A global Corynebacterium diphtheriae genomic framework sheds light on current diphtheria reemergence
Background: Diphtheria, caused by Corynebacterium diphtheriae, reemerges in Europe since 2022. Genomic sequencing can inform on transmission routes and genotypes of concern, but currently, no standard approach exists to detect clinically important genomic features and to interpret emergence in the g...
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Peer Community In
2023-08-01
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| Online Access: | https://peercommunityjournal.org/articles/10.24072/pcjournal.307/ |
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| author | Hennart, Mélanie Crestani, Chiara Bridel, Sébastien Armatys, Nathalie Brémont, Sylvie Carmi-Leroy, Annick Landier, Annie Passet, Virginie Fonteneau, Laure Vaux, Sophie Toubiana, Julie Badell, Edgar Brisse, Sylvain |
| author_facet | Hennart, Mélanie Crestani, Chiara Bridel, Sébastien Armatys, Nathalie Brémont, Sylvie Carmi-Leroy, Annick Landier, Annie Passet, Virginie Fonteneau, Laure Vaux, Sophie Toubiana, Julie Badell, Edgar Brisse, Sylvain |
| author_sort | Hennart, Mélanie |
| collection | DOAJ |
| description | Background: Diphtheria, caused by Corynebacterium diphtheriae, reemerges in Europe since 2022. Genomic sequencing can inform on transmission routes and genotypes of concern, but currently, no standard approach exists to detect clinically important genomic features and to interpret emergence in the global C. diphtheriae population framework. Methods: We developed the bioinformatics pipeline diphtOscan (available at https://gitlab.pasteur.fr/BEBP/diphtoscan) to extract from genomes of Corynebacteria of the diphtheriae species complex, medically relevant features including tox gene presence and disruption. We analyzed 101 human C. diphtheriae isolates collected in 2022 in metropolitan and overseas France (France-2022). To define the population background of this emergence, we sequenced 379 additional isolates (mainly from France, 2018-2021) and collated 870 publicly-available genomes. Results: The France-2022 isolates comprised 45 tox-positive (44 toxigenic) isolates, mostly imported, belonging to 10 sublineages (<500 distinct core genes). The global dataset comprised 245 sublineages and 33.9% tox-positive genomes, with diphtOscan predicting non-toxigenicity in 16.0% of these. 12% of the global isolates, and 43.6% of France-2022 ones, were multidrug resistant. Convergence of toxigenicity with penicillin and erythromycin resistance was observed in 2 isolates from France-2022. Phylogenetic lineages Gravis and Mitis contrasted strikingly in their pathogenicity-associated genes. Conclusions: This work provides a bioinformatics tool and global population framework to analyze C. diphtheriae genomes, revealing important heterogeneities in virulence and resistance features. Emerging genotypes combining toxigenicity and first-line antimicrobial resistance represent novel threats. Genomic epidemiology studies of C. diphtheriae should be intensified globally to improve understanding of reemergence and spatial spread.
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| first_indexed | 2024-03-10T07:25:06Z |
| format | Article |
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| institution | Directory Open Access Journal |
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| language | English |
| last_indexed | 2024-03-10T07:25:06Z |
| publishDate | 2023-08-01 |
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| spelling | doaj.art-6359ffe89653408588b8818397b0598e2023-11-22T14:22:09ZengPeer Community InPeer Community Journal2804-38712023-08-01310.24072/pcjournal.30710.24072/pcjournal.307A global Corynebacterium diphtheriae genomic framework sheds light on current diphtheria reemergence Hennart, Mélanie0https://orcid.org/0000-0002-1834-8246Crestani, Chiara1https://orcid.org/0000-0002-8948-1941Bridel, Sébastien2Armatys, Nathalie3Brémont, Sylvie4Carmi-Leroy, Annick5Landier, Annie6Passet, Virginie7Fonteneau, Laure8Vaux, Sophie9https://orcid.org/0000-0001-6648-6320Toubiana, Julie10https://orcid.org/0000-0001-9561-669XBadell, Edgar11https://orcid.org/0000-0001-6896-0495Brisse, Sylvain12https://orcid.org/0000-0002-2516-2108Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, F-75015, Paris, France; Institut Pasteur, National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, France; Sorbonne Université, Collège doctoral, F-75005 Paris, FranceInstitut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, F-75015, Paris, FranceInstitut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, F-75015, Paris, FranceInstitut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, F-75015, Paris, France; Institut Pasteur, National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, FranceInstitut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, F-75015, Paris, France; Institut Pasteur, National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, FranceInstitut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, F-75015, Paris, France; Institut