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, Gram-negative, motile, rod-shaped, human pathogen

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

NCBI tax id

NCBI tax idMatching level
564species
585054strain

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/bacdive4930.20250331.9.3

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

@refgram staincell shapemotilityconfidence
119305negativerod-shapedyes
125438negative99.75

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

@refgrowthtypetemperature
5121positivegrowth37
39147positivegrowth30
67770positivegrowth30
119305positivegrowth5-41

Physiology and metabolism

oxygen tolerance

  • @ref: 119305
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 92.6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11930529864mannitol+fermentation
11930516947citrate-carbon source
1193054853esculin+hydrolysis
11930517234glucose+fermentation
11930517716lactose-fermentation
11930517632nitrate+reduction
11930516301nitrite-reduction
11930515792malonate+assimilation
119305132112sodium thiosulfate-builds gas from
11930517234glucose+degradation
68371Potassium 5-ketogluconate-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
68371Potassium 2-ketogluconate+builds acid from
6837124265gluconate+builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol+builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose+builds acid from
6837117266L-sorbose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from

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
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
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
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382esterase lipase (C 8)+
68382esterase (C 4)+
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
68382lipase (C 14)-
68382alkaline phosphatase+3.1.3.1

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 sequenceAF5304751473nuccore585054
20218Escherichia fergusonii gene for 16S rRNA, partial sequence, strain: NBRC 102419AB6817751467nuccore564
67770Escherichia fergusonii strain ATCC 35469 16S ribosomal RNA gene, partial sequenceKP941767882nuccore564
124043Escherichia fergusonii ATCC 35469 gene for 16S rRNA, partial sequence.LC752358587nuccore585054
124043Escherichia fergusonii partial 16S rRNA gene, strain ATCC 35469, isolate a5, clone a5LS992079779nuccore585054
124043Escherichia fergusonii ATCC 35469 16S ribosomal RNA gene, partial sequence.OR6602521092nuccore585054

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

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno99.75no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.905no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no72.922yes
125438spore-formingspore-formingAbility to form endo- or exosporesno87.825no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97yes
125438motile2+flagellatedAbility to perform flagellated movementyes77.851no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno92.6
125439BacteriaNetmotilityAbility to perform movementno50.6
125439BacteriaNetgram_stainReaction to gram-stainingnegative88.9
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe88.8

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
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
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1