<i>P. falciparum</i> FP2 non-synonymous amino acid and nucleotide substitutions observed in Tororo, Uganda.

<p>All data are relative to reference sequence <i>PF3D7_1343700.</i></p><p>n = number of samples containing mutant allele.</p><p>N = number of samples sequenced at locus.</p>a<p>SNP reported in MalariaGen.</p>b<p>SNP reported in PlasmoDB, v. 11.0.</p>c<p>Different SNP in same codon has been previously reported (MalariaGen or PlasmoDB).</p>d<p>SNP reported to be present in culture adapted Cambodian strains by Ariey <i>et al</i>.<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105690#pone.0105690-Ariey1" target="_blank">[14]</a>.</p>e<p>Transmembrane boundaries as indicated in PlasmoDB v. 11.0 (amino acids 35–57).</p

<i>P. falciparum</i> K13-propeller amino acid and nucleotide substitutions observed in Tororo, Uganda.

<p>All data are relative to reference sequence <i>PF3D7_1343700.</i></p><p>n = number of samples containing mutant allele.</p><p>N = number of samples sequenced at locus.</p>a<p>SNP has been previously identified (MalariaGen).</p>b<p>Different SNP in same codon has been previously reported (MalariaGen).</p>c<p>Polymorphism identified in mixed <i>P. falciparum/P. ovale</i> infection.</p

Spatial overlap links seemingly unconnected genotype-matched TB cases in rural Uganda

<div><p>Introduction</p><p>Incomplete understanding of TB transmission dynamics in high HIV prevalence settings remains an obstacle for prevention. Understanding where transmission occurs could provide a platform for case finding and interrupting transmission.</p><p>Methods</p><p>From 2012–2015, we sought to recruit all adults starting TB treatment in a Ugandan community. Participants underwent household (HH) contact investigation, and provided names of social contacts, sites of work, healthcare and socializing, and two sputum samples. <i>Mycobacterium tuberculosis</i> culture-positive specimens underwent 24-loci MIRU-VNTR and spoligotyping. We sought to identify epidemiologic links between genotype-matched cases by analyzing social networks and mapping locations where cases reported spending ≥12 hours over the one-month pre-treatment. Sites of spatial overlap (≤100m) between genotype-matched cases were considered potential transmission sites. We analyzed social networks stratified by genotype clustering status, with cases linked by shared locations, and compared network density by location type between clustered vs. non-clustered cases.</p><p>Results</p><p>Of 173 adults with TB, 131 (76%) were enrolled, 108 provided sputum, and 84/131 (78%) were MTB culture-positive: 52% (66/131) tested HIV-positive. Of 118 adult HH contacts, 105 (89%) were screened and 3 (2.5%) diagnosed with active TB. Overall, 33 TB cases (39%) belonged to 15 distinct MTB genotype-matched clusters. Within each cluster, no cases shared a HH or reported shared non-HH contacts. In 6/15 (40%) clusters, potential epidemiologic links were identified by spatial overlap at specific locations: 5/6 involved health care settings. Genotype-clustered TB social networks had significantly greater network density based on shared clinics (p<0.001) and decreased density based on shared marketplaces (p<0.001), compared to non-clustered networks.</p><p>Conclusions</p><p>In this molecular epidemiologic study, links between MTB genotype-matched cases were only identifiable via shared locations, healthcare locations in particular, rather than named contacts. This suggests most transmission is occurring between casual contacts, and emphasizes the need for improved infection control in healthcare settings in rural Africa.</p></div

Unit Cost Estimates for Antiretroviral Therapy Delivery (2012 $US).

<p>Unit Cost Estimates for Antiretroviral Therapy Delivery (2012 $US).</p

Sensitivity Analyses of Varying Efficiency/Gain Scenarios.

<p>Sensitivity Analyses of Varying Efficiency/Gain Scenarios.</p

Estimated ART Delivery Costs under Modeled Scenarios of Efficient ART Scale-Up.

<p>Costs for ART delivery under six modeled scenarios are displayed inclusive of viral load testing. Model costs excluding viral load testing are also shown. <b>Model A:</b> steady-state patient load, MJAP program salary scale and standard core laboratory monitoring schedule. <b>Model B:</b> model A + lowest available ARV drug costs. <b>Model C:</b> model B + Uganda Ministry of Health 2013 salary scales. <b>Model D:</b> model C + increased healthcare worker efficiency due to full use of workday. <b>Model E:</b> model D + expansion of healthcare worker effort to full 8-hour workday. <b>Model F:</b> model E + higher MJAP program salary scales.</p

Potential epidemiologic links among patients in six of 15 MTB genotype clusters based on either co-location at a shared site or time spent at geographically adjacent locations (within 100 meters of one another) in the time leading up to TB diagnosis, using GPS coordinates of sites of work, clinic, socializing, and household.

<p>Patients in the remaining nine of 15 MTB genotype clusters had no shared or neighboring locations identified.</p

Demographic and clinical characteristics of MTB genotype non-clustered vs. clustered TB cases.

<p>Demographic and clinical characteristics of MTB genotype non-clustered vs. clustered TB cases.</p

Demographic Characteristics of Kakyerere Parish Community Health Campaign Participants.

<p>Demographic Characteristics of Kakyerere Parish Community Health Campaign Participants.</p

Social-location networks of genotype-clustered vs. non-clustered TB cases in Tororo, Uganda.

<p>Each network node represents a participant with culture-positive TB, with node size proportional to node degree. Each network edge represents a specific shared location, with edge colors indicating the location type, as indicated in the legend.</p