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Karmarkar EN, Fitzpatrick T, Himmelfarb ST, Chow EJ, Smith HZ, Lan KF, Matsumoto J, Graff NR, DeBolt C, Truong T, Bourassa L, Farquhar C, Fang FC, Kim HN, Pottinger PS. Cluster of Nontoxigenic Corynebacterium diphtheriae Infective Endocarditis and Rising Background C. diphtheriae Cases-Seattle, Washington, 2020-2023. Clin Infect Dis 2024; 78:1214-1221. [PMID: 38381586 DOI: 10.1093/cid/ciae094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/12/2024] [Accepted: 02/16/2024] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND Nontoxigenic Corynebacterium diphtheriae, often associated with wounds, can rarely cause infective endocarditis (IE). Five patients with C. diphtheriae IE were identified within 12 months at a Seattle-based hospital system. We reviewed prior C. diphtheriae-positive cultures to determine if detections had increased over time and evaluated epidemiologic trends. METHODS We conducted a formal electronic health record search to identify all patients aged ≥18 years with C. diphtheriae detected in a clinical specimen (ie, wound, blood, sputum) between 1 September 2020 and 1 April 2023. We collected patient demographics, housing status, comorbidities, substance-use history, and level of medical care required at detection. We extracted laboratory data on susceptibilities of C. diphtheriae isolates and on other pathogens detected at the time of C. diphtheriae identification. RESULTS Between 1 September 2020 and 1 April 2023, 44 patients (median age, 44 years) had a C. diphtheriae-positive clinical culture, with most detections occurring after March 2022. Patients were predominantly male (75%), White (66%), unstably housed (77%), and had a lifetime history of injecting drugs (75%). Most C. diphtheriae-positive cultures were polymicrobial, including wound cultures from 36 (82%) patients and blood cultures from 6 (14%) patients, not mutually exclusive. Thirty-four patients (77%), including all 5 patients with C. diphtheriae IE, required hospital admission for C. diphtheriae or a related condition. Of the 5 patients with IE, 3 died of IE and 1 from COVID-19. CONCLUSIONS Findings suggest a high-morbidity outbreak disproportionately affecting patients who use substances and are unstably housed.
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Affiliation(s)
- Ellora N Karmarkar
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Thomas Fitzpatrick
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Sarah T Himmelfarb
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Eric J Chow
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Communicable Disease Epidemiology and Immunization Section, Public Health-Seattle & King County, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Hayden Z Smith
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Kristine F Lan
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Jason Matsumoto
- Department of Laboratory Medicine and Pathology, University of Washington and Harborview Medical Center, Seattle, Washington, USA
| | - Nicholas R Graff
- Office of Communicable Disease Epidemiology, Washington State Department of Health, Shoreline, Washington, USA
| | - Chas DeBolt
- Center for Public Health Medical and Veterinary Science, Washington State Department of Health, Shoreline, Washington, USA
| | - Thao Truong
- Department of Laboratory Medicine and Pathology, University of Washington and Harborview Medical Center, Seattle, Washington, USA
| | - Lori Bourassa
- Department of Laboratory Medicine and Pathology, University of Washington and Harborview Medical Center, Seattle, Washington, USA
| | - Carey Farquhar
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Ferric C Fang
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington and Harborview Medical Center, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - H Nina Kim
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Paul S Pottinger
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
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Xiaoli L, Peng Y, Williams MM, Lawrence M, Cassiday PK, Aneke JS, Pawloski LC, Shil SR, Rashid MO, Bhowmik P, Weil LM, Acosta AM, Shirin T, Habib ZH, Tondella ML, Weigand MR. Genomic characterization of cocirculating Corynebacterium diphtheriae and non-diphtheritic Corynebacterium species among forcibly displaced Myanmar nationals, 2017-2019. Microb Genom 2023; 9:001085. [PMID: 37712831 PMCID: PMC10569726 DOI: 10.1099/mgen.0.001085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 07/23/2023] [Indexed: 09/16/2023] Open
Abstract
Respiratory diphtheria is a serious infection caused by toxigenic Corynebacterium diphtheriae, and disease transmission mainly occurs through respiratory droplets. Between 2017 and 2019, a large diphtheria outbreak among forcibly displaced Myanmar nationals densely settled in Bangladesh was investigated. Here we utilized whole-genome sequencing (WGS) to characterize recovered isolates of C. diphtheriae and two co-circulating non-diphtheritic Corynebacterium (NDC) species - C. pseudodiphtheriticum and C. propinquum. C. diphtheriae isolates recovered from all 53 positive cases in this study were identified as toxigenic biovar mitis, exhibiting intermediate resistance to penicillin, and formed four phylogenetic clusters circulating among multiple refugee camps. Additional sequenced isolates collected from two patients showed co-colonization with non-toxigenic C. diphtheriae biovar gravis, one of which exhibited decreased susceptibility to the first-line antibiotics and harboured a novel 23-kb multidrug resistance plasmid. Results of phylogenetic reconstruction and virulence-related gene contents of the recovered NDC isolates indicated they were likely commensal organisms, though 80.4 %(45/56) were not susceptible to erythromycin, and most showed high minimum inhibition concentrations against azithromycin. These results demonstrate the high resolution with which WGS can aid molecular investigation of diphtheria outbreaks, through the quantification of bacterial genetic relatedness, as well as the detection of virulence factors and antibiotic resistance markers among case isolates.
