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Shamsuzzaman M, Dahal RH, Kim S, Kim J. Genome insight and probiotic potential of three novel species of the genus Corynebacterium. Front Microbiol 2023; 14:1225282. [PMID: 37485528 PMCID: PMC10358988 DOI: 10.3389/fmicb.2023.1225282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/14/2023] [Indexed: 07/25/2023] Open
Abstract
Three bacterial strains, B5-R-101T, TA-R-1T, and BL-R-1T, were isolated from the feces of a healthy Korean individual. Cells of these strains were Gram-stain-positive, facultatively anaerobic, oxidase-negative, catalase-positive, rod-shaped, and non-motile. They were able to grow within a temperature range of 10-42°C (optimum, 32-37°C), at a pH range of 2.0-10.0 (optimum, pH 5.5-8.0), and at NaCl concentration of 0.5-10.5% (w/v). All the three strains exhibited 2,2-Diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activities ranging from 58 ± 1.62 to 79 ± 1.46% (% inhibition). These strains survived in lower pH (2.0) and in 0.3% bile salt concentration for 4 h. They did not show hemolytic activity and exhibited antimicrobial activity against pathogenic bacteria, such as Escherichia coli, Acinetobacter baumannii, Staphylococcus aureus, and Salmonella enterica. The genomic analysis presented no significant concerns regarding antibiotic resistance or virulence gene content, indicating these strains could be potential probiotic candidates. Phylogenetic analysis showed that they belonged to the genus Corynebacterium, with 98.5-99.0% 16S rRNA gene sequence similarities to other members of the genus. Their major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The abundant cellular fatty acids were C16:0, C18:1ω9c, and anteiso-C19:0. Genomic analysis of these isolates revealed the presence of genes necessary for their survival and growth in the gut environment, such as multi-subunit ATPases, stress response genes, extracellular polymeric substance biosynthesis genes, and antibacterial genes. Furthermore, the genome of each strain possessed biosynthetic gene clusters with antioxidant and antimicrobial potentials, including terpenes, saccharides, polyketides, post-translationally modified peptides (RIPPs), and non-ribosomal peptides (NRPs). In silico DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values were lower than the thresholds to distinguish novel species. Based on phenotypic, genomic, phylogenomic, and phylogenetic analysis, these potential probiotic strains represent novel species within the genus Corynebacterium, for which the names Corynebacterium intestinale sp. nov. (type strain B5-R-101T = CGMCC 1.19408T = KCTC 49761T), Corynebacterium stercoris sp. nov. (type strain TA-R-1T = CGMCC 1.60014T = KCTC 49742T), and Corynebacterium faecium sp. nov. (type strain BL-R-1T = KCTC 49735T = TBRC 17331T) are proposed.
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Affiliation(s)
- Md Shamsuzzaman
- Department of Biomedical Science, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Ram Hari Dahal
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Shukho Kim
- Department of Biomedical Science, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Jungmin Kim
- Department of Biomedical Science, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
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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] [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.
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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
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3
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Ramos JN, Baio PVP, Veras JFC, Vieira ÉMD, Mattos-Guaraldi AL, Vieira VV. Novel configurations of type I-E CRISPR-Cas system in Corynebacterium striatum clinical isolates. Braz J Microbiol 2023; 54:69-80. [PMID: 36477756 PMCID: PMC9944170 DOI: 10.1007/s42770-022-00881-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) are a prokaryotic adaptive immune system that, through Cas proteins, promote the degradation of foreign nucleic acids such as phages and plasmids. We analyzed 10 genomes of Corynebacterium striatum clinical isolates from a public hospital in Rio de Janeiro, Brazil, the most emergent multidrug-resistant Corynebacterium species. All isolates were submitted to antimicrobial susceptibility testing. The occurrence and diversity of the CRISPR system were investigated by bioinformatics tools. Our analysis revealed that the isolates exhibited type I-E gene arrangements, and 3 more multidrug-resistant isolates, alternative type I-E gene arrangements, showing a divergent gene arrangement within the cas operon. Phylogenetic analysis of the cas1 gene of this type I-E CRISPR-Cas system alternative arrangement, termed here type I-E', showed a cluster in a distinct clade of the type I-E CRISPR-Cas system. The systems' guanine-cytosine (GC) content is lower than the genomic DNA's GC content, and mobile genetic elements were found in some isolates near the CRISPR-Cas system. Most CRISPR spacers are unknown indicating that there is a reservoir of unexplored corynebacteriophages and plasmids. Some spacers showed perfect homologies with phage and plasmid sequences. Intact phage regions were found in 3 of our isolates, ranging from 9.1 to 43.8 kb, with regions showing similarity to Rhodococcus and Corynebacterium phages. Our results may contribute to research about the CRISPR-Cas system diversity in C. striatum, where there are no published data to date.
