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Background: Pulicat Lake is one of India's most valuable ecosystems. Correct species identification is essential for the conservation and management of finite resources. Molecular signatures and character-based keys could be used for faster identification. This will be a powerful tool to obtain a significant amount of accurate information quickly and conveniently and could be used for forensic applications and the conservation of fish in Indian waters. Methods: In addition to morphological identification, the species were identified using various approaches, such as Neighbourjoining (NJ), Maximum Likelihood (ML) trees and the Character-based method. For each species, the LOGic (BLOG 2.0) DNA Barcode analysis method was used to identify different positions of key diagnostic nucleotides in a given set. Result: DNA barcodes were generated from twenty-nine species of fish representing seven orders, 26 genera and 21 families in this study. The current study's findings show that the 16S rRNA barcodes facilitated successful fish species identification and also provided phylogenetic information to differentiate the fishes. The character-based molecular diagnostic keys for fishes were also developed in-silico from the data set comprising 393 mitochondrial 16S rRNA sequences including the sequences generated in the present study and other published resources. [ABSTRACT FROM AUTHOR]

This article communicates thermal performance of a low cost solar parabolic dish collector. The parabolic dish collector is developed from low cost technology and is tested in the outdoors on a sunny day by measuring stagnation temperature on the flat absorber. The absorber, made of aluminum alloys and coated with black paint, is placed on the focal receiver. The calculated overall heat transfer co-efficient varies from 130 to 180 W/m2 K for the actual climate conditions at Tiruchirappalli, India. The thermal efficiency of the thermal collector is found to be 60% and the cost is minimized to half the cost of a collector that is available in the market with the same specifications. [ABSTRACT FROM PUBLISHER]

HAART has dramatically improved survival and quality of life among people living with HIV and AIDS globally. However, drug resistant mutations of HIV are a great challenge to the benefits of HAART. Antiviral resistance can be mediated either by changes in the molecular target of therapy (the primary mechanism observed in HIV-1) or in other viral proteins that indirectly interfere with a drug's activity. Drug resistant mutations easily evolve in the presence of sub-optimal adherence. With the introduction of generic HAART, there has been a steep increase in the number of patients put on HAART in India. It should also be noted that since most patients pay for medications out of their own pockets, interruptions in therapy due to monetary constraints are not uncommon. There is little information on HIV drug resistance in resource constrained settings like India where the predominant circulating HIV-1 sub-type is C. The transmissibility of drug-resistant forms of the virus is also a major concern especially when formulating treatment guidelines. This article reviews published data available on the patterns of HIV-1 drug resistance among treatment naïve in India. [ABSTRACT FROM AUTHOR]

Abstract: Objective: To elucidate the medicinally important herbs and their role in the health cares of the villagers living in Sivagangai district of Tamil Nadu, India. Methods: Interviews and detailed personal discussions were conducted with the herbalist and local people to identify plants and collect the medicinal informations for 12 months (from June 2009 to May 2010). The medicinal important plants were botanically identified. Results: Totally 71 species of 61 genera belonging to 36 families were reported with ethnomedicinal values. Leaves are the mostly used part to prepare medicine. Generally fresh parts are used. Conclusions: Attention should be made on proper exploitation and utilization of these medicinally important plants. [Copyright &y& Elsevier]

Background: Mycobacterium tuberculosis (Mtb) is an obligate, persistent, intracellular human pathogen. Host immune pressure and associated Mtb immune evasion that drive the evolution of Mtb, is crucial for diagnosing and designing effective vaccine. Human T cell responses are essential for containment of Mtb through secretion of IFNγ and TNFα, previous studies have shown that Mtb T cell epitopes (TCEs) are hyperconserved, suggesting there is little evidence for immune selection pressure and indicating that antigenic variation may contribute to bacterial persistence. Thus, the aim of this study was to provide an in-depth analysis of the pattern of changes in TCEs in circulating Indian Mtb strains. Methods & Materials: We analyzed 79 Mtb whole genome sequences generated from strains isolated from South Indian pulmonary TB patients. Extensive bioinformatic analyses were employed, but not limited to determine i) phylogenetic relationships ii) extent and nature of mutations harbored within TCEs and iii) binding affinity of novel mutated TCEs (mTCEs). Results: Phylogenetic trees revealed clustering of 79 strains to three lineages: EAI, CAS and Beijing. We identified that 13% of 1101 examined TCEs within the Mtb genome were mutated in atleast one strain, with 67% of mutations resulting in single amino acid changes. We report for the first time, focused mutations in 16 of 66 highly immunodominant CD4 T cell antigens comprising experimentally verified epitopes. More than 80% of the sequenced strains had common mutations across this antigenic group, with 4-6 mutated immunodominant antigens occurring per strain. The most impacted functional category of mutated immunodominant antigens belonged to the cell wall and cell processes. Furthermore, we identified three mTCEs (one each in mce2A, hemK and espA antigens) have not previously been identified to be immunodominant, but present in all the strains studied. Binding affinity of the majority of mTCEs to common Indian HLA alleles was marginally higher than the corresponding parent TCEs. Conclusion: Presently, investigating the impact of these novel mutants and their corresponding parent epitopes inCD4T cell functional assays that enable the evaluation of the immunogenicity of candidates peptides. Together, our data provide novel insights into the importance of immune selection pressure in Mtb evolution in India. [ABSTRACT FROM AUTHOR]

