Strain identifier

BacDive ID: 14652

Type strain: Yes

Species: Staphylococcus nepalensis

Strain Designation: CW1

Strain history: CIP <- 2003, CCM <- H.J. Busse <- J. Spergser: strain CW1

NCBI tax ID(s): 214473 (species)

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General

@ref: 5727

BacDive-ID: 14652

DSM-Number: 15150

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, coccus-shaped, animal pathogen

description: Staphylococcus nepalensis CW1 is an aerobe, mesophilic, Gram-positive animal pathogen that was isolated from nasal mucosa of a goat.

NCBI tax id

  • NCBI tax id: 214473
  • Matching level: species

strain history

@refhistory
5727<- J. Spergser; CW1
121270CIP <- 2003, CCM <- H.J. Busse <- J. Spergser: strain CW1

doi: 10.13145/bacdive14652.20230509.8.1

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 nepalensis
  • full scientific name: Staphylococcus nepalensis Spergser et al. 2003

@ref: 5727

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Staphylococcaceae

genus: Staphylococcus

species: Staphylococcus nepalensis

full scientific name: Staphylococcus nepalensis Spergser et al. 2003

strain designation: CW1

type strain: yes

Morphology

cell morphology

  • @ref: 121270
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

colony morphology

  • @ref: 121270

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5727TRYPTICASE 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
38263MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121270CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5727positivegrowth37mesophilic
38263positivegrowth30mesophilic
58425positivegrowth30mesophilic
121270positivegrowth10-41
121270nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
58425aerobe
121270obligate aerobe

antibiogram

  • @ref: 5727
  • medium: Mueller-Hinton Agar
  • incubation temperature: 37
  • Penicillin G: 40
  • oxacillin: 28
  • ampicillin: 40
  • ticarcillin: 42
  • mezlocillin: 34
  • cefalotin: 40
  • cefazolin: 34-36
  • cefotaxime: 30
  • aztreonam: 0
  • imipenem: 48-50
  • tetracycline: 36-38
  • chloramphenicol: 36
  • gentamycin: 34-36
  • amikacin: 36-38
  • vancomycin: 24
  • erythromycin: 22
  • lincomycin: 20
  • ofloxacin: 28
  • norfloxacin: 26-28
  • colistin: 12-14
  • pipemidic acid: 10-12
  • nitrofurantoin: 28
  • bacitracin: 12
  • polymyxin b: 18
  • kanamycin: 34-36
  • neomycin: 30
  • doxycycline: 38-40
  • ceftriaxone: n.d.
  • clindamycin: n.d.
  • fosfomycin: n.d.
  • moxifloxacin: n.d.
  • linezolid: n.d.
  • nystatin: n.d.
  • quinupristin/dalfopristin: n.d.
  • teicoplanin: n.d.
  • piperacillin/tazobactam: n.d.

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
121270hippurate+hydrolysis606565
121270nitrate+reduction17632
121270nitrite-reduction16301
68375urea+hydrolysis16199
68375arginine-hydrolysis29016
68375ornithine-degradation18257
68375esculin+hydrolysis4853
68375D-glucose+fermentation17634
68375D-fructose+fermentation15824
68375D-mannose+fermentation16024
68375maltose+fermentation17306
68375lactose+fermentation17716
68375trehalose+fermentation27082
68375D-mannitol+fermentation16899
68375raffinose-fermentation16634
68375D-ribose-fermentation16988
68375cellobiose-fermentation17057
68375nitrate+reduction17632
68375sucrose+fermentation17992
68375N-acetylglucosamine+fermentation59640
68375turanose-fermentation32528
68375arabinose+fermentation22599
68381arginine+hydrolysis29016
68381D-ribose-builds acid from16988
68381D-mannitol+builds acid from16899
68381sorbitol-builds acid from30911
68381lactose+builds acid from17716
68381trehalose+builds acid from27082
68381raffinose-builds acid from16634
68381sucrose+builds acid from17992
68381L-arabinose-builds acid from30849
68381D-arabitol-builds acid from18333
68381alpha-cyclodextrin-builds acid from40585
68381hippurate+hydrolysis606565
68381glycogen-builds acid from28087
68381pullulan-builds acid from27941
68381maltose-builds acid from17306
68381melibiose-builds acid from28053
68381melezitose-builds acid from6731
68381methyl beta-D-glucopyranoside-builds acid from320055
68381D-tagatose-builds acid from16443
68381urea+hydrolysis16199

antibiotic resistance

  • @ref: 68375
  • ChEBI: 28368
  • metabolite: novobiocin
  • is antibiotic: yes
  • is resistant: yes
  • resistance conc.: 1.8 µg

metabolite production

@refChebi-IDmetaboliteproduction
6837515688acetoinno
12127035581indoleno
6838115688acetoinno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
6838115688acetoin-
6837515688acetoin-
12127015688acetoin-
12127017234glucose+

