1976 research outputs found
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Optimal Dual RNA-Seq Mapping for Accurate Pathogen Detection in Complex Eukaryotic Hosts
Full text linkDual RNA-Seq technology has significantly advanced the study of biological interactions between two organisms by
allowing parallel transcriptomic analysis. Existing analysis methods employ various combinations of open-source
bioinformatics tools to process dual RNA-Seq data. Upon reviewing these methods, we intend to explore crucial criteria for selecting standard tools and methods, especially focusing on critical steps such as trimming and mapping reads to the reference genome. In order to validate the different combinatorial approaches, we performed benchmarking using top�ranking tools and a publicly available dual RNA-Seq Sequence Read Archive (SRA) dataset. An important observation while evaluating the mapping approach is that when the adapter trimmed reads are first mapped to the pathogen genome, more reads align to the pathogen genome than the unmapped reads derived from the traditional host-first mapping approach. This mapping method prevents the misalignment of pathogen reads to the host genome due to their shorter length. In this way, the pathogenic read information found at lesser proportions in a complex eukaryotic dataset is precisely obtained. This
protocol presents a comprehensive comparison of these possible approaches, resulting in a robust unified standard
methodology
Impact of rpoB gene mutations and Rifampicin-resistance levels on treatment outcomes in Rifampicin-resistant tuberculosis
Full text linkAlthough many studies have examined the connection between mutations in the rpoB gene and drug resistance, the impact of common mutations on treatment outcomes for RR-TB is not yet fully understoo
Efficacy and safety data on pretomanid for drug-resistant TB
Full text linkTo summarise the efficacy and safety of pretomanid (Pa) based regimens in patients with drug-resistant TB (DR-TB).
We included clinical trials, operational research and observational studies reporting the efficacy and safety of Pa-based regimens in DR-TB. The duration of the treatment was at least 24 weeks. Efficacy was reported as a favourable/unfavourable outcome and culture conversion. Safety was reported in terms of death and frequency of adverse events of special interest. Of the 127 articles identified, 13 were included. The proportion of favourable outcomes reported was 76−100%, and the median time to culture conversion was 4−6 weeks. Culture conversion rates ranged from 80–100% by the end of 3 months of treatment, regardless of the type of drug resistance. Treatment completion rates in the operational research studies varied between 18–93%. Safety events were not proportionate among the studies included, possibly due to the differing linezolid dosing (more frequent in the 1,200 mg dose regimen). Our review supports the use of Pa-based regimens in patients with DR-TB. The results indicate that Pa-based regimens are efficacious with tolerable safety profile in DR-TB patients
Economic Burden of TB Deaths in India (2021): A Retrospective Cross-sectional Study
Full text linkWe aimed to estimat the economic burden of TB deaths in terms of gross domestic product (GDP) across Indian states, regions, and different demographic groups. Using the Human Capital Approach, we estimated the non-health GDP losses due to TB deaths in India for 2021 at subnational level. The total monetary value for the years of life lost due to TB deaths was calculated
Identification of non-tuberculous mycobacteria in slaughtered cattle from Chennai, India
Full text linkNon-tuberculous mycobacteria (NTM) are emerging pathogens in human and veterinary medicine, with a globally increasing incidence. In India, sporadic studies have identified an upward trend in NTM infections, but accurate prevalence estimates are lacking due to the absence of nationwide surveillance. Non-tuberculous mycobacteria have been reported in clinically healthy cattle and wildlife globally, complicating tuberculosis (TB) diagnostics and surveillance. This study aimed to characterize NTM species isolated from tissue samples of slaughtered cattle in Chennai using culture and targeted hsp65 gene sequencing. A total of 118 presumed NTM samples from 115 animals were processed, and 49 isolates were confirmed as NTMs by PCR. Sequencing identified 18 different species, with Mycobacterium
intracellulare (9/49) being the most frequent, followed by Mycobacterium sp. strain 79_MI18_10584 (6/49) and Mycobacterium elephantis (6/49). Several identified
species, including M. intracellulare, M. fortuitum (5/49), M. kansasii (4/49), and M. avium, have caused infections in humans as well. NTMs in cattle lymph nodes
without visible lesions suggest their asymptomatic persistence, albeit there being a possibility of transient colonization. Non-tuberculous mycobacteria complicate
bovine tuberculosis (bTB) diagnostics by inducing cross-reactive immune responses and forming granulomatous lesions resembling those caused by Mycobacterium tuberculosis complex (MTBC). This study highlights the presence and diversity of NTMs in Indian cattle and emphasizes the need for better surveillance, improved molecular characterization, and better understanding of their epidemiological and immunological roles in both veterinary and public health contexts
Long term outcomes in drug resistant tuberculosis with Bedaquiline, Pretomanid and varying doses of Linezolid