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Affiliation(s)
- Juliana Nunes Ramos
- Laboratório de Difteria E Corinebactérias de Importância Clínica (LDCIC), Faculdade de Ciências Médicas, Universidade Do Estado Do Rio de Janeiro, Av. 28 de Setembro, 87, Fundos, 3º Andar, Vila Isabel, Rio de Janeiro, RJ, Brazil.
| | - Paulo Victor Pereira Baio
- Laboratório Químico-Farmacêutico Do Exército Brasileiro (LQFEx), Ministério da Defesa, Brasília, Brazil
| | - João Flávio Carneiro Veras
- Laboratório Interdisciplinar de Pesquisas Médicas (LIPMED), Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Érica Miranda Damásio Vieira
- Laboratório Interdisciplinar de Pesquisas Médicas (LIPMED), Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Ana Luiza Mattos-Guaraldi
- Laboratório de Difteria E Corinebactérias de Importância Clínica (LDCIC), Faculdade de Ciências Médicas, Universidade Do Estado Do Rio de Janeiro, Av. 28 de Setembro, 87, Fundos, 3º Andar, Vila Isabel, Rio de Janeiro, RJ, Brazil
| | - Verônica Viana Vieira
- Laboratório Interdisciplinar de Pesquisas Médicas (LIPMED), Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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Point-Counterpoint: What's in a Name? Clinical Microbiology Laboratories Should Use Nomenclature Based on Current Taxonomy. J Clin Microbiol 2023; 61:e0173222. [PMID: 36625570 PMCID: PMC9879091 DOI: 10.1128/jcm.01732-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
INTRODUCTION The mnemonic SPICE (Serratia, Pseudomonas, indole-positive Proteus, Citrobacter, and Enterobacter) has served as a reminder to consider when a Gram-negative organism may carry a chromosomal copy of blaampC, with the associated risk of developing resistance to first-, second-, and third-generation cephalosporins. However, in 2017, there was a well-founded proposal to rename Enterobacter aerogenes to Klebsiella aerogenes, based on whole-genome sequencing (WGS), and the SPICE mnemonic lost its relevance. With the increased use of WGS for taxonomy, it seems like bacteria and fungi are undergoing constant name changes. These changes create unique challenges for clinical microbiology laboratories, who would like to issue reports that are readily understood and that help clinicians determine empirical antibiotic therapy, interpret antimicrobial resistance, and understand clinical significance. In this Point-Counterpoint, Drs. Karen Carroll and Erik Munson discuss the pros of updating bacterial taxonomy and why clinical labs must continue to update reporting, while Drs. Susan Butler-Wu and Sheila Patrick argue for caution in adopting new names for microorganisms.
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Prygiel M, Polak M, Mosiej E, Wdowiak K, Formińska K, Zasada AA. New Corynebacterium Species with the Potential to Produce Diphtheria Toxin. Pathogens 2022; 11:1264. [PMID: 36365015 PMCID: PMC9693595 DOI: 10.3390/pathogens11111264] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/20/2022] [Accepted: 10/27/2022] [Indexed: 07/30/2023] Open
Abstract
Only three Corynebacterium species are known to produce a lethal exotoxin called diphtheria toxin. These are C. diphtheriae, C. ulcerans and C. pseudotuberculosis. The diphtheria toxin gene (tox) is carried in a family of closely related corynebacteriophages and therefore the toxin can be produced only through lysogenisation, in which the corynephage encoding tox is stably inserted into the chromosome. However, 'nontoxigenic tox gene-bearing' (NTTB) strains, which are genotypically tox-positive but do not express the protein, have been described. The emergence of NTTB strains was first observed during the 1990s diphtheria epidemic in Eastern Europe and nowadays such isolates have been detected in many countries in the world. Recently, novel species of Corynebacterium genus have been described which might have the potential of producing the diphtheria toxin due to the possession of the diphtheria toxin gene but it has not produced toxin in laboratory tests. The circulation of NTTB strains could be related to the increased risk for diphtheria disease arising from the risk of re-emerging toxin expression. The article presents the mechanism of diphtheria toxin expression and action, recently described novel species of NTTB corynebacteria as well as the taxonomic changes within the C. diphtheriae group.
