Chapter 12 References

1 Stone AC, Wilbur AK, Buikstra JE et al. Tuberculosis and leprosy in perspective. American Journal of Physical Anthropology 2009;140:66–94. doi:10.1002/ajpa.21185

2 Public Health England. Tuberculosis in England 2017 report ( presenting data to end of 2016 ) About Public Health England. 2017.

3 The World Health Organization. BCG vaccine:WHO position paper. Weekly epidemiological record 2018;1–24.

4 Roy A, Eisenhut M, Harris RJ et al. Effect of BCG vaccination against Mycobacterium tuberculosis infection in children: systematic review and meta-analysis. BMJ (Clinical research ed) 2014;349:g4643–3.

5 Zwerling A, Behr MA, Verma A et al. The BCG world atlas: A database of global BCG vaccination policies and practices. PLoS medicine 2011;8:e1001012.

6 McElreath, Richard. Statistical Rethinking. 1st ed. Chapman; Hall/CRC 2018.

7 Anderson RM, May RM. Infectious Diseases of Humans: Dynamics and Control (Oxford Univ. Press, Oxford 1991.

8 Keeling MJ, Rohani P. Modeling Infectious Diseases in Humans and Animals. Epidemiology Department, Ben-Gurion University of the Negev, Beer-Sheva, Israel. rbalicer@netvision.net.il: 2007.

9 Funk S, Camacho A, Kucharski AJ et al. Real-time forecasting of infectious disease dynamics with a stochastic semi-mechanistic model. Epidemics 2016;22:56–61.

10 King AA, Nguyen D, Ionides EL. Statistical Inference for Partially Observed Markov Processes via the R Package pomp. Journal Of Statistical Software 2016;69:1–43.

11 Houben RMGJ, Dodd PJ. The Global Burden of Latent Tuberculosis Infection: A Re-estimation Using Mathematical Modelling. PLoS medicine 2016;13:e1002152–13.

12 Gideon HP, Flynn JL. Latent tuberculosis: What the host "sees"? Immunologic Research 2011;50:202–12.

13 Sepkowitz K. How contagious is tuberculosis? Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 1996;23:954–62.

14 Rottenberg ME, Pawlowski A, Jansson M et al. Tuberculosis and HIV Co-Infection. PLoS Pathogens 2012;8:e1002464.

15 Bhatti N, Law MR, Morris JK et al. Increasing incidence of tuberculosis in England and Wales: a study of the likely causes. BMJ (Clinical research ed) 1995;310:967–9.

16 Narasimhan P, Wood J, Macintyre CR et al. Risk Factors for Tuberculosis. 2013;2013.

17 Story A, Murad S, Roberts W et al. Tuberculosis in London: the importance of homelessness, problem drug use and prison. Thorax 2007;62:667–72.

18 World Health Organization. Global Tuberculosis Report. 2016.

19 World Health Organisation. Global Tuberculosis Report. 2018.

20 PHE. Tuberculosis in England 2016 Report (presenting data to end of 2015). Public Health England 2016;Version 1.:173.

21 Public Health England. Tuberculosis in England: 2018. 2019;1–218.

22 Luca S, Mihaescu T. History of bcg vaccine. Maedica 2013;8.http://europepmc.org/articles/PMC3749764

23 Rodrigues LC, Diwan VK, Wheeler JG. Protective effect of BCG against tuberculous meningitis and miliary tuberculosis: a meta-analysis. International journal of epidemiology 1993;22:1154–8.

24 Colditz GA, Brewer TF, Berkey CS et al. Efficacy of BCG Vaccine in the Prevention of Tuberculosis. JAMA 1994;271:698.

25 Mangtani P, Abubakar I, Ariti C et al. Protection by BCG Vaccine Against Tuberculosis: A Systematic Review of Randomized Controlled Trials. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2014;58:470–80.

26 Hart PDA, Sutherland IAN. BCG and vole bacillus vaccines in the prevention of tuberculosis in adolescence and early adult life. The American Statistician 1972;46:371–85.

27 Zwerling A, Behr MA, Verma A et al. The BCG World Atlas: a database of global BCG vaccination policies and practices. PLoS medicine 2011;8:e1001012.

28 Abubakar I, Pimpin L, Ariti C et al. Systematic review and meta-analysis of the current evidence on the duration of protection by bacillus Calmette-Guérin vaccination against tuberculosis. Health technology assessment 2013;17:1–372, v–vi.

29 Mangtani P, Nguipdop-Djomo P, Keogh RH et al. Original article The duration of protection of school-aged BCG vaccination in England : a population -based case control study. International journal of epidemiology 2017;0:1–9.