The present investigation evaluates three satellite precipitation products (SPPs), Multi-Source Weighted-Ensemble Precipitation (MSWEP), Global Precipitation Climatology Centre (GPCC), Climate Hazard Infrared Precipitation with Station Data (CHIRPS), and two reanalysis datasets, namely, the ERA5 atmosphere reanalysis dataset (ERA5) and Indian Monsoon Data Assimilation and Analysis (IMDAA), against the good quality gridded reference dataset (1991-2022) developed by the India Meteorological Department (IMD). The evaluation was carried out in terms of the rainfall detection ability and estimation accuracy of the products using metrics such as the false alarm ratio (FAR), probability of detection (POD), misses, root mean square error (RMSE), and percent bias (PBIAS). Among all the rainfall products, ERA5 had the best ability to capture rainfall events with a higher POD, followed by MSWEP. Both MSWEP and ERA5 had PODs of 70-100% in more than 90% of the grids and less than 35% of missing rainfall events in the entire Tamil Nadu. In the case of the rainfall estimation accuracy evaluation, the MSWEP exhibited superior performance, with lower RMSEs and biases ranging from - 25 to 25% at the annual and seasonal scales. In northeast monsoon (NEM), CHIRPS demonstrated a comparable performance to that of MSWEP in terms of the RMSE and PBIAS. These findings will help product users select the best reliable rainfall dataset for improved research, diversified applications in various sectors, and policy-making decisions., (© 2024. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

Introduction: Tuberculosis (TB) remains a significant health concern in India, and its complexity is exacerbated by the rising occurrence of non-communicable diseases such as diabetes mellitus (DM). Recognizing that DM is a risk factor for active TB, the emerging comorbidity of TB and PDM (TB-PDM) presents a particular challenge. Our study focused on the impact of PDM on cytokine and chemokine profiles in patients with pulmonary tuberculosis TB) who also have PDM., Materials and Methods: We measured and compared the cytokine (GM-CSF, IFN-γ, IL-1α/IL-1F1, IL-1β/IL-1F2, IL-2, IL-4, IL-5, IL-6, IL-10, IL-12p70, IL-13, IL-17/IL-17A, IL-18/IL-1F4, TNF-α) and chemokine (CCL1, CCL2, CCL3, CCL4, CCL11, CXCL1, CXCL2, CXCL9, CXCL10, and CXCL11) levels in plasma samples of TB-PDM, only TB or only PDM using multiplex assay., Results: We observed that PDM was linked to higher mycobacterial loads in TB. Patients with coexisting TB and PDM showed elevated levels of various cytokines (including IFNγ, TNFα, IL-2, IL-17, IL-1α, IL-1β, IL-6, IL-12, IL-18, and GM-CSF) and chemokines (such as CCL1, CCL2, CCL3, CCL4, CCL11, CXCL1, CXCL9, CXCL10, and CXCL11). Additionally, cytokines such as IL-18 and GM-CSF, along with the chemokine CCL11, were closely linked to levels of glycated hemoglobin (HbA1c), hinting at an interaction between glycemic control and immune response in TB patients with PDM., Conclusion: Our results highlight the complex interplay between metabolic disturbances, immune responses, and TB pathology in the context of PDM, particularly highlighting the impact of changes in HbA1c levels. This emphasizes the need for specialized approaches to manage and treat TB-PDM comorbidity., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Rajamanickam, Kothandaraman, Kumar, Viswanathan, Shanmugam, Hissar, Nott, Kornfeld and Babu.)

Background: Hemoglobin (Hb), a red pigment of red blood cells (RBCs), carries oxygen from the lungs to different organs of the body and transports carbon dioxide back to the lungs. Any fault present in the Hb structure leads to undesirable functional effects of the RBCs, such as sickle cell anemia (SCA), thalassemia, etc. Hemoglobinopathies affect around 7% of people in both developed and developing countries globally. The aim of the present study was to determine the prevalence and carrier frequencies of hemoglobinopathies including SCA, thalassemia, and other abnormal Hb variants among Malayali tribes in the Jawadhu hills of Tiruvannamalai district, Tamil Nadu, India., Methods: A community-based cross-sectional study was carried out among 443 Malayali tribes inhabiting the Jawadhu hills of Tiruvannamalai district from July 2022 to September 2022. The RBC indices were analyzed using an automated 5-part hematology analyzer (Mindray, BC-5150) and hemoglobin fractions were done using the HPLC system (Bio-Rad, D-10) following standard protocols., Findings: A total of 443 participants were screened, out of whom 14.67% had an abnormal Hb fraction, 83.30% were identified as normal, and 2.03% were borderline. Notably, the study revealed a prevalence of 0.68% for the α-thalassemia trait and 13.99% for the β-thalassemia trait., Interpretation: Haemoglobinopathies, specifically the β-thalassemia trait, were most prevalent among the Malayali tribal population of Tamil Nadu residing in the Jawadhu hills of Tiruvannamalai district. Hence, we need special attention for creating awareness, increasing hemoglobinopathies screening programs, and improving the importance of tribal health conditions by the government and non-governmental organizations (NGOs) for the betterment of the ethnic tribes.