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Munson E. Microbial Taxonomy Revision: Enough Is Enough! Or Is It? Clin Chem 2021; 68:138-142. [PMID: 34969113 DOI: 10.1093/clinchem/hvab189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022]
Affiliation(s)
- Erik Munson
- Department of Medical Laboratory Science, Marquette University, Milwaukee, WI, USA.,Wisconsin Clinical Laboratory Network Laboratory Technical Advisory Group, Madison, WI, USA
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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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Whole genome sequence of a non-toxigenic Corynebacterium diphtheriae strain from a hospital in southeastern China. BMC Genom Data 2021; 22:42. [PMID: 34656079 PMCID: PMC8520229 DOI: 10.1186/s12863-021-00998-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/06/2021] [Indexed: 12/02/2022] Open
Abstract
Background Sporadic cases of infection with non-toxigenic Corynebacterium diphtheriae (C. diphtheriae) isolates have been reported in regions covered by the Diphtheria-Tetanus-Pertussis vaccine, but no information describing the whole genome of non-toxigenic strains collected in China is available. Therefore, in this work, the complete genome of a non-toxigenic strain of C. diphtheriae from a hospital located in southeastern China was performed. Results This non-toxigenic isolate belonged to the belfanti biotype and possessed a unique ST (assigned as ST799 in pubMLST). ErmX was present in the genome sequence and this isolate owned the resistance to erythromycin and clindamycin. Genes coding for virulence factors involved in adherence, iron-uptake and regulation of diphtheria toxin were also found. Two genes were involved in the interaction between pathogen and host. The phylogenetic analysis revealed that this newly isolated strain was similar to the strain NCTC10838, CMCNS703 and CHUV2995. Conclusion Non-toxigenic C. diphtheriae strain contained virulence factors, thus it is able to cause an infectious disease, aspect that could be clarified by performing the whole genome sequencing analysis. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-00998-9.
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Pathogenic Determinants of the Mycobacterium kansasii Complex: An Unsuspected Role for Distributive Conjugal Transfer. Microorganisms 2021; 9:microorganisms9020348. [PMID: 33578772 PMCID: PMC7916490 DOI: 10.3390/microorganisms9020348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/02/2021] [Accepted: 02/05/2021] [Indexed: 01/15/2023] Open
Abstract
The Mycobacterium kansasii species comprises six subtypes that were recently classified into six closely related species; Mycobacterium kansasii (formerly M. kansasii subtype 1), Mycobacterium persicum (subtype 2), Mycobacterium pseudokansasii (subtype 3), Mycobacterium ostraviense (subtype 4), Mycobacterium innocens (subtype 5) and Mycobacterium attenuatum (subtype 6). Together with Mycobacterium gastri, they form the M. kansasii complex. M. kansasii is the most frequent and most pathogenic species of the complex. M. persicum is classically associated with diseases in immunosuppressed patients, and the other species are mostly colonizers, and are only very rarely reported in ill patients. Comparative genomics was used to assess the genetic determinants leading to the pathogenicity of members of the M. kansasii complex. The genomes of 51 isolates collected from patients with and without disease were sequenced and compared with 24 publicly available genomes. The pathogenicity of each isolate was determined based on the clinical records or public metadata. A comparative genomic analysis showed that all M. persicum, M. ostraviense, M innocens and M. gastri isolates lacked the ESX-1-associated EspACD locus that is thought to play a crucial role in the pathogenicity of M. tuberculosis and other non-tuberculous mycobacteria. Furthermore, M. kansasii was the only species exhibiting a 25-Kb-large genomic island encoding for 17 type-VII secretion system-associated proteins. Finally, a genome-wide association analysis revealed that two consecutive genes encoding a hemerythrin-like protein and a nitroreductase-like protein were significantly associated with pathogenicity. These two genes may be involved in the resistance to reactive oxygen and nitrogen species, a required mechanism for the intracellular survival of bacteria. Three non-pathogenic M. kansasii lacked these genes likely due to two distinct distributive conjugal transfers (DCTs) between M. attenuatum and M. kansasii, and one DCT between M. persicum and M. kansasii. To our knowledge, this is the first study linking DCT to reduced pathogenicity.
