Workshop and Q&A October 6th

Strain identifier

BacDive ID: 4907

Type strain: Yes

Species: Escherichia coli

Strain Designation: U5/41

Strain history: ATCC <- NCTC <- F. Kauffmann, U5/41

NCBI tax ID(s): 866789 (strain), 562 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 9115

BacDive-ID: 4907

DSM-Number: 30083

keywords: human pathogen, antibiotic resistance, mesophilic, Bacteria, 16S sequence, genome sequence

description: Escherichia coli U5/41 is a mesophilic human pathogen that has multiple antibiotic resistances and was isolated from urine.

NCBI tax id

NCBI tax idMatching level
866789strain
562species

strain history

doi: 10.13145/bacdive4907.20220920.7

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: 9115

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: U5/41

type strain: yes

Morphology

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_30083_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_30083_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_30083_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_30083_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_30083_5.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_30083_6.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_30083_7.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9115NUTRIENT AGAR (DSMZ Medium 1)yeshttps://bacmedia.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
38566MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)

culture temp

@refgrowthtypetemperaturerange
9115positivegrowth37mesophilic
38566positivegrowth30mesophilic
67770positivegrowth37mesophilic
67772positiveoptimum37mesophilic

Physiology and metabolism

antibiogram

@refmediumincubation temperatureoxygen conditionPenicillin Goxacillinampicillinticarcillinmezlocillincefalotincefazolincefotaximeaztreonamimipenemtetracyclinechloramphenicolgentamycinamikacinvancomycinerythromycinlincomycinofloxacinnorfloxacincolistinpipemidic acidnitrofurantoinbacitracinpolymyxin bkanamycinneomycindoxycyclineceftriaxoneclindamycinfosfomycinmoxifloxacinlinezolidnystatinquinupristin/dalfopristinteicoplaninpiperacillin/tazobactamincubation time
9115Mueller-Hinton Agar37aerob00203026182634-363430-3226-2828-30222268-10032-3436-3814262401620182232030-3232-34000026
9115Mueller-Hinton Agar37aerob00203226182836363226302022-24810032-3440144024-2601420-2216-1820-223203234000026-281
9115Mueller-Hinton Agar0018-2030261826-28383634283022-242401003438142826014-1624202234028-3034000026
9115Mueller-Hinton Agar37aerob002030282028-3036-3836-383426-28262222010032-3438-4014-16302801622202234-3603232-340000281
9115Mueller-Hinton Agar370014221812182424222018-201414060222282216010161416n.d.n.d.n.d.n.d.n.d.n.d.n.d.n.d.n.d.
9115Mueller-Hinton Agar37aerob001828241824-263232302228202201003234-36142624014-162218203003032000024
9115Mueller-Hinton Agar37aerob001828241824-263232302228202201003234-36142624014-162218203003032000024

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate+builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose+builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose+builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose-builds acid from17992
68371melibiose+builds acid from28053
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371cellobiose-builds acid from17057
68371salicin+builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol+builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose+builds acid from62345
68371L-sorbose+builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose+builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
68368nitrate+reduction17632
68368L-arabinose+fermentation30849
68368amygdalin-fermentation27613
68368melibiose+fermentation28053
68368sucrose-fermentation17992
68368L-rhamnose+fermentation62345
68368sorbitol+fermentation30911
68368myo-inositol-fermentation17268
68368D-mannitol+fermentation16899
68368D-glucose+fermentation17634
68368gelatin-hydrolysis5291
68368tryptophan+energy source27897
68368urea-hydrolysis16199
68368citrate-assimilation16947
68368ornithine+degradation18257
68368arginine-hydrolysis29016

metabolite production

@refChebi-IDmetaboliteproduction
6836816301nitriteyes
6836815688acetoinno
6836835581indoleyes
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole+

enzymes

@refvalueactivityec
68368cytochrome oxidase-1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOXNO2
9115+-++----+--++-++-+-+-+
9115+-++----+--++-++-+-+
9115+-+/-+----+--++-++-+-+
9115+-++----+--++-++-+-+
9115+-++----+--++-++-+-+-
9115+-++----+--++-++-+-+-
9115+-++----+--++-++-+-+-
9115+-++----+--++-++-+-+-
9115+-++----+--++-++-+-+-
9115+-++----+--++-++-+-+-