In December 2023, we observed a notable shift in the COVID-19 landscape, when JN.1 omicron emerged as the predominant SARS-CoV-2 variant with a 95% incidence. We characterized the clinical profile, and genetic changes in JN.1, an emerging SARS-CoV-2 variant of interest. Whole genome sequencing was performed on SARS-CoV-2 positive clinical specimens, followed by sequence analysis. Mutations within the spike protein sequences were analysed and compared with the previously reported lineages and sub-lineages, to identify the potential impact of the unique mutations on protein structure and possible alterations in the functionality. Several unique and dynamic mutations were identified herein. Molecular docking analysis showed changes in the binding affinity, and key interacting residues of wild-type and mutated structures with key host cell receptors of SARS-CoV-2 entry viz., ACE2, CD147, CD209L and AXL. Our data provides key insights on the emergence of newer variants and highlights the necessity for robust and sustained global genomic surveillance of SARS-CoV-2., (© 2024. The Author(s).)

Kangayam cattle are one of the drought breeds in India with distinct attributes. Agricultural transformation has led to a decline in many pure-breed indigenous cattle, including the Kangayam breed. Hence, a study on the reproductive physiology of male Kangayam breed cattle is necessary to disentangle problems in the area of livestock improvement. In this study, we investigated the relationship between serum hormones and bio-constituents and ascertained the potential of saliva as an indicator of the reproductive status of Kangayam cattle (Bos indicus). The present study confirms that cholesterol was higher in intact males and lower in prepubertal and castrated males. Testosterone levels were also higher in intact males than in castrated or prepubertal males. Hence, it can be inferred that high cholesterol levels contribute to active derivatization of testosterone in intact males. In contrast, reduced cholesterol availability leads to decreased testosterone synthesis in castrated and prepubertal males. Furthermore, it is reasonable to speculate that testosterone could have influenced salivary fern patterns in intact males, and thus, fern-like crystallization in the saliva was apparent. The unique salivary compounds identified through GC-MS across various reproductive statuses of Kangayam males may advertise their physiological status to conspecifics. In addition, the presence of odorant-binding protein (OBP) in saliva further supports its role in olfactory communication. This study attested to a posssible interlink between gonadal status and serum biochemical profiles. The salivary fern pattern revealed in this study can be used as a predictive tool, and the presence of putative volatiles and OBP adds evidence to the role of saliva in chemical communication., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

The presence of toxic trace elements (TEs) has resulted in a worldwide deterioration in freshwater ecosystem quality. This study aimed to analyze the distribution of TEs, including chromium (Cr), nickel (Ni), arsenic (As), mercury (Hg), cadmium (Cd), and lead (Pb), in water, sediment, and organs of Tilapia (Oreochromis mossambicus) collected from selected inland water bodies in Tamil Nadu, India. The water samples exhibited a range of concentrations for TEs: Cr varied from 0.014 to 5.193 µg/L, Ni ranged from 0.283 to 11.133 µg/L, As ranged from 0.503 to 1.519 µg/L, Cd from 0.001 to 0.616 µg/L, and Pb ranged from non-detectable (ND) to 6.103 µg/L. The concentrations of TEs in sediment were found to vary within the following ranges: 5.259 to 32.621 mg/kg for Cr, 1.932 to 30.487 mg/kg for Ni, 0.129 to 0.563 mg/kg for As, 0.003 to 0.011 mg/kg for Cd, ND to 0.003 mg/kg for Hg, and 0.404 to 1.575 mg/kg for Pb. The study found that the accumulation pattern of TE in fishes across all selected areas was liver > bone > gill > muscle. The organs had TE concentrations of Cr (ND-0.769 mg/kg), Ni (ND-1.053 mg/kg), As (0.002-0.080 mg/kg), Pb (ND-0.411 mg/kg), and Hg (ND-0.067 mg/kg), which was below the maximum residual limit prescribed by EC and FSSAI. The bioconcentration factor (BCF) of TEs exhibited a greater magnitude in comparison with the biota-sediment accumulation factor due to the higher concentration of TEs in fish and lower level in water. The assessment of both carcinogenic and non-carcinogenic risks suggests that the consumption of Tilapia from the study region does not pose any significant risks., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