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Munson E, Carroll KC. Summary of Novel Bacterial Isolates Derived from Human Clinical Specimens and Nomenclature Revisions Published in 2018 and 2019. J Clin Microbiol 2021; 59:e01309-20. [PMID: 32967902 PMCID: PMC8111135 DOI: 10.1128/jcm.01309-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Knowledge of novel prokaryotic taxon discovery and nomenclature revisions is of importance to clinical microbiology laboratory practice, infectious disease epidemiology, and studies of microbial pathogenesis. Relative to bacterial isolates derived from human clinical specimens, we present an in-depth summary of novel taxonomic designations and revisions to prokaryotic taxonomy that were published in 2018 and 2019. Included are several changes pertinent to former designations of or within Propionibacterium spp., Corynebacterium spp., Clostridium spp., Mycoplasma spp., Methylobacterium spp., and Enterobacteriaceae Future efforts to ascertain clinical relevance for many of these changes may be augmented by a document development committee that has been appointed by the Clinical and Laboratory Standards Institute.
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Affiliation(s)
- Erik Munson
- College of Health Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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11
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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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12
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Dylus D, Pillonel T, Opota O, Wüthrich D, Seth-Smith HMB, Egli A, Leo S, Lazarevic V, Schrenzel J, Laurent S, Bertelli C, Blanc DS, Neuenschwander S, Ramette A, Falquet L, Imkamp F, Keller PM, Kahles A, Oberhaensli S, Barbié V, Dessimoz C, Greub G, Lebrand A. NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test. Front Microbiol 2020; 11:591093. [PMID: 33424794 PMCID: PMC7793906 DOI: 10.3389/fmicb.2020.591093] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/19/2020] [Indexed: 12/31/2022] Open
Abstract
Whole genome sequencing (WGS) enables high resolution typing of bacteria up to the single nucleotide polymorphism (SNP) level. WGS is used in clinical microbiology laboratories for infection control, molecular surveillance and outbreak analyses. Given the large palette of WGS reagents and bioinformatics tools, the Swiss clinical bacteriology community decided to conduct a ring trial (RT) to foster harmonization of NGS-based bacterial typing. The RT aimed at assessing methicillin-susceptible Staphylococcus aureus strain relatedness from WGS and epidemiological data. The RT was designed to disentangle the variability arising from differences in sample preparation, SNP calling and phylogenetic methods. Nine laboratories participated. The resulting phylogenetic tree and cluster identification were highly reproducible across the laboratories. Cluster interpretation was, however, more laboratory dependent, suggesting that an increased sharing of expertise across laboratories would contribute to further harmonization of practices. More detailed bioinformatic analyses unveiled that while similar clusters were found across laboratories, these were actually based on different sets of SNPs, differentially retained after sample preparation and SNP calling procedures. Despite this, the observed number of SNP differences between pairs of strains, an important criterion to determine strain relatedness given epidemiological information, was similar across pipelines for closely related strains when restricting SNP calls to a common core genome defined by S. aureus cgMLST schema. The lessons learned from this pilot study will serve the implementation of larger-scale RT, as a mean to have regular external quality assessments for laboratories performing WGS analyses in a clinical setting.
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Affiliation(s)
- David Dylus
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Trestan Pillonel
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Onya Opota
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Daniel Wüthrich
- Division of Clinical Bacteriology and Mycology, University Hospital of Basel, Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Helena M B Seth-Smith
- Division of Clinical Bacteriology and Mycology, University Hospital of Basel, Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Adrian Egli
- Division of Clinical Bacteriology and Mycology, University Hospital of Basel, Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Stefano Leo
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Genetics Laboratory Medicine and Pathology, Geneva University Hospitals, Geneva, Switzerland
| | - Vladimir Lazarevic
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Genetics Laboratory Medicine and Pathology, Geneva University Hospitals, Geneva, Switzerland
| | - Jacques Schrenzel
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Genetics Laboratory Medicine and Pathology, Geneva University Hospitals, Geneva, Switzerland
| | - Sacha Laurent
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Claire Bertelli
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Dominique S Blanc
- Service of Hospital Preventive Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | | | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Laurent Falquet
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Frank Imkamp
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Peter M Keller
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Andre Kahles
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Biomedical Informatics, Swiss Federal Institute of Technology (ETH Zürich), ETH Zürich, Zurich, Switzerland
| | - Simone Oberhaensli
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Interfaculty Bioinformatics Unit, University of Bern, Bern, Switzerland
| | - Valérie Barbié
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Christophe Dessimoz
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Department of Genetics, Evolution and Environment, University College London, London, United Kingdom.,Department of Computer Science, University College London, London, United Kingdom
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Aitana Lebrand
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
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13
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Borisova O, Chaplin A, Gadua N, Pimenova A, Alexeeva I, Rakitsky G, Afanas'ev S, Donskikh E, Kafarskaya L. Characterization of the genotype and the phenotype of nontoxigenic strains of Corynebacterium diphtheriae subsp. lausannense isolated in Russian residents. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2020. [DOI: 10.24075/brsmu.2020.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In 2018, a few sequencing studies were published revealing the existence of two monophyletic clusters within the C. diphtheriae species, meaning that this species can be divided into two subspecies: C. diphtheriae subsp. diphtheriae and C. diphtheriae subsp. lausannense. The objective of our study was to describe the genotype and the phenotype of 2 nontoxigenic C. diphtheriae strains isolated in Russia in 2017–2018, which were classified by us as C. diphtheriae subsp. lausannense based on the aggregated data yielded by a variety of techniques, including microbiological and molecular genetic techniques, as well as a bioinformatic search for subspecies-specific genes in the publicly available genomes of C. diphtheriae. The isolated strains had morphological and biochemical characteristics of C. diphtheriae. The strains were assigned to the MLST type ST199 included in the clonal complex associated with subsp. lausannense. PCR revealed that both analyzed strains of C. diphtheriae subsp. lausannense carried the ptsI gene encoding phosphoenolpyruvate-protein phosphotransferase and did not carry the narG gene encoding the synthesis of nitrate reductase subunits, whereas the strains of C. diphtheriae subsp. diphtheriae had the narG gene and did not have ptsI. We experimentally proved the ability of lausannense strains to ferment N-acetylglucosamine. Our findings expand the knowledge of the biological diversity of C. diphtheriae and indicate the need for estimating the spread of these microorganisms in Russia, as well as their pathogenic potential.