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Affiliation(s)
- Lingzi Xiaoli
- ASRT, Inc, Atlanta, GA, USA
- Present address: Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Yanhui Peng
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Margaret M. Williams
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Present address: Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Marlon Lawrence
- Laboratory Leadership Service, Division of Scientific Education and Professional Development, Center for Surveillance, Epidemiology, and Laboratory Services, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Present address: Public Health Laboratory, Virgin Islands Department of Health, US Virgin Islands, USA
| | - Pamela K. Cassiday
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Janessa S. Aneke
- IHRC, Inc., Atlanta, GA, USA
- Present address: Université de Paris Cité, Learning Planet Institute, Paris, France
| | - Lucia C. Pawloski
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sadhona Rani Shil
- Institute of Epidemiology, Disease Control & Research, National Influenza Center, Dhaka, Bangladesh
| | - Mamun Or Rashid
- Institute of Epidemiology, Disease Control & Research, National Influenza Center, Dhaka, Bangladesh
| | - Proshanta Bhowmik
- Institute of Epidemiology, Disease Control & Research, National Influenza Center, Dhaka, Bangladesh
| | - Lauren M. Weil
- Epidemic Intelligence Service, Division of Scientific Education and Professional Development, Center for Surveillance, Epidemiology, and Laboratory Services, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Present address: Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Anna M. Acosta
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Present address: Director of Medical and Clinical Affairs, GSK Vaccines, USA
| | - Tahmina Shirin
- Institute of Epidemiology, Disease Control & Research, National Influenza Center, Dhaka, Bangladesh
| | - Zakir Hossain Habib
- Institute of Epidemiology, Disease Control & Research, National Influenza Center, Dhaka, Bangladesh
| | - M. Lucia Tondella
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Michael R. Weigand
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
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3
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Guglielmini J, Hennart M, Badell E, Toubiana J, Criscuolo A, Brisse S. Genomic Epidemiology and Strain Taxonomy of Corynebacterium diphtheriae. J Clin Microbiol 2021; 59:e0158121. [PMID: 34524891 PMCID: PMC8601238 DOI: 10.1128/jcm.01581-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 09/03/2021] [Indexed: 12/13/2022] Open
Abstract
Corynebacterium diphtheriae is highly transmissible and can cause large diphtheria outbreaks where vaccination coverage is insufficient. Sporadic cases or small clusters are observed in high-vaccination settings. The phylogeography and short timescale evolution of C. diphtheriae are not well understood, in part due to a lack of harmonized analytical approaches of genomic surveillance and strain tracking. We combined 1,305 genes with highly reproducible allele calls into a core genome multilocus sequence typing (cgMLST) scheme. We analyzed cgMLST gene diversity among 602 isolates from sporadic clinical cases, small clusters, or large outbreaks. We defined sublineages based on the phylogenetic structure within C. diphtheriae and strains based on the highest number of cgMLST mismatches within documented outbreaks. We performed time-scaled phylogenetic analyses of major sublineages. The cgMLST scheme showed high allele call rate in C. diphtheriae and the closely related species C. belfantii and C. rouxii. We demonstrate its utility to delineate epidemiological case clusters and outbreaks using a 25 mismatches threshold and reveal a number of cryptic transmission chains, most of which are geographically restricted to one or a few adjacent countries. Subcultures of the vaccine strain PW8 differed by up to 20 cgMLST mismatches. Phylogenetic analyses revealed a short-timescale evolutionary gain or loss of the diphtheria toxin and biovar-associated genes. We devised a genomic taxonomy of strains and deeper sublineages (defined using a 500-cgMLST-mismatch threshold), currently comprising 151 sublineages, only a few of which are geographically widespread based on current sampling. The cgMLST genotyping tool and nomenclature was made publicly accessible (https://bigsdb.pasteur.fr/diphtheria). Standardized genome-scale strain genotyping will help tracing transmission and geographic spread of C. diphtheriae. The unified genomic taxonomy of C. diphtheriae strains provides a common language for studies of ecology, evolution, and virulence heterogeneity among C. diphtheriae sublineages.