30 Fine P. Stopping routine vaccination for tuberculosis in schools. BMJ (Clinical research ed) 2005;331:647–8.

31 Teo SSS, Shingadia DV. Does BCG have a role in tuberculosis control and prevention in the United Kingdom? Archives of Disease in Childhood 2006;91:529–31.

32 Kleinnijenhuis J, Quintin J, Preijers F et al. Bacille Calmette-Guerin induces NOD2-dependent nonspecific protection from reinfection via epigenetic reprogramming of monocytes. Proceedings of the National Academy of Sciences of the United States of America 2012;109:17537–42.

33 Garly ML, Martins CL, Balé C et al. BCG scar and positive tuberculin reaction associated with reduced child mortality in West Africa: A non-specific beneficial effect of BCG? Vaccine 2003;21:2782–90.

34 Higgins JPT, Soares-weiser K, López-lópez JA et al. Association of BCG , DTP , and measles containing vaccines with childhood mortality : systematic review. BMJ (Clinical research ed) 2016;i5170.

35 Rieckmann A, Villumsen M, Sørup S et al. Vaccinations against smallpox and tuberculosis are associated with better long-term survival: a Danish case-cohort study 19712010. International journal of epidemiology 2016;0:1–11.

36 Jeremiah K, Praygod G, Faurholt-Jepsen D et al. BCG vaccination status may predict sputum conversion in patients with pulmonary tuberculosis: a new consideration for an old vaccine? Thorax 2010;65:1072–6.

37 Zimmermann, Petra, Finn, Adam, Curtis, Nigel. Does BCG Vaccination Protect Against Nontuberculous Mycobacterial Infection? A Systematic Review and Meta-Analysis. J Infect Dis 2018;218:679–87.

38 The World Health Organization. BCG Vaccine. Weekly epidemiological record 2004;79:27–48.

39 World Health Organization. Global Tuberculosis Report. 2017.

40 Mangtani P, Abubakar I, Ariti C et al. Protection by BCG vaccine against tuberculosis: A systematic review of randomized controlled trials. Clinical Infectious Diseases 2014;58:470–80.

41 Sutherland I, Springett VH. The effects of the scheme for BCG vaccination of schoolchildren in England and Wales and the consequences of discontinuing the scheme at various dates. Journal of epidemiology and community health 1989;43:15–24.

42 Schrager LK, Harris RC, Vekemans J. Research and development of new tuberculosis vaccines: a review. F1000Research 2018;7:1732–32.

43 R Core Team. R: a language and environment for statistical computing. 2019.

44 Abbott S. getTBinR: an R package for accessing and summarising the World Health Organisation Tuberculosis data. Journal of Open Source Software 2019;4:1260. doi:10.21105/joss.01260

45 French CE, Antoine D, Gelb D et al. Tuberculosis in non-UK-born persons, England and Wales, 2001-2003. Int J Tuberc Lung Dis 2007;11:577–84.

46 Kruijshaar M, French C, Anderson C et al. Tuberculosis in the UK, Annual report on tuberculosis surveillance and control in the UK 2007. Thorax 2007;50:703–3.

47 Public Health England. The Green Book. 2013;391–409.

48 Sterne JAC, White IR, Carlin JB et al. Multiple imputation for missing data in epidemiological and clinical research: potential and pitfalls. Bmj 2009;338:b2393–3.

49 Pillaye J, Clarke A. An evaluation of completeness of tuberculosis notification in the United Kingdom. BMC Public Health 2003;3:31.

50 PHE. Tuberculosis in England 2016 Report (presenting data to end of 2015). 2016.

51 van Buuren S, Groothuis-Oudshoorn K. mice: Multivariate imputation by chained equations in r. Journal of Statistical Software 2011;45:1–67.https://www.jstatsoft.org/v45/i03/

52 Sterne JA, Davey Smith G. Sifting the evidence-what’s wrong with significance tests? Bmj 2001;322:226–31.

53 Benchimol EI, Smeeth L, Guttmann A et al. The REporting of studies Conducted using Observational Routinely-collected health Data (RECORD) Statement. The American Statistician 2016;115-116:1–22.

54 Fewell Z, Davey Smith G, Sterne JAC. The impact of residual and unmeasured confounding in epidemiologic studies: A simulation study. American Journal of Epidemiology 2007;166:646–55.