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Affiliation(s)
- O.Yu. Borisova
- G. N. Gabrichevsky Research Institute for Epidemiology and Microbiology, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
| | - A.V. Chaplin
- G. N. Gabrichevsky Research Institute for Epidemiology and Microbiology, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
| | - N.T. Gadua
- G. N. Gabrichevsky Research Institute for Epidemiology and Microbiology, Moscow, Russia
| | - A.S. Pimenova
- G. N. Gabrichevsky Research Institute for Epidemiology and Microbiology, Moscow, Russia
| | - I.N. Alexeeva
- Regional Clinical Psychiatric Hospital, Khabarovsk, Russia
| | - G.F. Rakitsky
- Regional Clinical Psychiatric Hospital, Khabarovsk, Russia
| | - S.S. Afanas'ev
- G. N. Gabrichevsky Research Institute for Epidemiology and Microbiology, Moscow, Russia
| | - E.E. Donskikh
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - L.I. Kafarskaya
- Pirogov Russian National Research Medical University, Moscow, Russia
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14
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Corynebacterium rouxii sp. nov., a novel member of the diphtheriae species complex. Res Microbiol 2020; 171:122-127. [PMID: 32119905 DOI: 10.1016/j.resmic.2020.02.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 12/18/2022]
Abstract
A group of six clinical isolates previously identified as Corynebacterium diphtheriae biovar Belfanti, isolated from human cutaneous or peritoneum infections and from one dog, were characterized by genomic sequencing, biochemical analysis and MALDI-TOF mass spectrometry. The six isolates were negative for the diphtheria toxin gene. Phylogenetic analyses showed that the six isolates (including FRC0190T) are clearly demarcated from C. diphtheriae, Corynebacterium belfantii, Corynebacterium ulcerans and Corynebacterium pseudotuberculosis. The average nucleotide identity of FRC0190T with C. diphtheriae NCTC11397T was 92.6%, and was 91.8% with C. belfantii FRC0043T. C. diphtheriae subsp. lausannense strain CHUV2995T appeared to be a later heterotypic synonym of C. belfantii (ANI, 99.3%). Phenotyping data revealed an atypical negative or heterogeneous intermediate maltose fermentation reaction for the six isolates. MALDI-TOF mass spectrometry differentiated the new group from the other Corynebacterium taxa by the presence of specific spectral peaks. rpoB sequences showed identity to atypical, maltose-negative C. diphtheriae biovar Belfanti isolates previously described from two cats in the USA. We propose the name Corynebacterium rouxii sp. nov. for the novel group, with FRC0190T (= CIP 111752T = DSM 110354T) as type strain.
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15
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Rau J, Eisenberg T, Peters M, Berger A, Kutzer P, Lassnig H, Hotzel H, Sing A, Sting R, Contzen M. Reliable differentiation of a non-toxigenic tox gene-bearing Corynebacterium ulcerans variant frequently isolated from game animals using MALDI-TOF MS. Vet Microbiol 2019; 237:108399. [PMID: 31585651 DOI: 10.1016/j.vetmic.2019.108399] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/25/2019] [Accepted: 08/22/2019] [Indexed: 01/18/2023]
Abstract
Corynebacterium (C.) ulcerans is a zoonotic member of the C. diphtheriae group and is known to cause abscesses in humans and several animal species. Toxigenic strains, expressing the tox gene encoding diphtheria toxin, are also able to cause diphtheria in humans. In recent years, a non-toxigenic but tox gene-bearing (NTTB) variant of C. ulcerans has been identified that was frequently isolated from clinically healthy as well as from diseased wildlife animals, especially wild boars (Sus scrofa scrofa) in Germany and Austria. The described clinical cases showed similar signs of disease and the isolated corynebacteria displayed common genetic features as well as similar spectroscopic characteristics, therefore being assigned to a so called wild boar cluster (WBC). This study describes the establishment and validation of a method using MALDI-TOF mass spectrometry for a reliable differentiation between various members of the C. diphtheriae group at species level as well as a reliable sub-level identification of C. ulcerans isolates of the WBC variant. For this study 93 C. ulcerans isolates from wildlife animals, 41 C. ulcerans isolates from other animals and humans, and 53 isolates from further representatives of the C. diphtheriae group, as well as 26 non-diphtheriae group Corynebacteria collected via the MALDI user platform from seven MALDI users were used. By assigning 86 C. ulcerans isolates to the WBC the extensive geographical distribution of this previously less noticed variant in two Central European countries could be shown.
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Affiliation(s)
- Jörg Rau
- Chemisches und Veterinäruntersuchungsamt Stuttgart (CVUAS), Schaflandstr. 3/2, 70367 Fellbach, Germany.
| | - Tobias Eisenberg
- Landesbetrieb Hessisches Landeslabor (LHL), Schubertstr. 60 - Haus 13, 35392 Gießen, Germany.
| | - Martin Peters
- Chemisches und Veterinäruntersuchungsamt Westfalen, Zur Taubeneiche 10-12, 59821 Arnsberg, Germany.
| | - Anja Berger
- National Consiliar Laboratory on Diphtheria, Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), Veterinärstr. 2, 85764 Oberschleißheim, Germany.
