The use of whole genome sequencing for tuberculosis public health activities in Australia: a joint statement of the National Tuberculosis Advisory Committee and Communicable Diseases Genomics Network

Abstract

The public health utility of whole genome sequencing (WGS) for Mycobacterium tuberculosis includes genome-wide mutation analysis for genotypic drug susceptibility testing (DST), strain identification, differentiation of tuberculosis (TB) relapse from re-infection, transmission cluster detection to guide targeted public health responses and detection of laboratory cross contamination. This has the potential to optimise individual patient care and provide better targeted TB control measures compared to previous MIRU-VNTR genotyping methods. High resolution genotyping of TB should allow better targeting of contact tracing interventions and prevention strategies. WGS will be useful in programmatic evaluation of clinical and public health TB programs through the identification of relapse and cluster analyses to assess effectiveness of contact tracing activities. Characterising pathogens using WGS is usually less laborious and less expensive than traditional typing methods, and laboratory costs will likely further decrease as it is probable that WGS will soon reduce the need for routine phenotypic DST. However, resource, infrastructure and workforce (including information technology infrastructure and bioinformatics support) has limited implementation of WGS in some jurisdictions, though all mycobacterial reference laboratories in Australia have implemented WGS to some extent. Pathogen genomic data need to be integrated with clinical and public health data to realise their full value. Effective reporting strategies still need to be established, including analyses of key clinical variables and reporting of clusters over time, as well as processes for communicating clusters in a timely manner for public health benefit. NTAC and CDGN consider it a future requirement for all jurisdictions to have: center dot access to prospective WGS of TB isolates; center dot WGS results incorporated into routine laboratory reporting systems; center dot WGS results reported to clinicians and public health programs; center dot WGS results integrated into the routine TB surveillance system; center dot routine cross jurisdictional comparison of WGS data; and center dot continued education for public health staff and clinicians. Through increasing capacity for identification of transmission risk and opportunities to intervene and prevent reactivation, WGS will be an increasingly valuable tool for TB control and elimination in Australia.