Background: Progress on HIV treatment outcomes for people who inject drugs and men who have sex with men in India has been slow compared with that in other populations. We assessed whether HIV treatment incentives would improve outcomes among these groups., Methods: We did a matched-pair, cluster randomised trial in 16 sites (eight for people who inject drugs and eight for men who have sex with men) across 15 cities in India. We recruited cohorts of HIV-positive people who inject drugs or men who have sex with men who were antiretroviral therapy (ART)-naive or had less than 12 months of ART exposure. We randomised sites to provide incentives or usual care. At intervention sites, we provided incentive vouchers, which could be exchanged for food or household goods, for attending motivational interviewing sessions and timely appointments at government ART clinics. An ART-naive participant meeting all targets could earn the equivalent to 14 days' wages over 12 months. The primary outcome was survival with viral suppression at 12 months. We used an intention-to-treat analytic approach appropriate for matched-pair cluster randomised trials, adjusting for baseline viral suppression. This study was registered with ClinicalTrials.gov, NCT02969915, and is complete., Findings: Between Oct 30, 2017, and Oct 12, 2018, we recruited 1200 people who inject drugs and 1114 men who have sex with men living with HIV. Among people who inject drugs, 154 (12·8%) identified as female gender and 1046 (87·2%) as male. The site median percentage of participants earning one or more incentives was 96·1% (IQR 93·7-98·1). At 12 months, HIV viral suppression was 31·9% (n=383) among people who inject drugs and 52·1% (n=580) among men who have sex with men. The incentive intervention was not associated with significantly improved survival with viral suppression compared with usual care (adjusted prevalence difference 9·6 percentage points, 95% CI -4·4 to 23·7)., Interpretation: Despite high intervention engagement, incentives did not improve survival with viral suppression among people who inject drugs and men who have sex with men living with HIV in India. The poor outcomes overall underscore the need for innovative, multilevel approaches to engage marginalised people living with HIV in low-income and middle-income settings., Funding: US National Institutes of Health, Elton John AIDS Foundation., Competing Interests: Declaration of interests SSS has received grants, products and honoraria from Gilead Sciences and Abbott Laboratories. SSS also serves on the Board of Trustees of YR Gaitonde Medical Educational and Research Foundation. SHM receives materials support from Abbott Diagnostics. Other authors declare no competing interests., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Objective: To explore the relationship between occupational heat exposure, physiological heat strain indicators and adverse outcomes in pregnant women., Design: Prospective cohort., Setting: Workplaces in Tamil Nadu, India., Sample: A cohort of 800 pregnant women engaged in moderate to heavy physical work in 2017-2019 and 2021-2022., Methods: Participants were recruited at between 8 and 14 weeks of gestation. Occupational heat exposure and heat strain indicators were captured each trimester. 'Heat exposed' was defined as heat stress exceeding the threshold limit value (TLV) for safe manual work (with maximum wet-bulb globe temperatures of 27.5°C for a heavy workload and 28.0°C for a moderate workload). Physiological heat strain indicators (HSIs) such as core body temperature (CBT) and urine specific gravity (USG) were measured before and after each shift. Heat-related health symptoms were captured using the modified HOTHAPS questionnaire., Main Outcome Measures: The main outcome measures included (1) a composite measure of any adverse pregnancy outcome (APO) during pregnancy (including miscarriage, preterm birth, low birthweight, stillbirth, intrauterine growth restriction and birth defects), (2) a composite measure of adverse outcomes at birth (3) and miscarriage., Results: Of the 800 participants, 47.3% had high occupational heat exposure. A rise in CBT was recorded in 17.4% of exposed workers, and 29.6% of workers experienced moderate dehydration (USG ≥ 1.020). Heat-exposed women had a doubled risk of miscarriage (adjusted odds ratio, aOR 2.4; 95% confidence interval, 95% CI 1.0-5.7). High occupational heat exposure was associated with an increased risk of any adverse pregnancy and foetal outcome (aOR 2.3; 95% CI 1.4-3.8) and adverse outcome at birth (aOR 2.0; 95% CI 1.2-3.3)., Conclusions: High occupational heat exposure is associated with HSIs and adverse pregnancy outcomes in India., (© 2023 John Wiley & Sons Ltd.)

Peste des petits ruminants (PPR) presents economic challenges in enzootic countries impacting small ruminant productivity. The state of Karnataka, India, implemented a mass vaccination campaign in alignment with the PPR-Global Eradication Programme (GEP) and the National Strategic Plan for PPR eradication. This study was conducted from January to March 2023 to assess seroconversion in post-vaccinated goats and sheep at the epidemiological unit (epi-unit) level, aligning with the World Organisation for Animal Health (WOAH) and the Food and Agriculture Organization (FAO) guidelines in the PPR Global Control and Eradication Strategy (GCES). Before vaccination, 3466 random serum samples were collected from small ruminants of three age groups (6-12 months, 1-2 years, and >2 years) across 116 epi-units, spanning 82 taluks in 28 districts. Post-vaccination sero-monitoring included 1102 serum samples collected from small ruminants of the 6-12-month age group only, across 111 epi-units covering 64 taluks in 23 districts. The PPRV antibody status was determined using an indigenous hemagglutinin (H) protein monoclonal antibody-based competitive ELISA kit. Pre-vaccination, the PPR seropositivity rates were 55%, 62%, and 66% in the age groups of 6-12 months, 1-2 years, and >2 years, respectively, with a 61% PPRV antibody prevalence across all the age groups. Notably, 41% of the epi-units exhibited antibody prevalence rates of ≥70%, indicating a substantial population immunity, possibly attributed to the previous vaccination program in the state since 2011. In contrast, only 17% of the epi-units had below 30% seroprevalence rates, emphasizing the need for intensified vaccination. Statistical analysis of the data revealed significant correlations ( p < 0.05) between the presence of PPRV antibodies and host factors such as species, breed, and sex. Post-vaccination seroprevalence in the 6-12 months age group was found to be 73.4%, indicating the use of an efficacious vaccine. On the evaluation of vaccination immunity in the 6-12 months age group, it was revealed that over 69% of the epi-units achieved a response surpassing ≥70%, indicating a significant improvement from 42% of the epi-units in pre-vaccination. For active PPR eradication, a mass vaccination campaign (>95% coverage) targeting small ruminant populations aged >4 months is advocated, aiming to achieve the desired herd immunity of >80%. This study offers crucial insights into PPR baseline seroprevalence/immunity status and vaccine efficacy, guiding national strategies towards a PPR-free India and further supporting the global eradication initiative.

