Strain identifier
BacDive ID: 8528
Type strain:
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)
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
@ref | history |
---|---|
11935 | <- E. Tortoli; FI-01069 <- Nanetti |
67770 | CIP 107892 <-- E. Tortoli FI-01069 <-- A. Nanetti. |
118232 | CIP <- 2003, E. Tortoli, Firenze, Italy: strain FI-01069 <- A. Nanetti |
doi: 10.13145/bacdive8528.20230509.8.1
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 intracellulare subsp. chimaera
- full scientific name: Mycobacterium intracellulare subsp. chimaera (Tortoli et al. 2004) Nouioui et al. 2018
synonyms
@ref synonym 20215 Mycobacterium yongonense 20215 Mycobacterium chimaera 20215 Mycobacterium intracellulare subsp. yongonense
@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
@ref | cell shape | motility |
---|---|---|
29977 | ovoid-shaped | no |
118232 | rod-shaped | no |
colony morphology
@ref | incubation period | medium used | colony color |
---|---|---|---|
20080 | 10-14 days | 5006 | |
20080 | 10-14 days | BHI | |
20080 | 10-14 days | BUG | |
20080 | 10-14 days | MB7H9 | Cream (9001) |
pigmentation
- @ref: 29977
- production: no
multimedia
@ref | multimedia content | intellectual property rights | caption |
---|---|---|---|
11935 | https://www.dsmz.de/microorganisms/photos/DSM_44623-1.jpg | © Leibniz-Institut DSMZ | |
11935 | https://www.dsmz.de/microorganisms/photos/DSM_44623-2.jpg | © Leibniz-Institut DSMZ | |
11935 | https://www.dsmz.de/microorganisms/photos/DSM_44623-3.jpg | © Leibniz-Institut DSMZ | |
11935 | https://www.dsmz.de/microorganisms/photos/DSM_44623.jpg | © Leibniz-Institut DSMZ | Medium 645 37°C |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
11935 | MIDDLEBROOK MEDIUM (DSMZ Medium 645) | yes | https://mediadive.dsmz.de/medium/645 | Name: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled water |
20080 | BUG | yes | ||
20080 | BHI | yes | ||
20080 | 5006 | yes | Medium: 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 | |
20080 | MB7H9 | yes | Name: 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 | |
36332 | MEDIUM 55 - for Mycobacterium | yes | ||
118232 | CIP Medium 55 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
11935 | positive | growth | 37 | mesophilic |
20080 | positive | optimum | 37 | mesophilic |
29977 | positive | growth | 25-37 | mesophilic |
36332 | positive | growth | 37 | mesophilic |
59077 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
118232 | positive | growth | 22-30 | |
118232 | no | growth | 10 | psychrophilic |
118232 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
59077 | microaerophile |
118232 | obligate aerobe |
spore formation
- @ref: 29977
- spore formation: no
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
118232 | 606565 | hippurate | - | hydrolysis |
118232 | 17632 | nitrate | + | reduction |
118232 | 16301 | nitrite | - | reduction |
118232 | 17632 | nitrate | - | respiration |
68379 | 17632 | nitrate | + | reduction |
68379 | 4853 | esculin | - | hydrolysis |
68379 | 16199 | urea | + | hydrolysis |
68379 | 5291 | gelatin | - | hydrolysis |
68379 | 17634 | D-glucose | + | fermentation |
68379 | 16988 | D-ribose | - | fermentation |
68379 | 65327 | D-xylose | - | fermentation |
68379 | 16899 | D-mannitol | - | fermentation |
68379 | 17306 | maltose | + | fermentation |
68379 | 17716 | lactose | + | fermentation |
68379 | 17992 | sucrose | + | fermentation |
68379 | 28087 | glycogen | - | fermentation |
metabolite production
- @ref: 118232
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
29977 | catalase | + | 1.11.1.6 |
68379 | gelatinase | - | |
68379 | urease | + | 3.5.1.5 |
68379 | beta-glucosidase | - | 3.2.1.21 |
68379 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68379 | alpha-glucosidase | - | 3.2.1.20 |
68379 | beta-galactosidase | - | 3.2.1.23 |
68379 | beta-glucuronidase | - | 3.2.1.31 |
68379 | alkaline phosphatase | + | 3.1.3.1 |
68379 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68379 | pyrazinamidase | + | 3.5.1.B15 |
118232 | oxidase | - | |
118232 | beta-galactosidase | + | 3.2.1.23 |
118232 | gelatinase | - | |
118232 | amylase | - | |
118232 | caseinase | - | 3.4.21.50 |
118232 | catalase | + | 1.11.1.6 |
118232 | tween esterase | - | |
118232 | gamma-glutamyltransferase | + | 2.3.2.2 |
118232 | lecithinase | - | |
118232 | lipase | - | |
118232 | protease | - | |
118232 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API coryne
@ref | NIT | PYZ | PYRA | PAL | beta GUR | beta GAL | alpha GLU | beta NAG | ESC | URE | GEL | GLU | RIB | XYL | MAN | MAL | LAC | SAC | GLYG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
20080 | + | + | - | + | - | - | - | - | - | + | - | + | - | - | - | + | + | + | - |
API zym
@ref | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase | Control |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
20080 | - | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | |
118232 | - | + | + | - | + | - | - | - | - | + | + | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude | sampling date |
---|---|---|---|---|---|---|---|---|
11935 | bronchial lavage | Bologna | Italy | ITA | Europe | 44.499 | 11.3276 | |
