Distinct Genomic Features Characterize Two Clades of Corynebacterium diphtheriae: Proposal of Corynebacterium diphtheriae Subsp. diphtheriae Subsp. nov. and Corynebacterium diphtheriae Subsp. lausannense Subsp. nov.

Tagini, Florian; Pillonel, Trestan; Croxatto, Antony; Bertelli, Claire; Koutsokera, Angela; Lovis, Alban; Greub, Gilbert

doi:10.3389/fmicb.2018.01743

Cited by 40 publications

(23 citation statements)

References 64 publications

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“…lausannense . Of interest, members of the newly described subspecies lausannense show a larger genome size and are enriched in genes related to transport and metabolism of lipids and inorganic ion (62). On the other hand, the new subspecies lacks all genes involved in the synthesis of pili, molybdenum cofactor, and nitrate reductase.…”

Section: Microbiology and Pathogenicity Of C Diphtheriaementioning

confidence: 99%

Whole Genome Sequencing for Surveillance of Diphtheria in Low Incidence Settings

Seth-Smith

Egli

2019

Front. Public Health

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Corynebacterium diphtheriae ( C. diphtheriae ) is a relatively rare pathogen in most Western countries. While toxin producing strains can cause pharyngeal diphtheria with potentially fatal outcomes, the more common presentation is wound infections. The diphtheria toxin is encoded on a prophage and can also be carried by Corynebacterium ulcerans and Corynebacterium pseudotuberculosis . Currently, across Europe, infections are mainly diagnosed in travelers and refugees from regions where diphtheria is more endemic, patients from urban areas with poor hygiene, and intravenous drug users. About half of the cases are non-toxin producing isolates. Rapid identification of the bacterial pathogen and toxin production is a critical element of patient and outbreak management. Beside the immediate clinical management of the patient, public health agencies should be informed of toxigenic C. diphtheriae diagnoses as soon as possible. The collection of case-related epidemiological data from the patient is often challenging due to language barriers and social circumstances. However, information on patient contacts, vaccine status and travel/refugee route, where appropriate, is critical, and should be documented. In addition, isolates should be characterized using high resolution typing, in order to identify transmissions and outbreaks. In recent years, whole genome sequencing (WGS) has become the gold standard of high-resolution typing methods, allowing detailed investigations of pathogen transmissions. De-centralized sequencing strategies with redundancy in sequencing capacities, followed by data exchange may be a valuable future option, especially since WGS becomes more available and portable. In this context, the sharing of sequence data, using public available platforms, is essential. A close interaction between microbiology laboratories, treating physicians, refugee centers, social workers, and public health officials is a key element in successful management of suspected outbreaks. Analyzing bacterial isolates at reference centers may further help to provide more specialized microbiological techniques and to standardize information, but this is also more time consuming during an outbreak. Centralized communication strategies between public health agencies and laboratories helps considerably in establishing and coordinating effective surveillance and infection control. We review the current literature on high-resolution typing of C. diphtheriae and share our own experience with the coordination of a Swiss-German outbreak.

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Section: Microbiology and Pathogenicity Of C Diphtheriaementioning

confidence: 99%

Whole Genome Sequencing for Surveillance of Diphtheria in Low Incidence Settings

Seth-Smith

Egli

2019

Front. Public Health

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“…Hence, the five isolates were very closely related, showing that they belong to a single strain. In addition, this strain was phylogenetically distantly related (0.49% to 0.77% nucleotide p-distances) to all of the other C. belfantii isolates available in public repositories and from previous studies (16,21). One of the most closely related strains (separated from FRC0074 by a p-distance of 0.58%) was FRC0223, used as the outgroup in the SNP-based phylogeny of strains (Fig.…”