A state-wide prospective longitudinal investigation of the genomic surveillance of the omicron B.1.1.529 SARS-CoV-2 variant and its sublineages in Tamil Nadu, India, was conducted between December 2021 and March 2023. The study aimed to elucidate their mutational patterns and their genetic interrelationship in the Indian population. The study identified several unique mutations at different time-points, which likely could attribute to the changing disease characteristics, transmission, and pathogenicity attributes of omicron variants. The study found that the omicron variant is highly competent in its mutating potentials, and that it continues to evolve in the general population, likely escaping from natural as well as vaccine-induced immune responses. Our findings suggest that continuous surveillance of viral variants at the global scenario is warranted to undertake intervention measures against potentially precarious SARS-CoV-2 variants and their evolution., (© 2024 Wiley Periodicals LLC.)

Recurrent Tuberculosis patients contribute to a significant proportion of TB burden in India. A nationwide survey was conducted during 2019-2021 across India among adults to estimate the prevalence of TB. A total of 322480 individuals were screened and 1402 were having TB. Of this, 381 (27.1%) had recurrent TB. The crude prevalence (95% CI) of recurrent TB was 118 (107-131) per 100,000 population. The median duration between episodes of TB was 24 months. The proportion of drug resistant TB was 11.3% and 3.6% in the recurrent group and new TB patients respectively. Higher prevalence of recurrent TB was observed in elderly, males, malnourished, known diabetics, smokers, and alcohol users. (p<0.001). To prevent TB recurrence, all treated tuberculosis patients must be followed at least for 24 months, with screening for Chest X-ray, liquid culture every 6 months, smoking cessation, alcohol cessation, nutritional interventions and good diabetic management., Competing Interests: The authors have no conflict of interest to declare., (Copyright: © 2023 Giridharan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Swinepox is a sporadic virus disease of domestic and wild pigs that mainly occurs during the rainy season. Though the disease is known for a century, research on swinepox especially genetic characterization is scanty. Self-limiting nature of the disease, the non-availability of specific diagnostics as well as the resemblance of clinical signs with other pathogens are some of the issues in the slow progress in swinepox-related research. Recent whole genome sequencing data from the USA, India, and Germany enhanced our understanding of the biology of swinepox virus (SWPV). The objective of the present study is to investigate the molecular epidemiology of two swinepox outbreaks that occurred in 2015 and 2016 one each in Uttar Pradesh, and the Haryana states of India. The appearance of clinical signs in different swine breeds was recorded. The scab samples from infected pigs were collected, DNA extracted, host range genes of SWPV were PCR amplified, sequenced and analyzed for genetic and phylogenetic characterization. Desi (nondescript breed), Yorkshire White pigs, and Landrace cross were found to be infected with SWPV. Host range genes of SWPV analyzed from clinical samples showed very high nucleotide identity with each other. Phylogenetic analyses revealed that SWPVs circulating in India are distinct (Indian lineage) from the SWPV of the USA, Germany, and Russia (European-North American lineage). Our study affirms the existence of two distinct lineages of SWPV globally with differences in clinical lesions between breeds.

DNA barcoding, primarily focusing on cytochrome c oxidase subunit I (COI) gene has been appraised as an effective tool for species identification. In this study, we focused on the marine fishes of Family Nemipteridae, one of the commercially important group distributed within the Coromandel Coast. The Partial sequences of COI and 16S rRNA of mitochondrial genes were analyzed for species identification and phylogenetic relationship of Nemipterus species ( Nemipterus japonicus, Nemipterus peronii, Nemipterus bipunctatus, Nemipterus bathybius ). Character-based identification approaches that categorize specimens to species using classification rules that compactly identify species in terms of key diagnostic nucleotides in selected gene sequences. Using the BLOG 2.0 software, species-specific diagnostic nucleotides were identified for the selected group of species. A data set of 198 mtCOI sequences was obtained from published resources and used to screen character-based molecular diagnostic keys for species in silico . Partial sequences of both the genes provided sufficient phylogenetic information to distinguish the four Nemipterus species indicating the usefulness of mtDNA-based approach in species identification. This study proves the use of mtDNA genes sequence-based approach is a support tool along with traditional taxonomy for identifying fish species at a faster pace.

