Name: Mycobacterium intracellulare subsp. chimaera FI-01069
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 8528

Type strain:

Species: Mycobacterium intracellulare subsp. chimaera

Strain Designation: FI-01069

Culture col. no.: DSM 44623, CIP 107892, CCUG 50989, JCM 14737

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

NCBI tax ID(s): 222805 (subspecies)

SI-ID 132789

CIP 107892, DSM 44623, CCUG 50989, JCM 14737

Special Collections

Other strains from Mycobacterium intracellulare subsp. chimaera

Section

When using BacDive for research please cite our paper

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

ovoid-shaped
mesophilic
microaerophile
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Mycobacteriales*
	Family	*Mycobacteriaceae*
	Genus	*Mycobacterium*
	Species	**Mycobacterium intracellulare subsp. chimaera**
	Full Scientific Name (LPSN)	Mycobacterium intracellulare subsp. chimaera (Tortoli et al. 2004) Nouioui et al. 2018

	Synonym	Mycobacterium yongonense
	Synonym	Mycobacterium intracellulare subsp. yongonense
	Synonym	Mycobacterium chimaera

Information on morphological and physiological properties Morphology

[Ref.: #125439]	Gram stain	positive Confidence in %96.1

[Ref.: #29977]	Cell shape	ovoid-shaped
[Ref.: #118232]	Cell shape	rod-shaped

[Ref.: #29977]	Motility	no
[Ref.: #118232]	Motility	no

[Ref.: #20080]	Colony color	Cream (9001)
[Ref.: #20080]	Incubation period	10-14 days
[Ref.: #20080]	Cultivation medium used	MB7H9

[Ref.: #20080]	Incubation period	10-14 days
[Ref.: #20080]	Cultivation medium used	5006

[Ref.: #20080]	Incubation period	10-14 days
[Ref.: #20080]	Cultivation medium used	BHI

[Ref.: #20080]	Incubation period	10-14 days
[Ref.: #20080]	Cultivation medium used	BUG

[Ref.: #29977]

Pigment production

Multimedia content

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Intellectual property rights:

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Intellectual property rights:

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Intellectual property rights:

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Caption:

Medium 645 37°C

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Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

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Culture medium

MIDDLEBROOK MEDIUM (DSMZ Medium 645)

[Ref.: #11935]

Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #11935]

Culture medium composition

expand / minimize

[Ref.: #20080]

Culture medium

BUG

[Ref.: #20080]

Culture medium growth

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Culture medium

BHI

[Ref.: #20080]

Culture medium growth

[Ref.: #20080]

Culture medium

5006

[Ref.: #20080]

Culture medium growth

[Ref.: #20080]

Culture medium composition

expand / minimize

[Ref.: #20080]

Culture medium

MB7H9

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Culture medium growth

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Culture medium composition

expand / minimize

[Ref.: #36332]

Culture medium

MEDIUM 55 - for Mycobacterium

[Ref.: #36332]

Culture medium growth

[Ref.: #118232]

Culture medium

CIP Medium 55

[Ref.: #118232]

Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #11935]		growth	37 °C
[Ref.: #20080]		optimum	37 °C
[Ref.: #29977]		growth	25-37 °C
[Ref.: #36332]		growth	37 °C
[Ref.: #59077]		growth	37 °C
[Ref.: #67770]		growth	37 °C
[Ref.: #118232]		growth	22-30 °C
[Ref.: #118232]	no	growth	10 °C
[Ref.: #118232]	no	growth	45 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #59077]	Oxygen tolerance	microaerophile
[Ref.: #118232]	Oxygen tolerance	obligate aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %99

[Ref.: #29977]

