Whole-Genome Sequences of Four Clinical Isolates of Mycobacterium tuberculosis from Tamil Nadu, South India.
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ABSTRACT:
SUBMITTER: Narayanan S
PROVIDER: S-EPMC3707582 | biostudies-literature | 2013 Jun
REPOSITORIES: biostudies-literature
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Whole-Genome Sequences of Four Clinical Isolates of Mycobacterium tuberculosis from Tamil Nadu, South India.
Narayanan Sujatha S Deshpande Uday U
Genome announcements 20130620 3
We report the annotated genome sequences of four clinical isolates of Mycobacterium tuberculosis from Tamil Nadu, India. ...[more]
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Project description:We report the annotated genome sequence of two clinical isolates of Mycobacterium tuberculosis isolated from Kerala, India.
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Project description:Periodic drug resistance surveillance provides useful information on trends of drug resistance and effectiveness of tuberculosis (TB) control measures. The present study determines the prevalence of drug resistance among new sputum smear positive (NSP) and previously treated (PT) pulmonary TB patients, diagnosed at public sector designated microscopy centers (DMCs) in the state of Tamil Nadu, India. In this single-stage cluster-sampling prevalence survey, 70 of 700 DMCs were randomly selected using a probability-proportional to size method. A cluster size of 24 for NSP and a varying size of 0 to 99 for PT cases were fixed for each selected DMC. Culture and drug susceptibility testing was done on Lowenstein-Jensen medium using the economic variant of proportion sensitivity test for isoniazid (INH), rifampicin (RMP), ofloxacin (OFX) and kanamycin (KAN). Human Immunodeficiency Virus (HIV) status was collected from patient records. From June 2011 to August 2012, 1524 NSP and 901 PT patients were enrolled. Any RMP resistance and any INH resistance were observed in 2.6% and 15.1%, and in 10.4% and 30% respectively in NSP and PT cases. Among PT patients, multi drug resistant TB (MDR-TB) was highest in the treatment failure (35%) group, followed by relapse (13%) and treatment after default (10%) groups. Extensively drug resistant TB (XDRTB) was seen in 4.3% of MDR-TB cases. Any OFX resistance was seen in 10.4% of NSP, 13.9% of PT and 29% of PT MDR-TB patients. The HIV status of the patient had no impact on drug resistance levels. RMP resistance was present in 2.6% of new and 15.1% of previously treated patients in Tamil Nadu. Rates of OFX resistance were high among NSP and PT patients, especially among those with MDR-TB, a matter of concern for development of new treatment regimens for TB.
| S-EPMC4349813 | biostudies-literature
Project description:AimThe present study was carried out to find out the causative agent of exanthematous skin lesions in sheep maintained by Southern Regional Research Centre, Mannavanur, Kodai hills, Tamil Nadu.Materials and methodsPolymerase chain reaction (PCR) with Orf virus (ORFV) B2L gene-specific primers was carried out by employing the total genomic DNA isolated from the scabs as the template. The ORFV isolates from Kodai hills were characterized by the use of bioinformatics tools.ResultsThe amino acid identity of ORFV isolate 1 from Kodai hills is having 98.14%, 96.29%, and 83.59% identity with reference strains of ORFV, Pseudocowpox virus, and bovine papular stomatitis virus, respectively. Phylogenetic analysis revealed that ORFV isolates from Kodai hills clustered with the other ORFV isolates from different geographical areas of India.ConclusionThe etiological agent of exanthematous skin lesion among sheep of Kodai hills is ORFV.
| S-EPMC6702573 | biostudies-literature
Project description:BackgroundThe National Tuberculosis Elimination Programme (NTEP) of India is aiming to eliminate TB by 2025. The programme has increased its services and resources to strengthen the accurate and early detection of TB. It is important to estimate the cost of TB diagnosis in India considering the advancement and implementation of new diagnostic tools under the NTEP. The objective of this study was to estimate the unit costs of providing TB diagnostic services at different levels of public health facilities with different algorithms implemented under the NTEP in Chennai, Tamil Nadu, South India.MethodsThis costing study was conducted from the perspective of the health system. This study used only secondary data and information that were available in the public domain. Data were collected with the approval of health authorities. The patient's diagnostic path from the point of registration until the final diagnosis was considered in the costing exercise. The unit costs of different diagnostic tools used in the NTEP implemented by Chennai Corporation were calculated.ResultsWe estimated the unit cost of the eight laboratory tests (Ziehl-Neelsen [ZN], fluorescence microscopy [FM], x-ray, digital x-ray, gene Xpert MTB/RIF (cartridge-based nucleic acid amplification test [NAAT] that identifies rifampicin resistant Mycobacterium Tuberculosis) Mycobacterium Tuberculosis/Rifampicin [MTB/RIF], mycobacteria growth indicator tube [MGIT], line probe assay [LPA] and Lowenstein Jensen [LJ] culture) for diagnosis of drug-sensitive and drug-resistant TB. The unit costs included fixed and variable costs for smear examination by ZN microscopy (₹ [Indian Rupee] 326 [US${\$}$4.72], FM (₹104 [US${\$}$1.5]), x-ray (₹218 [US${\$}$3.15]), digital X-ray (₹281 [US${\$}$4.07]), gene Xpert MTB/RIF (₹1137 [US${\$}$16.47]), MGIT (₹7038 [US${\$}$102]), LPA (₹6448 [US${\$}$93.44]) and LJ culture (₹4850 [US${\$}$70.28]). Out of 10 diagnostic algorithms used for TB diagnosis, algorithms using only smear microscopy had the lowest cost, followed by smear microscopy with x-ray for drug-sensitive TB (₹104 [US${\$}$1.5] to ₹544 [US${\$}$7.88]). Diagnostic algorithms for drug-resistant TB involving LPA and gene Xpert MTB/RIF were the most expensive.ConclusionsUnderstanding the various costs contributing to TB diagnosis in India provides crucial evidence for policymakers, programme managers and researchers to optimise programme spending and efficiently use resources.