59077 | Human bronchial alveolar lavage,56-yr-old woman | Bologna | Italy | ITA | Europe | 2001 | ||
67770 | Bronchial lavage | Italy | ITA | Europe | ||||
118232 | Human, Lung | Bologna | Italy | ITA | Europe |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | biosafety level | biosafety level comment |
---|---|---|
11935 | 2 | Risk group (German classification) |
20080 | 2 | German classification |
118232 | 2 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Mycobacterium chimaera strain CIP 107892 16S ribosomal RNA gene, partial sequence | AY943208 | 493 | ena | 222805 |
20218 | Mycobacterium chimaera strain DSM 446232 16S ribosomal RNA gene, partial sequence | EF521894 | 1440 | ena | 222805 |
20218 | Mycobacterium chimaera strain DSM 446232 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequence | EF521902 | 438 | ena | 222805 |
20218 | Mycobacterium chimaera strain CIP107892 16S ribosomal RNA gene, partial sequence | GQ153281 | 1495 | ena | 222805 |
11935 | Mycobacterium chimaera 16S rRNA gene and ITS1, type strain FI-0169T | AJ548480 | 1766 | ena | 222805 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Mycobacterium intracellulare subsp. chimaera DSM 44623 | GCA_002219285 | complete | ncbi | 222805 |
66792 | Mycobacterium chimaera strain DSM 44623 | 222805.20 | wgs | patric | 222805 |
66792 | Mycobacterium chimaera strain DSM 44623 | 222805.39 | plasmid | patric | 222805 |
66792 | Mycobacterium chimaera strain DSM 44623 | 222805.24 | complete | patric | 222805 |
66792 | Mycobacterium chimaera strain DSM 44623 | 222805.42 | plasmid | patric | 222805 |
67770 | Mycobacterium intracellulare subsp. chimaera DSM 44623 | GCA_002101575 | contig | ncbi | 222805 |
67770 | Mycobacterium intracellulare subsp. chimaera JCM_14737 | GCA_001938095 | contig | ncbi | 222805 |
66792 | Mycobacterium intracellulare subsp. chimaera DSM 44623 | GCA_025822785 | scaffold | ncbi | 222805 |
GC content
- @ref: 67770
- GC-content: 67.7
- method: genome sequence analysis
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
flagellated | no | 98.961 | yes |
gram-positive | yes | 90.833 | no |
anaerobic | no | 99.561 | yes |
aerobic | yes | 89.651 | yes |
halophile | no | 91.356 | no |
spore-forming | no | 85.556 | no |
thermophile | no | 98.657 | yes |
glucose-util | yes | 65.876 | no |
motile | no | 94.339 | yes |
glucose-ferment | no | 90.642 | yes |
External links
@ref: 11935
culture collection no.: DSM 44623, CIP 107892, CCUG 50989, JCM 14737
straininfo link
- @ref: 77916
- straininfo: 132789
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 15280303 | Proposal 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 C | Int J Syst Evol Microbiol | 10.1099/ijs.0.02777-0 | 2004 | Aged, 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 Homology | Pathogenicity |
Phylogeny | 19625425 | Mycobacterium 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 D | Int J Syst Evol Microbiol | 10.1099/ijs.0.010405-0 | 2009 | Aged, 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/genetics | Pathogenicity |
Phylogeny | 22427442 | Mycobacterium 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 BJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.037465-0 | 2012 | DNA, 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 Korea | Pathogenicity |
Genetics | 29702266 | Genome 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 SG | Int J Infect Dis | 10.1016/j.ijid.2018.04.796 | 2018 | Diagnostic Errors, Genotype, Humans, Male, Middle Aged, Mycobacterium avium Complex/classification/genetics/*isolation & purification, Phylogeny, Tanzania, Tuberculosis, Multidrug-Resistant/diagnosis/*microbiology, Whole Genome Sequencing | Phylogeny |
Phylogeny | 29777159 | Identification of Mycobacterium chimaera in heater-cooler units in China. | Zhang X, Lin J, Feng Y, Wang X, McNally A, Zong Z | Sci Rep | 10.1038/s41598-018-26289-5 | 2018 | China/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/*methods | Pathogenicity |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
---|---|---|---|---|---|---|---|
11935 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44623) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44623 | ||||
20080 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM44623.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | ||||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | ||||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | ||
29977 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28776041 | 26345 | ||
36332 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5453 | |||||
59077 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 50989) | https://www.ccug.se/strain?id=50989 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
68379 | Automatically annotated from API Coryne | ||||||
68382 | Automatically annotated from API zym | ||||||
69479 | João 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 | ||||
77916 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID132789.1 | StrainInfo: A central database for resolving microbial strain identifiers | ||||
118232 | Curators of the CIP | Collection of Institut Pasteur (CIP 107892) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107892 |