Ability of spore formation

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68379]	D-glucose ChEBI	+	fermentation	* from API Coryne
[Ref.: #68379]	D-mannitol ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-ribose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-xylose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	esculin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #68379]	gelatin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #118232]	hippurate ChEBI	-	hydrolysis
[Ref.: #68379]	lactose ChEBI	+	fermentation	* from API Coryne
[Ref.: #68379]	maltose ChEBI	+	fermentation	* from API Coryne
[Ref.: #118232]	nitrate ChEBI	+	reduction
[Ref.: #118232]	nitrate ChEBI	-	respiration
[Ref.: #68379]	nitrate ChEBI	+	reduction	* from API Coryne
[Ref.: #118232]	nitrite ChEBI	-	reduction
[Ref.: #68379]	sucrose ChEBI	+	fermentation	* from API Coryne
[Ref.: #68379]	urea ChEBI	+	hydrolysis	* from API Coryne
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #118232]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68379]	alkaline phosphatase	+	3.1.3.1	* from API Coryne
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym, API Coryne
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #118232]	amylase	-
[Ref.: #118232]	beta-galactosidase	+	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym, API Coryne
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym, API Coryne
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym, API Coryne
[Ref.: #118232]	caseinase	-	3.4.21.50
[Ref.: #29977]	catalase	+	1.11.1.6
[Ref.: #118232]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #118232]	gamma-glutamyltransferase	+	2.3.2.2
[Ref.: #118232]	gelatinase	-
[Ref.: #68379]	gelatinase	-		* from API Coryne
[Ref.: #118232]	lecithinase	-
[Ref.: #118232]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym, API Coryne
[Ref.: #118232]	oxidase	-
[Ref.: #118232]	protease	-
[Ref.: #68379]	pyrazinamidase	+	3.5.1.B15	* from API Coryne
[Ref.: #68379]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API Coryne
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #118232]	tween esterase	-
[Ref.: #118232]	urease	-	3.5.1.5
[Ref.: #68379]	urease	+	3.5.1.5	* from API Coryne
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Coryne:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitrateNIT	PyrazinamidasePYZ	Pyrrolidonyl arylamidasePYRA	Alkaline phosphatasePAL	beta-Glucuronidasebeta GUR	beta-Galactosidasebeta GAL	alpha-Glucosidasealpha GLU	N-Acetyl-beta-Glucosidasebeta NAG	Esculin hydrolysis/beta-GlucosidaseESC	Urease/urea hydrolysisURE	Gelatinase/gelatin hydrolysisGEL	Control fermentationControl	Fermentation of D-glucoseGLU	Fermentation of D-riboseRIB	Fermentation of D-xyloseXYL	Fermentation of D-mannitolMAN	Fermentation of maltoseMAL	Fermentation of lactoseLAC	Fermentation of sucroseSAC	Fermentation of glycogenGLYG	CatalaseCAT
[Ref.: #20080]	429	+	+	-	+	-	-	-	-	-	+	-	not determinedn.d.	+	-	-	-	+	+	+	-	not determinedn.d.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #20080]	862	not determinedn.d.	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
[Ref.: #118232]	10727	-	-	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #11935]	Sample type/isolated from	bronchial lavage
[Ref.: #11935]	Geographic location (country and/or sea, region)	Bologna
[Ref.: #11935]	Country	Italy
[Ref.: #11935]	Country ISO 3 Code	ITA
[Ref.: #11935]	Continent	Europe
[Ref.: #11935]	Geographic location	44.4990°/11.3276°

[Ref.: #59077]	Sample type/isolated from	Human bronchial alveolar lavage,56-yr-old woman
[Ref.: #59077]	Sampling date	2001
[Ref.: #59077]	Geographic location (country and/or sea, region)	Bologna
[Ref.: #59077]	Country	Italy
[Ref.: #59077]	Country ISO 3 Code	ITA
[Ref.: #59077]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Bronchial lavage
[Ref.: #67770]	Country	Italy
[Ref.: #67770]	Country ISO 3 Code	ITA
[Ref.: #67770]	Continent	Europe

[Ref.: #118232]	Sample type/isolated from	Human, Lung
[Ref.: #118232]	Geographic location (country and/or sea, region)	Bologna
[Ref.: #118232]	Country	Italy
[Ref.: #118232]	Country ISO 3 Code	ITA
[Ref.: #118232]	Continent	Europe
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence GQ153281 (>99% sequence identity) for Mycobacterium from Microbeatlas

Aquatic Samples	4789
Soil Samples	12779
Animal Samples	3677
Plant Samples	2833
Total Samples	24078

