Strain identifier

BacDive ID: 8530

Type strain: Yes

Species: Mycobacterium cosmeticum

Strain Designation: LTA-388

Strain history: CIP <- 2003, R.C. Cooksey, CDC, Atlanta, GA USA: strain LTA-388 <- M. Yakrus, M.S., M.P.H., CDC, Tuberculosis Branch, Atlanta, GA USA <- J. de Waard, Inst. de Biomedicina, Caracas, Venezuela

NCBI tax ID(s): 258533 (species)

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General

@ref: 12011

BacDive-ID: 8530

DSM-Number: 44829

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, rod-shaped, human pathogen

description: Mycobacterium cosmeticum LTA-388 is an aerobe, mesophilic, rod-shaped human pathogen that was isolated from a granulomatous lesion of a female patient.

NCBI tax id

  • NCBI tax id: 258533
  • Matching level: species

strain history

@refhistory
12011<- CIP
67770CIP 108170 <-- R. C. Cooksey LTA-388 <-- M. Yakrus <-- J. de Waard.
118762CIP <- 2003, R.C. Cooksey, CDC, Atlanta, GA USA: strain LTA-388 <- M. Yakrus, M.S., M.P.H., CDC, Tuberculosis Branch, Atlanta, GA USA <- J. de Waard, Inst. de Biomedicina, Caracas, Venezuela

doi: 10.13145/bacdive8530.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Mycobacteriaceae
  • genus: Mycobacterium
  • species: Mycobacterium cosmeticum
  • full scientific name: Mycobacterium cosmeticum Cooksey et al. 2004

  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacterium cosmeticum

@ref: 12011

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium cosmeticum

full scientific name: Mycobacterium cosmeticum Cooksey et al. 2004 emend. Nouioui et al. 2018

strain designation: LTA-388

type strain: yes

Morphology

cell morphology

@refcell lengthcell widthcell shapemotilityconfidencegram stain
312971.5 µm0.55 µmrod-shapedno
69480no94.73
69480100positive
118762rod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
20128Ivory (1014)10-14 days5006
20128Ivory (1014)10-14 daysBUG
20128Ivory (1014)10-14 daysMB7H9
606032 days

pigmentation

  • @ref: 31297
  • production: yes

multimedia

  • @ref: 12011
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44829.jpg
  • caption: Medium 645 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12011MIDDLEBROOK MEDIUM (DSMZ Medium 645)yeshttps://mediadive.dsmz.de/medium/645Name: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled water
20128BUGyes
201285006yesMedium: 5006 Name: Composition (g/l) Sucrose 3,0 Dextrin 15,0 Meat extract 1,0 Yeast extract 2,0 Tryptone soy broth (Oxoid) 5,0 NaCl 0,5 K2HPO4 0,5 MgSO4 x 7 H2O 0,5 FeSO4 x 7 H2O 0,01 Agar 20,0 Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7,3 Usage: Maintenance Organisms: All Actinomycetes
20128MB7H9yesName: Middlebrook 7H9 (MB7H9) Broth Base Composition: Middelbrook 7H9 Broth Base 4.7 g/l Glycerol 2.0 g/l Casaminoacids 11.0 g/l Yeast extract 5.5 g/l Tween80 (20%) 2.5 g/l OADC-Enrichment 100 ml Agar 15.0 g/l Preparation: Dissolve in Milli-Q-H2O. Before Use add 10% OADC stock solution Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Maintenance and revitalization Organisms: Mycobacteria OADC stock solution old broth-name: OADC-Stock Composition: Bovine Serum Albumin, fraction V 5 % 1% Oleic Acid in 0.2N NaOH 5ml Glucose 2 % NaCl 0.85 % Comments: Melt 1% Oleic Acid in 65°C water bath. Dissolve all ingredients in 700ml of ddH2O. Adjust volume to 1L. Filter sterilize and store at 4°C. -To make 1% Oleic Acid in 0.2N NaOH: Dissolve 5g oleic acid (ampule) in 500ml 0.2N NaOH (300ml ddH2O + 20ml NaOH + adjust volume to 500ml). Heat solution to 55°C for oleic acid to melt. Store at -20°C in 50ml aliquots. There is no need to sterilize this. Sterilisation: 20 minutes Temperature:121°C PH before: PH after: Biological details Culture type: suitable for: Mycobacteria
36388MEDIUM 55 - for Mycobacteriumyes
118762CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperaturerange
12011positivegrowth37mesophilic
20128positiveoptimum37mesophilic
31297positiveoptimum35mesophilic
36388positivegrowth30mesophilic
60603positivegrowth30mesophilic
67770positivegrowth28mesophilic
118762positivegrowth25-45
118762nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
60603aerobe
118762obligate aerobe

spore formation

@refspore formationconfidence
31297no
69481no99
69480no99.965

halophily

@refsaltgrowthtested relationconcentration
31297NaClpositivegrowth0-5 %
31297NaClpositiveoptimum2.5 %