Introduction: Truenat MTB-RIF assay (Truenat), a nucleic acid amplification test (NAAT), is a real-time polymerase chain reaction (RT-PCR) chip-based assay that can detect Mycobacterium tuberculosis ( Mtb ) and rifampicin (RIF) drug resistance using portable, battery-operated devices. The National TB Elimination Program (NTEP) in India introduced this novel tool at the district and subdistrict level in 2020. This study aimed to assess the level and causes of inconclusive results (invalid results, errors, and indeterminate results) in MTB and RIF testing at NTEP sites and the root causes of these in the programmatic setting., Methods: Truenat testing data from 1,690 functional Truenat sites under the NTEP from April to June 2021 were analyzed to assess the rates of errors, invalid MTB results, and indeterminate RIF results. Following this analysis, 12 Truenat sites were selected based on site performance in Truenat testing, diversity of climatic conditions, and geographical terrain. These sites were visited to assess the root causes of their high and low rates of inconclusive results using a structured checklist., Results: A total of 327,649 Truenat tests performed for MTB and RIF testing were analyzed. The rate of invalid MTB results was 5.2% [95% confidence interval (CI): 5.11-5.26; n = 16,998] and the rate of errors was 2.5% (95% CI: 2.46-2.57; n = 8,240) in Truenat MTB chip testing. For Mtb-positive samples tested using the Truenat RIF chip for detection of RIF resistance ( n = 40,926), the rate of indeterminate results was 15.3% (95% CI: 14.97-15.67; n = 6,267) and the rate of errors was 1.6% (95% CI: 1.53-1.78; n = 675). There was a 40.1% retesting gap for Mtb testing and a 78.2% gap for inconclusive RR results. Among the inconclusive results retested, 27.9% (95% CI: 27.23-28.66; n = 4,222) were Mtb-positive, and 9.2% (95% CI: 7.84-10.76; n = 139) were detected as RR., Conclusion: The main causes affecting Truenat testing performance include suboptimal adherence to standard operating procedures (SOPs), inadequate training, improper storage of testing kits, inadequate sputum quality, lack of quality control, and delays in the rectification of machine issues. Root cause analysis identified that strengthening of training, external quality control, and supervision could improve the rate of inconclusive results. Ensuring hands-on training of technicians for Truenat testing and retesting of samples with inconclusive results are major recommendations while planning for Truenat scale-up. The recommendations from the study were consolidated into technical guidance documents and videos and disseminated to laboratory staff working at the tiered network of TB laboratories under the NTEP in order to improve Truenat MTB-RIF testing performance., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Gopalaswamy, Kumar, Vashistha, Rajendran, Kayesth, Peravali, Kashyap, Ghosh, Yumo, Moore, Anand, Ramachandran, Alavadi, Saini and Shanmugam.)

Background : Patients with first-line drug resistance (DR) to rifampicin (RIF) or isoniazid (INH) as a first-line (FL) line probe assay (LPA) were subjected to genotypic DST using second-line (SL) LPA to identify SL-DR (including pre-XDR) under the National TB Elimination Program (NTEP), India. SL-DR patients were initiated on different DR-TB treatment regimens and monitored for their outcomes. The objective of this retrospective analysis was to understand the mutation profile and treatment outcomes of SL-DR patients. Materials and Methods : A retrospective analysis of mutation profile, treatment regimen, and treatment outcome was performed for SL-DR patients who were tested at ICMR-NIRT, Supra-National Reference Laboratory, Chennai between the years 2018 and 2020. All information, including patient demographics and treatment outcomes, was extracted from the NTEP Ni-kshay database. Results : Between 2018 and 2020, 217 patients out of 2557 samples tested were identified with SL-DR by SL-LPA. Among them, 158/217 were FQ-resistant, 34/217 were SLID-resistant, and 25/217 were resistant to both. D94G (Mut3C) of gyrA and a1401g of rrs were the most predominant mutations in the FQ and SLID resistance types, respectively. Favorable (cured and treatment complete) and unfavorable outcomes (died, lost to follow up, treatment failed, and treatment regimen changed) were recorded in a total of 82/217 and 68/217 patients in the NTEP Ni-kshay database. Conclusions : As per the testing algorithm, SL- LPA is used for genotypic DST following identification of first-line resistance, for early detection of SL-DR in India. The fluoroquinolone resistance pattern seen in this study population corelates with the global trend. Early detection of fluoroquinolone resistance and monitoring of treatment outcome can help achieve better patient management.

The prevalence of diabetes is increasing at an alarming rate globally, particularly in India. In the urban areas, the prevalence of diabetes among adults aged ≥20 y, which was around 2% in the early 1970's, has increased by >20% in 50 y. The rapid nutrition transition due to high economic growth rates increased urbanization and globalization has resulted in higher intakes of processed refined grain staples, mainly white rice in Southern and Eastern India and refined wheat in Northern and Western India. This coupled with inadequate quantity and quality of protein; unhealthy fats; lower intake of vegetables, fruits, and fiber; and a sedentary lifestyle are the main drivers of the diabetes epidemic in India. This review attempts to discuss both the quality and quantity of Indian diets with specific reference to macronutrients. This review also outlines some of the strategies that can be employed to slow down the diabetes epidemic in this region. We believe that the lessons learned from India would be applicable to other developing nations as well, particularly to the South East Asian region., (Copyright © 2023 American Society for Nutrition. Published by Elsevier Inc. All rights reserved.)

