Tuberculosis in Australia's tropical north: a population-based genomic epidemiological study

Bright, 2020, Tuberculosis notifications in Australia, 2015–2018, Commun Dis Intell (2018), 44 2018, The National Tuberculosis Advisory Committee for the Communicable Diseases Network Australia. The strategic plan for control of tuberculosis in Australia, 2016–2020: towards disease elimination., Commun Dis Intell, 2019, 43 Tollefson, 2013, Burden of tuberculosis in Indigenous peoples globally: a systematic review, Int J Tuberc Lung Dis, 17, 1139, 10.5588/ijtld.12.0385 Teo, 2015, The epidemiology of tuberculosis in children in Australia, 2003–2012, Med J Aust, 203, 440, 10.5694/mja15.00717 Judge, 2016, Multidrug-resistant tuberculosis in the Northern Territory: a 10-year retrospective case series, Commun Dis Intell Q Rep, 40, E334 The Northern Territory Government. Northern Territory Economy: Population. https://nteconomy.nt.gov.au/population (accessed 10th June, 2021). Wyber, 2021, Formative evaluation of a community-based approach to reduce the incidence of Strep A infections and acute rheumatic fever, Aust NZ J Public health, 10.1111/1753-6405.13127 Quilty, 2019, Addressing profound disadvantages to improve Indigenous health and reduce hospitalisation: a collaborative community program in remote Northern Territory, Int J Environ Res Public Health, 16, 10.3390/ijerph16224306 Pai, 2016, Tuberculosis, Nat Rev Dis Primers, 2, 16076, 10.1038/nrdp.2016.76 Cormier, 2019, Proximate determinants of tuberculosis in Indigenous peoples worldwide: a systematic review, Lancet Glob Health, 7, e68, 10.1016/S2214-109X(18)30435-2 Krause, 1993, Tuberculosis in the tropics, Med J Aust, 159, 412, 10.5694/j.1326-5377.1993.tb137920.x Krause, 1991, Priorities for tuberculosis control in the Northern Territory, Intern Med J, 21, 595 Kelly, 2002, Tuberculosis in East Timorese refugees: implications for health care needs in East Timor, Int J Tuberc Lung Dis, 6, 980 Gray, 2008, Tuberculosis in illegal foreign fishermen: whose public health are we protecting?, Med J Aust, 188, 144, 10.5694/j.1326-5377.2008.tb01556.x Siegel M. Australia Adopts Tough Measures to Curb Asylum Seekers. The New York Times. July 19, 2013. https://www.nytimes.com/2013/07/20/world/asia/australia-adopts-tough-measures-to-curb-asylum-seekers.html (accessed 25th April, 2021). Ross, 1991, Differentiation of Mycobacterium tuberculosis strains by use of a nonradioactive Southern blot hybridization method, J Infect Dis, 163, 904, 10.1093/infdis/163.4.904 Votintseva, 2015, Mycobacterial DNA extraction for whole-genome sequencing from early positive liquid (MGIT) cultures, J Clin Microbiol, 53, 1137, 10.1128/JCM.03073-14 Sekizuka, 2015, TGS-TB: Total genotyping solution for Mycobacterium tuberculosis using short-read whole-genome sequencing, PLoS One, 10, 10.1371/journal.pone.0142951 Napier, 2020, Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies, Genome Med, 12, 114, 10.1186/s13073-020-00817-3 Phelan, 2019, Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs, Genome Med, 11, 41, 10.1186/s13073-019-0650-x Meehan, 2018, The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology, EBioMedicine, 37, 410, 10.1016/j.ebiom.2018.10.013 Walker, 2013, Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study, Lancet Infect Dis, 13, 137, 10.1016/S1473-3099(12)70277-3 Nguyen, 2015, Minh BQ. IQ–TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies, Mol Biol Evol, 32, 268, 10.1093/molbev/msu300 Yu, 2018, Two methods for mapping and visualizing associated data on phylogeny using ggtree, Mol Biol Evol, 35, 3041, 10.1093/molbev/msy194 Rambaut, 2016, Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen), Virus