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #11935]	Biosafety level	2	Risk group (German classification) According to TRBA 466
[Ref.: #20080]	Biosafety level	2	German classification
[Ref.: #118232]	Biosafety level	2	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #11935]	Mycobacterium chimaera 16S rRNA gene and ITS1, type strain FI-0169T	AJ548480	1766	GenBank ENA	222805 tax ID
[Ref.: #20218]	Mycobacterium chimaera strain CIP107892 16S ribosomal RNA gene, partial sequence	GQ153281	1495	GenBank ENA	222805 tax ID	*
[Ref.: #124043]	Mycobacterium chimaera strain CIP107892 16S ribosomal RNA gene, partial sequence.	GQ153265	1492	GenBank ENA	53378 tax ID	*
[Ref.: #124043]	Mycobacterium chimaera strain CIP107892 16S ribosomal RNA gene, partial sequence.	GQ153266	1492	GenBank ENA	53378 tax ID	*
[Ref.: #124043]	Mycobacterium chimaera strain CIP107892 16S ribosomal RNA gene, partial sequence.	GQ153267	1492	GenBank ENA	53378 tax ID	*
[Ref.: #124043]	Mycobacterium chimaera strain CIP107892 16S ribosomal RNA gene, partial sequence.	GQ153268	1492	GenBank ENA	53378 tax ID	*
[Ref.: #124043]	Mycobacterium chimaera strain CIP107892 16S ribosomal RNA gene, partial sequence.	GQ153269	1492	GenBank ENA	53378 tax ID	*
[Ref.: #20218]	Mycobacterium chimaera strain CIP 107892 16S ribosomal RNA gene, partial sequence	AY943208	493	GenBank ENA	222805 tax ID	*
[Ref.: #20218]	Mycobacterium chimaera strain DSM 446232 16S ribosomal RNA gene, partial sequence	EF521894	1440	GenBank ENA	222805 tax ID	*
[Ref.: #20218]	Mycobacterium chimaera strain DSM 446232 16S ribosomal RNA gene and 16S-23S ribosomal RNA intergenic spacer, partial sequence	EF521902	438	GenBank ENA	222805 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Mycobacterium intracellulare subsp. chimaera DSM 44623	GCA_002101575	contig	GenBank ENA	222805 tax ID
[Ref.: #67770]	Mycobacterium intracellulare subsp. chimaera JCM_14737	GCA_001938095	contig	GenBank ENA	222805 tax ID
[Ref.: #66792]	Mycobacterium intracellulare subsp. chimaera DSM 44623	GCA_025822785	scaffold	GenBank ENA	222805 tax ID	*
[Ref.: #66792]	Mycobacterium chimaera strain DSM 44623	222805.20	wgs	PATRIC	222805 tax ID	*
[Ref.: #66792]	Mycobacterium chimaera strain DSM 44623	222805.39	plasmid	PATRIC	222805 tax ID	*
[Ref.: #66792]	Mycobacterium chimaera strain DSM 44623	222805.24	complete	PATRIC	222805 tax ID	*

[Ref.: #67770]

GC-content

67.7 mol%

genome sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Mycobacterium intracellulare subsp. chimaera DSM 44623 NCBI: GCA_002219285.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	89.741	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	95.995	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	80.755	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	62.271	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	95.676	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	87.5	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Mycobacterium chimaera strain DSM 44623 PATRIC: 222805.24
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	56.9
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	78.5
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	96.1
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	99

Availability in culture collections External links

[Ref.: #11935]

Culture collection no.

DSM 44623, CIP 107892, CCUG 50989, JCM 14737

[Ref.: #77916]

SI-ID 132789

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	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	*
Genetics	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	*
Phylogeny	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	*
Phylogeny	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	*
Phylogeny	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	*

References

#11935

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44623

#20080

Wink, J.: 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.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#29977

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26345 (see below)

#36332 ; Curators of the CIP;
#59077 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 50989

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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.: MicrobeAtlas 1.0 beta .

#77916

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID132789.1 )

#118232 Collection of Institut Pasteur ; Curators of the CIP; CIP 107892

#124043

Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

#125438

Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )

#125439

Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .

#26345

IJSEM 1277 2004 ( DOI 10.1099/ijs.0.02777-0 , PubMed 15280303 )

* These data were automatically processed and therefore are not curated

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Mycobacterium intracellulare subsp. chimaera DSM 44623

Mycobacterium chimaera strain DSM 44623

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