Considering best practice standards for routine whole-genome sequencing for TB care and control

J T Denholm; G de Vries; R Anthony; E Robinson; M Backx; I F Laurenson; A L Seagar; H Modestil; L Trieu; J S Meissner; D H L Ng; J Y Tay; H H Lin; R Lee; V Sintchenko; B J Marais; E J Donnan

doi:10.5588/ijtldopen.24.0320

Considering best practice standards for routine whole-genome sequencing for TB care and control

IJTLD Open. 2024 Oct 1;1(10):431-436. doi: 10.5588/ijtldopen.24.0320. eCollection 2024 Oct.

Authors

J T Denholm^{1

2}, G de Vries³, R Anthony³, E Robinson⁴, M Backx⁵, I F Laurenson⁶, A L Seagar⁶, H Modestil⁷, L Trieu⁷, J S Meissner⁷, D H L Ng⁸, J Y Tay⁸, H H Lin⁹, R Lee¹⁰, V Sintchenko^{11

12}, B J Marais¹², E J Donnan^{12

13}

Affiliations

¹ Victorian Tuberculosis Program, Melbourne, VIC, Australia.
² Department of Infectious Diseases, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia.
³ Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.
⁴ TB Unit and National Mycobacterial Reference Service, United Kingdom Health Security Agency, London, UK.
⁵ Department of Microbiology, University Hospital of Wales, Cardiff, UK.
⁶ Scottish Mycobacteria Reference Laboratory, Royal Infirmary of Edinburgh, Edinburgh, Scotland, UK.
⁷ New York City Department of Health and Mental Hygiene, New York, NY, USA.
⁸ National Tuberculosis Programme, National Centre for Infectious Diseases, Singapore.
⁹ Institute of Epidemiology and Preventive Medicine, National Taiwan University College of Public Health, Taiwan.
¹⁰ Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada.
¹¹ NSW Mycobacterium Reference Laboratory, Institute of Clinical Pathology and Medical Research, NSW Health, Sydney, NSW, Australia.
¹² Sydney Infectious Diseases Institute, The University of Sydney, Sydney, NSW, Australia.
¹³ New South Wales Tuberculosis Program, Health Protection New South Wales, Sydney, NSW, Australia.

Abstract
in English, French

TB is a priority pathogen for the application of whole-genome sequencing (WGS) into routine public health practice. In low-incidence settings, a growing number of services have begun to incorporate routine WGS into standard practice. The increasing availability of real-time genomic information supports a variety of aspects of the public health response, including the detection of drug resistance, monitoring of laboratory and clinical practices, contact tracing investigations and active case finding. Optimal structures and approaches are needed to support the rapid translation of genomic information into practice and to evaluate outcomes and impact. In this consensus paper, we outline the elements needed to systemically incorporate routine WGS into the TB public health response, including the sustainability of services, multidisciplinary team models and monitoring and evaluation frameworks. If integrated in an efficient and thoughtful manner, routine WGS has the potential to significantly improve clinical TB care for individuals and the overall public health response.

La TB est un agent pathogène prioritaire pour l'application du séquençage du génome entier (WGS, pour l’anglais « whole-genome sequencing ») dans les pratiques courantes de santé publique. Dans des contextes à faible incidence, un nombre croissant de services ont commencé à intégrer le WGS de manière routinière dans la pratique standard. La disponibilité croissante de l'information génomique en temps réel soutient divers aspects de l'intervention de santé publique, notamment la détection de la résistance aux médicaments, la surveillance des pratiques de laboratoire et cliniques, les enquêtes de recherche des contacts et la recherche active des cas. Des structures et des approches optimales sont nécessaires pour soutenir l'application rapide de l'information génomique dans la pratique et pour évaluer les résultats et l'impact. Dans ce document de consensus, nous décrivons les éléments nécessaires à l'intégration systématique du WGS dans la riposte de santé publique à la TB, notamment la durabilité des services, les modèles d'équipe multidisciplinaire et les cadres de suivi et d'évaluation. S'il est intégré de manière efficace et réfléchie, le WGS de routine a le potentiel d'améliorer considérablement les soins cliniques de la TB pour les individus et la réponse globale de la santé publique.

Keywords: Mycobacterium tuberculosis; cluster analysis; computational biology; genomics; policy making; public health; tuberculosis.

Abstract in English, French

Abstract
in English, French