Verifying clustered mutation regions inside the newly-completed genome of a clinically-significant New Zealand Mycobacterium tuberculosis strain

Abstract

In 2019, active infections of Mycobacterium tuberculosis (Mtb) affected 10 million people globally, with 1.4 million deaths, and an additional 1.7-1.9 billion people infected without symptomatic disease (latent Mtb). While Mtb is often associated with Asia and Africa, New Zealand had 360 Mtb infections and 21 deaths in 2019, and roughly 20% of cases were caused by three strains unique to New Zealand. One is CS1 (formerly Rangipo), which is known to be more transmissible than its relatives and has been causing outbreaks in the Waikato region for 30 years. As CS1 has genetic features linked to virulence in unrelated Mtb strains, having a complete and accurate record of genetic features is important, in particular those with the potential to change protein structure (Variable Regions Inside Proteins, VRIPs). Resolving VRIPs would simultaneously remove sequencing mistakes and increase knowledge about Mtb virulence. The aim of this project was to investigate the genetic cause of improved transmissibility in CS1 and produce a closed genome. Sequencing data from Illumina and PacBio reads was processed, assembled, and checked for quality discrepancies which would require more sequencing to resolve. VRIPs were mapped alongside regions of low-quality data, low data-coverage, and repeat regions. Characteristics of the CS1 genome, such as repeat levels and size, were found by comparing with the reference strain H37Rv. The read data and assembly were found to be good quality, and the genome is of high enough quality to be considered closed. As expected, some regions of low coverage and poor quality were discovered inside large repeat regions, and more work on these would be valuable. 13 of the 32 VRIPs were verified, all linked with virulence factors. 5 verified VRIPs caused genes to split into domains, accumulating mutations in the non-coding region. Further work resolving the remaining 19 VRIPs is recommended.