Genome sequencing and annotation of multidrug resistant Mycobacterium tuberculosis (MDR-TB) PR10 strain.

Here, we report the draft genome sequence and annotation of a multidrug resistant Mycobacterium tuberculosis strain PR10 (MDR-TB PR10) isolated from a patient diagnosed with tuberculosis. The size of the draft genome MDR-TB PR10 is 4.34 Mbp with 65.6% of G + C content and consists of 4637 predicted genes. The determinants were categorized by RAST into 400 subsystems with 4286 coding sequences and 50 RNAs. The whole genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number CP010968.

Direct link to deposited data [provide URL below]

http://www.ncbi.nlm.nih.gov/bioproject/PRJNA196391

(Biosample: SAMN03290700).

Experimental design, materials and methods

Mycobacterium tuberculosis was isolated from the cerebrospinal fluid (CSF) of a patient diagnosed with tuberculosis at a local hospital. The sample was cultured in BBL™ MGIT™ Mycobacterial Growth Indicator Tube supplemented with BBL™ MGIT™ OADC enrichment and BBL™ MGIT™ PANTA™ antibiotic mixture (Becton-Dickinson, Oxford, United Kingdom). Since the isolate was found to be resistant to rifampicin and isoniazid, it was labeled as multidrug resistant M. tuberculosis strain PR10 (MDR-TB PR10). Genomic DNA was extracted and sequenced using MiSeq (Illumina, Ca, USA), generating a total of 10,595,456 reads in a 300-cycle run.

Raw reads were trimmed and assembled de novo using CLCbio (CLC Genomics Workbench version 7.0.3) (CLCbio, Aarhus, Denmark), producing 163 contigs with an average coverage of 334 ×. Annotation was performed using the Bacterial Annotation System (BASys) [1] and Rapid Annotation using Subsystem Technology (RAST) [2] online services, and the pathogenicity and virulence genes were determined. The genes identified were validated using the following external gene annotation databases: TubercuList (http://tuberculist.epfl.ch), UniProtKB (http://www.ebi.ac.uk/uniprot), Virulence Factor Database (VFDB) (http://www.mgc.ac.cn), and TBDatabase (TBDB) (http://www.tbdb.org).

The size of the draft genome MDR-TB PR10 is 4,347,484 bp with a G + C content of 65.6%. BASys annotation software predicted 4637 genes and 50 RNA-encoding elements. Using RAST, a total of 400 subsystems and 4286 protein-coding genes were annotated in the MDR-TB PR10 genome (Fig. 1).

Fig 1

Subsystem distribution of multidrug resistant Mycobacterium tuberculosis strain PR10 (based on RAST annotation server).

A gene that encodes DNA-directed RNA polymerase beta' subunit (rpoB) (EC 2.7.7.6) was annotated in MDR-TB PR10. The gene was reported to be involved in the invasion and intracellular resistance subsystem that may play a role in resistance towards certain drugs such as rifampicin. The rpoB gene is responsible for the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates catalyzed by DNA-dependent RNA polymerase. Mutations that occur in the rpoB gene may cause the changes in the protein translation of Mycobacterium that may confer resistance to rifampin [3], [4].

Comparison of genome sequences using RAST showed that the strains closest to PR10 are M. tuberculosis NCGM2209 (score of 521), followed by M. tuberculosis NA-A0008 (score of 459) and M. tuberculosis UM 1072388579 (score of 400).

This Whole Genome Shotgun project has been deposited at GenBank under the accession CP010968.

Nucleotide sequence accession number

The whole genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number CP010968.

Conflict of interest

The authors declare that there is no conflict of interests with respect to the work published in this paper.

Specifications
Organism/cell line/tissue	Mycobacterium tuberculosis
Strain	PR10
Sequencer or array type	Illumina Miseq Sequencer
Data format	Processed
Experimental factors	Microbial strain
Experimental features	Draft genome sequence of Mycobacterium tuberculosis PR10assembly and annotation
Consent	N/A
Sample source location	Kuala Lumpur, Malaysia4.1936°N103.7249°E