Section: Resultsmentioning

confidence: 70%

Carriage of a Single Strain of Nontoxigenic Corynebacterium diphtheriae bv. Belfanti ( Corynebacterium belfantii ) in Four Patients with Cystic Fibrosis

et al. 2019

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Cystic fibrosis (CF) patients are commonly colonized by bacterial pathogens, which can induce persistent lung inflammation and may contribute to clinical deterioration. Colonization of CF patients and cross-transmission by Corynebacterium diphtheriae have not been reported so far. The aim of this article was to investigate the possibility of a cross-transmission of C. diphtheriae biovar Belfanti between four patients of a CF center. C. diphtheriae biovar Belfanti (now formally called C. belfantii) isolates were collected from four patients in a single CF care center over a period of 6 years and analyzed by microbiological methods and whole-genome sequencing. Epidemiological links among patients were investigated. Ten isolates were collected from 4 patients. Whole-genome sequencing of one isolate from each patient showed that a single strain was shared among them. In addition, one patient was found to have the same strain in two consecutive samplings performed 9 months apart. The strain was nontoxigenic and was susceptible to most antimicrobial agents. Ciprofloxacin resistance was observed in one patient. The idea of transmission of the strain among patients was supported by the occurrence of same-day visits to the CF center. This study demonstrated colonization of CF patients by C. diphtheriae biovar Belfanti (C. belfantii), and the data suggest persistence and transmission of a unique strain during at least 6 years in a single CF patient care center.

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“…lausannense and C. belfantii was 99.3%. Besides, the former was positioned within the phylogenetic branch of C. belfantii ( Figure 1, S1 and S2 ), and the descriptions of both taxa are very similar (3, 13). Given that C. belfantii was validly published in October 2018, a few months before the taxonomic proposal C. diphtheriae subsp.…”

Section: Resultsmentioning

confidence: 85%

“…diphtheriae and C. diphtheriae subsp. lausannense (13). Here, we observed that the ANI value between the type strains of C. diphtheriae subsp.…”

Section: Resultsmentioning

confidence: 99%

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Description ofCorynebacterium rouxiisp. nov., a novel member of thediphtheriaespecies complex

Badell

Hennart

Rodrigues

et al. 2019

Preprint

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A group of six clinical isolates previously identified as Corynebacterium diphtheriae biovar Belfanti, isolated from human cutaneous or peritoneum infections and from one dog, were characterized by genomic sequencing, biochemical analysis and mass spectrometry (MALDI-TOF MS). The six isolates were negative for the diphtheria toxin gene. Phylogenetic analyses showed that the six isolates (including FRC0190T) are clearly demarcated from C. diphtheriae, C. belfantii, C. ulcerans and C. pseudotuberculosis. The average nucleotide identity of FRC0190T with C. diphtheriae NCTC 11397T was 92.6%, and was 91.8% with C. belfantii FRC0043T. C. diphtheriae subsp. lausannense strain CHUV2995T appeared to be a later heterotypic synonym of C. belfantii (ANI, 99.3%). Phenotyping data revealed an atypical negative or heterogeneous intermediate maltose fermentation reaction for the six isolates. MALDI-TOF MS differentiated the new group from the other Corynebacterium taxa by the presence of specific spectral peaks. rpoB sequences showed identity to atypical, maltose-negative C. diphtheriae biovar Belfanti isolates previously described from two cats in the USA. We propose the name Corynebacterium rouxii sp. nov. for the novel group, with FRC0190T (= CIP 111752T = DSM 110354T) as type strain.

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Distinct Genomic Features Characterize Two Clades of Corynebacterium diphtheriae: Proposal of Corynebacterium diphtheriae Subsp. diphtheriae Subsp. nov. and Corynebacterium diphtheriae Subsp. lausannense Subsp. nov.

Cited by 40 publications

References 64 publications

Whole Genome Sequencing for Surveillance of Diphtheria in Low Incidence Settings

Whole Genome Sequencing for Surveillance of Diphtheria in Low Incidence Settings

Carriage of a Single Strain of Nontoxigenic Corynebacterium diphtheriae bv. Belfanti ( Corynebacterium belfantii ) in Four Patients with Cystic Fibrosis

Description ofCorynebacterium rouxiisp. nov., a novel member of thediphtheriaespecies complex

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