55 Wickham H. Tidy Data. Journal of Statistical Software 2014;59:1–23.

56 R Core Team. R: A Language and Environment for Statistical Computing. Vienna, Austria: 2016.

57 Office for National Statistics. Accuracy of official high-age population estimates, in England and Wales: an evaluation. 2016. https://www.ons.gov.uk/peoplepopulationandcommunity/birthsdeathsandmarriages/ageing/methodologies/accuracyofofficialhighagepopulationestimatesinenglandandwalesanevaluation

58 NHS Trafford CCG Governing Body. Performance and Quality Report. 2015;1–47.

59 Office for National Statistics. A comparison of the 2011 Census and the Labour Force Survey ( LFS ) labour market indicators. 2012. https://www.ons.gov.uk/peoplepopulationandcommunity/populationandmigration/populationestimates/articles/acomparisonofthe2011censusandthelabourforcesurveylfslabourmarketindicators/2012-12-11

60 Stevenson M, Nunes T, Heuer C et al. epiR: Tools for the Analysis of Epidemiological Data. 2017.

61 Pilger D, Nguipdop-Djomo P, Abubakar I et al. BCG vaccination in England since 2005: A survey of policy and practice. BMJ Open 2012;2:e001303.

62 Joint Committee on Vaccination, panel IB. Minutes. 2002.

63 Joint Committee on Vaccination, panel IB. Minutes. 2003.

64 Sutherland I. Effectiveness of BCG vaccination in England and Wales in 1983. Tubercle 1987;68:81–92.

65 Springett VH, Darbyshire JH, Nunn AJ et al. Changes in tuberculosis notification rates in the white ethnic group in England and Wales between 1953 and 1983. Journal of epidemiology and community health 1988;42:370–6.

66 Borgdorff MW, Hof S van den, Kalisvaart N et al. Influence of sampling on clustering and associations with risk factors in the molecular epidemiology of tuberculosis. Am J Epidemiol 2011;174:243–51.

67 Fox J, Weisberg S. An R companion to applied regression. Third. Thousand Oaks CA:: Sage 2019. https://socialsciences.mcmaster.ca/jfox/Books/Companion/

68 Pereira SM, Barreto ML, Pilger D et al. Effectiveness and cost-effectiveness of first BCG vaccination against tuberculosis in school-age children without previous tuberculin test (BCG-REVAC trial): A cluster-randomised trial. Lancet Infectious Diseases 2012;12:300–6.

69 Barreto ML, Pilger D, Pereira SM et al. Causes of variation in BCG vaccine efficacy: Examining evidence from the BCG REVAC cluster randomized trial to explore the masking and the blocking hypotheses. Vaccine 2014;32:3759–64.

70 Fine PEM. Variation in protection by BCG: implications of and for heterologous immunity. Lancet 1995;346:1339–45.

71 Dye C. Making wider use of the world’s most widely used vaccine: Bacille Calmette-Guerin revaccination reconsidered. Journal of The Royal Society Interface 2013;10:20130365–5.

72 Usher C, Adams R, Schmitz S et al. Evaluating the neonatal BCG vaccination programme in Ireland. Archives of Public Health 2016;74:1–12.

73 Hersh AL, Tala-Heikkila M, Tala E et al. A cost-effectiveness analysis of universal versus selective immunization with Mycobacterium bovis bacille Calmette-Guérin in Finland. Int J Tuberc Lung Dis 2003;7:22–9.

74 Romanus V, Svensson Å, Hallander HO. The impact of changing BCG coverage on tuberculosis incidence in Swedish-born children between 1969 and 1989. Tubercle and Lung Disease 1992;73:150–61.

75 Guthmann JP, Antoine D, Fonteneau L et al. Assessing BCG vaccination coverage and incidence of paediatric tuberculosis following two major changes in BCG vaccination policy in France. 2011;1–6.

76 Abbott S, Christensen H, Welton NJ et al. Estimating the effect of the 2005 change in bcg policy in england: A retrospective cohort study, 2000 to 2015. Eurosurveillance 2019;24:1900220. doi:10.2807/1560-7917.ES.2019.24.49.1900220

77 Abbott S, Christensen H, Lalor MK et al. Exploring the effects of BCG vaccination in patients diagnosed with tuberculosis: Observational study using the Enhanced Tuberculosis Surveillance system. Vaccine 2019;1–6.

78 Parslow R, El-Shimy NA, Cundall DB et al. Tuberculosis, deprivation, and ethnicity in Leeds, UK, 1982-1997. Archives of disease in childhood 2001;84:109–13.

79 Roth A, Sodemann M, Jensen H et al. Tuberculin reaction, BCG scar, and lower female mortality. Epidemiology (Cambridge, Mass) 2006;17:562–8.

80 Aaby P, Nielsen J, Benn CS et al. Sex-differential and non-specific effects of routine vaccinations in a rural area with low vaccination coverage: An observational study from Senegal. Transactions of the Royal Society of Tropical Medicine and Hygiene 2014;109:77–84.

