Strain identifier

BacDive ID: 1778

Type strain: Yes

Species: Afipia felis

Strain Designation: B-91-007352, CSD1, CSD 1

Strain history: CIP <- 1992, ATCC <- Armed Forces Inst. Path.: strain CSD 1

NCBI tax ID(s): 883080 (strain), 1035 (species)

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General

@ref: 3001

BacDive-ID: 1778

DSM-Number: 7326

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, motile, human pathogen

description: Afipia felis B-91-007352 is an obligate aerobe, mesophilic, motile human pathogen that was isolated from human lymph node tissue.

NCBI tax id

NCBI tax idMatching level
1035species
883080strain

strain history

@refhistory
3001<- ATCC <- Armed Forces Institute of Pathology (cat scratch disease bacillus)
119298CIP <- 1992, ATCC <- Armed Forces Inst. Path.: strain CSD 1

doi: 10.13145/bacdive1778.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Nitrobacteraceae
  • genus: Afipia
  • species: Afipia felis
  • full scientific name: Afipia felis Brenner et al. 1992

@ref: 3001

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Nitrobacteraceae

genus: Afipia

species: Afipia felis

full scientific name: Afipia felis Brenner et al. 1992

strain designation: B-91-007352, CSD1, CSD 1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes94.664
6948099.999negative
119298yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3001BCYE-AGAR (DSMZ Medium 585)yeshttps://mediadive.dsmz.de/medium/585Name: BCYE AGAR (DSMZ Medium 585) Composition: OXOID Legionella CYE-Agar base
36858MEDIUM 23 - for Afipia and LegionellayesDistilled water make up to (1000.000 ml);Legionella agar (37.000 g);Legionella - enrichment mixture (10.000 ml)
119298CIP Medium 23yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=23

culture temp

@refgrowthtypetemperaturerange
3001positivegrowth30mesophilic
36858positivegrowth30mesophilic
50090positivegrowth37mesophilic
119298positivegrowth22-30
119298nogrowth37mesophilic
119298nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119298
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.991

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11929817632nitrate+reduction
11929816301nitrite-reduction
11929815792malonate-assimilation
11929817234glucose-degradation
11929817632nitrate-respiration

metabolite production

  • @ref: 119298
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
119298oxidase+
119298alcohol dehydrogenase-1.1.1.1
119298gelatinase-
119298catalase+1.11.1.6
119298lysine decarboxylase-4.1.1.18
119298ornithine decarboxylase-4.1.1.17
119298tryptophan deaminase-
119298urease+3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    50090C16:013.916
    50090C18:05.918
    5009011 methyl 18:1 ω7c8.118.081
    50090C16:1 ω7c5.715.819
    50090C17:0 CYCLO20.516.888
    50090C18:1 ω7c /12t/9t21.717.824
    50090C19:0 CYCLO ω8c24.118.9
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119298--++-+----+---------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
3001human lymph node tissueUSAUSAUSANorth America
50090Lymph node,patient with CSDWashington DCUSAUSANorth America1987
119298Human, Lymph node tissue

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Organ#Lymph node

taxonmaps

  • @ref: 69479
  • File name: preview.99_1530.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_297;97_329;98_1207;99_1530&stattab=map
  • Last taxonomy: Afipia
  • 16S sequence: HF970590
  • Sequence Identity:
  • Total samples: 807
  • soil counts: 269
  • aquatic counts: 275
  • animal counts: 203
  • plant counts: 60

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
3001yesyes2Risk group (German classification)
1192981Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Afipia felis ATCC 53690 strain B-91-007352 16S ribosomal RNA gene, partial sequenceM652481425ena883080
20218Afipia felis partial 16S rRNA gene, strain CIP 103515HF9705901411ena1035

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Afipia felis ATCC 53690GCA_000314735scaffoldncbi883080
66792Afipia felis ATCC 53690883080.3wgspatric883080
66792Afipia felis felis ATCC 536902537561903draftimg883080

GC content

  • @ref: 3001
  • GC-content: 62.5
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes75.881no
flagellatedno75.278no
gram-positiveno98.422no
anaerobicno97.856no
aerobicyes85.742no
halophileno95.496no
spore-formingno95.036no
thermophileno95.619yes
glucose-utilno50no
glucose-fermentno92.464no

External links

@ref: 3001

culture collection no.: DSM 7326, ATCC 53690, CCUG 30456, CIP 103515

straininfo link

  • @ref: 71425
  • straininfo: 12658

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Pathogenicity8991636Diagnostic value of the indirect immunofluorescence assay in cat scratch disease with Bartonella henselae and Afipia felis antigens.Amerein MP, De Briel D, Jaulhac B, Meyer P, Monteil H, Piemont YClin Diagn Lab Immunol10.1128/cdli.3.2.200-204.19961996Adult, Antibodies, Bacterial/biosynthesis/blood, Antigens, Bacterial/*immunology, Bartonella henselae/*immunology/isolation & purification, Cat-Scratch Disease/*diagnosis/immunology/microbiology, Female, Fluorescent Antibody Technique, Indirect, Humans, Male, Middle Aged, Predictive Value of Tests, Sensitivity and SpecificityEnzymology
Enzymology9137514Production and characterization of mouse monoclonal antibodies against Afipia felis.Engbaek K, Uttenthal LO, Koch CAPMIS10.1111/j.1699-0463.1997.tb00558.x1997Animals, *Antibodies, Bacterial/isolation & purification, *Antibodies, Monoclonal/isolation & purification, Antigens, Bacterial/*immunology, Cat-Scratch Disease/immunology/*microbiology, Electrophoresis, Polyacrylamide Gel, Female, Gram-Negative Bacteria/*immunology, Immunoglobulin G/classification/isolation & purification, Immunoglobulin M/classification/isolation & purification, Mice, Mice, Inbred BALB C, Molecular Weight, RabbitsPhylogeny
Phylogeny13130002Bosea minatitlanensis sp. nov., a strictly aerobic bacterium isolated from an anaerobic digester.Ouattara AS, Assih EA, Thierry S, Cayol JL, Labat M, Monroy O, Macarie HInt J Syst Evol Microbiol10.1099/ijs.0.02540-02003Aerobiosis, Bradyrhizobiaceae/classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Genes, Bacterial, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sewage/microbiology, Species SpecificityGenetics
Phylogeny15643932Isolation and properties of methanesulfonate-degrading Afipia felis from Antarctica and comparison with other strains of A. felis.Moosvi SA, Pacheco CC, McDonald IR, De Marco P, Pearce DA, Kelly DP, Wood APEnviron Microbiol10.1111/j.1462-2920.2004.00661.x2005Afipia/*classification/genetics/*isolation & purification/metabolism, Alcohol Oxidoreductases/genetics/metabolism, Antarctic Regions, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fresh Water/*microbiology, Genes, rRNA, Mesylates/*metabolism, Molecular Sequence Data, Oxygenases/genetics/metabolism, Phylogeny, Portugal, RNA, Ribosomal, 16S/genetics, Rivers/microbiology, Sequence Analysis, DNA, *Soil MicrobiologyMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3001Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7326)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7326
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
36858Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15321
50090Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 30456)https://www.ccug.se/strain?id=30456
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
71425Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID12658.1StrainInfo: A central database for resolving microbial strain identifiers
119298Curators of the CIPCollection of Institut Pasteur (CIP 103515)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103515