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Affiliation(s)
- Julien Guglielmini
- Institut Pasteur, Université de Paris, Bioinformatics and Biostatistics Hub, Department of Computational Biology, Paris, France
| | - Melanie Hennart
- Institut Pasteur, Université de Paris, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Edgar Badell
- Institut Pasteur, Université de Paris, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
- National Reference Center for the Corynebacteria of the Diphtheriae Complex, Paris, France
| | - Julie Toubiana
- Institut Pasteur, Université de Paris, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
- National Reference Center for the Corynebacteria of the Diphtheriae Complex, Paris, France
- Université de Paris, Service de Pédiatrie Générale et Maladies Infectieuses, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Alexis Criscuolo
- Institut Pasteur, Université de Paris, Bioinformatics and Biostatistics Hub, Department of Computational Biology, Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Université de Paris, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
- National Reference Center for the Corynebacteria of the Diphtheriae Complex, Paris, France
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Molecular and Epidemiological Characterization of Toxigenic and Nontoxigenic Corynebacterium diphtheriae, Corynebacterium belfantii, Corynebacterium rouxii, and Corynebacterium ulcerans Isolates Identified in Spain from 2014 to 2019. J Clin Microbiol 2021; 59:JCM.02410-20. [PMID: 33298610 DOI: 10.1128/jcm.02410-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/21/2020] [Indexed: 11/20/2022] Open
Abstract
This study examines the microbiological and epidemiological characteristics of toxigenic and nontoxigenic Corynebacterium isolates submitted to the national reference laboratory in Spain, between 2014 and 2019, in order to describe the current situation and improve our knowledge regarding these emerging pathogens. Epidemiological information was extracted from the Spanish Surveillance System. Microbiological and molecular characterization was carried out using phenotypic methods, multilocus sequence typing (MLST), whole-genome sequencing (WGS), and core genome MLST (cgMLST). Thirty-nine isolates were analyzed. Twenty-one isolates were identified as Corynebacterium diphtheriae (6 toxigenic), 14 as C. belfantii, 4 as C. ulcerans (3 toxigenic), and 1 as C. rouxii One C. diphtheriae isolate was identified as nontoxigenic tox gene bearing (NTTB). Ages of patients ranged from 1 to 89 years, with 10% (3/30) of nontoxigenic and 22% (2/9) of toxigenic isolates collected from children less than 15 years. Twenty-five of the patients were males (17/30 in nontoxigenic; 8/9 in toxigenic). MLST identified 28 sequence types (STs), of which 7 were described for the first time in Spain. WGS analysis showed that 10 isolates, including 3 toxigenic isolates, harbored a variety of antibiotic resistance genes in addition to the high prevalence of penicillin resistance phenotypically demonstrated. Phylogenetic analysis revealed one cluster of isolates from family members. Risk information was available for toxigenic isolates (9/39); 3 patients reported recent travels to countries of endemicity and 3 had contact with cats/dogs. One unvaccinated child with respiratory diphtheria had a fatal outcome. Including nontoxigenic Corynebacterium infections in disease surveillance and using WGS could further improve current surveillance.
