Schematic of ODE model.

<p>Boxes indicate ODE compartments, arrows represent fluxes between compartments; broad arrows indicate immigration and emigration in and out of the compartments. See main text for complete model description, and Fig A in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0192282#pone.0192282.s005" target="_blank">S1 Appendix</a> for detailed figure.</p

Estimates for transmission rate, fraction recent LTBI in 1995 and contribution of different routes to LTBI in the Netherlands for three ethnic groups–Morocco-, Turkey- and Indonesia-born communities.

<p>In brackets the 95% confidence regions of the multivariate sensitivity analysis.</p

Best fit model to diagnosed (E)PTB cases.

<p>Number of diagnosed (A) PTB and (B) EPTB cases among Moroccan-born (grey bars; left axis). The black line represents the best-fit line to the diagnosed cases (left axis), the blue line represents yearly immigration figures from Morocco (right axis). Turkish-born (C) PTB, (D) EPTB cases, and Indonesian-born (E) PTB, (F) EPTB cases.</p

Model parameters.

<p>Model parameters.</p

Additional file 2: of Whole genome sequencing reveals mycobacterial microevolution among concurrent isolates from sputum and blood in HIV infected TB patients

SNPs and SNP functions identified by comparing concurrent sputum and blood M. tuberculosis strains from HIV-infected individuals. (DOC 30 kb

Results for studies on clinical algorithms for diagnosis of smear-negative TB in patients presenting with symptoms (“rule-in”) and for screening of HIV-infected individuals (“rule-out”).

a<p>Excluding one that generated an algorithm that was subsequently evaluated in a separate (prediction) dataset.</p>b<p>Additional diagnostic procedures evaluated include bronchoalveolar lavage, nasopharyngeal aspirate, stool culture, fluorescence microscopy, PCR, urinary lipoarabinomannan, microscopic observation of drug susceptibility (MODS), endobroncheal ultrasound, repeat of smear examination after 1 mo.</p>c<p>These studies also assessed effects on health outcomes.</p>d<p>Excluding one multi-country study <a href="http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.1001358#pmed.1001358-Cain1" target="_blank">[65]</a>.</p>e<p>Excluding two multi-country studies <a href="http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.1001358#pmed.1001358-Cain1" target="_blank">[65]</a>,<a href="http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.1001358#pmed.1001358-Monkongdee1" target="_blank">[66]</a>.</p>f<p>Number of studies evaluating effects on health outcomes.</p

Results for studies on provision of second-line treatment for multidrug-resistant TB.

a<p>Studies covering multiple sites or periods.</p>b<p>Including eight studies that evaluated treatment outcomes.</p>c<p>Including two studies that did so by (also) evaluating treatment outcomes.</p>d<p>Studies testing a hypothesis about measures to improve treatment completion or adherence.</p>e<p>As specific study objective, no hypothesis testing about measures to improve treatment completion or adherence.</p>f<p>Also addressing treatment outcomes.</p>g<p>Number of studies evaluating effects on health.</p

Additional file 1: of Whole genome sequencing reveals mycobacterial microevolution among concurrent isolates from sputum and blood in HIV infected TB patients

A tabular list of all SNPs and indels per M. tuberculosis isolate, sputum and blood, created using nesoni nway program. Key: Highlighted = SNPs between concurrent sputum and blood M. tuberculosis isolates, p = patient. (XLS 15043 kb

Results for studies on preventive therapy in HIV-infected individuals and in household contacts.

a<p>For example, comparing patients with positive versus negative tuberculin skin tests.</p>b<p>Including studies that addressed effects on treatment outcomes.</p>c<p>Studies testing a hypothesis about measures to improve treatment completion or adherence.</p>d<p>As specific study objective, no hypothesis testing about measures to improve treatment completion or adherence.</p>e<p>Two multi-country studies situated at locations with different TB incidences and HIV prevalence; one of these in various regions.</p>f<p>Number of studies evaluating effects on health outcomes.</p><p>HAART, highly active antiretroviral treatment.</p

Distribution of published studies on preventive therapy of household contacts of infectious TB patients, by geography, objective, and study setting.

<p>Effectiveness studies relate to studies designed to address effectiveness as well as mixed effectiveness-efficacy for health-related outcomes, done in routine or mixed routine-research settings. Delivery studies relate to studies designed to address treatment completion and adherence, practices, and organization of services. Two non-comparative delivery studies were also included as effectiveness studies.</p