We report the draft genome sequence of Mycobacterium obuense strain UC1 from a patient sputum sample. This is the first draft genome sequence of Mycobacterium obuense, a rapidly growing scotochromogenic mycobacterium

Chiu, Charles Y

Cunningham, Gail

Greninger, Alexander L

Hsu, Elaine D

Miller, Steve

Yu, Joanna M

English

PubMed

eScholarship - University of California

UCSFUC San Francisco Previously Published WorksTitleDraft Genome Sequence of Mycobacterium obuense Strain UC1, Isolated from Patient SputumPermalinkhttps://escholarship.org/uc/item/2zn4h77zJournalMicrobiology Resource Announcements, 3(3)ISSN2576-098XAuthorsGreninger, Alexander LCunningham, GailHsu, Elaine Det al.Publication Date2015-06-25DOI10.1128/genomea.00612-15 Peer reviewedeScholarship.org Powered by the California Digital LibraryUniversity of CaliforniaDraft Genome Sequence of Mycobacterium obuense Strain UC1,Isolated from Patient SputumAlexander L. Greninger, Gail Cunningham, Elaine D. Hsu, Joanna M. Yu, Charles Y. Chiu, Steve MillerDepartment of Laboratory Medicine, UCSF, San Francisco, California, USAWe report the draft genome sequence of Mycobacterium obuense strain UC1 from a patient sputum sample. This is the first draftgenome sequence of Mycobacterium obuense, a rapidly growing scotochromogenic mycobacterium.Received 6 May 2015 Accepted 7 May 2015 Published 11 June 2015Citation Greninger AL, Cunningham G, Hsu ED, Yu JM, Chiu CY, Miller S. 2015. Draft genome sequence of Mycobacterium obuense strain UC1, isolated from patient sputum.Genome Announc 3(3):e00612-15. doi:10.1128/genomeA.00612-15.Copyright © 2015 Greninger et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.Address correspondence to Steve Miller, steve.miller@ucsf.edu.Mycobacterium obuense is a rapidly growing scotochromoge-nic member of the genus Mycobacterium that has beenpreviously isolated from soil and the sputum of a patient withpulmonary disease (1). The unique biochemical properties ofM. obuense that resulted in it being classified as a species include itsability to degrade p-aminosalicylate and salicylate into black prod-ucts. Smooth colonies of this species have been reported to bemobile, along with several other environmental mycobacteria (2).A heat-killed suspension of M. obuense has been investigated as apotential treatment for melanoma due to its stimulation of anti-tumor T cell response (3, 4).Rapidly growing mycobacteria constitute a commonly isolatedpopulation of acid-fast bacilli in the clinical microbiology lab ofvarying clinical importance (5). Their speciation via molecularmethods is becoming increasingly important given the expandingnumbers of immunosuppressed individuals in which they can bepathogenic. We sequenced the first draft genome of Mycobacte-rium obuense in order to enhance molecular methods of detectionand to understand mycobacterial genetic diversity.The patient had a history of non–small cell lung cancer andpresented with patchy lung infiltrates. A sputum culture for acid-fast bacilli yielded a rapidly growing scotochromogen identifiedby high-performance liquid chromatography as M. obuense/M. aurum. DNA from isolated colonies of strain UC1 was ex-tracted using the Qiagen EZ1 DNA tissue kit and paired-end li-braries were prepared using the Nextera XT DNA library kitfollowed by sequencing on the Illumina MiSeq. Sequences wereadapter and quality (Q20) trimmed using cutadapt, de novo as-sembled using SPAdes version 3.5, metagenomically screenedwith SURPI, and annotated with Prokka version 1.1 (6–9). A totalof 10,848,516 paired-end reads of average length 111.7 nucleo-tides were recovered after trimming. De novo assembly