| S-EPMC8643484 | biostudies-literature
Project description:The rising geriatric population and the increased susceptibility of this age group to tuberculosis (TB), the deadliest single infectious agent, is bothersome for India. This study tried to explore the demographic and treatment outcome differences between the elderly (aged 60 years and above) and non-elderly TB (<60 years) patients from South India. This study was part of a large ongoing cohort study under the RePORT India consortium. Newly diagnosed TB patients recruited into the cohort between 2014 and 2018 were included in this study. Pretested and standardized questionnaire and tools were used to collect data and were stored securely for the entire cohort. Required demographic, anthropometric and treatment related variables were extracted from this database and analyzed using Stata version 14.0. Prevalence of elderly TB was summarized as percentage with 95% confidence interval (CI). Generalized linear modelling was attempted to find the factors associated with elderly TB. A total of 1,259 eligible TB patients were included into this present study. Mean (SD) of the participants in the elderly and non-elderly group was 65.8 (6.2) and 40.2 (12.0) respectively. Prevalence of elderly TB was 15.6% (95%CI: 13.6%-17.6%) with nearly 71% belonging to 60-69 age category. Male sex, OBC caste, poor education, unemployment, marriage, alcohol consumption and unable to work as per Karnofsky score were found to be significantly associated with an increased prevalence of elderly TB. Unfavorable outcomes (12% vs 6.5%, p value: 0.018), including death (9.3% vs 3.4%, p value: 0.001) were significantly higher among the elderly group when compared to their non-elderly counterparts. The current TB programme should have strategies to maintain follow up with due attention to adverse effects, social support and outcomes. Additional research should focus on predictors for unfavorable outcomes among the elderly TB group and explore ways to handle the same. Rendering adequate social support from the health system side and family side would be a good start.
| S-EPMC8396735 | biostudies-literature
Project description:We aimed to define characteristics of TB patients in Puducherry and two districts of Tamil Nadu, India and calculate the population attributable fractions (PAF) of TB from malnutrition and alcohol.New smear-positive TB cases were enrolled into the Regional Prospective Observational Research for Tuberculosis (RePORT India) cohort. Census and National Family Health Survey data were used for comparisons.Data were analyzed for 409 participants enrolled between May 2014-June 2016; 307 (75.1%) were male, 60.2% were malnourished (body mass index [BMI] <18.5 kg/m2), and 29.1% severely malnourished (BMI <16). "Hazardous" alcohol use (based on AUDIT-C score) was reported by 155/305 (50.8%) of males. Tuberculosis cases were more likely than the Puducherry population to be malnourished (62.6% v 10.2% males and 71.7% v 11.3% of females; both p<0.001), and male cases were more likely to use alcohol than male non-cases (84.4% v 41%; p < .001). The PAF of malnutrition was 57.4% in males and 61.5% in females; the PAF for alcohol use was 73.8% in males and 1.7% in females.Alcohol use in men and malnutrition are helping drive the TB epidemic in Southern India. Reducing the TB burden in this population will require efforts to mitigate these risk factors.
| S-EPMC5568341 | biostudies-other
Project description:BACKGROUND:Vitamin D has multifarious roles in maintenance of health and prevention of disease. The present study was undertaken to assess the vitamin D status of a rural adult south Indian population and to identify its associations with socioeconomic status and cultural practices. METHODS:Between June 2015 and July 2016, 424 healthy adults residing in Kattankulathur block in Tamil Nadu, India, provided venous blood samples and answered questions by personal interview. 25-hydroxy vitamin D was estimated by ELISA. RESULTS:Fifty nine (13.9%) of the 424 participants had 25OHD levels below 12?ng/mL (vitamin D deficient) and 175 (41.3%) had 25OHD levels between 12 to 20?ng/mL (vitamin D insufficiency). In univariate analysis, demographic factors associated with vitamin D status included education, occupation, socioeconomic class, and birthplace; lifestyle factors included sun exposure time, skin surface exposed to sunlight, use of sunscreen, awareness of vitamin D, and consumption of fish; and hygiene related factors included source of drinking water, availability of tap water at home, and closed toilet at home. In ordinal logistic regression, the following variables were found to be independently associated with vitamin D sufficiency: Duration of daily sun exposure below 30?min (Odds ratio 0.31, 95% confidence intervals 0.14-0.71, P?=?0.006), sun exposure 30-60?min (OR 0.49, 95% CI 0.30-0.80, P?=?0.004), male gender (OR 2.00, 95% CI 1.30-3.09, P?=?0.002), higher level of education (OR 0.80, 95% CI 0.69-0.94, P?=?0.005), non-consumption of fatty fish (OR 0.48, 95% CI 0.24-0.85, P?=?0.035) and presence of closed toilet system at home (OR 0.59, 95% CI 0.37-0.93). CONCLUSION:VDD and VDI are highly prevalent in this rural Indian community. The study identifies socioeconomic and behavior patterns that negatively impact vitamin D sufficiency, thus providing a basis for targeted intervention.
