We report here the draft genome sequence of Mycobacterium heckeshornense strain RLE isolated from a sputum sample from a patient with shortness of breath. This is the first draft genome sequence of M. heckeshornense

Chiu, Charles Y

Cunningham, Gail

Greninger, Alexander L

Miller, Steve

English

PubMed

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UCSFUC San Francisco Previously Published WorksTitleDraft Genome Sequence of Mycobacterium heckeshornense Strain RLEPermalinkhttps://escholarship.org/uc/item/8cs6q1qkJournalMicrobiology Resource Announcements, 3(4)ISSN2576-098XAuthorsGreninger, Alexander LCunningham, GailChiu, Charles Yet al.Publication Date2015-08-27DOI10.1128/genomea.00930-15 Peer reviewedeScholarship.org Powered by the California Digital LibraryUniversity of CaliforniaDraft Genome Sequence of Mycobacterium heckeshornense Strain RLEAlexander L. Greninger, Gail Cunningham, Charles Y. Chiu, Steve MillerDepartment of Laboratory Medicine, UCSF, San Francisco, California, USAWe report here the draft genome sequence of Mycobacterium heckeshornense strain RLE isolated from a sputum sample from apatient with shortness of breath. This is the first draft genome sequence of M. heckeshornense.Received 8 July 2015 Accepted 21 July 2015 Published 27 August 2015Citation Greninger AL, Cunningham G, Chiu CY, Miller S. 2015. Draft genome sequence of Mycobacterium heckeshornense strain RLE. Genome Announc 3(4):e00930-15. doi:10.1128/genomeA.00930-15.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 heckeshornense is a slowly growing scotochro-mogenic mycobacterium that was originally isolated in 1994from a cavitary lung lesion and is named after the HeckeshornLung Clinic in Berlin (1). M. heckeshornense has since been iso-lated from a broad range of clinical cases, such as septicemia, os-teomyelitis, diskitis, peritonitis, tenosynovitis, and lymphadenitis,as well as from porcine and feline lymph nodes (2–8). It is phylo-genetically and phenotypically close to Mycobacterium xenopi,which is a common source of confusion and misidentification (1,5, 9). We sequenced the first draft genome of M. heckeshornenseisolated from a 2008 sputum sample from a 50-year-old male withHIV and CD4 count of 60 who presented with shortness ofbreath and cough and was concurrently diagnosed with Pneumo-cystis jirovecii pneumonia.DNA from M. heckeshornense strain RLE was extracted usingthe Qiagen EZ1 kit, and paired-end libraries were prepared usingthe Nextera XT DNA library kit, followed by 2  80-bp sequenc-ing on Illumina MiSeq. The sequences were adapter and quality(Q20) trimmed using cutadapt, de novo assembled using SPAdesversion 3.5, metagenomically screened for contaminating se-quence with SURPI, and annotated via Prokka version 1.1 (10–13). A total of 8,091,536 paired-end reads were recovered aftertrimming. De novo assembly yielded 191 contigs of 500 bp for atotal assembly size of 5,010,173 bp, with an N50 of 95,235 bp, anaverage coverage of 126, and a total of 4,882 coding sequences.Contiguity was interrupted due to the short read length, highGC content (66%), and presence of many high-copy-numberintegrases, transposases, and tyrosine recombinases that alignedwith between 70 and 85% identity at the nucleotide level to avariety of actinobacteria, such as Gordonia bronchialis DSM43247, Rhodococcus aetherivorans strain lcdP1, Mycobacteriumkansasii 824, Mycobacterium marinum strain M, and Rhodococcusjostii RHA1.BLASTn analysis of the complete 16S sequence from strainRLE showed 100% identity to M. heckeshornense type strain S369(NCBI reference sequence NR_028759) and Mycobacterium cf.xenopi (i.e., a Mycobacterium sp. very similar to Mycobacteriumxenopi) strain Hymi_Wue Tb_939/99 (GenBank accession no.AJ243481) and Mycobacterium sydneyiensis (GenBank accessionno. AF101243), as has been noted for M. heckeshornense (14). Asno publications are available for these two strains nor have anysequences been deposited, they likely should be renamed as strainsof M. heckeshornense. BLASTn of the full-length rpoB gene re-vealed 91% nucleotide identity to rpoB genes from Mycobacteriumbranderi ATCC 51789, Mycobacterium celatum ATCC 51130, My-cobacterium kyorinense KUM 060204, and a variety of Mycobacte-rium avium strains, including 104, 2285, and DJO-44271. Nohigh-confidence antibiotic resistance genes were identified by theComprehensive Antibiotic Resistance Database analysis (15).Nucleotide sequence accession numbers. This whole-genomeshotgun project has been deposited at DDBJ/ENA/GenBank un-der the accession no. LFOF00000000. The assembly described inthis paper is the first version, LFOF01000000.ACKNOWLEDGMENTThis work was supported by the University of California, San FranciscoDepartment of Laboratory Medicine.REFERENCES1. 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The Comprehensive AntibioticResistance Database. Antimicrob Agents Chemother 57:3348 –3357.http://dx.doi.org/10.1128/AAC.00419-13.Greninger et al.Genome Announcements2 genomea.asm.org July/August 2015 Volume 3 Issue 4 e00930-15

Draft Genome Sequence of Mycobacterium heckeshornense Strain RLE

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Draft Genome Sequence of Mycobacterium heckeshornense Strain RLE.

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