yielded 249contigs 500 nucleotides for a total assembly size of 6,382,135 bpwith an N50 of 55,467 bp, an average coverage of 148, and a totalof 6,193 coding sequences. Contiguity was most likely disruptedby high GC content (68%), and several high-copy-number inte-grases and transposases longer than the sequence read length. Ofnote, three contigs 18 kb each demonstrated 4 higher coveragethan other sequences and aligned to plasmids present in M. ab-scessus strains with approximately 80% identity, suggesting thatthe UC1 strain has one or more plasmids.Pairwise alignment of available sequenced genes from Myco-bacterium obuense type strain CIP 106803 (16S, hsp65, gyrB, rpoB,sod) with strain UC1 revealed 99 to 100% identity, confirming theidentify as Mycobacterium obuense. The closest related completegenome to M. obuense UC1 was Mycobacterium chubuense NBB4(81.3% identity), while the closest NCBI WGS database entry wasMycobacterium rufum JS14 (92.2% identity). Analysis by theComprehensive Antibiotic Resistant Database identified putativeresistance genes marA (55% amino acid identity to Frankia spp.),aminoglycoside resistance protein/kinase (62% amino acid iden-tity to M. rufum JS14), two metallo-beta-lactamases (86% and89% amino acid identity to M. rufum JS14), blaF beta-lactamase(79% amino acid to M. rufum JS14), and beta-lactamase (43%amino acid to Gordonia spp.) (10, 11).Nucleotide sequence accession numbers. This whole-genomeshotgun project has been deposited at DDBJ/ENA/GenBank un-der the accession number LAUZ00000000. The version describedin this paper is the second version, LAUZ02000000.ACKNOWLEDGMENTThis work was supported by the University of California San FranciscoDepartment of Laboratory Medicine.REFERENCES1. Tsukamura M, Mizuno S. 1971. Mycobacterium obuense, a rapidly grow-ing scotochromogenic mycobacterium capable of forming a black productfrom p-aminosalicylate and salicylate. J Gen Microbiol 68:129 –134.http://dx.doi.org/10.1099/00221287-68-2-129.2. Agustí G, Astola O, Rodríguez-Güell E, Julián E, Luquin M. 2008.Surface spreading motility shown by a group of phylogenetically related,rapidly growing pigmented mycobacteria suggests that motility is a com-mon property of mycobacterial species but is restricted to smooth colo-nies. J Bacteriol 190:6894 – 6902. http://dx.doi.org/10.1128/JB.00572-08.3. Stebbing J, Dalgleish A, Gifford-Moore A, Martin A, Gleeson C, WilsonG, Brunet LR, Grange J, Mudan S. 2012. An intra-patient placebo-controlled phase I trial to evaluate the safety and tolerability of intrader-mal IMM-101 in melanoma. Ann Oncol 23:1314 –1319. http://dx.doi.org/10.1093/annonc/mdr363.4. Fowler DW, Copier J, Wilson N, Dalgleish AG, Bodman-Smith MD.crossmarkGenome AnnouncementsMay/June 2015 Volume 3 Issue 3 e00612-15 genomea.asm.org 12012. 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McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, Baylay AJ,Bhullar K, Canova MJ, De Pascale G, Ejim L, Kalan L, King AM, KotevaK, Morar M, Mulvey MR, O’Brien JS, Pawlowski AC, Piddock LJ,Spanogiannopoulos P, Sutherland AD, Tang I, Taylor PL, Thaker M,Wang W, Yan M, Yu T, Wright GD. 2013. The Comprehensive Antibi-otic Resistance Database. Antimicrob Agents Chemother 57:3348 –3357.http://dx.doi.org/10.1128/AAC.00419-13.Greninger et al.Genome Announcements2 genomea.asm.org May/June 2015 Volume 3 Issue 3 e00612-15

Draft Genome Sequence of Mycobacterium obuense Strain UC1, Isolated from Patient Sputum

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Draft Genome Sequence of Mycobacterium obuense Strain UC1, Isolated from Patient Sputum.

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