Differential carriage of virulence-associated loci in the New Zealand Rangipo outbreak strain of Mycobacterium tuberculosis

Abstract

Background: The Rangipo strain of Mycobacterium tuberculosis achieved notoriety in New Zealand due to its role in several tuberculosis (TB) outbreaks. Why this strain should be the source of relatively large clusters of the disease is unknown. In this work, we performed an in-depth analysis of the genome of the Rangipo strain to determine whether it offers clues to understanding its prevalence.

Methods: Next-generation sequencing was performed on nine isolates which matched the Rangipo genotypic profile. Sequence reads were assembled against the H37Rv reference genome and single-locus variants identified. Unmapped reads were compared against the genome sequences of other M. tuberculosis strains, in particular CDC1551, Haarlem and Erdman.

Results: Across the nine Rangipo strains, a total of 727 single-locus variants were identified with respect to H37Rv, of which 700 were common to all Rangipo strains sequenced. Within the common variants, 386 were non-synonymous, with 12 occurring in genes associated with M. tuberculosis virulence. Next-generation and Sanger sequencing determined the presence of three genes in the Rangipo isolates, which are absent in H37Rv, but which have been reported to be important for the pathogenicity of M. tuberculosis. The differentially encoded Rangipo genes consisted of transcriptional regulator EmbR2, and molybdopterin cofactor biosynthesis proteins A and B. The Rangipo strain also harbours an extended DNA helicase and an additional adenylate cyclase.

Conclusions: Our study provides new insights into the genomic content of the New Zealand Rangipo strain of M. tuberculosis and highlights the presence of additional virulence-related loci not found in H37Rv.

Keywords:

• Mycobacterium tuberculosis
• CDC1551
• EmbR2
• whole-genome sequencing

Disclosure statement

The authors report no conflicts of interest.

Additional information

Funding

RFOT is a recipient of a School of Medicine Research Development Grant, University of Tasmania and Royal Hobart Hospital Research Foundation grant (17-104). SSG is a recipient of a School of Medicine/Faculty of Health PhD Scholarship. Micheál Mac Aogáin was funded by Irish Research Council (EPSPD/2015/32).