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5
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Viana MVC, Profeta R, da Silva AL, Hurtado R, Cerqueira JC, Ribeiro BFS, Almeida MO, Morais-Rodrigues F, Soares SDC, Oliveira M, Tavares L, Figueiredo H, Wattam AR, Barh D, Ghosh P, Silva A, Azevedo V. Taxonomic classification of strain PO100/5 shows a broader geographic distribution and genetic markers of the recently described Corynebacterium silvaticum. PLoS One 2020; 15:e0244210. [PMID: 33347470 PMCID: PMC7751848 DOI: 10.1371/journal.pone.0244210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 12/04/2020] [Indexed: 12/19/2022] Open
Abstract
The bacterial strain PO100/5 was isolated from a skin abscess taken from 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 C. diphtheriae group. Taxonomic analysis reclassified it and three others strains as 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 livestock and a different geographical region, has the unique sequence type ST709, and could be could produce the diphtheriae toxin, along with strain 05–13. Genomic analysis of PO100/5 showed four prophages, and eight conserved genomic islands in comparison to C. ulcerans. Pangenome analysis of 38 C. silvaticum and 76 C. ulcerans genomes suggested that C. silvaticum is a genetically homogeneous species, with 73.6% of its genes conserved and a pangenome near to be closed (α > 0.952). There are 172 genes that are unique to C. silvaticum in comparison to C. ulcerans. Most of these conserved genes are related to nutrient uptake and metabolism, prophages or immunity against them, and could be genetic markers for species identification. Strains PO100/5 (livestock) and KL0182T (wild boar) were predicted to be potential human pathogens. This information may be useful for identification and surveillance of this pathogen.
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Affiliation(s)
- Marcus Vinicius Canário Viana
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Department of Genetics, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Rodrigo Profeta
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Alessandra Lima da Silva
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Raquel Hurtado
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Janaína Canário Cerqueira
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Bruna Ferreira Sampaio Ribeiro
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marcelle Oliveira Almeida
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Francielly Morais-Rodrigues
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Siomar de Castro Soares
- Department of Immunology, Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Manuela Oliveira
- Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisboa, Portugal
| | - Luís Tavares
- Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisboa, Portugal
| | - Henrique Figueiredo
- National Reference Laboratory of Aquatic Animal Disease, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Alice Rebecca Wattam
- Biocomplexity Institute, University of Virginia, Charlottesville, Virginia, United States of America
| | - Debmalya Barh
- Institute of Integrative Omics and Applied Biotechnology, Purba Medinipur, West Bengal, India
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Artur Silva
- Department of Genetics, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Vasco Azevedo
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- * E-mail:
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Hennart M, Panunzi LG, Rodrigues C, Gaday Q, Baines SL, Barros-Pinkelnig M, Carmi-Leroy A, Dazas M, Wehenkel AM, Didelot X, Toubiana J, Badell E, Brisse S. Population genomics and antimicrobial resistance in Corynebacterium diphtheriae. Genome Med 2020; 12:107. [PMID: 33246485 PMCID: PMC7694903 DOI: 10.1186/s13073-020-00805-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 11/11/2020] [Indexed: 12/21/2022] Open
Abstract
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. Supplementary information Supplementary information accompanies this paper at 10.1186/s13073-020-00805-7.
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Affiliation(s)
- Melanie Hennart
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France.,Collège doctoral, Sorbonne Université, F-75005, Paris, France
| | - Leonardo G Panunzi
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France.,Institut Français de Bioinformatique, CNRS UMS 3601, Evry, France
| | - Carla Rodrigues
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Quentin Gaday
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, Université de Paris, F-75015, Paris, France
| | - Sarah L Baines
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | | | - Annick Carmi-Leroy
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France.,Institut Pasteur, National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, France
| | - Melody Dazas
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France.,Institut Pasteur, National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, France
| | - Anne Marie Wehenkel
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, Université de Paris, F-75015, Paris, France
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, UK
| | - Julie Toubiana
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, 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, France
| | - Edgar Badell
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France.,Institut Pasteur, National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France. .,Institut Pasteur, National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, France.
