Strain identifier

BacDive ID: 4930

Type strain: Yes

Species: Escherichia fergusonii

Strain Designation: 568-73

Strain history: CIP <- 1996, PAD Grimont, Inst. Pasteur, Paris, France <- CDC: strain 568-73 <- Missouri State Hlth. Dept.

NCBI tax ID(s): 585054 (strain), 564 (species)

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General

@ref: 5121

BacDive-ID: 4930

DSM-Number: 13698

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, motile, human pathogen

description: Escherichia fergusonii 568-73 is a facultative anaerobe, mesophilic, motile human pathogen that was isolated from faeces of 1-year-old boy.

NCBI tax id

NCBI tax idMatching level
585054strain
564species

strain history

@refhistory
5121<- ATCC <- CDC <- Missouri State Health Dept.
67770IAM 14443 <-- ATCC 35469 <-- CDC 0568-73 <-- Missouri State Health Dept., USA.
119305CIP <- 1996, PAD Grimont, Inst. Pasteur, Paris, France <- CDC: strain 568-73 <- Missouri State Hlth. Dept.

doi: 10.13145/bacdive4930.20230509.8.1

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 fergusonii
  • full scientific name: Escherichia fergusonii Farmer et al. 1985

@ref: 5121

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Escherichia

species: Escherichia fergusonii

full scientific name: Escherichia fergusonii Farmer et al. 1985

strain designation: 568-73

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.301
6948099.979negative
119305yesnegativerod-shaped

colony morphology

  • @ref: 119305
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5121COLUMBIA 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
5121TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
39147MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
119305CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
119305CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5121positivegrowth37mesophilic
39147positivegrowth30mesophilic
67770positivegrowth30mesophilic
119305positivegrowth5-41

Physiology and metabolism

oxygen tolerance

  • @ref: 119305
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.56

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
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose-builds acid from17992
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
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
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose+builds acid from62345
68371L-sorbose-builds acid from17266
68371methyl beta-D-xylopyranoside-builds acid from74863
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
119305mannitol+fermentation29864
119305citrate-carbon source16947
119305esculin+hydrolysis4853
119305glucose+fermentation17234
119305lactose-fermentation17716
119305nitrate+reduction17632
119305nitrite-reduction16301
119305malonate+assimilation15792
119305sodium thiosulfate-builds gas from132112
119305glucose+degradation17234

antibiotic resistance

  • @ref: 119305
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 119305
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11930515688acetoin-
11930517234glucose+

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
119305oxidase-
119305beta-galactosidase+3.2.1.23
119305alcohol dehydrogenase-1.1.1.1
119305gelatinase-
119305catalase+1.11.1.6
119305lysine decarboxylase+4.1.1.18
119305ornithine decarboxylase+4.1.1.17
119305phenylalanine ammonia-lyase-4.3.1.24
119305tryptophan deaminase-
119305urease-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
119305-+++-+----++-+-+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119305+/---+++-+/--+/-+/-+/-+/--+--+/----+-+/-+/-+/-+++/-+/--+--+/----+/------+-++-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119305++++-----+-----+-+-+++-+--+----+-+---+--+--++----+----+++--++++----+-------+---++-----+--++++++-+-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5121faeces of 1-year-old boyMissouriUSAUSANorth America
46882Feces,1-yr-old boyUSAUSANorth America
67770Human stool
119305Human, Child, fecesMichiganUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host Body Product#Gastrointestinal tract#Feces (Stool)
#Host#Human#Child

taxonmaps

  • @ref: 69479
  • File name: preview.99_8.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_7;98_7;99_8&stattab=map
  • Last taxonomy: Enterobacteriaceae
  • 16S sequence: AF530475
  • Sequence Identity:
  • Total samples: 97630
  • soil counts: 2111
  • aquatic counts: 5613
  • animal counts: 88071
  • plant counts: 1835

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
5121yesyes2Risk group (German classification)
1193051Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Escherichia fergusonii 16S ribosomal RNA gene, partial sequenceAF5304751473ena585054
20218Escherichia fergusonii gene for 16S rRNA, partial sequence, strain: NBRC 102419AB6817751467ena564
67770Escherichia fergusonii strain ATCC 35469 16S ribosomal RNA gene, partial sequenceKP941767882ena564

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Escherichia fergusonii ATCC 35469 ATCC 35469TGCA_000026225completencbi585054
66792Escherichia fergusonii ATCC 35469585054.5completepatric585054
66792Escherichia fergusonii ATCC 35469 strain type strain: ATCC 35469 strain ATCC 35469T585054.21plasmidpatric585054
66792Escherichia fergusonii strain FDAARGOS_1499564.206completepatric564
66792Escherichia fergusonii strain NCTC12128564.28wgspatric564
66792Escherichia fergusonii UMN026, ATCC 35469643692022completeimg564
67770Escherichia fergusonii NCTC12128GCA_900450565contigncbi564
66792Escherichia fergusonii strain FDAARGOS_1499564.336completepatric564
66792Escherichia fergusonii strain FDAARGOS_1499564.246completepatric564
66792Escherichia fergusonii strain FDAARGOS_1499564.285completepatric564

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.209no
flagellatedno51.584no
gram-positiveno98.108no
anaerobicno96.565no
aerobicyes88.233no
halophileno83.861no
spore-formingno94.006no
glucose-utilyes92.715no
thermophileno98.735yes
glucose-fermentyes90.975no

External links

@ref: 5121

culture collection no.: DSM 13698, ATCC 35469, CDC 0568-73, CCUG 18766, JCM 21226, CIP 103357, CIP 104947, IAM 14443, LMG 7866, NBRC 102419, NCTC 12128

straininfo link

  • @ref: 74427
  • straininfo: 2807

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny3968204Escherichia fergusonii and Enterobacter taylorae, two new species of Enterobacteriaceae isolated from clinical specimens.Farmer JJ 3rd, Fanning GR, Davis BR, O'Hara CM, Riddle C, Hickman-Brenner FW, Asbury MA, Lowery VA 3rd, Brenner DJJ Clin Microbiol10.1128/jcm.21.1.77-81.19851985Aged, Animals, Anti-Bacterial Agents/pharmacology, DNA, Bacterial/genetics, Drug Resistance, Microbial, Enterobacter/*classification/drug effects/genetics/metabolism, Enterobacteriaceae/*classification, Escherichia/*classification/drug effects/genetics/metabolism, Female, Fermentation, Humans, Male, Microbial Sensitivity Tests, Middle Aged, Nucleic Acid Hybridization, Terminology as TopicPathogenicity
Phylogeny22252367Pathogenic and multidrug-resistant Escherichia fergusonii from broiler chicken.Forgetta V, Rempel H, Malouin F, Vaillancourt R Jr, Topp E, Dewar K, Diarra MSPoult Sci10.3382/ps.2011-017382012Animals, Anti-Bacterial Agents/pharmacology, *Chickens, *Drug Resistance, Multiple, Bacterial, Enterobacteriaceae Infections/microbiology/*veterinary, Escherichia/*classification/*drug effects/pathogenicity, Genome, Bacterial, Phylogeny, Poultry Diseases/*microbiology, VirulencePathogenicity
Metabolism25317751Degradation of curcuminoids by in vitro pure culture fermentation.Tan S, Rupasinghe TW, Tull DL, Boughton B, Oliver C, McSweeny C, Gras SL, Augustin MAJ Agric Food Chem10.1021/jf50311682014Animals, Biotransformation, Curcumin/analogs & derivatives/chemistry/*metabolism, Escherichia/growth & development/*metabolism, Escherichia coli/growth & development/metabolism, Feces/microbiology, Fermentation, Gastrointestinal Tract/microbiology, Humans, In Vitro Techniques, SwinePathogenicity
Phylogeny25851592Escherichia marmotae sp. nov., isolated from faeces of Marmota himalayana.Liu S, Jin D, Lan R, Wang Y, Meng Q, Dai H, Lu S, Hu S, Xu JInt J Syst Evol Microbiol10.1099/ijs.0.0002282015Animals, Base Composition, China, DNA, Bacterial/genetics, Escherichia/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Feces/*microbiology, Marmota/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny28599915Multiplex polymerase chain reaction for identification of Escherichia coli, Escherichia albertii and Escherichia fergusonii.Lindsey RL, Garcia-Toledo L, Fasulo D, Gladney LM, Strockbine NJ Microbiol Methods10.1016/j.mimet.2017.06.0052017Cross Infection, DNA Primers/genetics, DNA, Bacterial/*genetics, Enterobacteriaceae/genetics, Escherichia/*classification/genetics/*isolation & purification, Escherichia coli/*classification/genetics/*isolation & purification, Escherichia coli Infections/diagnosis/microbiology, Escherichia coli Proteins/genetics, Genome, Bacterial, Humans, Multiplex Polymerase Chain Reaction/*methods, Sensitivity and SpecificityEnzymology
Phylogeny32744988Intestinirhabdus alba gen. nov., sp. nov., a novel genus of the family Enterobacteriaceae, isolated from the gut of plastic-eating larvae of the Coleoptera insect Zophobas atratus.Xu Z, Xia M, Huo YX, Yang YInt J Syst Evol Microbiol10.1099/ijsem.0.0043642020Animals, Bacterial Typing Techniques, Base Composition, China, Coleoptera/*microbiology, DNA, Bacterial/genetics, Enterobacteriaceae/*classification/isolation & purification, Fatty Acids/chemistry, *Gastrointestinal Microbiome, Genes, Bacterial, Larva/microbiology, *Phylogeny, Plastics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome
35783086Crystal structure of the BREX phage defence protein BrxA.Beck IN, Picton DM, Blower TRCurr Res Struct Biol10.1016/j.crstbi.2022.06.0012022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5121Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13698)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13698
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
39147Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16912
46882Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 18766)https://www.ccug.se/strain?id=18766
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
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
74427Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2807.1StrainInfo: A central database for resolving microbial strain identifiers
119305Curators of the CIPCollection of Institut Pasteur (CIP 104947)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104947