81 Teale C, Goldman JM, Pearson SB. The association of age with the presentation and outcome of tuberculosis: a five-year survey. Age and ageing 1993;22:289–93.

82 Abubakar I, Laundy MT, French CE et al. Epidemiology and treatment outcome of childhood tuberculosis in England and Wales: 1999-2006. Archives of Disease in Childhood 2008;93:1017–21.

83 Djuretic T, Herbert J, Drobniewski F et al. Antibiotic resistant tuberculosis in the United Kingdom : 2002;477–82.

84 Barnard J, Rubin DB. Miscellanea. Small-sample degrees of freedom with multiple imputation. Biometrika 1999;86:948–55.

85 Roy a, Eisenhut M, Harris RJ et al. Effect of BCG vaccination against Mycobacterium tuberculosis infection in children: systematic review and meta-analysis. BMJ (Clinical research ed) 2014;349:g4643–3.

86 Kandasamy R, Voysey M, McQuaid F et al. Non-specific immunological effects of selected routine childhood immunisations: systematic review. BMJ (Clinical research ed) 2016;355:i5225.

87 Pollard AJ, Finn A, Curtis N. Non-specific effects of vaccines: plausible and potentially important, but implications uncertain. Archives of Disease in Childhood 2017;102:archdischild–2015–310282.

88 Thomas HL, Harris RJ, Muzyamba MC et al. Reduction in tuberculosis incidence in the UK from 2011 to 2015: a population-based study. Thorax 2018;thoraxjnl–2017–211074.

89 Parikh SR, Andrews NJ, Beebeejaun K et al. Effectiveness and impact of a reduced infant schedule of 4CMenB vaccine against group B meningococcal disease in England : a national observational cohort study. The Lancet 2013;388:2775–82.

90 Vehtari A, Gelman A, Gabry J. Practical Bayesian model evaluation using leave-one-out cross-validation and WAIC. The American Statistician 2016;27:1–20.

91 ai H. R Interface for H2O. 2018.

92 Bürkner P-C. brms: An R package for Bayesian multilevel models using Stan. Journal of Statistical Software 2017;80:1–28. doi:10.18637/jss.v080.i01

93 Carpenter B, Gelman A, Hoffman M et al. Stan: A probabilistic programming language. Journal of Statistical Software, Articles 2017;76:1–32. doi:10.18637/jss.v076.i01

94 Davies R, Jones M, Lloyd-Williams H. Age and Work-Related Health: Insights from the UK Labour Force Survey. British Journal of Industrial Relations 2016;54:136–59.

95 Lindley J. The over-education of UK immigrants and minority ethnic groups: Evidence from the Labour Force Survey. Economics of Education Review 2009;28:80–9.

96 Manissero D, Lopalco PL, Levy-Bruhl D et al. Assessing the impact of different BCG vaccination strategies on severe childhood TB in low-intermediate prevalence settings. Vaccine 2008;26:2253–9.

97 Feiring B, Laake I, Molden T et al. Do selective immunisation against tuberculosis and hepatitis B reach the targeted populations ? A nationwide register-based study evaluating the recommendations in the Norwegian Childhood Immunisation Programme. Vaccine 2016;34:2015–20.

98 Nguipdop-Djomo P, Mangtani P, Pedrazzoli D et al. Uptake of neonatal BCG vaccination in England: Performance of the current policy recommendations. Thorax 2014;69:87–9.

99 Vynnycky E, Fine PE. The annual risk of infection with Mycobacterium tuberculosis in England and Wales since 1901. Int J Tuberc Lung Dis 1997;1:389–96.

100 Harris RC, Dodd PJ, White RG. The potential impact of BCG vaccine supply shortages on global paediatric tuberculosis mortality. BMC Med 2016;14:138.

101 Ragonnet R, Trauer JM, Scott N et al. Optimally capturing latency dynamics in models of tuberculosis transmission. Epidemics 2017;21:39–47.

102 Brooks-Pollock E, Cohen T, Murray M. The impact of realistic age structure in simple models of tuberculosis transmission. PLoS ONE 2010;5:3–8.

103 Manissero D, Lopalco PL, Levy-Bruhl D et al. Assessing the impact of different BCG vaccination strategies on severe childhood TB in low-intermediate prevalence settings. Vaccine 2008;26:2253–9.

104 Trunz BB, Fine P, Dye C. Effect of BCG vaccination on childhood tuberculous meningitis and miliary tuberculosis worldwide: a meta-analysis and assessment of cost-effectiveness. Lancet 2006;367:1173–80.

