Strain identifier

BacDive ID: 137262

Type strain: No

Species: Shigella flexneri

Strain Designation: 3591-52

Strain history: CIP <- 1994, ATCC <- CDC: strain 3591-52

NCBI tax ID(s): 623 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 8.1 (current version)

General

@ref: 37166

BacDive-ID: 137262

keywords: genome sequence, Bacteria, facultative anaerobe, mesophilic, motile

description: Shigella flexneri 3591-52 is a facultative anaerobe, mesophilic, motile bacterium of the family Enterobacteriaceae.

NCBI tax id

  • NCBI tax id: 623
  • Matching level: species

strain history

  • @ref: 37166
  • history: CIP <- 1994, ATCC <- CDC: strain 3591-52

doi: 10.13145/bacdive137262.20230509.8.1

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 flexneri
  • full scientific name: Shigella flexneri Castellani and Chalmers 1919 (Approved Lists 1980)

@ref: 37166

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacterales

family: Enterobacteriaceae

genus: Shigella

species: Shigella flexneri

strain designation: 3591-52

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.023
6948099.992negative
37166nonegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
37166MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
37166CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
37166positivegrowth30mesophilic
37166positivegrowth30-37mesophilic
37166nogrowth5psychrophilic
37166nogrowth10psychrophilic
37166nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 37166
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.663

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
6836829016arginine-hydrolysis
3716629864mannitol-fermentation
3716616947citrate-carbon source
3716617234glucose+fermentation
3716617716lactose+fermentation
3716617632nitrate-reduction
3716616301nitrite-reduction
3716615792malonate-assimilation
37166132112sodium thiosulfate-builds gas from
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: 37166
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6837435581indoleno
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
3716635581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6837435581indole-
6836815688acetoin+
6836835581indole-
3716615688acetoin+
3716617234glucose+

enzymes

@refvalueactivityec
68374L-aspartate arylamidase-3.4.11.21
68374alpha-maltosidase-
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
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
37166oxidase-
37166beta-galactosidase-3.2.1.23
37166alcohol dehydrogenase-1.1.1.1
37166gelatinase-
37166catalase+1.11.1.6
37166lysine decarboxylase-4.1.1.18
37166ornithine decarboxylase-4.1.1.17
37166phenylalanine ammonia-lyase-4.3.1.24
37166tryptophan deaminase-
37166urease-3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase-3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    50816C12:03.812
    50816C13:01.813
    50816C14:0814
    50816C15:09.615
    50816C16:024.316
    50816C17:01.617
    50816C13:0 3OH/C15:1 i I/H114.469
    50816C14:0 3OH/C16:1 ISO I6.615.485
    50816C15:1 ω8c0.514.792
    50816C16:1 ω5c0.515.908
    50816C16:1 ω7c5.215.819
    50816C17:0 CYCLO21.416.888
    50816C18:1 ω7c /12t/9t11.217.824
    50816C19:0 CYCLO ω8c4.518.9
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
37166--+-------++++-+----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
50816---------+-++------+-

API ID32E

@refODCADH ArgLDC LysURELARLGAT5KGLIPRPbeta GLUMANMALADOPLEbeta GURMNTINDbeta NAGbeta GALGLUSACLARADARLalpha GLUalpha GALTRERHAINOCELSORalphaMALAspA
50816-----+--+---------------++------

Safety information

risk assessment

  • @ref: 37166
  • biosafety level: 2
  • biosafety level comment: Risk group (French classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Shigella flexneri ATCC 12022GCA_000754175scaffoldncbi623
66792Shigella flexneri NCTC12698GCA_900457225contigncbi623
66792Shigella flexneri strain ATCC 12022623.156wgspatric623
66792Shigella flexneri strain NCTC12698623.1086wgspatric623

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.681no
flagellatedno66.426no
gram-positiveno98.387no
anaerobicno93.866no
aerobicyes81.28no
halophileno92.681no
spore-formingno93.893no
thermophileno98.854yes
glucose-utilyes94.666no
glucose-fermentyes91.734yes

External links

@ref: 37166

culture collection no.: CCUG 32079, CIP 104222, ATCC 12022, LMG 10472, WDCM 00126, CECT 4804, NCTC 12698

