On the analysis of tuberculosis studies with intermittent missing sputum data

In randomized studies evaluating treatments for tuberculosis (TB), individuals are scheduled to be routinely evaluated for the presence of TB using sputum cultures. One important endpoint in such studies is the time of culture conversion, the first visit at which a patient’s sputum culture is negative and remains negative. This article addresses how to draw inference about treatment effects when sputum cultures are intermittently missing on some patients. We discuss inference under a novel benchmark assumption and under a class of assumptions indexed by a treatment-specific sensitivity parameter that quantify departures from the benchmark assumption. We motivate and illustrate our approach using data from a randomized trial comparing the effectiveness of two treatments for adult TB patients in Brazil.Fil: Scharfstein, Daniel. University Johns Hopkins; Estados UnidosFil: Rotnitzky, Andrea Gloria. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Torcuato Di Tella. Departamento de Economía; ArgentinaFil: Abraham, Maria. Statistics Collaborative; Estados UnidosFil: McDermott, Aidan. University Johns Hopkins; Estados UnidosFil: Chaisson, Richard. University Johns Hopkins; Estados UnidosFil: Geiter, Lawrence. Otsuka Novel Products; Estados Unido

Tuberculosis and Human Immunodeficiency Virus Infection

Progressive human immunodeficiency virus infection eventually leads to activation and dissemination of a wide variety of microorganisms normally held in check by the cellular immune system. Mycobacterium tuberculosis is one of these pathogens, and the disease caused by it has become a common presenting infection in the patient with AIDS. Dr. Richard E. Chaisson and Dr. Gary Slutkin have studied tuberculosis in the United States and worldwide, respectively. In this AIDS Commentary they address the unique nature of this infection, its diagnosis, and its treatment in the patient with AID

Reply to “At the crossroads between early or delayed antiretroviral therapy initiation during TB/HIV coinfection”

La digitalització dels textos, iniciada en la dècada dels setanta, ha originat sistemes i productes diversos que poden ser molt útils en la investigació literària. Un dels més coneguts, lâhipertext, és un bon exemple de les possibilitats de la lectura no seqüencial que caracteritza les obres de referència o determinades recerques en lâàmbit de la filologia, com ara lâedició de textos. La digitalització destaca les característiques tant hipertextuals com intertextuals de la literatura i ajuda a entendre, així, alguns dels seus trets constitutius. Dâaltra banda, la publicació en línia de textos de molt difícil abast proposada per comunitats científiques molt presents a Internet és una oferta plena de possibilitats i suggereix un camí a seguir per comunitats encara poc implantades, com ara la filologia catalana. | Digitisation of text, begun in the 1970s, has produced a diversity of systems and products that could be very useful for literary research. One of the better known examples, hypertext, demonstrates the potential for non-sequential reading that characterises the use made of reference works or specific searches performed in the field of philology, such as for text publishing. Digitisation highlights both | La digitalización de textos, iniciada en la década de los años setenta, ha dado lugar a sistemas y productos diversos que pueden ser muy útiles en la investigación literaria. Uno de los más conocidos, el hipertexto, constituye un buen ejemplo de las posibilidades de la lectura secuencial que caracteriza las obras de referencia o determinadas investigaciones en el ámbito de la Filología, como, por ejemplo, la edición de textos. La digitalización destaca las características tanto hipertextuales como intertextuales de la literatura facilitando, por tanto, su comprensión. Por otro lado, la publicación en línea de textos de muy difícil acceso, propuesta por comunidades científicas muy presentes en Internet, es una oferta llena de posibilidades y abre un camino a seguir por parte de comunidades poco implantadas todavía como es el caso de la Filología catalana

Building clinical trials capacity for tuberculosis drugs in high-burden countries

The long duration of TB therapy, the high prevalence of HIV coinfection, and the growing prevalence of drug-resistant TB underscore the urgent need for more effective treatments

Discovery and genotyping of structural variation from long-read haploid genome sequence data

