Strain identifier
BacDive ID: 138208
Type strain:
Species: Haemophilus ducreyi
Strain Designation: X2, 379
Strain history: CIP <- 1954, P. Kirsche, Inst. Pasteur, Hanoi, Vietnam: strain X2 <- H.K. Killian: strain 379
NCBI tax ID(s): 730 (species)
General
@ref: 39281
BacDive-ID: 138208
DSM-Number: 8925
keywords: genome sequence, Bacteria, microaerophile, mesophilic, Gram-negative, rod-shaped
description: Haemophilus ducreyi X2 is a microaerophile, mesophilic, Gram-negative bacterium of the family Pasteurellaceae.
NCBI tax id
- NCBI tax id: 730
- Matching level: species
strain history
- @ref: 39281
- history: CIP <- 1954, P. Kirsche, Inst. Pasteur, Hanoi, Vietnam: strain X2 <- H.K. Killian: strain 379
doi: 10.13145/bacdive138208.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Pasteurellales
- family: Pasteurellaceae
- genus: Haemophilus
- species: Haemophilus ducreyi
- full scientific name: Haemophilus ducreyi (Neveu-Lemaire 1921) Bergey et al. 1923 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Coccobacillus ducreyi
@ref: 39281
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pasteurellales
family: Pasteurellaceae
genus: Haemophilus
species: Haemophilus ducreyi
strain designation: X2, 379
type strain: yes
Morphology
cell morphology
- @ref: 39281
- gram stain: negative
- cell shape: rod-shaped
- motility: no
colony morphology
@ref | incubation period |
---|---|
44749 | 2 days |
39281 |
Culture and growth conditions
culture medium
@ref | name | growth | composition | link |
---|---|---|---|---|
39281 | MEDIUM 10 - Chocolate medium for Actinobacillus pleuropneumoniae, Capnocytophaga cynodegmi, Haemophilus and Neisseria | yes | Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml);PolyVitex mischung (10.000 ml) | |
39281 | CIP Medium 10 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=10 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
39281 | positive | growth | 30 | mesophilic |
44749 | positive | growth | 33 | mesophilic |
39281 | positive | growth | 25-30 | mesophilic |
39281 | no | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 44749
- oxygen tolerance: microaerophile
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
39281 | 4853 | esculin | - | hydrolysis |
39281 | 606565 | hippurate | - | hydrolysis |
39281 | 17632 | nitrate | + | reduction |
39281 | 16301 | nitrite | - | reduction |
68377 | 17634 | D-glucose | - | builds acid from |
68377 | 15824 | D-fructose | - | builds acid from |
68377 | 17306 | maltose | - | builds acid from |
68377 | 17992 | sucrose | - | builds acid from |
68377 | 18257 | ornithine | - | degradation |
68377 | 16199 | urea | - | hydrolysis |
68377 | 27897 | tryptophan | - | energy source |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68377 | 35581 | indole | no |
39281 | 35581 | indole | no |
metabolite tests
- @ref: 68377
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
68377 | tryptophan deaminase | - | 4.1.99.1 |
68377 | gamma-glutamyltransferase | - | 2.3.2.2 |
68377 | proline-arylamidase | - | 3.4.11.5 |
68377 | beta-galactosidase | - | 3.2.1.23 |
68377 | alkaline phosphatase | + | 3.1.3.1 |
68377 | lipase | - | |
68377 | urease | - | 3.5.1.5 |
68377 | ornithine decarboxylase | - | 4.1.1.17 |
68377 | beta-lactamase | - | 3.5.2.6 |
39281 | oxidase | + | |
39281 | beta-galactosidase | - | 3.2.1.23 |
39281 | alcohol dehydrogenase | - | 1.1.1.1 |
39281 | catalase | + | 1.11.1.6 |
39281 | gamma-glutamyltransferase | - | 2.3.2.2 |
39281 | lysine decarboxylase | - | 4.1.1.18 |
39281 | ornithine decarboxylase | - | 4.1.1.17 |
39281 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | - | |
68382 | esterase lipase (C 8) | - | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
fatty acid profile
fatty acids
@ref fatty acid percentage ECL 44749 C12:0 0.4 12 44749 C14:0 18.8 14 44749 C16:0 23.8 16 44749 C18:0 4.7 18 44749 C12:0 ALDE ? 1.8 10.915 44749 C13:0 ISO 2OH 0.3 13.814 44749 C14:0 3OH/C16:1 ISO I 6.2 15.485 44749 C16:1 ω7c 22.7 15.819 44749 C18:1 ω9c 9.9 17.769 44749 C18:2 ω6,9c/C18:0 ANTE 10.9 17.724 44749 unknown 14.503 0.6 14.503 - type of FA analysis: whole cell analysis
- method/protocol: CCUG
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
39281 | - | + | - | - | - | + | - | - | - | - | + | + | - | - | - | - | - | - | - | - |
API NH
@ref | PEN | GLU | FRU | MAL | SAC | ODC | URE | LIP | PAL | beta GAL | ProA | GGT | IND |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
44749 | - | - | - | - | - | - | - | - | + | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | geographic location | country | origin.country | continent | sample type | sampling date | isolation date |
---|---|---|---|---|---|---|---|
39281 | Hanoi | Vietnam | VNM | Asia | |||
44749 | Hanoï | Vietnam | VNM | Asia | Human chancroid | 1954 | |
39281 | Hanoi | Vietnam | VNM | Asia | Human, Chancroid | 1954 |
isolation source categories
Cat1 | Cat2 |
---|---|
#Host | #Human |
#Infection | #Disease |
#Infection | #Patient |
Safety information
risk assessment
- @ref: 39281
- biosafety level: 2
- biosafety level comment: Risk group (French classification)
Sequence information
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | [Haemophilus] ducreyi CIP 54.2 | GCA_001043455 | chromosome | ncbi | 730 |
66792 | [Haemophilus] ducreyi CCUG 4438 | GCA_002015155 | scaffold | ncbi | 730 |
66792 | [Haemophilus] ducreyi ATCC 33940 | GCA_900109315 | contig | ncbi | 730 |
66792 | [Haemophilus] ducreyi strain ATCC 33940 | 730.36 | wgs | patric | 730 |
66792 | [Haemophilus] ducreyi strain CCUG 4438 | 730.53 | wgs | patric | 730 |
66792 | Haemophilus ducreyi ATCC 33940 | 2597490374 | draft | img | 730 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 90.367 | no |
flagellated | no | 97.638 | no |
gram-positive | no | 98.95 | no |
anaerobic | no | 93.884 | no |
aerobic | no | 97.203 | no |
halophile | yes | 56.245 | no |
spore-forming | no | 98.689 | no |
thermophile | no | 97.075 | yes |
glucose-util | no | 64.25 | no |
glucose-ferment | no | 56.033 | no |
External links
@ref: 39281
culture collection no.: CIP 54.2, ATCC 33940, CCUG 4438, DSM 8925, NCTC 10945, CIP 542
straininfo link
- @ref: 94981
- straininfo: 46305
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Cultivation | 1625315 | Cytopathic effect of Haemophilus ducreyi for human foreskin cell culture. | Alfa MJ | J Med Microbiol | 10.1099/00222615-37-1-43 | 1992 | Bacterial Adhesion, Carcinoma, Cell Line, Culture Media, Fibroblasts/*microbiology, Haemophilus ducreyi/growth & development/*pathogenicity/ultrastructure, Haemophilus influenzae/growth & development/physiology, Humans, Lung Neoplasms, Male, Microscopy, Electron, Penis/cytology, Skin/cytology, Tumor Cells, Cultured | Pathogenicity |
Pathogenicity | 3517183 | Use of dot-immunobinding and immunofluorescence assays to investigate clinically suspected cases of chancroid. | Schalla WO, Sanders LL, Schmid GP, Tam MR, Morse SA | J Infect Dis | 10.1093/infdis/153.5.879 | 1986 | Antibodies, Bacterial/*analysis, Antibodies, Monoclonal, Bacterial Outer Membrane Proteins/immunology, Chancroid/*diagnosis/epidemiology/microbiology, Disease Outbreaks, Female, Fluorescent Antibody Technique, Haemophilus/immunology, Haemophilus ducreyi/*immunology/isolation & purification, Haemophilus influenzae/immunology, Humans, Immunoenzyme Techniques, Immunoglobulin G/analysis, Immunoglobulin M/analysis, Male | Enzymology |
Pathogenicity | 7817258 | Characterization of the cytopathic effect of Haemophilus ducreyi. | Hollyer TT, DeGagne PA, Alfa MJ | Sex Transm Dis | 10.1097/00007435-199409000-00002 | 1994 | Bacterial Adhesion, Biological Assay, Cell Line, Cells, Cultured, Evaluation Studies as Topic, Exotoxins/*metabolism, Fibroblasts/*microbiology, Haemophilus ducreyi/classification/*pathogenicity/physiology, Humans, Indicators and Reagents, Male, Penis/cytology, Serotyping, Tetrazolium Salts | Metabolism |
Pathogenicity | 8440935 | In vitro model of Haemophilus ducreyi adherence to and entry into eukaryotic cells of genital origin. | Lammel CJ, Dekker NP, Palefsky J, Brooks GF | J Infect Dis | 10.1093/infdis/167.3.642 | 1993 | Adenocarcinoma/microbiology, Bacterial Adhesion/*physiology, Cell Line, Chancroid/*microbiology, Endometrial Neoplasms/microbiology, Escherichia coli/pathogenicity, Female, Haemophilus ducreyi/*pathogenicity/ultrastructure, HeLa Cells, Humans, Male, Microscopy, Electron, Scanning, Models, Biological, Time Factors, Tumor Cells, Cultured, Virulence | |
Enzymology | 8828227 | Organization of the Haemophilus ducreyi 35000 chromosome. | Hobbs MM, Leonardi MJ, Zaretzky FR, Wang TH, Kawula TH | Microbiology (Reading) | 10.1099/00221287-142-9-2587 | 1996 | Blotting, Southern, *Chromosome Mapping, Cloning, Molecular, Electrophoresis, Gel, Pulsed-Field, Genome, Haemophilus ducreyi/*genetics, Haemophilus influenzae/genetics, Operon, Polymorphism, Restriction Fragment Length | Genetics |
9234768 | Structurally defined epitopes of Haemophilus ducreyi lipooligosaccharides recognized by monoclonal antibodies. | Ahmed HJ, Frisk A, Mansson JE, Schweda EK, Lagergard T | Infect Immun | 10.1128/iai.65.8.3151-3158.1997 | 1997 | Animals, Antibodies, Monoclonal/*immunology, Enzyme-Linked Immunosorbent Assay, *Epitopes, Haemophilus ducreyi/*immunology, Immune Sera/immunology, Immunoblotting, Lipopolysaccharides/*immunology, Neuraminidase/pharmacology, Rabbits | ||
Pathogenicity | 9756778 | Haemophilus ducreyi is susceptible to protegrin. | Fortney K, Totten PA, Lehrer RI, Spinola SM | Antimicrob Agents Chemother | 10.1128/AAC.42.10.2690 | 1998 | Anti-Bacterial Agents, Anti-Infective Agents/*pharmacology, Antimicrobial Cationic Peptides, Diffusion, Dose-Response Relationship, Drug, Haemophilus ducreyi/*drug effects, Humans, Microbial Sensitivity Tests, Proteins/*pharmacology | |
Pathogenicity | 11339253 | The effect of temperature on the interaction of Haemophilus ducreyi with human epithelial cells. | Makakole SC, Sturm AW | J Med Microbiol | 10.1099/0022-1317-50-5-449 | 2001 | *Bacterial Adhesion, Cell Line, Haemophilus ducreyi/cytology/*physiology/ultrastructure, Humans, Keratinocytes/cytology/*microbiology/ultrastructure, Kinetics, Microscopy, Electron, Species Specificity, Temperature, Time Factors | Enzymology |
Metabolism | 11517937 | Neutrophil degranulation induced by Haemophilus ducreyi. | Odhav B, Hoosen A, Sturm W | Biol Chem | 10.1515/BC.2001.100 | 2001 | Cathepsin D/analysis/metabolism, Coculture Techniques, Cytoplasmic Granules/enzymology/metabolism/*pathology, Haemophilus ducreyi/*pathogenicity, HeLa Cells, Humans, Microscopy, Confocal, Microscopy, Electron, Muramidase/analysis/metabolism, Necrosis, Neutrophils/*microbiology/pathology/ultrastructure, Peroxidase/analysis/metabolism | Pathogenicity |
Pathogenicity | 15784585 | Haemophilus ducreyi Outer membrane determinants, including DsrA, define two clonal populations. | White CD, Leduc I, Olsen B, Jeter C, Harris C, Elkins C | Infect Immun | 10.1128/IAI.73.4.2387-2399.2005 | 2005 | Amino Acid Sequence, Bacterial Outer Membrane Proteins/chemistry/genetics/*physiology, Blood Bactericidal Activity, Haemophilus ducreyi/classification/*immunology, Humans, Lipopolysaccharides/analysis, Molecular Sequence Data | Genetics |
Metabolism | 16552053 | Immunization with the Haemophilus ducreyi hemoglobin receptor HgbA protects against infection in the swine model of chancroid. | Afonina G, Leduc I, Nepluev I, Jeter C, Routh P, Almond G, Orndorff PE, Hobbs M, Elkins C | Infect Immun | 10.1128/IAI.74.4.2224-2232.2006 | 2006 | Animals, Antibodies, Bacterial/biosynthesis/blood/metabolism, Bacterial Proteins/administration & dosage/*immunology, Binding Sites, Antibody, Carrier Proteins/administration & dosage/*immunology, Chancroid/immunology/microbiology/pathology/*prevention & control, Disease Models, Animal, Haemophilus Vaccines/administration & dosage/*immunology, Haemophilus ducreyi/*immunology, Hemoglobins/*metabolism, Immunoglobulin G/metabolism/physiology, Protein Binding/immunology, *Swine |
Reference
@id | authors | title | doi/url | catalogue |
---|---|---|---|---|
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |
39281 | Curators of the CIP | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2054.2 | Collection of Institut Pasteur (CIP 54.2) | |
44749 | Curators of the CCUG | https://www.ccug.se/strain?id=4438 | Culture Collection University of Gothenburg (CCUG) (CCUG 4438) | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
68377 | Automatically annotated from API NH | |||
68382 | Automatically annotated from API zym | |||
94981 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID46305.1 |