Genome sequence and analysis of Mycobacterium tuberculosis strain SWLPK.

OBJECTIVES: Multidrug-resistant Mycobacterium tuberculosis poses a global threat, particularly in developing countries such as Pakistan. Genome sequencing, comparative genomic analysis and drug resistance gene analysis could be beneficial for understanding and monitoring M. tuberculosis disease severity in Pakistan by elucidating the biology of M. tuberculosis.

METHODS: Here the draft genome of M. tuberculosis strain SWLPK was sequenced, assembled and annotated using an Illumina MiSeq system. De novo genomic assembly was conducted using Geneious Pro™ v.10. The assembled genome of strain SWLPK was annotated using the Rapid Annotation using Subsystem Technology (RAST) server, tRNAscan-SE 1.21 and RNAmmer v.1.2, which provide high-quality functional annotation.

RESULTS: Mycobacterium tuberculosis strain SWLPK yielded an average read depth of 68.5-fold, which covered 97% of the genome of reference strain H37Rv. The genome contains 4305 protein-coding genes, including key drug resistance and virulence-associated genes such as type seven secretion systems. Additionally, it has a 65.6% GC content and contains 48 RNAs and 12 contigs. We determined that all proteins encoded by this strain contain conserved domains, except OxyR, which is associated with first-line antituberculosis drugs such as ethambutol, rifampicin, streptomycin, pyrazinamide and isoniazid.

CONCLUSIONS: This genome sequence provides information regarding the drug resistance genes and virulence propensity of M. tuberculosis strain SWLPK. Strain SWLPK appears to be multidrug-resistant, similar to the Beijing genotype, as it clusters in the same group. These findings will pave the way for genomic characterisation, which will provide further insights into adaptation and evolution in human hosts by transcriptome studies and gene manipulation.