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Spatially targeted interventions may be effective alternatives to individual or populationbased prevention strategies against tuberculosis (TB). However, their efficacy may depend on the mechanisms that lead to geographically constrained hotspots. Local TB incidence may reflect high levels of local transmission; conversely, they may point to frequent travel of community members to high-risk areas. We used whole-genome sequencing to explore patterns of TB incidence and transmission in Lima, Peru. Between 2009 and 2012, we recruited incident pulmonary TB patients and their household contacts, whom we followed for the occurrence of TB disease. We used whole-genome sequences of 2,712 Mycobacterial tuberculosis isolates from 2,440 patients to estimate pariwise genomic distances and compared these to the spatial distance between patients’ residences. Genomic distances increased rapidly as spatial distances increased and remained high beyond 2 km of separation. Next, we divided the study catchment area into 1 × 1 km grid-cell surface units and used household spatial coordinates to locate each TB patient to a specific cell. We estimated cell-specific transmission by calculating the proportion of patients in each cell with a pairwise genomic distance of 10 or fewer single-nucleotide polymorphisms. We found that cell-specific TB incidence and local transmission varied widely but that cell-specific TB incidence did not correlate closely with our estimates of local transmission (Cohen’s k = 0.27). These findings indicate that an understanding of the spatial heterogeneity in the relative proportion of TB due to local transmission may help guide the implementation of spatially targeted interventions. [ABSTRACT FROM AUTHOR]

Background South Africa has the highest tuberculosis incidence globally (781/100,000), with an estimated 4.3% of cases being rifampicin resistant (RR). Control and elimination strategies will require detailed spatial information to understand where drug-resistant tuberculosis exists and why it persists in those communities. We demonstrate a method to enable drug-resistant tuberculosis monitoring by identifying high-burden communities in the Western Cape Province using routinely collected laboratory data. Methods and findings We retrospectively identified cases of microbiologically confirmed tuberculosis and RR-tuberculosis from all biological samples submitted for tuberculosis testing (n = 2,219,891) to the Western Cape National Health Laboratory Services (NHLS) between January 1, 2008, and June 30, 2013. Because the NHLS database lacks unique patient identifiers, we performed a series of record-linking processes to match specimen records to individual patients. We counted an individual as having a single disease episode if their positive samples came from within two years of each other. Cases were aggregated by clinic location (n = 302) to estimate the percentage of tuberculosis cases with rifampicin resistance per clinic. We used inverse distance weighting (IDW) to produce heatmaps of the RR-tuberculosis percentage across the province. Regression was used to estimate annual changes in the RR-tuberculosis percentage by clinic, and estimated average size and direction of change was mapped. We identified 799,779 individuals who had specimens submitted from mappable clinics for testing, of whom 222,735 (27.8%) had microbiologically confirmed tuberculosis. The study population was 43% female, the median age was 36 years (IQR 27-44), and 10,255 (4.6%, 95% CI: 4.6-4.7) cases had documented rifampicin resistance. Among individuals with microbiologically confirmed tuberculosis, 8,947 (4.0%) had more than one disease episode during the study period. The percentage of tuberculosis cases with rifampicin resistance documented among these individuals was 11.4% (95% CI: 10.7-12.0). Overall, the percentage of tuberculosis cases that were RR-tuberculosis was spatially heterogeneous, ranging from 0% to 25% across the province. Our maps reveal significant yearly fluctuations in RR-tuberculosis percentages at several locations. Additionally, the directions of change over time in RR-tuberculosis percentage were not uniform. The main limitation of this study is the lack of unique patient identifiers in the NHLS database, rendering findings to be estimates reliant on the accuracy of the person-matching algorithm. Conclusions Our maps reveal striking spatial and temporal heterogeneity in RR-tuberculosis percentages across this province. We demonstrate the potential to monitor RR-tuberculosis spatially and temporally with routinely collected laboratory data, enabling improved resource targeting and more rapid locally appropriate interventions., Author(s): Avery I. McIntosh 1, Helen E. Jenkins 1, Laura F. White 1, Marinus Barnard 2, Dana R. Thomson 3, Tania Dolby 2, John Simpson 2, Elizabeth M. Streicher 4, [...]

Resistant TB Is a Serious Threat to Global Health Tuberculosis (TB) remains the leading cause of death from a largely preventable and curable infectious disease, with an estimated 1.7 million [...]

Background Several studies have suggested that diabetes mellitus (DM) increases the risk of active tuberculosis (TB). The rising prevalence of DM in TB-endemic areas may adversely affect TB control. We conducted a systematic review and a meta-analysis of observational studies assessing the association of DM and TB in order to summarize the existing evidence and to assess methodological quality of the studies. Methods and Findings We searched the PubMed and EMBASE databases to identify observational studies that had reported an age-adjusted quantitative estimate of the association between DM and active TB disease. The search yielded 13 observational studies (n= 1,786,212 participants) with 17,698 TB cases. Random effects meta-analysis of cohort studies showed that DM was associated with an increased risk of TB (relative risk = 3.11, 95% CI 2.27-4.26). Case-control studies were heterogeneous and odds ratios ranged from 1.16 to 7.83. Subgroup analyses showed that effect estimates were higher in non-North American studies. Conclusion DM was associated with an increased risk of TB regardless of study design and population. People with DM may be important targets for interventions such as active case finding and treatment of latent TB and efforts to diagnose, detect, and treat DM may have a beneficial impact on TB control., The Editors' Summary of this article follows the references. Introduction Despite the availability of effective therapy, tuberculosis (TB) continues to infect an estimated one-third of the world's population, to cause [...]

The comparative-genomic sequencing of two Mycobacterium tuberculosis strains enabled us to identify single nucleotide polymorphism (SNP) markers for studies of evolution, pathogenesis, and epidemiology in clinical M. tuberculosis. Phylogenetic analysis using these 'comparative-genome markers' (CGMs) produced a highly unusual phylogeny with a complete absence of secondary branches. To investigate CGM-based phylogenies, we devised computer models to simulate sequence evolution and calculate new phylogenies based on an SNP format. We found that CGMs represent a distinct class of phylogenetic markers that depend critically on the genetic distances between compared 'reference strains.' Properly distanced reference strains generate CGMs that accurately depict evolutionary relationships, distorted only by branch collapse. Improperly distanced reference strains generate CGMs that distort and reroot outgroups. Applying this understanding to the CGM-based phylogeny of M. tuberculosis, we found evidence to suggest that this species is highly clonal without detectable lateral gene exchange. We noted indications of evolutionary bottlenecks, including one at the level of the PHRI 'C' strain previously associated with particular virulence characteristics. Our evidence also suggests that loss of IS6110 to fewer than seven elements per genome is uncommon. Finally, we present population-based evidence that KasA, an important component of mycolic acid biosynthesis, develops G312S polymorphisms under selective pressure.

A 19-year-old man who experienced symptoms of ascending abnormal sensations (paresthesias), progressive weakness of the legs, rash, and upper respiratory infection was finally diagnosed as having Mycoplasma pneumoniae infection. He was successfully treated with antibiotics, and was able to walk and run again and control his bladder and bowels. Mycoplasma pneumoniae can cause upper respiratory illness in young adults, with symptoms of sore throat, bronchitis, skin rash, high levels of white blood cells (leukocytosis) and elevated red blood cell sedimentation rates. It can also cause neurologic symptoms such as myelopathies (lesions of the spinal cord). Tests for Lyme disease were negative. Guillain-Barre syndrome, spinal cord and nerve involvement caused by Lyme disease, a growing brain lesion, and a growing spinal cord lesion causing acute transverse myelopathy were other conditions that doctors considered but ruled out.

Abstract Background Tuberculosis (TB) is known to disproportionately affect the most economically disadvantaged strata of society. Many studies have assessed the association between poverty and TB, but only a few have assessed the direct financial burden TB treatment and care can place on households. Patient costs can be particularly burdensome for TB-affected households in sub-Saharan Africa where poverty levels are high; these costs include the direct costs of medical and non-medical expenditures and the indirect costs of time utilizing healthcare or lost wages. In order to comprehensively assess the existing evidence on the costs that TB patients incur, we undertook a systematic review of the literature. Methods PubMed, EMBASE, Science Citation Index, Social Science Citation Index, EconLit, Dissertation Abstracts, CINAHL, and Sociological Abstracts databases were searched, and 5,114 articles were identified. Articles were included in the final review if they contained a quantitative measure of direct or indirect patient costs for treatment or care for pulmonary TB in sub-Saharan Africa and were published from January 1, 1994 to Dec 31, 2010. Cost data were extracted from each study and converted to 2010 international dollars (I$). Results Thirty articles met all of the inclusion criteria. Twenty-one studies reported both direct and indirect costs; eight studies reported only direct costs; and one study reported only indirect costs. Depending on type of costs, costs varied from less than I$1 to almost I$600 or from a small fraction of mean monthly income for average annual income earners to over 10 times average annual income for income earners in the income-poorest 20% of the population. Out of the eleven types of TB patient costs identified in this review, the costs for hospitalization, medication, transportation, and care in the private sector were largest. Conclusion TB patients and households in sub-Saharan Africa often incurred high costs when utilizing TB treatment and care, both within and outside of Directly Observed Therapy Short-course (DOTS) programs. For many households, TB treatment and care-related costs were considered to be catastrophic because the patient costs incurred commonly amounted to 10% or more of per capita incomes in the countries where the primary studies included in this review were conducted. Our results suggest that policies to decrease direct and indirect TB patient costs are urgently needed to prevent poverty due to TB treatment and care for those affected by the disease.

Abstract Background Multiple studies of tuberculosis treatment have indicated that patients with diabetes mellitus may experience poor outcomes. We performed a systematic review and meta-analysis to quantitatively summarize evidence for the impact of diabetes on tuberculosis outcomes. Methods We searched PubMed, EMBASE and the World Health Organization Regional Indexes from 1 January 1980 to 31 December 2010 and references of relevant articles for reports of observational studies that included people with diabetes treated for tuberculosis. We reviewed the full text of 742 papers and included 33 studies of which 9 reported culture conversion at two to three months, 12 reported the combined outcome of failure and death, 23 reported death, 4 reported death adjusted for age and other potential confounding factors, 5 reported relapse, and 4 reported drug resistant recurrent tuberculosis. Results Diabetes is associated with an increased risk of failure and death during tuberculosis treatment. Patients with diabetes have a risk ratio (RR) for the combined outcome of failure and death of 1.69 (95% CI, 1.36 to 2.12). The RR of death during tuberculosis treatment among the 23 unadjusted studies is 1.89 (95% CI, 1.52 to 2.36), and this increased to an effect estimate of 4.95 (95% CI, 2.69 to 9.10) among the 4 studies that adjusted for age and other potential confounding factors. Diabetes is also associated with an increased risk of relapse (RR, 3.89; 95% CI, 2.43 to 6.23). We did not find evidence for an increased risk of tuberculosis recurrence with drug resistant strains among people with diabetes. The studies assessing sputum culture conversion after two to three months of tuberculosis therapy were heterogeneous with relative risks that ranged from 0.79 to 3.25. Conclusions Diabetes increases the risk of failure and death combined, death, and relapse among patients with tuberculosis. This study highlights a need for increased attention to treatment of tuberculosis in people with diabetes, which may include testing for suspected diabetes, improved glucose control, and increased clinical and therapeutic monitoring.