Full text linkAssess the effectiveness of bedaquiline, pretomanid and linezolid (BPaL) regimens with varying doses and duration of linezolid at the end of 48 weeks post treatment among drug resistant tuberculosis (DR TB) patients
Predictive Markers of Incident Tuberculosis in Close Contacts in Brazil and India
No full textThere are insufficient predictors of progression to tuberculosis among contacts. A case-control study within RePORT-Brazil matched 20 QuantiFERON-positive progressors and 40 nonprogressors by sex, age, and exposure duration. Twentynine cytokines were measured using a Luminex assay with QuantiFERON-TB Gold Plus supernatants collected at baseline and evaluated using machine learning for tuberculosis prediction. The same markers were evaluated in 8 QuantiFERON-positive progressors and 12 nonprogressors from India. Interleukin 8, interleukin 10, and CCL3 levels predicted incident tuberculosis (area under the receiver operating characteristic curve, 0.75) in 2 years with sensitivity and specificity >80%, in both cohorts. This signature predicted tuberculosis progression in close contacts meeting World Health Organization goals
Estimating the epidemiological and economic mpact of providing nutritional care for tuberculosis-affected households across India: a modelling study
Full text linkApproximately 20% of global tuberculosis incidence is ttributable to undernutrition, increasing to more than a third in India. Targeting nutritional interventions to tuberculosis-affected households is a policy priority, but understanding of epidemiological and economic impacts is limited. We aimed to estimate the population-level epidemiological and economic effect of such an intervention
Diagnostic accuracy of screening and diagnostic tests used in a state-wide tuberculosis prevalence survey in India
Full text linkPrevalence surveys and active case findings for tuberculosis (TB) typically use symptoms and Chest X-ray for screening and a diagnostic test for microbiological confirmation. We report the performance of screening and diagnostic tests from a state-wide prevalence survey in India. We screened 130,932 individuals using chest X-ray (CXR) and symptom checklist. Sputum samples were obtained from eligible participants and subjected to Xpert/MTB RIF, smear microscopy, and culture. Cough over two weeks had higher sensitivity (41.6%, 95% CI: 31.6–52.1) and lower specificity (72.8%, 95% CI: 72.1–73.5) among all the symptoms. The sensitivity and specificity of abnormal CXR were 86.4% (95%
CI:77.9–92.5) and 42.12% (95% CI, 41.3–42.8), respectively. Xpert/MTB RIF in the reference laboratory had the highest sensitivity (96.55% 95% CI: 88.0-99.5), and smear microscopy had the highest specificity (99.7% 95% CI: 99.6–99.8). The combined sensitivity and specificity of Xpert MTB/RIF along
symptom screening and CXR were 97.9% (95% CI:92.6–99.7) and 4.9% (95% CI:4.67–5.33), respectively. The mobile van Xpert MTB/RIF was found to be highly specific (99.3%). We recommend a diagnostic algorithm consisting of symptom screening and CXR followed by WHO-recommended rapid molecular assays (mWRD) for future prevalence surveys and active case finding
Clinico-demographic profile of pre-extensively drug-resistant pulmonary tuberculosis patients in India
Full text linkDrug-resistant tuberculosis (DR TB) is a major public health problem and an important area of research. Identification of various risk factors is essential for its prevention and management. Adults weighing more than 30 kg, aged 18 years or more diagnosed with pre extensively drug resistant TB (pre-XDR TB) were initiated on bedaquiline and linezolid based regimens along with pretomanid/delamanid as part of two multicentric clinical trials in India. Pre-XDR TB was defined as patients infected with M. tb strains resistant to rifampicin (may or may not be resistant to isoniazid) with additional resistance to fluoroquinolones and/or second line injectable as per the existing World Health Organization (WHO) definitions during the trial period. We describe here the baseline demographic and clinical profile of patients with pre-XDR TB and enrolled in those two trials. Of 554 Pre-XDR TB patients, 297 (54 %) were males. Median age (IQR) was 27 years [22.0–36.3] and body mass index was 17.4 [15.7–20.1] kg/m2. Of all, 326 (59 %) had BMI <18.5 kg/m2. History of previous episodes of TB was reported by 415 (75 %) patients. Among them, 142 (34 %) had taken treatment more than once, 279 (67 %) had treatment failure during the previous episodes. Persons with a known history of diabetes were 67 (12 %). Cough, cough with expectoration, fever and weight loss were the presenting complaints in 539 (97 %) and 487 (88 %), 337 (61 %) and 314 (57 %) respectively. Sputum smear microscopy showed more than ++ acid-fast bacilli in 264 (48 %). Chest x-ray showed bilateral lung involvement in 329 (60 %) with more than two zones involvement in 304 (55 %) and presence of cavities in 264 (48 %) patients. Persons in the younger age group, those with malnutrition and previous history of TB treatment were observed to be more in these cohort of patients with PreXDR TB. High rates of treatment failure during the earlier episodes of TB with increased disease severity and drug resistance during the current episode is a matter of grave concern. Improved treatment success during the management of drug sensitive TB, addressing the nutritional challenges are some of key areas of focus in the prevention of DRTB burden