enzymes

@refvalueactivityec
68381urease+3.5.1.5
68381beta-mannosidase-3.2.1.25
68381glycyl tryptophan arylamidase-
68381N-acetyl-beta-glucosaminidase-3.2.1.52
68381pyrrolidonyl arylamidase+3.4.19.3
68381beta-galactosidase+3.2.1.23
68381Alanyl-Phenylalanyl-Proline arylamidase-
68381alkaline phosphatase+3.1.3.1
68381alpha-galactosidase-3.2.1.22
68381beta-glucuronidase+3.2.1.31
68381beta-glucosidase+3.2.1.21
68381arginine dihydrolase+3.5.3.6
68375beta-glucuronidase+3.2.1.31
68375pyrrolidonyl arylamidase+3.4.19.3
68375alkaline phosphatase+3.1.3.1
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
68375urease+3.5.1.5
121270oxidase-
121270beta-galactosidase+3.2.1.23
121270alcohol dehydrogenase-1.1.1.1
121270gelatinase+/-
121270amylase-
121270DNase-
121270caseinase-3.4.21.50
121270catalase+1.11.1.6
121270coagulase-
121270tween esterase+
121270gamma-glutamyltransferase-2.3.2.2
121270lecithinase-
121270lipase-
121270lysine decarboxylase-4.1.1.18
121270ornithine decarboxylase-4.1.1.17
121270phenylalanine ammonia-lyase-4.3.1.24
121270urease+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
121270-+++------++-++-----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121270----------+/-+/-+/------------+/-+/-----+/-+/------------------

API ID32STA

@refUREADH ArgODCESCGLUFRUMNEMALLACTREMANRAFRIBCELNITVPbeta GALArgAPALPyrANOVOSACNAGTURARAbeta GUR
5727+--++++++++---+-+-+++++-++
5727+--++++++++---+-+-+++++-++

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
5727++-+-+-+-++-+-----++--+--------+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121270++-++--+-+++------++++++--+-+--+-+++-----------------+-----++------------+-+----------+---++--+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
5727nasal mucosa of a goatChitwan areaNepalNPLAsia
58425Goat nasal mucosaChitwanNepalNPLAsia
121270Nasal mucosa of a goatChitwanNepalNPLAsia1999

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Caprinae (Sheep/Goat)
#Host Body-Site#Organ#Nose

taxonmaps

  • @ref: 69479
  • File name: preview.99_1035.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_3;97_3;98_3;99_1035&stattab=map
  • Last taxonomy: Staphylococcus
  • 16S sequence: AJ517414
  • Sequence Identity:
  • Total samples: 759
  • soil counts: 26
  • aquatic counts: 20
  • animal counts: 679
  • plant counts: 34

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
5727yes2Risk group (German classification)
1212701Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Staphylococcus nepalensis strain DSM 15150 16S ribosomal RNA gene, partial sequenceAY688080464ena214473
5727Staphylococcus nepalensis 16S rRNA gene, strain CW1TAJ5174141470ena214473

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Staphylococcus nepalensis CCM 7045GCA_014635045scaffoldncbi214473
66792Staphylococcus nepalensis DSM 15150GCA_002902745scaffoldncbi214473
66792Staphylococcus nepalensis strain CCM 7045214473.24wgspatric214473
66792Staphylococcus nepalensis strain DSM 15150214473.15wgspatric214473
66792Staphylococcus nepalensis DSM 151502917442331draftimg214473

GC content

  • @ref: 5727
  • GC-content: 33

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno93.895no
gram-positiveyes90.812no
anaerobicno99.207yes
aerobicyes92.736yes
halophileyes96.187no
spore-formingno92.307no
thermophileno99.88yes
glucose-utilyes89.92no
motileno88.959no
glucose-fermentyes83.715yes

External links

@ref: 5727

culture collection no.: DSM 15150, CCUG 48991, CCM 7045, CIP 108211

straininfo link

  • @ref: 83779
  • straininfo: 128020

literature

  • topic: Phylogeny
  • Pubmed-ID: 14657137
  • title: Staphylococcus nepalensis sp. nov., isolated from goats of the Himalayan region.
  • authors: Spergser J, Wieser M, Taubel M, Rossello-Mora RA, Rosengarten R, Busse HJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02646-0
  • year: 2003
  • mesh: Altitude, Animals, DNA Fingerprinting, Geography, Goats/*microbiology, India, Microbial Sensitivity Tests, Molecular Sequence Data, *Phylogeny, Polymerase Chain Reaction, Staphylococcus/*classification/genetics/isolation & purification/physiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5727Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15150)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15150
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
38263Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5809
58425Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48991)https://www.ccug.se/strain?id=48991
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)
68371Automatically annotated from API 50CH acid
68375Automatically annotated from API ID32STA
68381Automatically annotated from API rID32STR
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
83779Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID128020.1StrainInfo: A central database for resolving microbial strain identifiers
121270Curators of the CIPCollection of Institut Pasteur (CIP 108211)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108211