Strain identifier

BacDive ID: 8528

Type strain: Yes

Species: Mycobacterium intracellulare subsp. chimaera

Strain Designation: FI-01069

Strain history: CIP <- 2003, E. Tortoli, Firenze, Italy: strain FI-01069 <- A. Nanetti

NCBI tax ID(s): 222805 (subspecies)

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General

@ref: 11935

BacDive-ID: 8528

DSM-Number: 44623

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, ovoid-shaped

description: Mycobacterium intracellulare subsp. chimaera FI-01069 is a microaerophile, mesophilic, ovoid-shaped bacterium that was isolated from bronchial lavage.

NCBI tax id

  • NCBI tax id: 222805
  • Matching level: subspecies

strain history

@refhistory
11935<- E. Tortoli; FI-01069 <- Nanetti
67770CIP 107892 <-- E. Tortoli FI-01069 <-- A. Nanetti.
118232CIP <- 2003, E. Tortoli, Firenze, Italy: strain FI-01069 <- A. Nanetti

doi: 10.13145/bacdive8528.20250331.9.3

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 intracellulare subsp. chimaera
  • full scientific name: Mycobacterium intracellulare subsp. chimaera (Tortoli et al. 2004) Nouioui et al. 2018

  • synonyms

    @refsynonym
    20215Mycobacterium yongonense
    20215Mycobacterium intracellulare subsp. yongonense
    20215Mycobacterium chimaera

@ref: 11935

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium intracellulare subsp. chimaera

full scientific name: Mycobacterium intracellulare subsp. chimaera (Tortoli et al. 2004) Nouioui et al. 2018

strain designation: FI-01069

type strain: yes

Morphology

cell morphology

@refcell shapemotilitygram stainconfidence
29977ovoid-shapedno
118232rod-shapedno
125439positive96.1

colony morphology

@refincubation periodmedium usedcolony color
2008010-14 days5006
2008010-14 daysBHI
2008010-14 daysBUG
2008010-14 daysMB7H9Cream (9001)

pigmentation

  • @ref: 29977
  • production: no

multimedia

@refmultimedia contentintellectual property rightscaption
11935https://www.dsmz.de/microorganisms/photos/DSM_44623-1.jpg© Leibniz-Institut DSMZ
11935https://www.dsmz.de/microorganisms/photos/DSM_44623-2.jpg© Leibniz-Institut DSMZ
11935https://www.dsmz.de/microorganisms/photos/DSM_44623-3.jpg© Leibniz-Institut DSMZ
11935https://www.dsmz.de/microorganisms/photos/DSM_44623.jpg© Leibniz-Institut DSMZMedium 645 37°C

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11935MIDDLEBROOK 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
20080BUGyes
20080BHIyes
200805006yesMedium: 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
20080MB7H9yesName: 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
36332MEDIUM 55 - for Mycobacteriumyes
118232CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperature
11935positivegrowth37
20080positiveoptimum37
29977positivegrowth25-37
36332positivegrowth37
59077positivegrowth37
67770positivegrowth37
118232positivegrowth22-30
118232nogrowth10
118232nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
59077microaerophile
118232obligate aerobe
125439obligate aerobe99

spore formation

  • @ref: 29977
  • spore formation: no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837917992sucrose+fermentation
6837917716lactose+fermentation
6837917306maltose+fermentation
6837916899D-mannitol-fermentation
6837965327D-xylose-fermentation
6837916988D-ribose-fermentation
683795291gelatin-hydrolysis
6837916199urea+hydrolysis
6837917632nitrate+reduction
118232606565hippurate-hydrolysis
11823217632nitrate+reduction
11823216301nitrite-reduction
11823217632nitrate-respiration
6837928087glycogen-fermentation
6837917634D-glucose+fermentation
683794853esculin-hydrolysis

