penicillin, the genomic determinants and population dynamics of resistance are largely unknown for this neglected human pathogen. Methods Here, we analyzed the associations of antimicrobial susceptibility phenotypes, diphtheria toxin production, and genomic features in C. diphtheriae. We used 247 strains collected over several decades in multiple world regions, including the 163 clinical isolates collected prospectively from 2008 to 2017 in France mainland and overseas territories. Results Phylogenetic analysis revealed multiple deep-branching sublineages, grouped into a Mitis lineage strongly associated with diphtheria toxin production and a largely toxin gene-negative Gravis lineage with few toxin-producing isolates including the 1990s ex-Soviet Union outbreak strain. The distribution of susceptibility phenotypes allowed proposing ecological cutoffs for most of the 19 agents tested, thereby defining acquired antimicrobial resistance. Penicillin resistance was found in 17.2% of prospective isolates. Seventeen (10.4%) prospective isolates were multidrug-resistant (≥ 3 antimicrobial categories), including four isolates resistant to penicillin and macrolides. Homologous recombination was frequent (r/m = 5), and horizontal gene transfer contributed to the emergence of antimicrobial resistance in multiple sublineages. Genome-wide association mapping uncovered genetic factors of resistance, including an accessory penicillin-binding protein (PBP2m) located in diverse genomic contexts. Gene pbp2m is widespread in other Corynebacterium species, and its expression in C. glutamicum demonstrated its effect against several beta-lactams. A novel 73-kb C. diphtheriae multiresistance plasmid was discovered. Conclusions This work uncovers the dynamics of antimicrobial resistance in C. diphtheriae in the context of phylogenetic structure, biovar, and diphtheria toxin production and provides a blueprint to analyze re-emerging diphtheria.

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“…For this, we carried out parallel whole genome-based phylogeny assessments of all validly published species of the family Sphingobacteriaceae using pairwise genomic dissimilarity measures based on substitution events and BLAST-based whole-genome average nucleotide identities (ANIb) analyses. The former method performs alignment-free, pairwise whole-genome comparisons and has been used previously for resolving phylogenies from large genomic datasets (Parks et al, 2018 ; Badell et al, 2020 ; Tarlachkov et al, 2020 ). Although the genus Parapedobacter derives its name from Pedobacter based on 16S rRNA gene sequence similarity (Kim et al, 2007 ), the inferred trees from both the described methods revealed a close association of Parapedobacter with the genus Olivibacter ( Figures 1A,B ).…”

Section: Resultsmentioning

confidence: 99%

Phylogenetic Relationships and Potential Functional Attributes of the Genus Parapedobacter: A Member of Family Sphingobacteriaceae

et al. 2020

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The genus Parapedobacter was established to describe a novel genus within the family Sphingobacteriaceae and derives its name from Pedobacter , with which it is shown to be evolutionarily related. Despite this, Parapedobacter and Pedobacter do not share very high 16S rRNA gene sequence similarities. Therefore, we hypothesized whether these substantial differences at the 16S rRNA gene level depict the true phylogeny or that these genomes have actually diverged. Thus, we performed genomic analysis of the four available genomes of Parapedobacter to better understand their phylogenomic position within family Sphingobacteriaceae . Our results demonstrated that Parapedobacter is more closely related to species of Olivibacter , as opposed to the genus Pedobacter . Further, we identified a significant class of enzymes called pectinases with potential industrial applications within the genomes of Parapedobacter luteus DSM 22899 T and Parapedobacter composti DSM 22900 T . These enzymes, specifically pectinesterases and pectate lyases, are presumed to have largely different catalytic activities based on very low sequence similarities to already known enzymes and thus may be exploited for industrial applications. We also determined the complete Bacteroides aerotolerance (Bat) operon ( batA, batB, batC, batD, batE , hypothetical protein, moxR , and pa3071 ) within the genome of Parapedobacter indicus RK1 T . This expands the definition of genus Parapedobacter to containing members that are able to tolerate oxygen stress using encoded oxidative stress responsive systems. By conducting a signal propagation network analysis, we determined that BatD, BatE, and hypothetical proteins are the major controlling hubs that drive the expression of Bat operon. As a key metabolic difference, we also annotated the complete iol operon within the P . indicus RK1 T genome for utilization of all three stereoisomers of inositol, namely myo-inositol, scyllo-inositol, and 1D-chiro-inositol, which are abundant sources of organic phosphate found in soils. The results suggest that the genus Parapedobacter holds promising applications owing to its environmentally relevant genomic adaptations, which may be exploited in the future.

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Corynebacterium rouxii sp. nov., a novel member of the diphtheriae species complex

Cited by 50 publications

References 28 publications

Taxonomic classification of strain PO100/5 shows a broader geographic distribution and genetic markers of the recently describedCorynebacterium silvaticum

Taxonomic classification of strain PO100/5 shows a broader geographic distribution and genetic markers of the recently describedCorynebacterium silvaticum

Population genomics and antimicrobial resistance in Corynebacterium diphtheriae

Phylogenetic Relationships and Potential Functional Attributes of the Genus Parapedobacter: A Member of Family Sphingobacteriaceae

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