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7
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Loire E, Ibrahim AI, Manso-Silván L, Lignereux L, Thiaucourt F. A whole-genome worldwide molecular epidemiology approach for contagious caprine pleuropneumonia. Heliyon 2020; 6:e05146. [PMID: 33083610 PMCID: PMC7550919 DOI: 10.1016/j.heliyon.2020.e05146] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 08/16/2020] [Accepted: 09/29/2020] [Indexed: 12/03/2022] Open
Abstract
Contagious caprine pleuropneumonia is an infectious and contagious disease affecting goats and wildlife ruminants, mostly in Africa and Asia. It is caused by a mycoplasma, Mycoplasma capricolum susbp. capripneumoniae, which is very fastidious. This may be the reason why there are few reports of its isolation and characterization. This study describes the development of a whole genome typing strategy based on sequencing reads assemblies on a reference genome (Abomsa, GenBank accession LM995445) and extraction of informative single nucleotide polymorphism. FASTA sequences inferred from the variant calling files were used to establish a comprehensive phylogenetic tree based on 2880 SNPs. This tree included a total of 34 strains originating from all the regions where CCPP has been detected, as well as strains isolated from wildlife. A recent isolate from West-Niger was positioned closely to another 1995 East-Niger isolate, an indication that CCPP may be extending westward in Africa. Six 2013 Tanzanian isolates had identical sequences in spite of diverse geographical origins. This could be explained by the clonal expansion of a virulent strain at that time in East Africa. Although all strains isolated from wildlife in the Middle East were in the same phylogenetic group, this may not sign an adaptation to new hosts. The most probable explanation for wildlife contamination remains the contact with goats. This strategy will easily accommodate new data in the near future and should become a gold-standard high-resolution typing procedure for the surveillance of contagious caprine pleuropneumonia.
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Affiliation(s)
- Etienne Loire
- CIRAD-ASTRE, Montpellier, France.,OIE/FAO World Reference Laboratory for CCPP, France.,INRA, UMR1309 ASTRE, Montpellier, France
| | | | - Lucía Manso-Silván
- CIRAD-ASTRE, Montpellier, France.,OIE/FAO World Reference Laboratory for CCPP, France.,INRA, UMR1309 ASTRE, Montpellier, France
| | - Louis Lignereux
- Research Unit for Epidemiology and Risk Analysis Applied to Veterinary Sciences (UREAR-ULiège), Centre of Fundamental and Applied Research for Animals and Health (FARAH), Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.,School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, 5371, South Australia, Australia
| | - François Thiaucourt
- CIRAD-ASTRE, Montpellier, France.,OIE/FAO World Reference Laboratory for CCPP, France.,INRA, UMR1309 ASTRE, Montpellier, France
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Husada D, Soegianto SDP, Kurniawati IS, Hendrata AP, Irawan E, Kartina L, Puspitasari D, Basuki PS, Ismoedijanto. First-line antibiotic susceptibility pattern of toxigenic Corynebacterium diphtheriae in Indonesia. BMC Infect Dis 2019; 19:1049. [PMID: 31829153 PMCID: PMC6907133 DOI: 10.1186/s12879-019-4675-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 11/29/2019] [Indexed: 11/21/2022] Open
Abstract
Background Diphtheria has been reported as an outbreak in some regions in Indonesia, most especially in East Java Province. Resistance to penicillin, erythromycin, and other antibiotics, single or multiple, has been reported in several studies. This study aims to evaluate the first-line antibiotic susceptibility pattern of toxigenic Corynebacterium diphtheriae isolates. Methods This descriptive observational study was performed from August to November 2018. C. diphtheriae isolates were collected from diphtheria patients and carriers in East Java from 2012 to 2017 and kept at the Balai Besar Laboratorium Kesehatan Daerah Surabaya or the Public Health Laboratory of Surabaya. Sample selection was done by random cluster sampling. The sensitivity test by E-test®of the five antibiotics (penicillin, oxacillin, erythromycin, azithromycin, and clarithromycin) was done to determine the minimum inhibitory concentration (MIC). The Clinical and Laboratory Standards Institute M45A (2015) Corynebacterium spp. for penicillin and erythromycin was used as standard. Results From 114 targeted isolates, 108 were viable and toxigenic. The E-test was performed on the viable isolates. The majority of the hosts were male (58.3%), with median (range) age of 6.5 (1–14) years. Half of the samples were from the 1 to 5-year-old age group. The isolates were acquired much more from patients (78.7%) than carriers (21.3%) and from pharyngeal swab (74.1%). Most of these isolates were from Madura Island (47.2%) and the northern and eastern parts of the province (horseshoe area). Mitis isolates were the major variant (76.9%). The susceptibility pattern of C. diphtheriae to erythromycin was better than that to penicillin. The E-test result for penicillin was 68.52% susceptible, 31.48% intermediate, and 0% resistant (MIC range, < 0.016 to 2 μg/L) and for erythromycin (MIC range, < 0.016 to > 256 μg/L) was 85.2% susceptible, 12% intermediate, and 2.8% resistant The MIC range for oxacillin was 1 to 96 μg/L, while for both azithromycin and clarithromycin were < 0.016 to > 256 μg/L. Conclusion The susceptibility rate of C. diphtheriae to erythromycin is higher than that to penicillin. The regular update of antibiotic selection to the national guidelines is recommended. The MIC reference standard to azithromycin and clarithromycin is also needed.