metabolite production

  • @ref: 118232
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
29977catalase+1.11.1.6
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-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
118232oxidase-
118232beta-galactosidase+3.2.1.23
118232gelatinase-
118232amylase-
118232caseinase-3.4.21.50
118232catalase+1.11.1.6
118232tween esterase-
118232gamma-glutamyltransferase+2.3.2.2
118232lecithinase-
118232lipase-
118232protease-
118232urease-3.5.1.5
68379urease+3.5.1.5
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68382alpha-galactosidase-3.2.1.22
68382valine arylamidase-
68379gelatinase-
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase-3.2.1.23
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase+3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20080++-+-----+-+---+++-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20080-++----------------
118232-++-+----++---------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudesampling date
11935bronchial lavageBolognaItalyITAEurope44.49911.3276
59077Human bronchial alveolar lavage,56-yr-old womanBolognaItalyITAEurope2001
67770Bronchial lavageItalyITAEurope
118232Human, LungBolognaItalyITAEurope

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Oral cavity and airways
#Host Body Product#Oral cavity and Airways#Bronchial wash

taxonmaps

  • @ref: 69479
  • File name: preview.99_402.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_37;97_39;98_43;99_402&stattab=map
  • Last taxonomy: Mycobacterium
  • 16S sequence: GQ153281
  • Sequence Identity:
  • Total samples: 24078
  • soil counts: 12779
  • aquatic counts: 4789
  • animal counts: 3677
  • plant counts: 2833

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
119352Risk group (German classification)
200802German classification
1182322Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium chimaera strain CIP 107892 16S ribosomal RNA gene, partial sequenceAY943208493nuccore222805
20218Mycobacterium chimaera strain DSM 446232 16S ribosomal RNA gene, partial sequenceEF5218941440nuccore222805
20218Mycobacterium chimaera strain DSM 446232 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequenceEF521902438nuccore222805
20218Mycobacterium chimaera strain CIP107892 16S ribosomal RNA gene, partial sequenceGQ1532811495nuccore222805
11935Mycobacterium chimaera 16S rRNA gene and ITS1, type strain FI-0169TAJ5484801766nuccore222805
124043Mycobacterium chimaera strain CIP107892 16S ribosomal RNA gene, partial sequence.GQ1532651492nuccore53378
124043Mycobacterium chimaera strain CIP107892 16S ribosomal RNA gene, partial sequence.GQ1532661492nuccore53378
124043Mycobacterium chimaera strain CIP107892 16S ribosomal RNA gene, partial sequence.GQ1532671492nuccore53378
124043Mycobacterium chimaera strain CIP107892 16S ribosomal RNA gene, partial sequence.GQ1532681492nuccore53378
124043Mycobacterium chimaera strain CIP107892 16S ribosomal RNA gene, partial sequence.GQ1532691492nuccore53378

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium intracellulare subsp. chimaera DSM 44623GCA_002219285completencbi222805
66792Mycobacterium chimaera strain DSM 44623222805.20wgspatric222805
66792Mycobacterium chimaera strain DSM 44623222805.39plasmidpatric222805
66792Mycobacterium chimaera strain DSM 44623222805.24completepatric222805
66792Mycobacterium chimaera strain DSM 44623222805.42plasmidpatric222805
67770Mycobacterium intracellulare subsp. chimaera DSM 44623GCA_002101575contigncbi222805
67770Mycobacterium intracellulare subsp. chimaera JCM_14737GCA_001938095contigncbi222805
66792Mycobacterium intracellulare subsp. chimaera DSM 44623GCA_025822785scaffoldncbi222805

GC content

  • @ref: 67770
  • GC-content: 67.7
  • method: genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes89.741no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.995yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes80.755no
125438spore-formingspore-formingAbility to form endo- or exosporesno62.271yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.676yes
125438motile2+flagellatedAbility to perform flagellated movementno87.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno56.9
125439BacteriaNetmotilityAbility to perform movementno78.5
125439BacteriaNetgram_stainReaction to gram-stainingpositive96.1
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99

