Strain identifier

BacDive ID: 4326

Type strain: No

Species: Citrobacter freundii

Strain Designation: LRA 117.03.76

Strain history: CIP <- 1992, R. Mercier, bioMérieux, La Balme les Grottes, France: strain LRA 117.03.76 <- Mandrin, Saint Eloi Hosp., Montpellier, France

NCBI tax ID(s): 546 (species)

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General

@ref: 17656

BacDive-ID: 4326

DSM-Number: 24397

keywords: genome sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Citrobacter freundii LRA 117.03.76 is an aerobe, mesophilic, Gram-negative bacterium of the family Enterobacteriaceae.

NCBI tax id

  • NCBI tax id: 546
  • Matching level: species

strain history

@refhistory
17656<- LMG; LMG 21265 <- ATCC; ATCC 43864 <- bioMerieux;
119458CIP <- 1992, R. Mercier, bioMérieux, La Balme les Grottes, France: strain LRA 117.03.76 <- Mandrin, Saint Eloi Hosp., Montpellier, France

doi: 10.13145/bacdive4326.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Citrobacter
  • species: Citrobacter freundii
  • full scientific name: Citrobacter freundii (Braak 1928) Werkman and Gillen 1932 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Bethesda ballerupensis
    20215Bacterium freundii

@ref: 17656

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Citrobacter

species: Citrobacter freundii

full scientific name: Citrobacter freundii (Braak 1928) Werkman and Gillen 1932

strain designation: LRA 117.03.76

type strain: no

Morphology

cell morphology

  • @ref: 119458
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17656TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
41707MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
17656COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
119458CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
119458CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
17656positivegrowth37mesophilic
41707positivegrowth30mesophilic
60027positivegrowth30mesophilic
119458positivegrowth10-41
119458nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
60027aerobe
119458facultative anaerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836830849L-arabinose+fermentation
6836828053melibiose+fermentation
6836817992sucrose+fermentation
6836862345L-rhamnose+fermentation
6836830911sorbitol+fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
11945816947citrate+carbon source
11945817632nitrate+reduction
11945816301nitrite+reduction
11945815792malonate-assimilation
6837418257ornithine-degradation
6837429016arginine-hydrolysis
6837425094lysine-degradation
6837416199urea-hydrolysis
6837418403L-arabitol-builds acid from
6837418024D-galacturonic acid+builds acid from
68374Potassium 5-ketogluconate+builds acid from
6837416899D-mannitol+builds acid from
6837417306maltose+builds acid from
6837415963ribitol-builds acid from
6837418394palatinose-builds acid from
6837415792malonate-assimilation
6837427897tryptophan-energy source
6837417634D-glucose+builds acid from
6837417992sucrose+builds acid from
6837430849L-arabinose+builds acid from
6837418333D-arabitol-builds acid from
6837427082trehalose+builds acid from
6837462345L-rhamnose+builds acid from
6837417268myo-inositol+builds acid from
6837417057cellobiose-builds acid from
6837430911sorbitol+builds acid from

antibiotic resistance

  • @ref: 119458
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6837435581indoleno
6836835581indoleno
6836816136hydrogen sulfideyes
11945835581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6837435581indole-
6836835581indole-
11945815688acetoin-
11945817234glucose+

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
68374L-aspartate arylamidase+3.4.11.21
68374alpha-maltosidase-
68374alpha-galactosidase+3.2.1.22
68374alpha-glucosidase-3.2.1.20
68374beta-galactosidase+3.2.1.23
68374N-acetyl-beta-glucosaminidase-3.2.1.52
68374beta-glucuronidase-3.2.1.31
68374beta-glucosidase+3.2.1.21
68374lipase-
68374urease-3.5.1.5
68374lysine decarboxylase-4.1.1.18
68374arginine dihydrolase-3.5.3.6
68374ornithine decarboxylase-4.1.1.17
68368cytochrome oxidase-1.9.3.1
68368gelatinase-
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368beta-galactosidase+3.2.1.23
119458oxidase-
119458beta-galactosidase+3.2.1.23
119458alcohol dehydrogenase-1.1.1.1
119458gelatinase-
119458catalase+1.11.1.6
119458lysine decarboxylase-4.1.1.18
119458ornithine decarboxylase-4.1.1.17
119458urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    60027C12:04.312
    60027C13:00.713
    60027C14:08.414
    60027C15:04.115
    60027C16:023.416
    60027C17:01.217
    60027C13:0 3OH/C15:1 i I/H114.469
    60027C14:0 3OH/C16:1 ISO I7.915.485
    60027C16:1 ω7c29.215.819
    60027C17:0 CYCLO316.888
    60027C18:1 ω7c /12t/9t16.917.824
  • 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
119458--------------------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
17656+---++-----+++++++-+-
17656+---++-+-+-+++/-++++-+-
17656++--++---+-+++++++++-
17656++--++---+-+++++++++-

API ID32E

@refODCADH ArgLDC LysURELARLGAT5KGLIPRPbeta GLUMANMALADOPLEbeta GURMNTINDbeta NAGbeta GALGLUSACLARADARLalpha GLUalpha GALTRERHAINOCELSORalphaMALAspA
60027-----++-++++------++++--++++-+-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119458---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refgeographic locationcountryorigin.countrycontinentsample typeisolation date
41707MontpellierFranceFRAEurope
60027MontpellierFranceFRAEuropeHuman clinical isolate
119458MontpellierFranceFRAEurope1976

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Infection#Patient
#Infection#Medical environment#Clinic
#Infection#Patient#Specimen

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
176562Risk group (German classification)
1194581Risk group (French classification)

Sequence information

Genome sequences

  • @ref: 66792
  • description: Citrobacter freundii strain ATCC 43864
  • accession: 546.359
  • assembly level: plasmid
  • database: patric
  • NCBI tax ID: 546

External links

@ref: 17656

culture collection no.: CCUG 53829, CCM 7187, CIP 103547, DSM 24397, ATCC 43864, LMG 21265, WDCM 00006, CECT 7464, NCTC 13639

straininfo link

  • @ref: 73818
  • straininfo: 42090

literature

  • topic: Pathogenicity
  • Pubmed-ID: 23529729
  • title: Characterization of qnrB-like genes in Citrobacter species of the American Type Culture Collection.
  • authors: Saga T, Sabtcheva S, Mitsutake K, Ishii Y, Tateda K, Yamaguchi K, Kaku M
  • journal: Antimicrob Agents Chemother
  • DOI: 10.1128/AAC.02396-12
  • year: 2013
  • mesh: Anti-Bacterial Agents/*pharmacology, Bacterial Proteins/genetics, Citrobacter/*classification/*drug effects/genetics, Drug Resistance, Bacterial/*genetics, *Genes, Bacterial, Humans, Molecular Sequence Data, Plasmids/genetics, Quinolones/*pharmacology, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
17656Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24397)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24397
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
41707Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15357
60027Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53829)https://www.ccug.se/strain?id=53829
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)
68368Automatically annotated from API 20E
68374Automatically annotated from API ID32E
68382Automatically annotated from API zym
73818Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42090.1StrainInfo: A central database for resolving microbial strain identifiers
119458Curators of the CIPCollection of Institut Pasteur (CIP 103547)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103547