straininfo link

  • @ref: 94199
  • straininfo: 4970

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Cultivation10340667The effectiveness of triclosan-incorporated plastic against bacteria on beef surfaces.Cutter CNJ Food Prot10.4315/0362-028x-62.5.4741999Animals, Anti-Infective Agents, Local/*pharmacology, Bacteria/*growth & development, Cattle, Colony Count, Microbial, Culture Media, *Food Packaging, Gram-Negative Bacteria/drug effects/growth & development/isolation & purification, Gram-Positive Bacteria/drug effects/growth & development/isolation & purification, Meat/*microbiology, Microbial Sensitivity Tests, Plastics/*chemistry, Triclosan/*pharmacology, VacuumEnzymology
Biotechnology20932087Viable but nonculturable state of foodborne pathogens in grapefruit juice: a study of laboratory.Nicolo MS, Gioffre A, Carnazza S, Platania G, Silvestro ID, Guglielmino SPFoodborne Pathog Dis10.1089/fpd.2009.04912010Bacteria/*growth & development, Beverages/*microbiology, Citrus paradisi/*microbiology, Colony Count, Microbial, Escherichia coli O157/growth & development, *Food Microbiology, Foodborne Diseases/*microbiology, Fruit/microbiology, Humans, Listeria monocytogenes/growth & development, Microbial Viability, Salmonella typhi/growth & development, Shigella flexneri/growth & developmentPathogenicity
Enzymology23181593Antibacterial, antifungal and antioxidant activities of the ethanol extract of the stem bark of Clausena heptaphylla.Fakruddin M, Mannan KS, Mazumdar RM, Afroz HBMC Complement Altern Med10.1186/1472-6882-12-2322012Anti-Bacterial Agents/chemistry/isolation & purification/*pharmacology, Antifungal Agents/chemistry/isolation & purification/*pharmacology, Antioxidants/chemistry/isolation & purification/*pharmacology, Bacteria/drug effects, Clausena/*chemistry, Fungi/drug effects, Microbial Sensitivity Tests, Plant Bark/*chemistry, Plant Extracts/chemistry/isolation & purification/*pharmacologyPhylogeny
Biotechnology24075344Production of microbial medium from defatted brebra (Milletia ferruginea) seed flour to substitute commercial peptone agar.Andualem B, Gessesse AAsian Pac J Trop Biomed10.1016/S2221-1691(13)60157-42013Agar/*chemistry, Bacteria/growth & development, Colony Count, Microbial, Culture Media/*chemistry, Peptones/*chemistry, Seeds/*chemistryCultivation
24330657Temperature-regulated expression of outer membrane proteins in Shigella flexneri.Harikrishnan H, Ismail A, Banga Singh KKGut Pathog10.1186/1757-4749-5-382013
25359907Genome Assembly of Shigella flexneri ATCC 12022, a Quality Control Reference Strain.Daligault HE, Davenport KW, Minogue TD, Bishop-Lilly KA, Broomall SM, Bruce DC, Chain PS, Coyne SR, Freitas T, Frey KG, Gibbons HS, Jaissle J, Lo CC, Meincke L, Munk AC, Redden CL, Rosenzweig CN, Johnson SLGenome Announc10.1128/genomeA.01052-142014
Pathogenicity25716124Design, synthesis and in vitro bactericidal/fungicidal screening of some vanadyl(IV)complexes with mono- and di-substituted ONS donor triazoles.Sumrra SH, Hanif M, Chohan ZHJ Enzyme Inhib Med Chem10.3109/14756366.2014.9765652015Anti-Bacterial Agents/chemical synthesis/chemistry/*pharmacology, Antifungal Agents/chemical synthesis/chemistry/*pharmacology, Bacteria/*drug effects, Dose-Response Relationship, Drug, *Drug Design, Fungi/*drug effects, Microbial Sensitivity Tests, Molecular Structure, Organometallic Compounds/chemical synthesis/chemistry/*pharmacology, Structure-Activity Relationship, Triazoles/chemistry/pharmacology, Vanadates/chemistry/pharmacology
Pathogenicity25930687Antibacterial activity of Lactobacillus spp. isolated from the feces of healthy infants against enteropathogenic bacteria.Davoodabadi A, Soltan Dallal MM, Rahimi Foroushani A, Douraghi M, Sharifi Yazdi MK, Amin Harati FAnaerobe10.1016/j.anaerobe.2015.04.0142015*Antibiosis, Bacterial Adhesion, Drug Resistance, Bacterial, Epithelial Cells/microbiology, Feces/*microbiology, Healthy Volunteers, Humans, Hydrogen-Ion Concentration, Infant, Lactobacillus/*isolation & purification/*physiology, Microbial Viability/drug effects, Salmonella enteritidis/*growth & development, Shigella/*growth & development, Yersinia enterocolitica/*growth & developmentEnzymology
Phylogeny26844762Epigenetic Activation of Antibacterial Property of an Endophytic Streptomyces coelicolor Strain AZRA 37 and Identification of the Induced Protein Using MALDI TOF MS/MS.Kumar J, Sharma VK, Singh DK, Mishra A, Gond SK, Verma SK, Kumar A, Kharwar RNPLoS One10.1371/journal.pone.01478762016Anti-Bacterial Agents/biosynthesis/chemistry/*pharmacology, Azacitidine/pharmacology, Bacterial Proteins/biosynthesis/chemistry/*pharmacology, Chromatography, High Pressure Liquid, *Epigenesis, Genetic, *Gene Expression Regulation, Bacterial, Humans, Microbial Sensitivity Tests, Phylogeny, RNA, Ribosomal, 16S/genetics, Secondary Metabolism, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Streptomyces coelicolor/classification/drug effects/*genetics/isolation & purification/*metabolismPathogenicity