External links

@ref: 11935

culture collection no.: DSM 44623, CIP 107892, CCUG 50989, JCM 14737

straininfo link

  • @ref: 77916
  • straininfo: 132789

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15280303Proposal to elevate the genetic variant MAC-A, included in the Mycobacterium avium complex, to species rank as Mycobacterium chimaera sp. nov.Tortoli E, Rindi L, Garcia MJ, Chiaradonna P, Dei R, Garzelli C, Kroppenstedt RM, Lari N, Mattei R, Mariottini A, Mazzarelli G, Murcia MI, Nanetti A, Piccoli P, Scarparo CInt J Syst Evol Microbiol10.1099/ijs.0.02777-02004Aged, DNA Fingerprinting, DNA Transposable Elements, DNA, Bacterial/chemistry, DNA, Ribosomal/chemistry, DNA, Ribosomal Spacer/chemistry, Female, Genes, rRNA, Humans, Male, Microbial Sensitivity Tests, Middle Aged, Molecular Sequence Data, Mycobacterium avium Complex/chemistry/*classification/*genetics/isolation & purification, Mycobacterium avium-intracellulare Infection/microbiology, Mycolic Acids/analysis, Nucleic Acid Hybridization, Phylogeny, Polymorphism, Restriction Fragment Length, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence HomologyPathogenicity
Phylogeny19625425Mycobacterium mantenii sp. nov., a pathogenic, slowly growing, scotochromogenic species.van Ingen J, Lindeboom JA, Hartwig NG, de Zwaan R, Tortoli E, Dekhuijzen PN, Boeree MJ, van Soolingen DInt J Syst Evol Microbiol10.1099/ijs.0.010405-02009Aged, Aged, 80 and over, Bacterial Proteins/genetics, Child, Preschool, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Female, Humans, Infant, Lymph Nodes/microbiology, Male, Molecular Sequence Data, Mycobacterium/classification/*isolation & purification/metabolism/pathogenicity, Mycobacterium Infections/*microbiology, Phylogeny, Pigments, Biological/*metabolism, RNA, Ribosomal, 16S/geneticsPathogenicity
Phylogeny22427442Mycobacterium yongonense sp. nov., a slow-growing non-chromogenic species closely related to Mycobacterium intracellulare.Kim BJ, Math RK, Jeon CO, Yu HK, Park YG, Kook YH, Kim BJInt J Syst Evol Microbiol10.1099/ijs.0.037465-02012DNA, Bacterial/genetics, DNA, Ribosomal Spacer/genetics, Genes, Bacterial, Humans, Lipids/analysis, Lung Diseases/*microbiology, Molecular Sequence Data, Mycobacterium/*classification/genetics/isolation & purification, Mycobacterium Infections/*microbiology, Mycobacterium avium Complex/genetics, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of KoreaPathogenicity
Genetics29702266Genome sequence of Mycobacterium yongonense RT 955-2015 isolate from a patient misdiagnosed with multidrug-resistant tuberculosis: First clinical detection in Tanzania.Mnyambwa NP, Kim DJ, Ngadaya E, Chun J, Ha SM, Petrucka P, Addo KK, Kazwala RR, Mfinanga SGInt J Infect Dis10.1016/j.ijid.2018.04.7962018Diagnostic Errors, Genotype, Humans, Male, Middle Aged, Mycobacterium avium Complex/classification/genetics/*isolation & purification, Phylogeny, Tanzania, Tuberculosis, Multidrug-Resistant/diagnosis/*microbiology, Whole Genome SequencingPhylogeny
Phylogeny29777159Identification of Mycobacterium chimaera in heater-cooler units in China.Zhang X, Lin J, Feng Y, Wang X, McNally A, Zong ZSci Rep10.1038/s41598-018-26289-52018China/epidemiology, Cross Infection/microbiology, DNA, Bacterial/genetics, Disease Outbreaks, *Equipment Contamination, Humans, Mycobacterium/*classification/genetics/isolation & purification, Mycobacterium Infections/*epidemiology/microbiology, Phylogeny, Polymorphism, Single Nucleotide, Water Microbiology, Whole Genome Sequencing/*methodsPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
11935Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44623)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44623
20080Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44623.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
29977Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126345
36332Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5453
59077Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 50989)https://www.ccug.se/strain?id=50989
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
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
77916Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID132789.1StrainInfo: A central database for resolving microbial strain identifiers
118232Curators of the CIPCollection of Institut Pasteur (CIP 107892)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107892
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1