The present study describes the isolation and characterization of Bacillus tropicus LS27 capable of keratinolytic protease production from Russell Market, Shivajinagar, Bangalore, Karnataka, with its diverse application. The ability of this strain to hydrolyze chicken feathers and skim milk was used to assess its keratinolytic and proteolytic properties. The strain identification was done using biochemical and molecular characterization using the 16S rRNA sequencing method. Further a sequential and systematic optimization of the factors affecting the keratinase production was done by initially sorting out the most influential factors (NaCl concentration, pH, inoculum level and incubation period in this study) through one factor at a time approach followed by central composite design based response surface methodology to enhance the keratinase production. Under optimized levels of NaCl (0.55 g/L), pH (7.35), inoculum level (5%) and incubation period (84 h), the keratinase production was enhanced from 41.62 U/mL to 401.67 ± 9.23 U/mL (9.65 fold increase) that corresponds to a feather degradation of 32.67 ± 1.36% was achieved. With regard to the cost effectiveness of application studies, the crude enzyme extracted from the optimized medium was tested for its potential dehairing, destaining and metal recovery properties. Complete dehairing was achieved within 48 h of treatment with crude enzyme without any visible damage to the collagen layer of goat skin. In destaining studies, combination of crude enzyme and detergent solution [1 mL detergent solution (5 mg/mL) and 1 mL crude enzyme] was found to be most effective in removing blood stains from cotton cloth. Silver recovery from used X-ray films was achieved within 6 min of treatment with crude enzyme maintained at 40 °C., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Inc. All rights reserved.)

This paper demarcated the most vulnerable regions within the Poiney sub-basin (Tamil Nadu state in India) with respect to the groundwater quality. An index-based vulnerability assessment was carried out by measuring the physico-chemical variables such as pH, electrical conductivity, total dissolved solids, magnesium, sodium, chloride, sulphate, bicarbonate and fluoride in the pre-monsoon and post-monsoon samples. Water quality index varied across the sub-basin due to differences in the water quality induced by anthropogenic activities related to land use practices and presence of industries. The MT3D engine coupled with visual MODFLOW identified that sulphate released from tanneries and leather factories is the main effluent contaminating the groundwater. Model reveals that both the flow and contaminant transport is towards southeast with maximum and minimum calculated head of 201.82 mg/l and 265.92 mg/l and calculated sulphate concentration of 394.40 mg/l and 46.79 mg/l respectively., (© 2023. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

A major challenge in tuberculosis is identifying correlates of a protective immune response. The Mycobacterial Growth Inhibition Assay (MGIA) is a functional assay providing an integrated measure of the host immune response to mycobacteria. However, its feasibility is limited by reliance on biosafety level 3 facilities, and its performance has not been widely evaluated in TB-endemic settings. Here, we compared two mycobacterial strains (M. tuberculosis H37Rv versus attenuated M. bovis BCG) in the performance of whole-blood MGIA in 30 TB-exposed children (median age 2 years) in Chennai, India. The time-to-positivity in both assays was similar (5.7 days vs 6 days) and the mycobacterial growth of M. tuberculosis H37Rv and M. bovis BCG were correlated (r = 0.64, p<0.0001). In Bland-Altman analysis, the bias was -0.54 days (95% limit of agreement -2.08, 0.99). Collectively, our results indicate that M. tuberculosis H37Rv can be substituted with the less virulent M. bovis BCG strain to improve feasibility of the MGIA assay, particularly in low-income settings., Competing Interests: Declaration of competing interest The authors have no conflicts of interest to declare., (Copyright © 2022. Published by Elsevier Ltd.)

Purpose: This study aimed to evaluate the knowledge, awareness and attitude of eye donation among non-clinical staff of tertiary eye hospitals and to convey a positive attitude toward eye donation by enhancing their awareness and knowledge., Methods: An online cross-sectional study was conducted among the non-clinical staff from all centers of a tertiary eye care hospital across Tamil Nadu. Quiz link was emailed to non-clinical staff of all the centers. On completion of the quiz, the participants viewed their respective scores and the correct answers to all questions. This activity was presumed to subsequently improve their knowledge and clear up the myths on eye donation., Results: Two hundred twenty-eight non-clinical staff from 11 hospitals participated in the quiz. Mean age was 35.3 ± 9.8 years and 130 were female staff (57.05%). One hundred eighty-one participants (79.39%) scored over 50% of the total 17 queries. One hundred eighty-six (81.58%) and 142 (62.28%) participants scored over 50% in the awareness section and knowledge section, respectively. Eye bank volunteers (73, 32.02%) were the main source of information. Twenty-four (10.53%) had already taken pledge for eye donation and 175 (76.75%) were willing to pledge, 29 (12.72%) were not willing to pledge. Twenty-two out of these 29 (75.86%) had no specific reason for not pledging. Family, religious reasons, lack of clarity and fear were least cited reasons (13.79%)., Conclusion: Non-clinical staff of an eye hospital are easily approachable and are expected to be more knowledgeable by the general public around them. They might act as primary motivators in raising awareness within their family, friends, relatives and neighbors., Competing Interests: None

