Invited Speaker Australian Society for Microbiology Annual Scientific Meeting 2021

Antimicrobial resistance determination of Mycobacterium tuberculosis via WGS on DNA extracted from MGIT tubes – a pilot study. (#269)

Linda T Viberg 1 , Maria Globan 1 , Katherine Bond 2 , Norelle Sherry 3 , Kristy Horan 3 , Deborah Williamson 2 3
  1. Mycobacterium Reference Laboratory, Victorian Infectious Diseases Reference Laboratory, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
  2. Department of Microbiology, Royal Melbourne Hospital, Melbourne, VIC, Australia
  3. Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia

Mycobacterium tuberculosis (MTB) is the causative agent of tuberculosis (TB). In 2019, TB caused 1.4 million deaths globally and is considered to be the leading cause of death from an infectious agent1. Australia is a low TB prevalence country with less than 10 cases per 100,000 population per year1. In Victoria ~350 new cases are identified annually. MTB is a very slow growing organism. The process of obtaining an isolate for phenotypic susceptibility testing is protracted involving culturing of primary specimen on traditional solid media as well as liquid media (Mycobacterial Growth Indicator Tube, MGIT). Growth generally occurs faster within the MGIT tube when compared to solid media. Total time from receipt of primary specimen to obtaining a phenotypic susceptibility result is approximately 6-8 weeks. Current process within the Victorian Mycobacterium Reference Laboratory, is that DNA extraction is performed for whole genome sequencing (WGS) from solid culture growth at the same time as phenotypic susceptibilities. WGS allows for the in silico detection of known resistance mutations to predict drug susceptibilities (DST). To decrease the time for DST a pilot study has been set up to extract DNA directly from positive MGIT cultures. A total of 96 MGIT extractions have been performed and 81 of these have passed sequencing quality controls. Results of WGS from 55 of the 81 MGIT broths that passed, were compared to results obtained from DNA extracted from the equivalent solid culture isolate. Results were concordant in all cases except one where the DST pipeline quality requirements were not met. Results of automating the extraction procedure will also be presented. The pilot study shows promising results, with the potential for a much shortened turnaround time for DST, leading to potential improvements to patient care and clinical outcomes.

  1. 1. WHO 2020 Global tuberculosis report