Pasteur, National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, FranceInstitut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, F-75015, Paris, France; Institut Pasteur, National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, FranceInstitut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, F-75015, Paris, France; Institut Pasteur, National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, FranceSanté publique France, Saint-Maurice, FranceSanté publique France, Saint-Maurice, FranceInstitut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, F-75015, Paris, France; Institut Pasteur, National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, France; Department of General Pediatrics and Pediatric Infectious Diseases, Hôpital Necker-Enfants Malades, APHP, Université de Paris, Paris, FranceInstitut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, F-75015, Paris, France; Institut Pasteur, National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, FranceInstitut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, F-75015, Paris, France; Institut Pasteur, National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, FranceBackground: Diphtheria, caused by Corynebacterium diphtheriae, reemerges in Europe since 2022. Genomic sequencing can inform on transmission routes and genotypes of concern, but currently, no standard approach exists to detect clinically important genomic features and to interpret emergence in the global C. diphtheriae population framework. Methods: We developed the bioinformatics pipeline diphtOscan (available at https://gitlab.pasteur.fr/BEBP/diphtoscan) to extract from genomes of Corynebacteria of the diphtheriae species complex, medically relevant features including tox gene presence and disruption. We analyzed 101 human C. diphtheriae isolates collected in 2022 in metropolitan and overseas France (France-2022). To define the population background of this emergence, we sequenced 379 additional isolates (mainly from France, 2018-2021) and collated 870 publicly-available genomes. Results: The France-2022 isolates comprised 45 tox-positive (44 toxigenic) isolates, mostly imported, belonging to 10 sublineages (<500 distinct core genes). The global dataset comprised 245 sublineages and 33.9% tox-positive genomes, with diphtOscan predicting non-toxigenicity in 16.0% of these. 12% of the global isolates, and 43.6% of France-2022 ones, were multidrug resistant. Convergence of toxigenicity with penicillin and erythromycin resistance was observed in 2 isolates from France-2022. Phylogenetic lineages Gravis and Mitis contrasted strikingly in their pathogenicity-associated genes. Conclusions: This work provides a bioinformatics tool and global population framework to analyze C. diphtheriae genomes, revealing important heterogeneities in virulence and resistance features. Emerging genotypes combining toxigenicity and first-line antimicrobial resistance represent novel threats. Genomic epidemiology studies of C. diphtheriae should be intensified globally to improve understanding of reemergence and spatial spread. https://peercommunityjournal.org/articles/10.24072/pcjournal.307/diphtheria, genomic sequencing, antimicrobial resistance, virulence, epidemiology, transmission, 2022 reemergence, bioinformatics tool |
| spellingShingle | Hennart, Mélanie Crestani, Chiara Bridel, Sébastien Armatys, Nathalie Brémont, Sylvie Carmi-Leroy, Annick Landier, Annie Passet, Virginie Fonteneau, Laure Vaux, Sophie Toubiana, Julie Badell, Edgar Brisse, Sylvain A global Corynebacterium diphtheriae genomic framework sheds light on current diphtheria reemergence Peer Community Journal diphtheria, genomic sequencing, antimicrobial resistance, virulence, epidemiology, transmission, 2022 reemergence, bioinformatics tool |
| title | A global Corynebacterium diphtheriae genomic framework sheds light on current diphtheria reemergence
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| title_full | A global Corynebacterium diphtheriae genomic framework sheds light on current diphtheria reemergence
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| title_fullStr | A global Corynebacterium diphtheriae genomic framework sheds light on current diphtheria reemergence
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| title_full_unstemmed | A global Corynebacterium diphtheriae genomic framework sheds light on current diphtheria reemergence
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| title_short | A global Corynebacterium diphtheriae genomic framework sheds light on current diphtheria reemergence
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| title_sort | global corynebacterium diphtheriae genomic framework sheds light on current diphtheria reemergence |
| topic | diphtheria, genomic sequencing, antimicrobial resistance, virulence, epidemiology, transmission, 2022 reemergence, bioinformatics tool |
| url | https://peercommunityjournal.org/articles/10.24072/pcjournal.307/ |
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