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
9115-+-+++----++++++--++--+---+-+++-+------+--+-+--+--

Isolation, sampling and environmental information

isolation

@refsample typesampling date
9115urine
67770Urine
67772Urine1991

isolation source categories

  • Cat1: #Host Body Product
  • Cat2: #Fluids
  • Cat3: #Urine

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
9115yesyes2Risk group (German classification)
677722

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218E.coli (ATCC 11775T) gene for 16S rRNAX807251450ena866789
20218Escherichia coli strain DSM 30083 16S ribosomal RNA gene, partial sequenceHQ012019936ena866789
20218Escherichia coli gene for 16S ribosomal RNA, partial sequence, strain: JCM1649AB2429101110ena866789
20218Escherichia coli strain KCTC 2441 16S ribosomal RNA gene, partial sequenceEU0146891541ena562
20218Escherichia coli gene for 16S rRNA, partial sequence, strain: NBRC 102203AB6817281467ena562
67770Escherichia coli gene for 16S ribosomal RNA, partial sequence, strain: JCM 1649LC0690321464ena562

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Escherichia coli DSM 30083 = JCM 1649 = ATCC 11775 ATCC 11775GCA_003697165completencbi866789
66792Escherichia coli DSM 30083 = JCM 1649 = ATCC 11775 DSM 30083GCA_000690815contigncbi866789
66792Escherichia coli DSM 30083 = JCM 1649 = ATCC 11775 ATCC 11775GCA_000734955contigncbi866789
66792Escherichia coli NCTC9001GCA_900706755contigncbi562
66792Escherichia coli DSM 30083 = JCM 1649 = ATCC 11775 JCM 1649GCA_000613265contigncbi866789
66792Escherichia coli DSM 30083 = JCM 1649 = ATCC 11775866789.18completepatric866789
66792Escherichia coli DSM 30083 = JCM 1649 = ATCC 11775866789.7wgspatric866789
66792Escherichia coli DSM 30083 = JCM 1649 = ATCC 11775866789.6wgspatric866789
66792Escherichia coli DSM 30083 = JCM 1649 = ATCC 11775866789.5wgspatric866789
66792Escherichia coli strain NCTC9001562.7382completepatric562
66792Escherichia coli O1:K1:H7 U5/41, DSM 300832528311135draftimg866789
66792Escherichia coli ATCC 117752897341779completeimg562
66792Escherichia coli O1:K1:H7 U5/41, DSM 300832574180325draftimg866789
66792Escherichia coli O1:K1:H7 U5/41, DSM 300832588253787draftimg866789
66792Escherichia coli NCTC90012687453512completeimg562
67770Escherichia coli strain NCTC9001, whole genome shotgun sequencing projectCAADIS000000000ncbi562
67770Escherichia coli DSM 30083 = JCM 1649 = ATCC 11775 chromosome, complete genomeCP033092ena866789

GC content

  • @ref: 67770
  • GC-content: 49.2
  • method: thermal denaturation, midpoint method (Tm)

External links

@ref: 9115

culture collection no.: DSM 30083, ATCC 11775, CCM 5172, CIP 54.8, IAM 12119, JCM 1649, NCDO 1989, NCTC 9001, WDCM 00090, BCRC 10675, CCUG 24, CCUG 29300, CECT 515, CGMCC 1.2993, KCTC 2441, LMG 2092, NBRC 102203, NCIMB 11943, VTT E-94564, UCCCB113

straininfo link

@refpassport
20218http://www.straininfo.net/strains/11325
20218http://www.straininfo.net/strains/11317
20218http://www.straininfo.net/strains/11318
20218http://www.straininfo.net/strains/233878
20218http://www.straininfo.net/strains/11327
20218http://www.straininfo.net/strains/11328
20218http://www.straininfo.net/strains/11330
20218http://www.straininfo.net/strains/11332
20218http://www.straininfo.net/strains/866228

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9115Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 30083)https://www.dsmz.de/collection/catalogue/details/culture/DSM-30083
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
38566Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17456
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67772Curators of the UCCCBhttps://ucccb.uc.pt/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid