Strain identifier

BacDive ID: 5172

Type strain: Yes

Species: Shigella sonnei

Strain Designation: I virulent

Strain history: CIP <- 1982, ATCC <- D.J. Brenner, CDC: strain I virulent <- WRAIR, USA

NCBI tax ID(s): 624 (species)

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General

@ref: 2226

BacDive-ID: 5172

DSM-Number: 5570

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped, antibiotic resistance, human pathogen

description: Shigella sonnei I virulent is an aerobe, mesophilic, Gram-negative human pathogen that has multiple antibiotic resistances.

NCBI tax id

  • NCBI tax id: 624
  • Matching level: species

strain history

@refhistory
2226<- ATCC; ATCC 29930 <- D. J. Brenner; I virulent <- Walter Reed Army Institute of Research (WRAIR);
122678CIP <- 1982, ATCC <- D.J. Brenner, CDC: strain I virulent <- WRAIR, USA

doi: 10.13145/bacdive5172.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Shigella
  • species: Shigella sonnei
  • full scientific name: Shigella sonnei (Levine 1920) Weldin 1927 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Bacterium sonnei

@ref: 2226

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Shigella

species: Shigella sonnei

full scientific name: Shigella sonnei (Levine 1920) Weldin 1927

strain designation: I virulent

type strain: yes

Morphology

cell morphology

  • @ref: 122678
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2226NUTRIENT 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
41757MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
2226TRYPTICASE 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
2226COLUMBIA 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
122678CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
122678CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
2226positivegrowth37mesophilic
41757positivegrowth30mesophilic
63516positivegrowth30mesophilic
122678positivegrowth10-41
122678nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
63516aerobe
122678facultative anaerobe

antibiogram

  • @ref: 2226
  • medium: Mueller-Hinton Agar
  • Penicillin G: 0
  • oxacillin: 0
  • ampicillin: 22
  • ticarcillin: 32
  • mezlocillin: 26
  • cefalotin: 22
  • cefazolin: 30
  • cefotaxime: 40
  • aztreonam: 38
  • imipenem: 34
  • tetracycline: 6
  • chloramphenicol: 30-32
  • gentamycin: 20
  • amikacin: 22
  • vancomycin: 0
  • erythromycin: 10
  • lincomycin: 0
  • ofloxacin: 34
  • norfloxacin: 36-38
  • colistin: 14
  • pipemidic acid: 28
  • nitrofurantoin: 24-26
  • bacitracin: 0
  • polymyxin b: 14
  • kanamycin: 22
  • neomycin: 18
  • doxycycline: 10
  • ceftriaxone: 38
  • clindamycin: 0
  • fosfomycin: 34
  • moxifloxacin: 32
  • linezolid: 0
  • nystatin: 6
  • quinupristin/dalfopristin: 8
  • teicoplanin: 0
  • piperacillin/tazobactam: 26

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836830849L-arabinose+fermentation
6836827613amygdalin-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
12267829864mannitol+fermentation
12267816947citrate-carbon source
12267817234glucose+fermentation
12267817716lactose-fermentation
12267817632nitrate+reduction
12267816301nitrite+reduction
12267815792malonate-assimilation
122678132112sodium thiosulfate-builds gas from
12267817234glucose+degradation

antibiotic resistance

  • @ref: 122678
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836835581indoleno
6836816136hydrogen sulfideno
12267835581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836835581indole-
12267815688acetoin-
12267817234glucose+

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
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
122678oxidase-
122678beta-galactosidase+3.2.1.23
122678alcohol dehydrogenase-1.1.1.1
122678gelatinase-
122678catalase+1.11.1.6
122678lysine decarboxylase-4.1.1.18
122678ornithine decarboxylase+4.1.1.17
122678tryptophan deaminase-
122678urease-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
122678-++--++++-++-+-+----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
2226++/--+-------++--+---+-
2226+--+-----+-++--+---+-
2226++/--+-----+-++--+---+-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122678+++++-+-+++--++----++--++------+-+----------+---++----++---++------------+-+---++-+---+--++++-+---+

Isolation, sampling and environmental information

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: FR870445
  • 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
2226yesyes2Risk group (German classification)
1226782Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Shigella sonnei partial 16S rRNA gene, type strain CECT 4887T
  • accession: FR870445
  • length: 1530
  • database: ena
  • NCBI tax ID: 624

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Shigella sonnei ATCC 29930GCA_002950395completencbi624
66792Shigella sonnei NCTC12984GCA_900457155contigncbi624
66792Shigella sonnei strain ATCC 29930624.1345completepatric624
66792Shigella sonnei strain NCTC12984624.1595wgspatric624
66792Shigella sonnei ATCC 299302872158770completeimg624

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno62.212no
gram-positiveno98.171no
anaerobicno94.646yes
halophileno88.482no
spore-formingno94.22no
glucose-utilyes93.654no
aerobicyes83.507yes
thermophileno98.883no
motileyes88.571no
glucose-fermentyes92.435no

External links

@ref: 2226

culture collection no.: CCUG 68726, NCTC 12984, CECT 4887, DSM 5570, ATCC 29930, WDCM 00127, CIP 82.49

straininfo link

  • @ref: 74664
  • straininfo: 4971

literature

  • topic: Pathogenicity
  • Pubmed-ID: 23488799
  • title: Safety assessment and probiotic evaluation of Enterococcus faecium YF5 isolated from sourdough.
  • authors: Tan Q, Xu H, Aguilar ZP, Peng S, Dong S, Wang B, Li P, Chen T, Xu F, Wei H
  • journal: J Food Sci
  • DOI: 10.1111/1750-3841.12079
  • year: 2013
  • mesh: Amoxicillin/pharmacology, Animals, *Antibiosis, Chloramphenicol/pharmacology, Cronobacter sakazakii, *Drug Resistance, Bacterial, Enterococcus faecium/drug effects/genetics/*isolation & purification/*physiology, Escherichia coli O157, Feces/chemistry/microbiology, HT29 Cells, Humans, Listeria monocytogenes, Male, Mice, Mice, Inbred BALB C, Microbial Sensitivity Tests, Phenotype, *Probiotics, Salmonella typhimurium, Shigella flexneri, Shigella sonnei, Staphylococcus aureus, Vancomycin/pharmacology, Virulence, Virulence Factors/genetics
  • topic2: Phenotype

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2226Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5570)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5570
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
41757Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11321
63516Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 68726)https://www.ccug.se/strain?id=68726
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
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
74664Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID4971.1StrainInfo: A central database for resolving microbial strain identifiers
122678Curators of the CIPCollection of Institut Pasteur (CIP 82.49)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2082.49