In an effort to more fully understand the full spectrum of human genetic variation, we generated deep single-molecule, real-time (SMRT) sequencing data from two haploid human genomes. By using an assembly-based approach (SMRT-SV), we systematically assessed each genome independently for structural variants (SVs) and indels resolving the sequence structure of 461,553 genetic variants from 2 bp to 28 kbp in length. We find that &gt;89% of these variants have been missed as part of analysis of the 1000 Genomes Project even after adjusting for more common variants (MAF &gt; 1%). We estimate that this theoretical human diploid differs by as much as ∼16 Mbp with respect to the human reference, with long-read sequencing data providing a fivefold increase in sensitivity for genetic variants ranging in size from 7 bp to 1 kbp compared with short-read sequence data. Although a large fraction of genetic variants were not detected by short-read approaches, once the alternate allele is sequence-resolved, we show that 61% of SVs can be genotyped in short-read sequence data sets with high accuracy. Uncoupling discovery from genotyping thus allows for the majority of this missed common variation to be genotyped in the human population. Interestingly, when we repeat SV detection on a pseudodiploid genome constructed in silico by merging the two haploids, we find that ∼59% of the heterozygous SVs are no longer detected by SMRT-SV. These results indicate that haploid resolution of long-read sequencing data will significantly increase sensitivity of SV detection.</jats:p

Tuberculosis and Hepatic Steatosis Are Prevalent Liver Pathology Findings among HIV-Infected Patients in South Africa

Liver disease epidemiology in sub-Saharan Africa has shifted as a result of HIV and the increased use of antiretroviral therapy leading to a need for updated data on common causes of liver disease. We retrospectively reviewed records from all hospitalized patients who had liver biopsy at a single hospital in South Africa from 2001 to 2009 and compared diagnosis by HIV status. During the period of study 262 patients had liver biopsy, 108 (41%) were HIV-infected, 25 (10%) were HIV-sero-negative, and 129 (49%) had unknown or unrecorded HIV status. Overall 81% of biopsies provided additional diagnostic data. Malignancy was the most common finding reported on 56 (21%) biopsies followed by granuloma or TB, hepatic steatosis, and fibrosis or cirrhosis. HIV-infected patients were more likely to have granulomas and steatosis. Half of patients with granulomas were already on TB treatment, suggesting paradoxical reactions or drug induced liver injury may have been important causes of liver inflammation among these patients. We note that TB, paradoxical reactions during TB treatment, possible drug induced liver injury, and hepatic steatosis are important causes of liver pathology among HIV-infected hospitalized patients with unclear etiology of liver disease after initial assessment. Among HIV sero-negative patients, malignancy was the major cause of liver disease. Our findings re-enforce the importance of TB as a diagnosis among HIV-infected individuals.\ud \u

Mortality associated with delays between clinic entry and ART initiation in resource-limited settings: results of a transition-state model.

OBJECTIVE: To estimate the mortality impact of delay in antiretroviral therapy (ART) initiation from the time of entry into care. DESIGN: A state-transition Markov process model. This technique allows for assessing mortality before and after ART initiation associated with delays in ART initiation among a general population of ART-eligible patients without conducting a randomized trial. METHODS: We used patient-level data from 3 South African cohorts to determine transition probabilities for pre-ART CD4 count changes and pre-ART and on-ART mortality. For each parameter, we generated probabilities and distributions for Monte Carlo simulations with 1-week cycles to estimate mortality 52 weeks from clinic entry. RESULTS: We estimated an increase in mortality from 11.0% to 14.7% (relative increase of 34%) with a 10-week delay in ART for patients entering care with our pre-ART cohort CD4 distribution. When we examined low CD4 ranges, the relative increase in mortality delays remained similar; however, the absolute increase in mortality rose. For example, among patients entering with CD4 count 50-99 cells per cubic millimeter, 12-month mortality increased from 13.3% with no delay compared with 17.0% with a 10-week delay and 22.9% with a 6-month delay. CONCLUSIONS: Delays in ART initiation, common in routine HIV programs, can lead to important increases in mortality. Prompt ART initiation for patients entering clinical care and eligible for ART, especially those with lower CD4 counts, could be a relatively low-cost approach with a potential marked impact on mortality

A trial of mass isoniazid preventive therapy for tuberculosis control.

BACKGROUND: Tuberculosis is epidemic among workers in South African gold mines. We evaluated an intervention to interrupt tuberculosis transmission by means of mass screening that was linked to treatment for active disease or latent infection. METHODS: In a cluster-randomized study, we designated 15 clusters with 78,744 miners as either intervention clusters (40,981 miners in 8 clusters) or control clusters (37,763 miners in 7 clusters). In the intervention clusters, all miners were offered tuberculosis screening. If active tuberculosis was diagnosed, they were referred for treatment; if not, they were offered 9 months of isoniazid preventive therapy. The primary outcome was the cluster-level incidence of tuberculosis during the 12 months after the intervention ended. Secondary outcomes included tuberculosis prevalence at study completion. RESULTS: In the intervention clusters, 27,126 miners (66.2%) underwent screening. Of these miners, 23,659 (87.2%) started taking isoniazid, and isoniazid was dispensed for 6 months or more to 35 to 79% of miners, depending on the cluster. The intervention did not reduce the incidence of tuberculosis, with rates of 3.02 per 100 person-years in the intervention clusters and 2.95 per 100 person-years in the control clusters (rate ratio in the intervention clusters, 1.00; 95% confidence interval [CI], 0.75 to 1.34; P=0.98; adjusted rate ratio, 0.96; 95% CI, 0.76 to 1.21; P=0.71), or the prevalence of tuberculosis (2.35% vs. 2.14%; adjusted prevalence ratio, 0.98; 95% CI, 0.65 to 1.48; P=0.90). Analysis of the direct effect of isoniazid in 10,909 miners showed a reduced incidence of tuberculosis during treatment (1.10 cases per 100 person-years among miners receiving isoniazid vs. 2.91 cases per 100 person-years among controls; adjusted rate ratio, 0.42; 95% CI, 0.20 to 0.88; P=0.03), but there was a subsequent rapid loss of protection. CONCLUSIONS: Mass screening and treatment for latent tuberculosis had no significant effect on tuberculosis control in South African gold mines, despite the successful use of isoniazid in preventing tuberculosis during treatment. (Funded by the Consortium to Respond Effectively to the AIDS TB Epidemic and others; Thibela TB Current Controlled Trials number, ISRCTN63327174.)

Reconstructing complex regions of genomes using long-read sequencing technology

Cataloged from PDF version of article.Obtaining high-quality sequence continuity of complex regions of recent segmental duplication remains one of the major challenges of finishing genome assemblies. In the human and mouse genomes, this was achieved by targeting large-insert clones using costly and laborious capillary-based sequencing approaches. Sanger shotgun sequencing of clone inserts, however, has now been largely abandoned, leaving most of these regions unresolved in newer genome assemblies generated primarily by next-generation sequencing hybrid approaches. Here we show that it is possible to resolve regions that are complex in a genome-wide context but simple in isolation for a fraction of the time and cost of traditional methods using long-read single molecule, real-time (SMRT) sequencing and assembly technology from Pacific Biosciences (PacBio). We sequenced and assembled BAC clones corresponding to a 1.3-Mbp complex region of chromosome 17q21.31, demonstrating 99.994% identity to Sanger assemblies of the same clones. We targeted 44 differences using Illumina sequencing and find that PacBio and Sanger assemblies share a comparable number of validated variants, albeit with different sequence context biases. Finally, we targeted a poorly assembled 766-kbp duplicated region of the chimpanzee genome and resolved the structure and organization for a fraction of the cost and time of traditional finishing approaches. Our data suggest a straightforward path for upgrading genomes to a higher quality finished state

Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics