1
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
2
|
Berger A, Badell E, Åhman J, Matuschek E, Zidane N, Kahlmeter G, Sing A, Brisse S. Corynebacterium diphtheriae and Corynebacterium ulcerans: development of EUCAST methods and generation of data on which to determine breakpoints. J Antimicrob Chemother 2024; 79:968-976. [PMID: 38497937 DOI: 10.1093/jac/dkae056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/20/2024] [Indexed: 03/19/2024] Open
Abstract
BACKGROUND Evidence-based clinical susceptibility breakpoints have been lacking for antimicrobial agents used for diphtheria. OBJECTIVES We aimed to evaluate broth microdilution and disc diffusion methods and create a dataset of MIC values and inhibition zone diameters (ZDs) from which breakpoints could be determined. METHODS We included 400 recent clinical isolates equally distributed by species (Corynebacterium diphtheriae and Corynebacterium ulcerans) and by national surveillance programmes (France and Germany). Non-duplicate toxigenic and non-toxigenic isolates were chosen to enable the inclusion of a diversity of susceptibility levels for the 13 agents tested. Broth microdilution and disc diffusion, using EUCAST methodology for fastidious organisms, were used. RESULTS The distributions of MIC and ZD values were largely in agreement among methods and countries. Breakpoints to allow categorization of WT isolates as susceptible, i.e. susceptible (S) or susceptible, increased exposure (I) were determined for 12 agents. The data supported a breakpoint for benzylpenicillin and amoxicillin of resistant (R) > 1 mg/L since WT isolates were inhibited by 1 mg/L or less. WT isolates were categorized as I (S ≤ 0.001 mg/L) for benzylpenicillin, emphasizing the need for increased exposure, and S (S ≤ 1 mg/L) for amoxicillin. Erythromycin breakpoints were set at S ≤ 0.06 mg/L and R > 0.06 mg/L. The corresponding ZD breakpoints were determined for all agents except amoxicillin, for which categorization was based on benzylpenicillin results. CONCLUSIONS This work provided a large set of antimicrobial susceptibility data for C. diphtheriae and C. ulcerans, using a harmonized methodology. The dataset allowed EUCAST and experts in the diphtheria field to develop evidence-based breakpoints in January 2023.
Collapse
Affiliation(s)
- Anja Berger
- National Consiliary Laboratory for Diphtheria, Bavarian Food and Health Authority (LGL), Oberschleissheim, Germany
| | - Edgar Badell
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, 25-28 rue du Docteur Roux, F-75724, Paris, France
- Institut Pasteur, National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, France
| | - Jenny Åhman
- EUCAST Development Laboratory (EDL), Växjö, Sweden
| | | | - Nora Zidane
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, 25-28 rue du Docteur Roux, F-75724, Paris, France
| | | | - Andreas Sing
- National Consiliary Laboratory for Diphtheria, Bavarian Food and Health Authority (LGL), Oberschleissheim, Germany
| | - Sylvain Brisse
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, 25-28 rue du Docteur Roux, F-75724, Paris, France
- Institut Pasteur, National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, France
| |
Collapse
|
3
|
Tessier E, Hennart M, Badell E, Passet V, Toubiana J, Biron A, Gourinat AC, Merlet A, Colot J, Brisse S. Genomic Epidemiology of Corynebacterium diphtheriae in New Caledonia. Microbiol Spectr 2023; 11:e0461622. [PMID: 37042786 PMCID: PMC10269643 DOI: 10.1128/spectrum.04616-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 03/16/2023] [Indexed: 04/13/2023] Open
Abstract
An increasing number of isolations of Corynebacterium diphtheriae has been observed in recent years in the archipelago of New Caledonia. We aimed to analyze the clinical and microbiological features of samples with C. diphtheriae. All C. diphtheriae isolates identified in New Caledonia from May 2015 to May 2019 were included. For each case, a retrospective consultation of the patient files was conducted. Antimicrobial susceptibility phenotypes, tox gene and diphtheria toxin expression, biovar, and the genomic sequence were determined. Core genome multilocus sequence typing (cgMLST), 7-gene MLST, and search of genes of interest were performed from genomic assemblies. Fifty-eight isolates were included, with a median age of patients of 28 years (range: 9 days to 78 years). Cutaneous origin accounted for 51 of 58 (87.9%) isolates, and C. diphtheriae was associated with Staphylococcus aureus and/or Streptococcus pyogenes in three-quarters of cases. Half of cases came either from the main city Noumea (24%, 14/58) or from the sparsely populated island of Lifou (26%, 15/58). Six tox-positive isolates were identified, associated with recent travel to Vanuatu; 5 of these cases were linked and cgMLST confirmed recent transmission. Two cases of endocarditis in young female patients with a history of rheumatic fever involved tox-negative isolates. The 58 isolates were mostly susceptible to commonly used antibiotics. In particular, no isolate was resistant to the first-line molecules amoxicillin or erythromycin. Resistance to tetracycline was found in a genomic cluster of 17 (29%) isolates, 16 of which carried the tetO gene. There were 13 cgMLST sublineages, most of which were also observed in the neighboring country Australia. Cutaneous infections may harbor nontoxigenic C. diphtheriae isolates, which circulate largely silently in nonspecific wounds. The possible introduction of tox-positive strains from a neighboring island illustrates that diphtheria surveillance should be maintained in New Caledonia, and that immunization in neighboring islands must be improved. Genomic sequencing uncovers how genotypes circulate locally and across neighboring countries. IMPORTANCE The analysis of C. diphtheriae from the tropical archipelago of New Caledonia revealed a high genetic diversity with sublineages that may be linked to Polynesia, Australia, or metropolitan France. Genomic typing allowed confirming or excluding suspected transmission events among cases and contacts. A highly prevalent tetracycline-resistant sublineage harboring the tetO gene was uncovered. Toxigenic isolates were observed from patients returning from Vanuatu, showing the importance of improving vaccination coverage in settings where it is insufficient. This study also illustrates the importance for diphtheria surveillance of the inclusion of isolates from cutaneous sources in addition to respiratory cases, in order to provide a more complete epidemiological picture of the diversity and transmission of C. diphtheriae.
Collapse
Affiliation(s)
- Eve Tessier
- CHU Nantes, Service de Bactériologie et des Contrôles Microbiologiques, Nantes, France
- Microbiology Laboratory, Centre Hospitalier Territorial Gaston Bourret, Nouméa, New Caledonia
| | - Melanie Hennart
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
- Sorbonne Université, Collège doctoral, Paris, France
| | - Edgar Badell
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
- National Reference Center for the Corynebacteria of the diphtheriae complex, Paris, France
| | - Virginie Passet
- Institut Pasteur, Université Paris Cité, 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 Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
- National Reference Center for the Corynebacteria of the diphtheriae complex, Paris, France
- Université Paris Cité, Department of General Pediatrics and Pediatric Infectious Diseases, Hôpital Necker–Enfants Malades, APHP, Paris, France
| | - Antoine Biron
- Microbiology Laboratory, Centre Hospitalier Territorial Gaston Bourret, Nouméa, New Caledonia
| | - Ann-Claire Gourinat
- Microbiology Laboratory, Centre Hospitalier Territorial Gaston Bourret, Nouméa, New Caledonia
| | - Audrey Merlet
- Infectious diseases unit, Centre Hospitalier Territorial Gaston Bourret, Nouméa, New Caledonia
| | - Julien Colot
- Microbiology Laboratory, Centre Hospitalier Territorial Gaston Bourret, Nouméa, New Caledonia
- Institut Pasteur de Nouvelle Calédonie, Groupe de Bactériologie médicale et environnementale Nouméa, New Caledonia
| | - Sylvain Brisse
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
- National Reference Center for the Corynebacteria of the diphtheriae complex, Paris, France
| |
Collapse
|
4
|
Marosevic DV, Berger A, Kahlmeter G, Payer SK, Hörmansdorfer S, Sing A. Antimicrobial susceptibility of Corynebacterium diphtheriae and Corynebacterium ulcerans in Germany 2011-17. J Antimicrob Chemother 2021; 75:2885-2893. [PMID: 32747952 DOI: 10.1093/jac/dkaa280] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 05/26/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Diphtheria is mainly caused by diphtheria-toxin-producing strains of Corynebacterium diphtheriae and Corynebacterium ulcerans. The recommended first-line antibiotic is penicillin or erythromycin, but reliable susceptibility data are scarce. OBJECTIVES To define WT MIC distributions of 12 antimicrobial agents and provide data for the determination of tentative epidemiological cut-off values (TECOFFs) for potentially toxigenic corynebacteria and to evaluate the potential usefulness of a gradient test (Etest) for susceptibility testing of penicillin, erythromycin and clindamycin. METHODS For the 421 human or veterinary isolates from the period 2011-17, MICs of 12 antimicrobial agents were determined. Etest performance was evaluated for penicillin, erythromycin and clindamycin. RESULTS MIC distributions were characterized and TECOFFs could be set for 11 out of 24 antibiotic/species combinations. The current EUCAST clinical breakpoints, predominantly determined for Corynebacterium species other than C. diphtheriae and C. ulcerans, divide the WT MIC distributions of penicillin and clindamycin, thereby making reproducible susceptibility testing of C. diphtheriae and C. ulcerans difficult. For erythromycin, 4% of C. diphtheriae and 2% of C. ulcerans had MICs higher than those for WT isolates. Phenotypically detectable resistance to other antibiotics was rare. Etest underestimated MICs of penicillin and lower concentrations needed to be included for erythromycin, while for clindamycin the Etest was not a good surrogate method. CONCLUSIONS MIC distributions based on reference broth microdilution for potentially toxigenic Corynebacterium spp. were developed. For five and six agents, TECOFFs were suggested for C. diphtheriae and C. ulcerans, respectively, but for Corynebacterium pseudotuberculosis the number of isolates was too low.
Collapse
Affiliation(s)
- Durdica V Marosevic
- Public Health Microbiology, Bavarian Health and Food Safety Authority, Oberschleißheim, Germany.,European Programme for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Anja Berger
- Public Health Microbiology, Bavarian Health and Food Safety Authority, Oberschleißheim, Germany.,Consultant Laboratory for Diphtheria, Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Gunnar Kahlmeter
- Clinical Microbiology and the EUCAST Development Laboratory, Central Hospital, Växjö, Sweden
| | - Sarah Katharina Payer
- Public Health Microbiology, Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Stefan Hörmansdorfer
- Public Health Microbiology, Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Andreas Sing
- Public Health Microbiology, Bavarian Health and Food Safety Authority, Oberschleißheim, Germany.,Consultant Laboratory for Diphtheria, Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| |
Collapse
|
5
|
Schaeffer J, Huhulescu S, Stoeger A, Allerberger F, Ruppitsch W. Assessing the Genetic Diversity of Austrian Corynebacterium diphtheriae Clinical Isolates, 2011 to 2019. J Clin Microbiol 2021; 59:e02529-20. [PMID: 33268541 DOI: 10.1128/JCM.02529-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/25/2020] [Indexed: 02/01/2023] Open
Abstract
Diphtheria is a vaccine-preventable disease with a high potential for reemergence. One of its causative agents is Corynebacterium diphtheriae, with some strains producing diphtheria toxin. From 2011 to 2019, 57 clinical C. diphtheriae strains were isolated in Austria, either from the respiratory tract or from skin infections. The aim of this study was to investigate the genetic diversity of these C. diphtheriae isolates using whole-genome sequencing. Isolates were characterized by genome-wide comparisons using single nucleotide polymorphism analysis or core genome multilocus sequence typing and by searching sequence data for antimicrobial resistance genes and genes involved in diphtheria toxin production. The genetic diversity among the isolates was high, with no clear distribution over time or place. Corynebacterium belfantii isolates were separated from other strains and were strongly associated with respiratory infections (odds ratio [OR] = 57). Two clusters, limited in time and space, were identified. Almost 40% of strains carried resistance genes against tetracycline or sulfonamides, mostly from skin infections. Microbiological tests showed that 55% of isolates were resistant to penicillin but did not carry genes conferring β-lactam resistance. A diphtheria toxin gene with no nonsynonymous mutation was found in three isolates only. This study showed that sequencing can provide valuable information complementing routine microbiological and epidemiological investigations. It allowed us to identify unknown clusters, evaluate antimicrobial resistance more broadly, and support toxigenicity results obtained by PCR. For these reasons, C. diphtheriae surveillance could strongly benefit from the routine implementation of whole-genome sequencing.
