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Crestani C, Passet V, Rethoret-Pasty M, Zidane N, Brémont S, Badell E, Criscuolo A, Brisse S. Microevolution and genomic epidemiology of the diphtheria-causing zoonotic pathogen Corynebacterium ulcerans. Nat Commun 2025; 16:4843. [PMID: 40413184 PMCID: PMC12103533 DOI: 10.1038/s41467-025-60065-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Accepted: 05/13/2025] [Indexed: 05/27/2025] Open
Abstract
Corynebacterium ulcerans is an emerging zoonotic pathogen which causes diphtheria-like infections. Although C. ulcerans is found in multiple domestic and wild animal species, most human cases are linked with pets. Our ability to decipher cross-host species transmission dynamics and to understand the emergence of clinically relevant clones (e.g., diphtheria toxin-positive) is currently hampered by a limited knowledge of C. ulcerans strain diversity and genome evolution. Here, we explore the genomic population structure and evolution of C. ulcerans with 582 isolates from diverse hosts and geographical locations. A newly developed core genome genotyping scheme captures the population structure of C. ulcerans both at deep and shallow phylogenetic levels, uncovering its main sublineages and offering high strain subtyping resolution for epidemiological surveillance. Additionally, we reveal the diversity and distribution of the diphtheria toxin gene (tox), and those of its associated mobile elements. Considering the entire Corynebacterium diphtheriae Species Complex, we find four diphtheria toxin families, five tox-prophage families, and a novel tox-carrying genetic element. We show that some toxin families are shared across Corynebacterium species, revealing tox-prophage cross-species transfer. Our work enhances knowledge on the ecology and evolution of C. ulcerans and provides a genomic framework for tracking the dissemination of emerging sublineages.
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Affiliation(s)
- Chiara Crestani
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Virginie Passet
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Martin Rethoret-Pasty
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Nora Zidane
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Sylvie Brémont
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
- Institut Pasteur, National Reference Center for Corynebacteria of the diphtheriae complex, Paris, France
| | - Edgar Badell
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
- Institut Pasteur, National Reference Center for Corynebacteria of the diphtheriae complex, Paris, France
| | - Alexis Criscuolo
- Institut Pasteur, Université Paris Cité, Biological Resource Center of Institut Pasteur, Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France.
- Institut Pasteur, National Reference Center for Corynebacteria of the diphtheriae complex, Paris, France.
- Institut Pasteur, Université Paris Cité, Biological Resource Center of Institut Pasteur, Paris, France.
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2
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Mori G, Errico G, Giancristoforo S, Visentin D, Castagna A, Viel L, Dellamaria D, Lorenzin G, Ortalli G, Scarparo C, Lanzafame M. When an underestimated zoonosis and antimicrobial resistance collide: Corynebacterium ulcerans. Access Microbiol 2024; 6:000898.v3. [PMID: 39697998 PMCID: PMC11652731 DOI: 10.1099/acmi.0.000898.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Accepted: 11/04/2024] [Indexed: 12/20/2024] Open
Abstract
In the European region, diphtheria is now rarely suspected in patients presenting with upper respiratory tract symptoms. Corynebacterium ulcerans is the underestimated zoonosis that is replacing C. diphtheria infections in industrialized countries, but extensive human and animal prevalence studies are lacking. The range of hosts that can act as reservoirs for C. ulcerans is very broad, companion pets currently being the main source of human infection. We report a case of macrolide-resistant C. ulcerans infection with no apparent zoonotic transmission and outline the efforts required for the public and zooprophylactic management of these cases. We describe the main critical issues to be addressed to comprehensively tackle this zoonosis in the future.
