Strain identifier

BacDive ID: 5171

Type strain: Yes

Species: Shigella flexneri

Strain Designation: 24570

Strain history: CIP <- 1982, ATCC <- D.J. Brenner, CDC: strain 24570

NCBI tax ID(s): 623 (species)

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General

@ref: 1822

BacDive-ID: 5171

DSM-Number: 4782

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

description: Shigella flexneri 24570 is an aerobe, mesophilic, Gram-negative human pathogen that has multiple antibiotic resistances.

NCBI tax id

  • NCBI tax id: 623
  • Matching level: species

strain history

@refhistory
1822<- ATCC; ATCC 29903 <- D. J. Brenner; 24570
67771<- DSM <- ATCC <- DJ Brenner, 24570
119397CIP <- 1982, ATCC <- D.J. Brenner, CDC: strain 24570

doi: 10.13145/bacdive5171.20230509.8.1

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: 1822

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Shigella

species: Shigella flexneri

full scientific name: Shigella flexneri Castellani and Chalmers 1919

strain designation: 24570

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
67771negative
119397negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
36625MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
1822TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium92.pdf
1822COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium693.pdf
119397CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
1822positivegrowth37mesophilic
36625positivegrowth30mesophilic
60957positivegrowth30mesophilic
67771positivegrowth37mesophilic
119397positivegrowth30-41
119397nogrowth5psychrophilic
119397nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
60957aerobe
67771aerobe
119397facultative anaerobe

antibiogram

@refmediumPenicillin Goxacillinampicillinticarcillinmezlocillincefalotincefazolincefotaximeaztreonamimipenemtetracyclinechloramphenicolgentamycinamikacinvancomycinerythromycinlincomycinofloxacinnorfloxacincolistinpipemidic acidnitrofurantoinbacitracinpolymyxin bkanamycinneomycindoxycyclineceftriaxoneclindamycinfosfomycinmoxifloxacinlinezolidnystatinquinupristin/dalfopristinteicoplaninpiperacillin/tazobactamincubation temperatureoxygen condition
1822Mueller-Hinton Agar8-1002432302430-324038-4034-3630342222012-14034341630280163218-2026-284003432-34000030
1822Mueller Hinton6-8024-263028-302428-30403836-383034-362220-22016038401630-3224-260182218-20283603036-38100603030aerob

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836830849L-arabinose+fermentation
6836827613amygdalin-fermentation
6836828053melibiose+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
11939729864mannitol+fermentation
11939716947citrate-carbon source
11939717234glucose+fermentation
11939717716lactose-fermentation
11939717632nitrate+reduction
11939716301nitrite+reduction
11939715792malonate-assimilation
119397132112sodium thiosulfate-builds gas from
11939717234glucose+degradation
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: 119397
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6837435581indoleyes
6836835581indoleyes
6836816136hydrogen sulfideno
11939735581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6837435581indole+
6836835581indole+
11939715688acetoin-
11939717234glucose+

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
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
119397oxidase-
119397beta-galactosidase-3.2.1.23
119397alcohol dehydrogenase-1.1.1.1
119397gelatinase-
119397catalase+1.11.1.6
119397lysine decarboxylase-4.1.1.18
119397ornithine decarboxylase-4.1.1.17
119397phenylalanine ammonia-lyase-4.3.1.24
119397tryptophan deaminase-
119397urease-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
119397-+---++-+-++---+----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
1822--------+--++----+-+-
1822--------+--++---++-+-
1822--------++-++----+-+-

API ID32E

@refODCADH ArgLDC LysURELARLGAT5KGLIPRPbeta GLUMANMALADOPLEbeta GURMNTINDbeta NAGbeta GALGLUSACLARADARLalpha GLUalpha GALTRERHAINOCELSORalphaMALAspA
60957-----+--+-------+------++-------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119397+++++-+-+++---+-----+---+------+-+---------------+----++---++--------------+---++-----+------+-----

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: X96963
  • 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
1822yesyes2Risk group (German classification)
1193972Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: S.flexneri 16S rRNA gene
  • accession: X96963
  • length: 1488
  • database: ena
  • NCBI tax ID: 623

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Shigella flexneri 2a ATCC 29903GCA_002950215completencbi42897
66792Shigella flexneri 2a strain ATCC 2990342897.55completepatric42897
66792Shigella flexneri ATCC 299032859793810completeimg623

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno61.18no
gram-positiveno98.291yes
anaerobicno93.965yes
halophileno91.396no
spore-formingno93.654no
glucose-utilyes94.302no
aerobicyes82.644yes
thermophileno98.836yes
motileyes88.686no
glucose-fermentyes91.958no

External links

@ref: 1822

culture collection no.: DSM 4782, ATCC 29903, KCTC 22192, WDCM 00125, CCUG 56439, CIP 82.48, BCRC 13984, KCTC 22529, CECT 8175, NCTC 13631

straininfo link

  • @ref: 74663
  • straininfo: 44862

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics1624118Virulence phenotypes of Shigella flexneri 2a avirulent mutant 24570 can be complemented by the plasmid-coded positive regulator virF gene.Qi MS, Yoshikura H, Watanabe HFEMS Microbiol Lett10.1111/j.1574-6968.1992.tb05264.x1992Antigens, Bacterial/analysis, Base Sequence, DNA, Bacterial/*genetics, Genes, Regulator/*genetics, Genetic Complementation Test, Molecular Sequence Data, Mutation/genetics, Plasmids/genetics, Polymerase Chain Reaction, Serotyping, Shigella flexneri/*genetics/pathogenicity, Virulence/geneticsPhenotype
Pathogenicity2188429[Membrane component of Shigella flexneri and their relationship to bacteria antigenicity and virulence].Jin L, Su XWei Sheng Wu Xue Bao1990Animals, Antigens, Bacterial/*immunology, Bacterial Outer Membrane Proteins/*immunology, Convalescence, Dysentery, Bacillary/immunology, Guinea Pigs, Humans, Immune Sera/*immunology, Shigella flexneri/immunology/*pathogenicity, Virulence
Pathogenicity9621565[Mechanism of resistance of Shigella flexneri 2a resistant to new quinolone antibiotics].Oonaka K, Fukuyama M, Tanaka M, Sato K, Ohnishi K, Ajima I, Murata MKansenshogaku Zasshi10.11150/kansenshogakuzasshi1970.72.3651998Anti-Infective Agents/*pharmacology, Drug Resistance, Microbial, *Fluoroquinolones, Humans, Naphthyridines/*pharmacology, Shigella flexneri/*drug effects/isolation & purificationEnzymology
Genetics26021915Draft Genome Sequence of 24570, the Type Strain of Shigella flexneri.Baker KS, Parkhill J, Thomson NRGenome Announc10.1128/genomeA.00393-152015
33304162Probiotic characteristics of Lactobacillus strains isolated from cheese and their antibacterial properties against gastrointestinal tract pathogens.Zhang X, Ali Esmail G, Fahad Alzeer A, Valan Arasu M, Vijayaraghavan P, Choon Choi K, Abdullah Al-Dhabi NSaudi J Biol Sci10.1016/j.sjbs.2020.10.0222020

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1822Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4782)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4782
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
36625Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11320
60957Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 56439)https://www.ccug.se/strain?id=56439
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68368Automatically annotated from API 20E
68374Automatically annotated from API ID32E
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
74663Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44862.1StrainInfo: A central database for resolving microbial strain identifiers
119397Curators of the CIPCollection of Institut Pasteur (CIP 82.48)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2082.48