28483960In Vitro Resistance Selection in Shigella flexneri by Azithromycin, Ceftriaxone, Ciprofloxacin, Levofloxacin, and Moxifloxacin.Allen GP, Harris KAAntimicrob Agents Chemother10.1128/AAC.00086-172017Anti-Bacterial Agents/*pharmacology, Azithromycin/*pharmacology, Ceftriaxone/*pharmacology, Ciprofloxacin/*pharmacology, DNA, Bacterial/genetics, Drug Resistance, Bacterial/genetics, Fluoroquinolones/*pharmacology, Levofloxacin/*pharmacology, Microbial Sensitivity Tests, Moxifloxacin, Mutation/genetics
31047673Oral immunization with LacVax(R) OmpA induces protective immune response against Shigella flexneri 2a ATCC 12022 in a murine model.Yagnik B, Sharma D, Padh H, Desai PVaccine10.1016/j.vaccine.2019.04.0532019Adaptive Immunity, Administration, Oral, Animals, Antibodies, Bacterial/*blood, Bacterial Outer Membrane Proteins/*immunology, Disease Models, Animal, Dysentery, Bacillary/*prevention & control, Female, Immunity, Cellular, Immunity, Mucosal, Immunization/*methods, Immunoglobulin A/analysis, Immunoglobulin G/blood, Lactobacillus/genetics/immunology, Mice, Mice, Inbred BALB C, Shigella Vaccines/administration & dosage/*immunology, Shigella flexneri, Specific Pathogen-Free Organisms, Th1 Cells/immunology
Phylogeny32439543Isolation and identification of potential probiotic Lactobacillus species from feces of infants in southwest Iran.Jomehzadeh N, Javaherizadeh H, Amin M, Saki M, Al-Ouqaili MTS, Hamidi H, Seyedmahmoudi M, Gorjian ZInt J Infect Dis10.1016/j.ijid.2020.05.0342020Anti-Bacterial Agents/pharmacology, Bacterial Adhesion, Child, Preschool, Feces/microbiology, Female, Humans, Infant, Iran, Lactobacillus/classification/genetics/*isolation & purification/physiology, Male, Probiotics/*chemistry/classification/isolation & purification/pharmacology, RNA, Ribosomal, 16S/genetics, Yersinia enterocolitica/drug effects/growth & developmentPathogenicity
Phylogeny32494347Isolation and structure elucidation of phenazine derivative from Streptomyces sp. strain UICC B-92 isolated from Neesia altissima (Malvaceae).Pratiwi RH, Hidayat I, Hanafi M, Mangunwardoyo WIran J Microbiol2020
Pathogenicity33188636Secondary Structural Transformation of Bovine Lactoferricin Affects Its Antibacterial Activity.Pei J, Xiong L, Bao P, Chu M, Yan P, Guo XProbiotics Antimicrob Proteins10.1007/s12602-020-09726-82020*Anti-Bacterial Agents/pharmacology, Disulfides, Escherichia coli/drug effects, *Lactoferrin/chemistry, Protein Structure, Secondary, Salmonella typhimurium/drug effects, Shigella flexneri/drug effects, Staphylococcus aureus/drug effects
34205938Phytochemical Profile and Microbiological Activity of Some Plants Belonging to the Fabaceae Family.Obistioiu D, Cocan I, Tirziu E, Herman V, Negrea M, Cucerzan A, Neacsu AG, Cozma AL, Nichita I, Hulea A, Radulov I, Alexa EAntibiotics (Basel)10.3390/antibiotics100606622021
34579365Antimicrobial Potential and Phytochemical Profile of Wild and Cultivated Populations of Thyme (Thymus sp.) Growing in Western Romania.Beicu R, Alexa E, Obistioiu D, Cocan I, Imbrea F, Pop G, Circioban D, Moisa C, Lupitu A, Copolovici L, Copolovici DM, Imbrea IMPlants (Basel)10.3390/plants100918332021
36076751Antibacterial Effect of Eugenol on Shigella flexneri and Its Mechanism.Bai X, Li X, Liu X, Xing Z, Su R, Wang Y, Xia X, Shi CFoods10.3390/foods111725652022
36367548Antibacterial Activity of Thymoquinone Against Shigella flexneri and Its Effect on Biofilm Formation.Wang M, Zhan X, Ma X, Wang R, Guo D, Zhang Y, Yu J, Chang Y, Lu X, Shi CFoodborne Pathog Dis10.1089/fpd.2022.00562022*Shigella flexneri, *Benzoquinones/pharmacology, Biofilms, Anti-Bacterial Agents/pharmacology
36467878The Antibacterial Effects of Cocktail and Single Forms of Lytic Phages Belonging to Podoviridae and Myoviridae Families from Sewage against Shigella sonnei and Shigella flexneri.Jokar J, Rahimian N, Ghasemian A, Najafipour SBiomed Res Int10.1155/2022/78335652022Animals, *Podoviridae, Myoviridae, Shigella sonnei, Shigella flexneri, *Bacteriophages, Sewage, Anti-Bacterial Agents

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
37166Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104222Collection of Institut Pasteur (CIP 104222)
50816Curators of the CCUGhttps://www.ccug.se/strain?id=32079Culture Collection University of Gothenburg (CCUG) (CCUG 32079)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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 OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
94199Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID4970.1