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Affiliation(s)
- Giovanni Mori
- Unit of Infectious Diseases, Ospedale Santa Chiara, APSS, Trento, Italy
- Università Vita-Salute San Raffaele, Milano, Italy
| | - Giulia Errico
- Unit of Infectious Diseases, Istituto Superiore di Sanità, Roma, Italy
| | | | | | | | - Laura Viel
- Microbiology and Diagnostic Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Villorba di Treviso, Italy
| | - Debora Dellamaria
- Microbiology and Diagnostic Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Trento, Italy
| | - Giovanni Lorenzin
- Unit of Microbiology and Virology, Ospedale Santa Chiara, APSS, Trento, Italy
| | - Gaia Ortalli
- Unit of Microbiology and Virology, Ospedale Santa Chiara, APSS, Trento, Italy
| | - Claudio Scarparo
- Unit of Microbiology and Virology, Ospedale Santa Chiara, APSS, Trento, Italy
| | - Massimiliano Lanzafame
- Unit of Infectious Diseases, Ospedale Santa Chiara, APSS, Trento, Italy
- Center for Medical Sciences (CISMed), University of Trento, Trento, Italy
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3
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Alvarez GV, Rupert DD, Sinclair S, Miyara SJ, Guevara S, Shih P, Hoey C. Cardiac arrest associated with non-toxigenic corynebacterium diphtheria strain: A case report. Front Med (Lausanne) 2023; 9:1003193. [PMID: 36698824 PMCID: PMC9868274 DOI: 10.3389/fmed.2022.1003193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023] Open
Abstract
Here we document a rare, acute, infection caused by non-toxigenic Corynebacterium diphtheriae and the resulting unique and severe clinical sequelae. Our patient was a young man with no known pre-existing conditions that presented in cardiopulmonary arrest. We contrast this case with prior instances of non-toxigenic C. diphtheriae strain infection in the United States and summarize the literature that suggests systemic infection can result in cardiogenic toxicity. We speculate on a possible missed, pre-existing condition that could have increased this patient's susceptibility to poor clinical outcome.
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Affiliation(s)
- George V. Alvarez
- Department of Family Medicine, Glen Cove Hospital, Northwell Health, Glen Cove, NY, United States,*Correspondence: George V. Alvarez,
| | - Deborah D. Rupert
- Medical Scientist Training Program, Stony Brook University, Stony Brook, NY, United States
| | - Samantha Sinclair
- Department of Infection Control, Huntington Hospital, Northwell Health, Huntington, NY, United States
| | - Santiago J. Miyara
- The Feinstein Institutes for Medical Research, Manhasset, NY, United States,Elmezzi Graduate School of Molecular Medicine, Manhasset, NY, United States
| | - Sara Guevara
- Department of Family Medicine, Glen Cove Hospital, Northwell Health, Glen Cove, NY, United States
| | - Peter Shih
- Department of Critical Care Medicine, Huntington Hospital, Northwell Health, Huntington, NY, United States
| | - Cynthia Hoey
- Department of Infectious Disease, Huntington Hospital, Northwell Health, Huntington, NY, United States
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Canário Viana MV, Profeta R, Cerqueira JC, Wattam AR, Barh D, Silva A, Azevedo V. Evidence of episodic positive selection in Corynebacterium diphtheriae complex of species and its implementations in identification of drug and vaccine targets. PeerJ 2022; 10:e12662. [PMID: 35190783 PMCID: PMC8857904 DOI: 10.7717/peerj.12662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 11/30/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Within the pathogenic bacterial species Corynebacterium genus, six species that can produce diphtheria toxin (C. belfantii, C. diphtheriae, C. pseudotuberculosis, C. rouxii, C. silvaticum and C. ulcerans) form a clade referred to as the C. diphtheria complex. These species have been found in humans and other animals, causing diphtheria or other diseases. Here we show the results of a genome scale analysis to identify positive selection in protein-coding genes that may have resulted in the adaptations of these species to their ecological niches and suggest drug and vaccine targets. METHODS Forty genomes were sampled to represent species, subspecies or biovars of Corynebacterium. Ten phylogenetic groups were tested for positive selection using the PosiGene pipeline, including species and biovars from the C. diphtheria complex. The detected genes were tested for recombination and had their sequences alignments and homology manually examined. The final genes were investigated for their function and a probable role as vaccine or drug targets. RESULTS Nineteen genes were detected in the species C. diphtheriae (two), C. pseudotuberculosis (10), C. rouxii (one), and C. ulcerans (six). Those were found to be involved in defense, translation, energy production, and transport and in the metabolism of carbohydrates, amino acids, nucleotides, and coenzymes. Fourteen were identified as essential genes, and six as virulence factors. Thirteen from the 19 genes were identified as potential drug targets and four as potential vaccine candidates. These genes could be important in the prevention and treatment of the diseases caused by these bacteria.