105 Rahman M, Sekimoto M, Takamatsu I et al. Economic evaluation of universal BCG vaccination of Japanese infants. International journal of epidemiology 2001;30:380–5.

106 Bhunu CP, Garira W, Mukandavire Z et al. Modelling the effects of pre-exposure and post-exposure vaccines in tuberculosis control. Journal of Theoretical Biology 2008;254:633–49.

107 Brooks-Pollock E, Cohen T, Murray M. The impact of realistic age structure in simple models of tuberculosis transmission. PLoS ONE 2010;5:3–8.

108 Menzies NA, Wolf E, Connors D et al. Review Progression from latent infection to active disease in dynamic tuberculosis transmission models : a systematic review of the validity of modelling assumptions. Lancet Infect Dis 2018;3099.

109 Mathema B, Andrews JR, Cohen T et al. Drivers of Tuberculosis Transmission. J Infect Dis 2018;216:S644–53.

110 Lefebvre N, Sotgiu G, Falzon D et al. Determinants of site of tuberculosis disease : An analysis of European surveillance data from 2003 to 2014. 2017;1–14.

111 Shaw JB, Wynn-Williams N. Infectivity of pulmonary tuberculosis in relation to sputum status. American review of tuberculosis 1954;69:724–32.

112 Tostmann A, Kik SV, Kalisvaart NA et al. Tuberculosis Transmission by Patients with Smear- Negative Pulmonary Tuberculosis in a Large Cohort in The Netherlands. Clinical Infectious Diseases 2008;47:1135–42.

113 Piccini P, Chiappini E, Tortoli E et al. Clinical peculiarities of tuberculosis. BMC Infect Dis 2014;14 Suppl 1:S4.

114 Houben RMGJ, Lalli M, Sumner T et al. TIME Impact - a new user-friendly tuberculosis (TB) model to inform TB policy decisions. BMC Medicine 2016;14:1–10.

115 Andrews JR, Lawn SD, Rusu C et al. The cost-effectiveness of routine tuberculosis screening with Xpert MTB/RIF prior to initiation of antiretroviral therapy: a model-based analysis. Aids 2012;26:987–95 10.1097/QAD.0b013e3283522d47.

116 Vynnycky E, Fine PE. The natural history of tuberculosis: the implications of age-dependent risks of disease and the role of reinfection. Epidemiology and infection 1997;119:183–201.

117 Houben RM, Lalli M, Sumner T et al. TIME Impact - a new user-friendly tuberculosis (TB) model to inform TB policy decisions. BMC Med 2016;14:56.

118 Vynnycky E, Fine PE. Interpreting the decline in tuberculosis: the role of secular trends in effective contact. Int J Epidemiol 1999;28:327–34.

119 Hens N, Jit M, Beutels P et al. Social Contacts and Mixing Patterns Relevant to the Spread of Infectious Diseases. PLoS medicine 2008;5:e74.

120 Lalor MK, Anderson LF, Hamblion EL et al. Recent household transmission of tuberculosis in England, 2010-2012: Retrospective national cohort study combining epidemiological and molecular strain typing data. BMC Medicine 2017;15:1–10.

121 Dowdy DW, Dye C, Cohen T. Data needs for evidence-based decisions : a tuberculosis modeler’s wish list. International Journal of Tuberculosis and Lung Disease 2013;17:866–77.

122 Egbetade S, Polytechnic T, Ibrahim MO. Modelling The Impact of BCG Vaccines on Tuberculosis Epidemics. 2011;1:49–55.

123 Murray LM. Bayesian State-Space Modelling on high-performance hardware using LibBi. Journal of Statistical Software 2015;67:1–36.

124 Jacob PE, Funk S. Rbi: R interface to libbi. 2019. https://CRAN.R-project.org/package=rbi

125 Funk S. RBI.helpers. Published Online First: 2019.https://github.com/sbfnk/RBi.helpers

126 Gelman A. Bayesian Data Analysis: Second Edition. 2004.

127 Marino S, Hogue IB, Ray CJ et al. A methodology for performing global uncertainty and sensitivity analysis in systems biology. J Theor Biol 2008;254:178–96.

128 Toni T, Welch D, Strelkowa N et al. Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems. Journal of The Royal Society Interface 2009;6:187–202.

129 Lintusaari J, Gutmann MU, Kaski S et al. On the identifiability of transmission dynamic models for infectious diseases. Genetics 2016;201:911–8.

130 Busetto AG, Numminen E, Corander J et al. Approximate bayesian computation. PLoS computational biology 2013;9:e1002803.