| S-EPMC6280507 | biostudies-other
Project description:OBJECTIVE: To isolate novel actinomycetes and to evaluate their antibacterial activity. METHODS: Three soil samples were collected from Vengodu (village) in Kanchipuram district, Tamil Nadu, India. Actinomycetes were isolated using serial dilution and plating method on actinomycetes isolation agar. RESULTS: Totally 35 isolates were obtained on the basis of colony characteristics on actinomycetes isolation agar. All the isolates were screened for antibacterial activity by cross streak method. Medium and optimization of day were done for the potent strains using Nathan's agar well diffusion method. Isolation of bioactive compounds from significant active isolates was done by using different media. The most active isolate VAS 10 was identified as Actinobacterium Loyola PBT VAS 10 (accession No. JF501398) using 16s rRNA sequence method. The hexane, ethyl acetate, dichloromethane and butanol extracts of VAS 10 were tested against bacteria. The maximum antibacterial activity was observed in dichloromethane and ethyl acetate; maximum zones of inhibition were observed against Enterococcus durans. The rRNA secondary structure and the restriction sites of Actinobacterium Loyola VAS 10 were predicted using Genebee and NEBCutter online tools respectively. CONCLUSIONS: The present study showed that among the isolated actinomycetes, Actinobacterium Loyola PBT VAS 10 (accession No. JF501398) showed good antibacterial activity against the tested bacteria.
| S-EPMC3621468 | biostudies-literature
Project description:PurposePrimary open angle glaucoma (POAG) is the most common type of glaucoma. Among the POAG genes identified so far, myocilin (MYOC) is the most frequently mutated gene in POAG patients worldwide. The MYOC Gln48His mutation is unique among Indian POAG patients. This mutation has not been observed in some populations within India and in other populations worldwide. The objectives of this work were to characterize and compare the mutation spectrum among POAG patients from two places of South India and identify the occurrence and prevalence of Gln48His mutation in our study populations.MethodsOne hundred-one (101) POAG patients from Chennai, South India were recruited for the study. Earlier, 100 patients from the southernmost part of India, Kanyakumari district, were screened. MYOC was screened by polymerase chain reaction based single stand conformation polymorphism (PCR-SSCP) methodology. DNA sequencing of deviant samples was performed. Secondary structures of the proteins with amino acid sequence variations were predicted.ResultsThe mutation frequency of MYOC among POAG patients in Chennai was 2%. Three types of mutations were observed. The MYOC Gln48His mutation was observed among 2 POAG patients from Chennai. However, absence of this mutation among patients from Kanyakumari suggests possible involvement of demographic factors in disease causation via this mutation. Two heterozygous sequence variants, Thr353Ile and Asn480Lys, in the same exon (exon III) of MYOC were observed in one POAG patient who had a severe disease phenotype. This is the first such report of a compound heterozygote individual with two mutations in the same exon of MYOC.ConclusionsThe presence of mutations at a rate similar to other studies suggests the causative role of MYOC among POAG patients from Chennai. Screening of more patients and families from all parts of India is required to identify the actual frequency of the Gln48His mutation and thus highlight its importance. The compound heterozygote with a severe disease phenotype reiterates the importance of MYOC in certain POAG patients.
| S-EPMC3244482 | biostudies-literature
Project description:Exposure to heat is associated with a substantial burden of disease and is an emerging issue in the context of climate change. Heat is of particular concern in India, which is one of the world's hottest countries and also most populous, where relatively little is known about personal heat exposure, particularly in rural areas. Here, we leverage data collected as part of a randomized controlled trial to describe personal temperature exposures of adult women (40-79 years of age) in rural Tamil Nadu. We also characterize measurement error in heat exposure assessment by comparing personal exposure measurements to the nearest ambient monitoring stations and to commonly used modeled temperature data products. We find that temperatures differ across individuals in the same area on the same day, sometimes by more than 5 °C within the same hour, and that some individuals experience sharp increases in heat exposure in the early morning or evening, potentially a result of cooking with solid fuels. We find somewhat stronger correlations between the personal exposure measurements and the modeled products than with ambient monitors. We did not find evidence of systematic biases, which indicates that adjusting for discrepancies between different exposure measurement methods is not straightforward.
| S-EPMC10785747 | biostudies-literature