observation

  • @ref: 31297
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3129722599arabinose+carbon source
3129716947citrate+carbon source
3129729864mannitol+carbon source
3129727082trehalose+carbon source
3129718222xylose+carbon source
3129717632nitrate+reduction
118762606565hippurate-hydrolysis
11876217632nitrate+reduction
11876216301nitrite-reduction
11876217632nitrate-respiration
6837917632nitrate-reduction
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837928087glycogen-fermentation

antibiotic resistance

  • @ref: 118762
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 118762
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31297arylsulfatase+3.1.6.1
68379gelatinase-
68379urease+3.5.1.5
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
118762oxidase-
118762beta-galactosidase-3.2.1.23
118762gelatinase-
118762amylase-
118762DNase-
118762caseinase-3.4.21.50
118762catalase+1.11.1.6
118762tween esterase+
118762gamma-glutamyltransferase+2.3.2.2
118762lecithinase-
118762lipase-
118762protease-
118762urease+3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382alpha-chymotrypsin-3.4.21.1
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
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYGControl
20128--------++-------+-
12011---+--+/---+----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20128-++-+--+-------+---
12011-+/-+-++/-+/---+----------
118762-++-+----+----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118762++-----------------+++-+----+--+++---------++----+----------+---+-----+-+-+-----++--+---+------++--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic locationisolation date
12011a granulomatous lesion of a female patientVenezuelaVENMiddle and South America
60603Human granulomatous subdermal lesionVenezuelaVENMiddle and South America2003Caracas
67770Granulomatous lesion of a female patientVenezuelaVENMiddle and South AmericaCaracas
118762Human, Granulomatous subdermal lesionVenezuelaVENMiddle and South AmericaCaracas2003

isolation source categories

Cat1Cat2Cat3
#Infection#Inflammation
#Infection#Patient
#Host#Human#Female

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
12011yes, in single cases1Risk group (German classification)
201282German classification
1187621Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium cosmeticum strain DSM 44829 16S ribosomal RNA gene, partial sequenceDQ124114532ena258533
12011Mycobacterium cosmeticum strain LTA-388 16S ribosomal RNA gene, partial sequenceAY4497281507ena258533

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium cosmeticum strain DSM 44829258533.3wgspatric258533
66792Mycolicibacterium cosmeticum strain DSM 44829258533.7wgspatric258533
66792Mycolicibacterium cosmeticum DSM 448292619619211draftimg258533
67770Mycolicibacterium cosmeticum DSM 44829GCA_000613185contigncbi258533
67770Mycolicibacterium cosmeticum DSM 44829GCA_005670675scaffoldncbi258533

GC content

  • @ref: 67770
  • GC-content: 68.2
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno91.91yes
gram-positiveyes86.339no
anaerobicno99.463yes
aerobicyes89.88no
halophileno95.585no
spore-formingno85.824yes
glucose-utilyes87.858no
flagellatedno97.732yes
thermophileno99.536yes
glucose-fermentno90.846yes

External links

@ref: 12011

culture collection no.: DSM 44829, ATCC BAA 878, CIP 108170, CCUG 55485, JCM 14739, KCTC 19713

straininfo link

  • @ref: 77918
  • straininfo: 127867

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15545488Mycobacterium cosmeticum sp. nov., a novel rapidly growing species isolated from a cosmetic infection and from a nail salon.Cooksey RC, de Waard JH, Yakrus MA, Rivera I, Chopite M, Toney SR, Morlock GP, Butler WRInt J Syst Evol Microbiol10.1099/ijs.0.63238-02004Bacterial Proteins/genetics, Bacterial Typing Techniques, *Beauty Culture, Chaperonin 60, Chaperonins/genetics, *Cosmetic Techniques, DNA Fingerprinting, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, DNA-Directed RNA Polymerases/genetics, Female, Genes, rRNA, Humans, Injections, Subcutaneous, Microinjections, Molecular Sequence Data, Mycobacterium/chemistry/*classification/*isolation & purification/physiology, Mycobacterium Infections/*microbiology, Mycolic Acids/analysis/isolation & purification, *Nails, Nucleic Acid Hybridization, Phylogeny, Pigments, Biological/biosynthesis, Polymorphism, Genetic, Polymorphism, Restriction Fragment Length, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Random Amplified Polymorphic DNA Technique, Sequence Analysis, DNA, Skin Diseases, Bacterial/*microbiology, Temperature, United States, VenezuelaEnzymology
Genetics24723727Draft Genome Sequence of Mycobacterium cosmeticum DSM 44829.Croce O, Robert C, Raoult D, Drancourt MGenome Announc10.1128/genomeA.00315-142014

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
12011Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44829)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44829
20128Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44829.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
31297Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127616
36388Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5763
60603Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55485)https://www.ccug.se/strain?id=55485
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
77918Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID127867.1StrainInfo: A central database for resolving microbial strain identifiers
118762Curators of the CIPCollection of Institut Pasteur (CIP 108170)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108170