Evol, 2, vew007, 10.1093/ve/vew007 R Core Team. R: A Language and Environment for Statistical Computing. https://www.R-project.org/ 2021 Bainomugisa, 2019, Cross-border movement of highly drug-resistant Mycobacterium tuberculosis from Papua New Guinea to Australia through Torres Strait Protected Zone, 2010–2015, Emerg Infect Dis, 25, 406, 10.3201/eid2503.181003 Mulholland, 2019, Dispersal of Mycobacterium tuberculosis driven by historical European trade in the South Pacific, Front Microbiol, 10, 2778, 10.3389/fmicb.2019.02778 Wilson, 2019, Tuberculosis in Far North Queensland, Australia: a retrospective clinical audit, Intern Med J, 49, 333, 10.1111/imj.13994 Aung, 2019, Reducing the burden of tuberculosis in the Maori, the Indigenous people of New Zealand, Lancet Glob Health, 7, e845, 10.1016/S2214-109X(19)30236-0 Aung, 2019, Tackling tuberculosis in the Indigenous people of New Zealand, Lancet Public Health, 4, e496, 10.1016/S2468-2667(19)30180-X Verrall, 2020, Towards elimination of tuberculosis in New Zealand, N Z Med J, 133, 89 D'Sylva, 2019, Chronic wet cough in Aboriginal children: it's not just a cough, J Paediatr Child Health, 55, 833, 10.1111/jpc.14305 Wakerman, 2019, Remote health workforce turnover and retention: what are the policy and practice priorities?, Hum Resour Health, 17, 99, 10.1186/s12960-019-0432-y Rosewarne, 2004, An analysis of the Primary Health Care Access Program in the Northern Territory: a major Aboriginal health policy reform, Aust J Primary Health, 10, 12, 10.1071/PY04052 Devlin, 2013, Ongoing transmission of tuberculosis in Aboriginal communities in NSW, N S W Public Health Bull, 24, 38, 10.1071/NB12113 Krause, 2002, TB Community Screening - a new TB threat promotes community action, The Northern Territory Disease Control Bulletin, 9, 3 Gardy, 2011, Whole-genome sequencing and social-network analysis of a tuberculosis outbreak, N Engl J Med, 364, 730, 10.1056/NEJMoa1003176 Sterling, 2011, Three months of rifapentine and isoniazid for latent tuberculosis infection, N Engl J Med, 365, 2155, 10.1056/NEJMoa1104875 Bryant, 2013, Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: a retrospective observational study, Lancet Respir Med, 1, 786, 10.1016/S2213-2600(13)70231-5 Guerra-Assuncao, 2015, Recurrence due to relapse or reinfection with Mycobacterium tuberculosis: a whole-genome sequencing approach in a large, population-based cohort with a high HIV infection prevalence and active follow–up, J Infect Dis, 211, 1154, 10.1093/infdis/jiu574 Lee, 2020, Previously undetected super-spreading of Mycobacterium tuberculosis revealed by deep sequencing, Elife, 9, 10.7554/eLife.53245 Devlin, 2019, The missing voices of Indigenous Australians in the social, cultural and historical experiences of tuberculosis: a systematic and integrative review, BMJ Glob Health, 4, 10.1136/bmjgh-2019-001794 Proust, 1991 Brynildsrud, 2018, Global expansion of Mycobacterium tuberculosis lineage 4 shaped by colonial migration and local adaptation, Sci Adv, 4, eaat5869, 10.1126/sciadv.aat5869 Lee, 2015, Reemergence and amplification of tuberculosis in the Canadian arctic, J Infect Dis, 211, 1905, 10.1093/infdis/jiv011 Menardo, 2021, Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim, F1000Res, 10, 60, 10.12688/f1000research.28318.2 O'Neill, 2019, Lineage specific histories of Mycobacterium tuberculosis dispersal in Africa and Eurasia, Mol Ecol, 28, 3241, 10.1111/mec.15120 Clark, 2013 Seraphin, 2019, Direct transmission of within-host Mycobacterium tuberculosis diversity to secondary cases can lead to variable between-host heterogeneity without de novo mutation: A genomic investigation, EBioMedicine, 47, 293, 10.1016/j.ebiom.2019.08.010