| | - Peter Kutzer
- Landeslabor Berlin-Brandenburg (LLBB), Gerhard-Neumann-Str. 2, 15236 Frankfurt (Oder), Germany.
| | - Heimo Lassnig
- Österreichische Agentur für Gesundheit und Ernährungssicherheit GmbH (AGES), Beethovenstr. 6, 8010 Graz, Austria.
| | - Helmut Hotzel
- Friedrich-Loeffler-Institut (FLI), Naumburger Str. 96a, 07743 Jena, Germany.
| | - Andreas Sing
- National Consiliar Laboratory on Diphtheria, Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), Veterinärstr. 2, 85764 Oberschleißheim, Germany.
| | - Reinhard Sting
- Chemisches und Veterinäruntersuchungsamt Stuttgart (CVUAS), Schaflandstr. 3/2, 70367 Fellbach, Germany; Consiliar Laboratory for Corynebacterium pseudotuberculosis (DVG).
| | - Matthias Contzen
- Chemisches und Veterinäruntersuchungsamt Stuttgart (CVUAS), Schaflandstr. 3/2, 70367 Fellbach, Germany.
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16
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Seth-Smith HMB, Egli A. Whole Genome Sequencing for Surveillance of Diphtheria in Low Incidence Settings. Front Public Health 2019; 7:235. [PMID: 31497588 PMCID: PMC6713046 DOI: 10.3389/fpubh.2019.00235] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/06/2019] [Indexed: 12/29/2022] Open
Abstract
Corynebacterium diphtheriae (C. diphtheriae) is a relatively rare pathogen in most Western countries. While toxin producing strains can cause pharyngeal diphtheria with potentially fatal outcomes, the more common presentation is wound infections. The diphtheria toxin is encoded on a prophage and can also be carried by Corynebacterium ulcerans and Corynebacterium pseudotuberculosis. Currently, across Europe, infections are mainly diagnosed in travelers and refugees from regions where diphtheria is more endemic, patients from urban areas with poor hygiene, and intravenous drug users. About half of the cases are non-toxin producing isolates. Rapid identification of the bacterial pathogen and toxin production is a critical element of patient and outbreak management. Beside the immediate clinical management of the patient, public health agencies should be informed of toxigenic C. diphtheriae diagnoses as soon as possible. The collection of case-related epidemiological data from the patient is often challenging due to language barriers and social circumstances. However, information on patient contacts, vaccine status and travel/refugee route, where appropriate, is critical, and should be documented. In addition, isolates should be characterized using high resolution typing, in order to identify transmissions and outbreaks. In recent years, whole genome sequencing (WGS) has become the gold standard of high-resolution typing methods, allowing detailed investigations of pathogen transmissions. De-centralized sequencing strategies with redundancy in sequencing capacities, followed by data exchange may be a valuable future option, especially since WGS becomes more available and portable. In this context, the sharing of sequence data, using public available platforms, is essential. A close interaction between microbiology laboratories, treating physicians, refugee centers, social workers, and public health officials is a key element in successful management of suspected outbreaks. Analyzing bacterial isolates at reference centers may further help to provide more specialized microbiological techniques and to standardize information, but this is also more time consuming during an outbreak. Centralized communication strategies between public health agencies and laboratories helps considerably in establishing and coordinating effective surveillance and infection control. We review the current literature on high-resolution typing of C. diphtheriae and share our own experience with the coordination of a Swiss-German outbreak.
