Strain identifier

BacDive ID: 4433

Type strain: No

Species: Escherichia coli

Strain Designation: Crooks, Crookes

Strain history: CIP <- 1953, NCIB <- ATCC <- I.C. Gunsalus, Cornell Univ., USA: strain Crookes

NCBI tax ID(s): 481805 (strain), 562 (species)

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General

@ref: 826

BacDive-ID: 4433

DSM-Number: 1576

keywords: genome sequence, Bacteria, facultative anaerobe, mesophilic, motile, antibiotic resistance, human pathogen

description: Escherichia coli Crooks is a facultative anaerobe, mesophilic, motile human pathogen that has multiple antibiotic resistances and was isolated from faeces.

NCBI tax id

NCBI tax idMatching level
481805strain
562species

strain history

@refhistory
826<- ATCC <- L.C. Gunsalus, strain Crooks <- G.C. Crooks
118679CIP <- 1953, NCIB <- ATCC <- I.C. Gunsalus, Cornell Univ., USA: strain Crookes

doi: 10.13145/bacdive4433.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Escherichia
  • species: Escherichia coli
  • full scientific name: Escherichia coli (Migula 1895) Castellani and Chalmers 1919 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Bacillus coli

@ref: 826

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Escherichia

species: Escherichia coli

full scientific name: Escherichia coli (Migula 1895) Castellani and Chalmers 1919

strain designation: Crooks, Crookes

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.163
6948099.975negative
118679yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
826NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
41827MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118679CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
826positivegrowth37mesophilic
41827positivegrowth30mesophilic
45377positivegrowth30-37mesophilic
118679positivegrowth30-41
118679nogrowth5psychrophilic
118679nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118679
  • oxygen tolerance: facultative anaerobe

antibiogram

@refmediumincubation temperatureincubation timeoxygen conditionPenicillin Goxacillinampicillinticarcillinmezlocillincefalotincefazolincefotaximeaztreonamimipenemtetracyclinechloramphenicolgentamycinamikacinvancomycinerythromycinlincomycinofloxacinnorfloxacincolistinpipemidic acidnitrofurantoinbacitracinpolymyxin bkanamycinneomycindoxycyclineceftriaxoneclindamycinfosfomycinmoxifloxacinlinezolidnystatinquinupristin/dalfopristinteicoplaninpiperacillin/tazobactam
826Mueller-Hinton Agar371aerob602030242026363432262824246100363614282401422-2420203203632600024-26
826Mueller-Hinton Agar802030222024-2636343226282226010-1203434122622-240142420203203832-34080024
826Mueller-Hinton Agar371aerob60203024202636343224282226010-1203636122822014242018-203403630-32680024
826Mueller-Hinton Agar37aerob6020302420-2226-2836363228-3028-3026260100363814-16282401622202234-3603836600026
826Mueller-Hinton Agar80203024-26222838383428302424-26010-120383814-163024-2601434202036038-4036000024-26
826Mueller-Hinton Agar37aerob602026-282218263232302626-2820-222461003432-34122620-220142218-20203003432-346-800022
826Mueller-Hinton Agar37aerob602026-282218263232302626-2820-222461003432-34122620-220142218-20203003432-346-800022
826Mueller Hinton30aerob8020-22322624284040322830-322422012040401630220162220223803636-38000026

spore formation

@refspore formationconfidence
69481no100
69480no99.657

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836830849L-arabinose+fermentation
6836828053melibiose+fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose+fermentation
6836830911sorbitol+fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan+energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine+degradation
11867929864mannitol+fermentation
11867916947citrate-carbon source
11867917234glucose+fermentation
11867917716lactose+fermentation
11867917632nitrate+reduction
11867916301nitrite+reduction
11867915792malonate-assimilation
118679132112sodium thiosulfate-builds gas from
11867917234glucose+degradation
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: 118679
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6837435581indoleyes
6836815688acetoinno
6836835581indoleyes
6836816136hydrogen sulfideno
11867935581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6837435581indole+
6836815688acetoin-
6836835581indole+
11867915688acetoin-
11867917234glucose+

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
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-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368beta-galactosidase+3.2.1.23
118679oxidase-
118679beta-galactosidase+3.2.1.23
118679alcohol dehydrogenase-1.1.1.1
118679gelatinase-
118679catalase+1.11.1.6
118679lysine decarboxylase+4.1.1.18
118679ornithine decarboxylase-4.1.1.17
118679tryptophan deaminase-
118679urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118679-+++++--++++-+++----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
826+-+-----+--++-++-+++
826+-+-----+--++-++-+++
826+-+-----+--++-++-+++-
826+-+-----+--++-++-+++-
826+++-----+--++-++-+-+-
826+-+-----+--++-++-+++-
826+-+-----+--++-++-+-+-

API ID32E

@refODCADH ArgLDC LysURELARLGAT5KGLIPRPbeta GLUMANMALADOPLEbeta GURMNTINDbeta NAGbeta GALGLUSACLARADARLalpha GLUalpha GALTRERHAINOCELSORalphaMALAspA
45377--+--+--++++--+-+-++-+--+++-----
45377--+--+--++++--+-+-++-+--+++---++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118679+++++-+-+++++++--+++++-++----+-+-+--+------+++-+++----+++--+++------++--+--++--++-+---+--++++++-+++

Isolation, sampling and environmental information

isolation

@refsample type
826faeces
45377Human feces
118679Human, Feces

isolation source categories

  • Cat1: #Host Body Product
  • Cat2: #Gastrointestinal tract
  • Cat3: #Feces (Stool)

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
826yesyes2Risk group (German classification)
1186791Risk group (French classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Escherichia coli ATCC 8739GCA_016864475completencbi481805
66792Escherichia coli ATCC 8739GCA_003591595completencbi481805
66792Escherichia coli ATCC 8739GCA_000019385completencbi481805
66792Escherichia coli NCTC12923GCA_900448245contigncbi562
66792Escherichia coli ATCC 8739GCA_001997065scaffoldncbi481805
66792Escherichia coli ATCC 8739481805.51completepatric481805
66792Escherichia coli ATCC 8739481805.6completepatric481805
66792Escherichia coli ATCC 8739 strain AgNO3 resistant481805.41completepatric481805
66792Escherichia coli strain ATCC 8739562.15132wgspatric562
66792Escherichia coli strain NCTC12923562.34149wgspatric562
66792Escherichia coli C ATCC 8739641522623completeimg481805
66792Escherichia coli ATCC 8739GCA_026016785completencbi481805

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno55.696no
gram-positiveno98.287no
anaerobicno94.63no
aerobicyes84.741no
halophileno90.038no
spore-formingno93.847no
thermophileno99.304yes
glucose-utilyes93.627no
motileyes89.562no
glucose-fermentyes93.923yes

External links

@ref: 826

culture collection no.: DSM 1576, ATCC 8739, NCIB 8545, WDCM 00012, CCUG 10979, CIP 53.126, NCTC 12923, CCM 4517, NCDO 904, NCIMB 8545, LMG 8063, CECT 516, IFO 3972, NBRC 3972, CMCC (B) 44102

straininfo link

  • @ref: 73923
  • straininfo: 92244

Reference

@idauthorscataloguedoi/urltitle
826Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1576)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1576
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
41827Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16667
45377Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 10979)https://www.ccug.se/strain?id=10979
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
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
73923Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92244.1StrainInfo: A central database for resolving microbial strain identifiers
118679Curators of the CIPCollection of Institut Pasteur (CIP 53.126)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2053.126