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Affiliation(s)
- Marcus Vinicius Canário Viana
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Departamento de Genética, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Rodrigo Profeta
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Janaína Canário Cerqueira
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Alice Rebecca Wattam
- Biocomplexity Institute, University of Virginia, Charlottesville, Virginia, United States
| | - Debmalya Barh
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Institute of Integrative Omics and Applied Biotechnology, Nonakuri, West Bengal, India
| | - Artur Silva
- Departamento de Genética, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Vasco Azevedo
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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AB 5 Enterotoxin-Mediated Pathogenesis: Perspectives Gleaned from Shiga Toxins. Toxins (Basel) 2022; 14:toxins14010062. [PMID: 35051039 PMCID: PMC8779504 DOI: 10.3390/toxins14010062] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/12/2022] [Accepted: 01/12/2022] [Indexed: 02/01/2023] Open
Abstract
Foodborne diseases affect an estimated 600 million people worldwide annually, with the majority of these illnesses caused by Norovirus, Vibrio, Listeria, Campylobacter, Salmonella, and Escherichia coli. To elicit infections in humans, bacterial pathogens express a combination of virulence factors and toxins. AB5 toxins are an example of such toxins that can cause various clinical manifestations, including dehydration, diarrhea, kidney damage, hemorrhagic colitis, and hemolytic uremic syndrome (HUS). Treatment of most bacterial foodborne illnesses consists of fluid replacement and antibiotics. However, antibiotics are not recommended for infections caused by Shiga toxin-producing E. coli (STEC) because of the increased risk of HUS development, although there are conflicting views and results in this regard. Lack of effective treatment strategies for STEC infections pose a public health threat during outbreaks; therefore, the debate on antibiotic use for STEC infections could be further explored, along with investigations into antibiotic alternatives. The overall goal of this review is to provide a succinct summary on the mechanisms of action and the pathogenesis of AB5 and related toxins, as expressed by bacterial foodborne pathogens, with a primary focus on Shiga toxins (Stx). The role of Stx in human STEC disease, detection methodologies, and available treatment options are also briefly discussed.
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Strauss RA, Herrera-Leon L, Guillén AC, Castro JS, Lorenz E, Carvajal A, Hernandez E, Navas T, Vielma S, Lopez N, Lopez MG, Aurenty L, Navas V, Rosas MA, Drummond T, Martínez JG, Hernández E, Bertuglia F, Andrade O, Torres J, May J, Herrera-Leon S, Eibach D. Molecular and epidemiologic characterization of the diphtheria outbreak in Venezuela. Sci Rep 2021; 11:6378. [PMID: 33737710 PMCID: PMC7973433 DOI: 10.1038/s41598-021-85957-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 03/09/2021] [Indexed: 11/09/2022] Open
Abstract
In 2016, Venezuela faced a large diphtheria outbreak that extended until 2019. Nasopharyngeal or oropharyngeal samples were prospectively collected from 51 suspected cases and retrospective data from 348 clinical records was retrieved from 14 hospitals between November 2017 and November 2018. Confirmed pathogenic Corynebactrium isolates were biotyped. Multilocus Sequence Typing (MLST) was performed followed by next-generation-based core genome-MLST and minimum spanning trees were generated. Subjects between 10 and 19 years of age were mostly affected (n = 95; 27.3%). Case fatality rates (CFR) were higher in males (19.4%), as compared to females (15.8%). The highest CFR (31.1%) was observed among those under 5, followed by the 40 to 49 age-group (25.0%). Nine samples corresponded to C. diphtheriae and 1 to C. ulcerans. Two Sequencing Types (ST), ST174 and ST697 (the latter not previously described) were identified among the eight C. diphtheriae isolates from Carabobo state. Cg-MLST revealed only one cluster also from Carabobo. The Whole Genome Sequencing analysis revealed that the outbreak seemed to be caused by different strains with C. diphtheriae and C. ulcerans coexisting. The reemergence and length of this outbreak suggest vaccination coverage problems and an inadequate control strategy.
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Affiliation(s)
| | | | | | - Julio S Castro
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | - Eva Lorenz
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Ana Carvajal
- Hospital Universitario de Caracas, Caracas, Venezuela
| | | | - Trina Navas
- Hospital General Los Magallanes de Catia, Caracas, Venezuela
| | | | | | - Maria G Lopez
- Hospital de Niños José Manuel de Los Ríos, Caracas, Venezuela
| | - Lisbeth Aurenty
- Hospital de Niños José Manuel de Los Ríos, Caracas, Venezuela
| | - Valeria Navas
- Hospital Universitario de Maracaibo, Maracaibo, Venezuela
| | - Maria A Rosas
- Ciudad Hospitalaria Dr Henrique Tejera, Carabobo, Venezuela
| | | | | | | | | | - Omaira Andrade
- Centro Clinico-Materno Leopoldo Aguerrevere, Caracas, Venezuela
| | - Jaime Torres
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | - Jürgen May
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | - Daniel Eibach
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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