Collapse
|
6
|
Xiaoli L, Benoliel E, Peng Y, Aneke J, Cassiday PK, Kay M, McKeirnan S, Duchin JS, Kawakami V, Lindquist S, Acosta AM, DeBolt C, Tondella ML, Weigand MR. Genomic epidemiology of nontoxigenic Corynebacterium diphtheriae from King County, Washington State, USA between July 2018 and May 2019. Microb Genom 2020; 6. [PMID: 33275088 PMCID: PMC8116682 DOI: 10.1099/mgen.0.000467] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Between July 2018 and May 2019, Corynebacterium diphtheriae was isolated from eight patients with non-respiratory infections, seven of whom experienced homelessness and had stayed at shelters in King County, WA, USA. All isolates were microbiologically identified as nontoxigenic C. diphtheriae biovar mitis. Whole-genome sequencing confirmed that all case isolates were genetically related, associated with sequence type 445 and differing by fewer than 24 single-nucleotide polymorphisms (SNPs). Compared to publicly available C. diphtheriae genomic data, these WA isolates formed a discrete cluster with SNP variation consistent with previously reported outbreaks. Virulence-related gene content variation within the highly related WA cluster isolates was also observed. These results indicated that genome characterization can readily support epidemiology of nontoxigenic C. diphtheriae.
Collapse
Affiliation(s)
| | | | - Yanhui Peng
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Pamela K Cassiday
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Meagan Kay
- Public Health Seattle and King County, Seattle, WA, USA
| | | | | | | | | | - Anna M Acosta
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Chas DeBolt
- Washington State Department of Health, Shoreline, WA, USA
| | - Maria Lucia Tondella
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Michael R Weigand
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| |
Collapse
|
7
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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.
| |
Collapse
|
8
|
Chorlton SD, Ritchie G, Lawson T, Romney MG, Lowe CF. Whole-Genome Sequencing of Corynebacterium diphtheriae Isolates Recovered from an Inner-City Population Demonstrates the Predominance of a Single Molecular Strain. J Clin Microbiol 2020; 58:e01651-19. [PMID: 31748323 DOI: 10.1128/JCM.01651-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 11/18/2019] [Indexed: 12/26/2022] Open
Abstract
In some parts of the world, Corynebacterium diphtheriae has reemerged as a pathogen, especially as a cause of infections among impoverished and marginalized populations. We performed whole-genome sequencing (WGS) on all cutaneous C. diphtheriae isolates (n = 56) from Vancouver's inner-city population over a 3-year time period (2015 to 2018). All isolates with complete genome assembly were toxin negative, contained a common set of 22 virulence factors, and shared a highly conserved accessory genome. One of our isolates harbored a novel plasmid conferring macrolide and lincosamide resistance. Fifty-two out of 56 isolates were multilocus sequence type 76, and single nucleotide variants (SNV) and core-genome multilocus sequence typing (cgMLST) analysis demonstrated tight clustering of our isolates relative to all publicly available C. diphtheriae genomes. All sequence type 76 (ST76) study isolates were within a median of 22 SNVs and 13 cgMLST alleles of each other, while NCBI genomes were within a median of 17,436 SNVs and 1,552 cgMLST alleles of each other (both P < 2.2 × 10-16). A single strain of C. diphtheriae appears to be causing cutaneous infections in the low-income population of Vancouver. Further research is needed to elucidate transmission networks in our study population and standardize C. diphtheriae epidemiological typing when whole genomes are sequenced.
Collapse
|
9
|
Chawla K, Gupta A, Gujral M, Singh A. Diphtheria resurgence in India: A case study from south Karnataka. J Family Med Prim Care 2020; 9:5776-5778. [PMID: 33532432 PMCID: PMC7842462 DOI: 10.4103/jfmpc.jfmpc_480_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/25/2020] [Accepted: 05/19/2020] [Indexed: 11/16/2022] Open
Abstract
Corynebacterium diphtheriae is a gram-positive bacillus with characteristic polar metachromatic granules. It was a significant public health problem, infecting the throat and upper airways and producing a highly potent exotoxin but with the advent of diphtheria vaccine, cases have rapidly decreased. Now over the last decade, the reemergence of this infection has been noted and case reports from India have been documented. India represents 78% of globally reported cases with significant mortality despite national immunization programs in place. This case study indicates the severity of an improperly managed case, the importance of microbiological diagnosis with a special interest in molecular detection, and reinforces a resurgence of diphtheria infection.
Collapse
|