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Affiliation(s)
- Helena M B Seth-Smith
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Adrian Egli
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
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17
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Carriage of a Single Strain of Nontoxigenic Corynebacterium diphtheriae bv. Belfanti ( Corynebacterium belfantii) in Four Patients with Cystic Fibrosis. J Clin Microbiol 2019; 57:JCM.00042-19. [PMID: 30814269 DOI: 10.1128/jcm.00042-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 02/17/2019] [Indexed: 12/16/2022] Open
Abstract
Cystic fibrosis (CF) patients are commonly colonized by bacterial pathogens, which can induce persistent lung inflammation and may contribute to clinical deterioration. Colonization of CF patients and cross-transmission by Corynebacterium diphtheriae have not been reported so far. The aim of this article was to investigate the possibility of a cross-transmission of C. diphtheriae biovar Belfanti between four patients of a CF center. C. diphtheriae biovar Belfanti (now formally called C. belfantii) isolates were collected from four patients in a single CF care center over a period of 6 years and analyzed by microbiological methods and whole-genome sequencing. Epidemiological links among patients were investigated. Ten isolates were collected from 4 patients. Whole-genome sequencing of one isolate from each patient showed that a single strain was shared among them. In addition, one patient was found to have the same strain in two consecutive samplings performed 9 months apart. The strain was nontoxigenic and was susceptible to most antimicrobial agents. Ciprofloxacin resistance was observed in one patient. The idea of transmission of the strain among patients was supported by the occurrence of same-day visits to the CF center. This study demonstrated colonization of CF patients by C. diphtheriae biovar Belfanti (C. belfantii), and the data suggest persistence and transmission of a unique strain during at least 6 years in a single CF patient care center.
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18
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Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2019; 69:5-9. [PMID: 30614438 DOI: 10.1099/ijsem.0.003174] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- Aharon Oren
- 1The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- 2Department of Microbiology and Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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19
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Ustinova VV, Smirnova TG, Sochivko DG, Varlamov DA, Larionova EE, Andreevskaya SN, Andrievskaya IY, Kiseleva EA, Chernousova LN, Ergeshov A. New assay to diagnose and differentiate between Mycobacterium tuberculosis complex and nontuberculous mycobacteria. Tuberculosis (Edinb) 2018; 114:17-23. [PMID: 30711153 DOI: 10.1016/j.tube.2018.10.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 10/02/2018] [Accepted: 10/07/2018] [Indexed: 11/29/2022]
Abstract
The purpose of the present study was to create a real-time PCR test system allowing simultaneous detection of nontuberculous mycobacteria (NTM) and Mycobacterium tuberculosis complex (MTBC) both in culture and sputum. NTM cultures (18 strains, 18 species), MTBC cultures (16 strains, 2 species) and non-mycobacterial microorganisms from the collection of the Central Research TB Institute (CTRI) were used for the preliminary evaluation of the test system. 301 NTM cultures from patients with mycobacteriosis were used to assess the sensitivity of the developed test system. Clinical respiratory samples (sputum) from 104 patients with mycobacteriosis, 3627 patients with tuberculosis and 118 patients with other lung diseases were used for diagnostic sensitivity and specificity testing. The specificity and sensitivity of the assay for MTBC was found to be 100% both in culture and sputum samples; for NTM, the specificity was 100% in culture and sputum, the sensitivity reached 100% in culture and 73.1% in sputum samples. Positive predictive value (PPV) and negative predictive value (NPV) of the assay for culture were both 100%, for clinical material 100% and 80.8%, respectively. The limit of detection at the probability of detection 95% (LoD95%) was estimated to be 16 cfu/ml for M. tuberculosis H37RV and 1200 cfu/ml for M. avium.
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Affiliation(s)
- Vera V Ustinova
- Microbiology Department, Central Tuberculosis Research Institute RAMS, Moscow, Russia.
| | - Tatiana G Smirnova
- Microbiology Department, Central Tuberculosis Research Institute RAMS, Moscow, Russia
| | | | - Dmitry A Varlamov
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Elena E Larionova
- Microbiology Department, Central Tuberculosis Research Institute RAMS, Moscow, Russia
| | - Sofya N Andreevskaya
- Microbiology Department, Central Tuberculosis Research Institute RAMS, Moscow, Russia
| | - Irina Yu Andrievskaya
- Microbiology Department, Central Tuberculosis Research Institute RAMS, Moscow, Russia
| | - Ekaterina A Kiseleva
- Microbiology Department, Central Tuberculosis Research Institute RAMS, Moscow, Russia
| | - Larisa N Chernousova
- Microbiology Department, Central Tuberculosis Research Institute RAMS, Moscow, Russia
| | - Atadzhan Ergeshov
- Microbiology Department, Central Tuberculosis Research Institute RAMS, Moscow, Russia
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