Search tips
Search criteria 


Logo of genannJournal InfoAuthorsPermissionsJournals.ASM.orggenomeA ArticleGenome Announcements
Genome Announc. 2016 May-Jun; 4(3): e00638-16.
Published online 2016 June 30. doi:  10.1128/genomeA.00638-16
PMCID: PMC4929519

First Draft Genome Sequence of a Mycobacterium gordonae Clinical Isolate


Here, we report the first draft genome sequence of the clinically relevant species Mycobacterium gordonae. The clinical isolate Mycobacterium gordonae 14-8773 was obtained from the sputum of a patient with mycobacteriosis.


Mycobacterium gordonae is a nontuberculous mycobacterium, named for Ruth E. Gordon, who first isolated the species. M. gordonae grows slowly, forming smooth, yellow- or orange-colored colonies. Of all the mycobacteria species, M. gordonae is one of the least pathogenic. Its isolation from samples of sputum obtained from patients is typically regarded as a contamination. Such a contamination can be associated with a patient’s use of tap water for mouth rinsing or for drinking to obtain better expectoration just before preparing a test sample (1). Despite its nonvirulent nature, there have been reports of clinically significant diseases caused by M. gordonae, including disseminated infections (2), urogenital tract diseases (3), gastrointestinal tract infections (4), soft tissue damage (5), and respiratory and pulmonary infections (6,8).

We report here the first draft genome sequence of M. gordonae clinical isolate 14-8773, which was obtained from the sputum of a patient admitted to a tuberculosis hospital with suspected pulmonary tuberculosis (confirmed by lung abnormalities in a chest X ray and positive test results from an acid-fast stain). Two isolates were obtained on Löwenstein-Jensen medium from two different portions of sputum. The genomic DNA of M. gordonae was extracted by the guanidiniumthiocyanate DNA isolation method with sorbtion on magnetic beads and purified by phenol-chloroform-isoamyl alcohol separation followed by ethanol precipitation. Species identification of the two cultures was carried out using the GenoType CM test system (Hain Lifescience, Germany). The identification result for clinical isolate 14-8773 was confirmed by 16S rRNA gene sequencing.

Paired-end libraries with an average insert size of 500 bp were generated using the Illumina Nextera XT DNA sample preparation kit according to the manufacturer’s protocol. Sequencing was performed on the Illumina MiSeq platform with a 2 × 250 paired-end run (theoretical coverage of 200×). The obtained reads were analyzed and quality-checked using FastQC version 0.11.3 (9), and subsequently trimmed. Illumina adapters, bases with quality lower than Q30, N bases, and reads shorter than 50 bp were removed using Trimmomatic version 0.33 (10). Reads were assembled using SPAdes version 3.5.0 (11) with the “--careful” option and with k values of 21, 33, 55, 77, 99, and 127. The final assembly consisted of 377 contigs comprising 7,552,315 bp with an N50 of 61,403 bp and a GC content of 66.76%. Annotation was carried out using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (12). PGAP annotation resulted in 6,889 predicted genes, 6,413 coding sequences, 424 pseudogenes, one 16S rRNA, one 23S rRNA, one 5S rRNA, 48 tRNAs, and one noncoding RNA.

This draft genome sequence and its functional annotation analysis will help to unravel the phylogeny of Mycobacterium gordonae, as well as its metabolic and pathogenic potential.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number LKTM00000000. The version described in this paper is the first version, LKTM01000000.


Whole-genome sequencing was performed at the Common-Use Center “Biotechnology” of the All-Russia Research Institute of Agriculture Biotechnology, Moscow. We thank the center staff for their help.


Citation Ustinova V, Smirnova T, Blagodatskikh K, Varlamov D, Sochivko D, Larionova E, Andreevskaya S, Andrievskaya I, Chernousova L. 2016. First draft genome sequence of a Mycobacterium gordonae clinical isolate. Genome Announc 4(3):e00638-16. doi:10.1128/genomeA.00638-16.


1. Arnow PM, Bakir M, Thompson K, Bova JL 2000. Endemic contamination of clinical specimens by Mycobacterium gordonae. Clin Infect Dis 31:472–476. doi:.10.1086/313940 [PubMed] [Cross Ref]
2. Weinberger M, Berg SL, Feuerstein IM, Pizzo PA, Witebsky FG 1992. Disseminated infection with Mycobacterium gordonae: report of a case and critical review of the literature. Clin Infect Dis 14:1229–1239. doi:.10.1093/clinids/14.6.1229 [PubMed] [Cross Ref]
3. Jarikre LN. 1992. Mycobacterium gordonae genitourinary disease. Genitourin Med 68:45–46. doi:.10.1136/sti.68.1.45 [PMC free article] [PubMed] [Cross Ref]
4. Mizoshita T, Tanida S, Mizushima T, Hirata Y, Murakami K, Shimura T, Mori Y, Kataoka H, Kamiya T, Joh T 2011. A rare case of infectious colitis with ulcers in the cecum caused by Mycobacterium gordonae. Intern Med 50:2583–2586. doi:.10.2169/internalmedicine.50.6238 [PubMed] [Cross Ref]
5. Foti C, Sforza V, Rizzo C, De Pascale G, Bonamonte D, Conserva A, Tarantino A, Stella C, Cantore S, Grassi RF, Ballini A, De Vito D, Angelini G 2009. Cutaneous manifestations of Mycobacterium gordonae infection described for the first time in Italy: a case report. Cases J 2:6828. [PMC free article] [PubMed]
6. Thomson R, Tolson C, Carter R, Coulter C, Huygens F, Hargreaves M 2013. Isolation of nontuberculous mycobacteria (NTM) from household water and shower aerosols in patients with pulmonary disease caused by NTM. J Clin Microbiol 51:3006–3011. doi:.10.1128/JCM.00899-13 [PMC free article] [PubMed] [Cross Ref]
7. Morimoto K, Kazumi Y, Shiraishi Y, Yoshiyama T, Murase Y, Ikushima S, Kurashima A, Kudoh S, Goto H, Maeda S 2015. Clinical and microbiological features of definite Mycobacterium gordonae pulmonary disease: the establishment of diagnostic criteria for low-virulence mycobacteria. Trans R Soc Trop Med Hyg 109:589–593. doi:.10.1093/trstmh/trv058 [PubMed] [Cross Ref]
8. Mazumder SA, Hicks A, Norwood J 2010. Mycobacterium gordonae pulmonary infection in an immunocompetent adult. N Am J Med Sci 2:205–207. [PMC free article] [PubMed]
9. Andrews S. 2010. FastQC: a quality control tool for high throughput sequence data.
10. Bolger AM, Lohse M, Usadel B 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. doi:.10.1093/bioinformatics/btu170 [PMC free article] [PubMed] [Cross Ref]
11. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi:.10.1089/cmb.2012.0021 [PMC free article] [PubMed] [Cross Ref]
12. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Ciufo S, Li W 2013. Prokaryotic genome annotation pipeline. The NCBI Handbook [Internet], 2nd ed NCBI, Bethesda, MD:

Articles from Genome Announcements are provided here courtesy of American Society for Microbiology (ASM)