Strain identifier

BacDive ID: 14562

Type strain: Yes

Species: Staphylococcus lugdunensis

Strain Designation: N860297

Strain history: CIP <- 1993, J. Freney, Med. Univ., Lyon, France: strain N860297 <- J. Fleurette, E. Herriot Hosp., Lyon, France

NCBI tax ID(s): 28035 (species)

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General

@ref: 1827

BacDive-ID: 14562

DSM-Number: 4804

keywords: 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, coccus-shaped

description: Staphylococcus lugdunensis N860297 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from axillary lymph node.

NCBI tax id

  • NCBI tax id: 28035
  • Matching level: species

strain history

@refhistory
1827<- J. Fleurette; <- Centre National des Staphylocoques, Lyon, France; N860297
120670CIP <- 1993, J. Freney, Med. Univ., Lyon, France: strain N860297 <- J. Fleurette, E. Herriot Hosp., Lyon, France

doi: 10.13145/bacdive14562.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Staphylococcaceae
  • genus: Staphylococcus
  • species: Staphylococcus lugdunensis
  • full scientific name: Staphylococcus lugdunensis Freney et al. 1988

@ref: 1827

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Staphylococcaceae

genus: Staphylococcus

species: Staphylococcus lugdunensis

full scientific name: Staphylococcus lugdunensis Freney et al. 1988

strain designation: N860297

type strain: yes

Morphology

cell morphology

  • @ref: 120670
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

colony morphology

@reftype of hemolysishemolysis ability
1827gamma
1206701

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1827COLUMBIA 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
1827TRYPTICASE 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
40750MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
120670CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
120670CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
1827positivegrowth37mesophilic
40750positivegrowth37mesophilic
48175positivegrowth37mesophilic
120670positivegrowth22-45
120670nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
48175microaerophile
120670facultative anaerobe

murein

  • @ref: 1827
  • murein short key: A11.02
  • type: A3alpha L-Lys-Gly5-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12067017632nitrate+reduction
12067016301nitrite-reduction
6837529016arginine-hydrolysis
6837518257ornithine+degradation
683754853esculin-hydrolysis
6837517634D-glucose+fermentation
6837515824D-fructose+fermentation
6837517306maltose+fermentation
6837517716lactose+fermentation
6837527082trehalose+fermentation
6837516899D-mannitol-fermentation
6837516634raffinose-fermentation
6837516988D-ribose-fermentation
6837517057cellobiose-fermentation
6837517632nitrate+reduction
6837517992sucrose+fermentation
6837559640N-acetylglucosamine+fermentation
6837522599arabinose-fermentation

metabolite production

@refChebi-IDmetaboliteproduction
6837515688acetoinyes
12067035581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-test
6837515688acetoin+
12067015688acetoin-

enzymes

@refvalueactivityec
1827catalase+1.11.1.6
1827cytochrome-c oxidase-1.9.3.1
68375beta-glucuronidase-3.2.1.31
68375L-arginine arylamidase-
68375beta-galactosidase-3.2.1.23
68375beta-glucosidase-3.2.1.21
68375ornithine decarboxylase+4.1.1.17
68375arginine dihydrolase-3.5.3.6
120670oxidase-
120670beta-galactosidase-3.2.1.23
120670alcohol dehydrogenase-1.1.1.1
120670gelatinase-
120670DNase+
120670catalase+1.11.1.6
120670coagulase-
120670gamma-glutamyltransferase-2.3.2.2
120670lecithinase+
120670lysine decarboxylase-4.1.1.18
120670ornithine decarboxylase+4.1.1.17
120670urease+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

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120670--++------++---+----

API ID32STA

@refUREADH ArgODCESCGLUFRUMNEMALLACTREMANRAFRIBCELNITVPbeta GALArgAPALPyrANOVOSACNAGTURARAbeta GUR
1827--+-++-+++----++---+-++---
1827--+-++++++----++--+/-+++++/---
1827+/--+-++++++----++---+/-+++---
1827--+-++++++----++---+/-++++--
1827+-+-++++++----++---++/-++---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120670++-++--+--++++---+--------+----+-----------------+---------++--------------+---++-----+-----+++----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
1827axillary lymph node
48175Human axillary lymph nodeLyonFranceFRAEurope
120670Other, Axillary adenopathyLyonFranceFRAEurope1986

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Host#Human
#Host Body-Site#Limb#Arm

taxonmaps

  • @ref: 69479
  • File name: preview.99_590.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_3;97_3;98_3;99_590&stattab=map
  • Last taxonomy: Staphylococcus
  • 16S sequence: AB009941
  • Sequence Identity:
  • Total samples: 3146
  • soil counts: 18
  • aquatic counts: 54
  • animal counts: 3062
  • plant counts: 12

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
18272Risk group (German classification)
1206701Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Staphylococcus lugdunensis strain DSM 4804 16S ribosomal RNA gene, partial sequenceAY688074464ena28035
20218S.lugdunensis gene for 16S ribosomal RNAZ26899771ena28035
1827Staphylococcus lugdunensis rrn gene for 16S ribosomal RNAAB0099411492ena28035

GC content

  • @ref: 1827
  • GC-content: 32.0

External links

@ref: 1827

culture collection no.: CCUG 25348, DSM 4804, ATCC 43809, CIP 103642, CCM 4069, NCTC 12217

straininfo link

  • @ref: 83692
  • straininfo: 7701

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Pathogenicity10467667False-positive beta-lactamase results with Staphylococcus lugdunensis in the Vitek AutoMicrobic system.Zbinden R, von Graevenitz A, Rossi J, Kumin E, Berger-Bachi B, Hachler H, Nadal DZentralbl Bakteriol10.1016/s0934-8840(99)80076-01999Diffusion, False Positive Reactions, Humans, Microbial Sensitivity Tests, Penicillin Resistance, Quality Control, Staphylococcus/drug effects/*enzymology, beta-Lactamases/*metabolismEnzymology
32038604Role of the LytSR Two-Component Regulatory System in Staphylococcus lugdunensis Biofilm Formation and Pathogenesis.Dahyot S, Oxaran V, Niepceron M, Dupart E, Legris S, Destruel L, Didi J, Clamens T, Lesouhaitier O, Zerdoumi Y, Flaman JM, Pestel-Caron MFront Microbiol10.3389/fmicb.2020.000392020

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1827Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4804)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4804
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
40750Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15462
48175Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 25348)https://www.ccug.se/strain?id=25348
68375Automatically annotated from API ID32STA
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
83692Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID7701.1StrainInfo: A central database for resolving microbial strain identifiers
120670Curators of the CIPCollection of Institut Pasteur (CIP 103642)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103642