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Affiliation(s)
- Dominicus Husada
- Department of Child Health, Faculty of Medicine Universitas Airlangga/Dr. Soetomo Academic General Hospital, Surabaya, Indonesia.
| | - Sugi Deny Pranoto Soegianto
- Department of Child Health, Faculty of Medicine Universitas Airlangga/Dr. Soetomo Academic General Hospital, Surabaya, Indonesia
| | | | | | - Eveline Irawan
- Balai Besar Laboratorium Kesehatan Daerah (BBLK), Surabaya, Indonesia
| | - Leny Kartina
- Department of Child Health, Faculty of Medicine Universitas Airlangga/Dr. Soetomo Academic General Hospital, Surabaya, Indonesia
| | - Dwiyanti Puspitasari
- Department of Child Health, Faculty of Medicine Universitas Airlangga/Dr. Soetomo Academic General Hospital, Surabaya, Indonesia
| | - Parwati Setiono Basuki
- Department of Child Health, Faculty of Medicine Universitas Airlangga/Dr. Soetomo Academic General Hospital, Surabaya, Indonesia
| | - Ismoedijanto
- Department of Child Health, Faculty of Medicine Universitas Airlangga/Dr. Soetomo Academic General Hospital, Surabaya, Indonesia
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Sharma NC, Efstratiou A, Mokrousov I, Mutreja A, Das B, Ramamurthy T. Diphtheria. Nat Rev Dis Primers 2019; 5:81. [PMID: 31804499 DOI: 10.1038/s41572-019-0131-y] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/25/2019] [Indexed: 01/09/2023]
Abstract
Diphtheria is a potentially fatal infection mostly caused by toxigenic Corynebacterium diphtheriae strains and occasionally by toxigenic C. ulcerans and C. pseudotuberculosis strains. Diphtheria is generally an acute respiratory infection, characterized by the formation of a pseudomembrane in the throat, but cutaneous infections are possible. Systemic effects, such as myocarditis and neuropathy, which are associated with increased fatality risk, are due to diphtheria toxin, an exotoxin produced by the pathogen that inhibits protein synthesis and causes cell death. Clinical diagnosis is confirmed by the isolation and identification of the causative Corynebacterium spp., usually by bacterial culture followed by enzymatic and toxin detection tests. Diphtheria can be treated with the timely administration of diphtheria antitoxin and antimicrobial therapy. Although effective vaccines are available, this disease has the potential to re-emerge in countries where the recommended vaccination programmes are not sustained, and increasing proportions of adults are becoming susceptible to diphtheria. Thousands of diphtheria cases are still reported annually from several countries in Asia and Africa, along with many outbreaks. Changes in the epidemiology of diphtheria have been reported worldwide. The prevalence of toxigenic Corynebacterium spp. highlights the need for proper clinical and epidemiological investigations to quickly identify and treat affected individuals, along with public health measures to prevent and contain the spread of this disease.
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Affiliation(s)
- Naresh Chand Sharma
- Laboratory Department, Maharishi Valmiki Infectious Diseases Hospital, Delhi, India
| | - Androulla Efstratiou
- WHO Collaborating Centre for Diphtheria and Streptococcal Infections, Reference Microbiology Division, Public Health England, London, UK
| | - Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Ankur Mutreja
- Global Health-Infectious Diseases, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Bhabatosh Das
- Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India
| | - Thandavarayan Ramamurthy
- Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India.
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