There is conflicting evidence about the association between dairy products and cardiometabolic risk (CMR). We aimed to assess the association of total dairy intake with CMR factors and to investigate the association of unfermented and fermented dairy intake with CMR in Asian Indians who are known to have greater susceptibility to type 2 diabetes and cardiovascular diseases compared to white Europeans. The study comprised 1033 Asian Indian adults with normal glucose tolerance chosen from the Chennai Urban Rural Epidemiological Study (CURES). Dietary intake was assessed using a validated open-ended semi-quantitative food frequency questionnaire. Metabolic syndrome (MS) was diagnosed based on the new harmonising criteria using central obesity, dyslipidaemia [low high-density lipoprotein cholesterol (HDL) and increased serum triglycerides (TG)], hypertension and glucose intolerance. Increased consumption of dairy (≥5 cups per day of total, ≥4 cups per day of unfermented or ≥2 cups per day of fermented dairy) was associated with a lower risk of high fasting plasma glucose (FPG) [hazards ratio (HR), 95% confidence interval (CI): 0.68, 0.48−0.96 for total dairy; 0.57, 0.34−0.94 for unfermented dairy; and 0.64, 0.46−0.90 for fermented dairy; p < 0.05 for all] compared to a low dairy intake (≤1.4 cups per day of total dairy; ≤1 cup per day of unfermented dairy; and ≤0.1 cup per day of fermented dairy). A total dairy intake of ≥5 cups per day was also protective against high blood pressure (BP) (HR: 0.65, 95% CI: 0.43−0.99, p < 0.05), low HDL (HR: 0.63, 95% CI: 0.43−0.92, p < 0.05) and MS (HR: 0.71, 95% CI: 0.51−0.98, p < 0.05) compared to an intake of ≤1.4 cups per day. A high unfermented dairy intake (≥4 cups per day) was also associated with a lower risk of high body mass index (BMI) (HR: 0.52, 95% CI: 0.31−0.88, p < 0.05) compared to a low intake (≤1 cup per day), while a reduced risk of MS was observed with a fermented dairy intake of ≥2 cups per day (HR: 0.71, 95% CI: 0.51−0.98, p < 0.05) compared to an intake of ≤0.1 cup per day. In summary, increased consumption of dairy was associated with a lower risk of MS and components of CMR.

We report the isolation of Mycobacterium orygis, a member of Mycobacterium tuberculosis complex (MTBC), from two black bucks (Antelope cervicapra) and one spotted deer (Axis axis) from the Guindy National Park forest range in Chennai, India. Lung tissue and lymph node samples collected during post-mortem examination were processed using NaOH method and cultured in solid and liquid media. DNA extracted from the cultured isolates was used to amplify the mpt64 gene by specific primers and the band visualized at 240 bps confirmed the isolates as a member of MTBC. Further examination of these isolates by spoligotyping and whole-genome sequencing confirmed the isolates as M. orygis and the phylogenetic tree revealed their well-clustered position with other M. orygis isolates around the globe. The deletion of RD7-RD10, RDOryx&#95;1, RDOryx&#95;4, RD12Oryx, RD301 and RD315 further substantiated these isolates as M. orygis. The exact source of infection in animals was untraceable and the pairwise comparison of the genomes based on single-nucleotide polymorphisms difference did not detect any events of transmission within the affected animals. Nevertheless, it would be wise to take into account the environment where there exists a high chance of transmission due to the increased human-animal interaction. Since it is well known that the pathogen is capable of causing infection in both human and animal hosts, systematic surveillance and screening of spotted deer, black buck as well as humans in the vicinity is essential for successful implementation of the One Health approach., (© 2022 Wiley-VCH GmbH.)

Purpose: Accurate HIV diagnosis is essential for appropriate patient care. This present study evaluated the performance of two different new rapid HIV diagnostic tests; 1) TRUSTline HIV-1/2 Ab rapid test (Athenese-DxPvt. Ltd, Chennai, India)and 2) OnSite HIV 1/2 Ab Plus Combo Rapid Test (CTK Biotech Inc., San Diego, USA) and also validated ALTA Rapid Test Reader (RTR-1) (CTK Biotech Inc., San Diego, USA), the device is a user-friendly and image-analysis based qualitative/semi-quantitative tabletop reader., Methods: A total of n ​= ​500 characterized specimens were used for this evaluation and the results of the new test kits (TRUSTline and OnSite) were also compared with 4 th generation ELISA kit (Genescreen™Ultra HIV Ag-Ab ELISA) and 3 other commercially available rapid tests that were in the market; 1)SD Bioline™ HIV 1/2 3.0, 2) Aspen® HIV 1/2 Rapid Ab Test and 3) Diagnostic enterprises HIVTRI-DOT. The test band intensities of the TRUSTline and OnSite tests were measured in an ALTA rapid test reader and compared with the naked eye reading., Results: The sensitivity, specificity, positive predictive value, negative predictive value and efficacy of TRUSTline and OnSite were 100%, 99.6%, 99.5%, 100% and 99.8% and 100%, 100%, 100%, 100% and 100% respectively., Conclusions: The 'TRUSTline HIV-1/2' and 'OnSite HIV 1/2' kits are suitable to use in the HIV testing algorithm. Use of the ALTA rapid test reader could be user's friendly in the field level testing in resource-limited settings"., Competing Interests: Declaration of competing interest The authors declare no conflicts of interest., (Copyright © 2022 Indian Association of Medical Microbiologists. Published by Elsevier B.V. All rights reserved.)

Background: Understanding the immune correlates of cardiovascular disease (CVD) risk in HIV infection is an important area of investigation in the current era of aging with HIV infection. Less is known about CVD risk and HIV infection in developing nations where additional risk factors may be playing a role in the CVD development. In this study, we assessed the effects of systemic inflammation, microbial translocation (MT), T cell immune activation (IA), and nadir CD4 counts on cardiac function and arterial stiffness as markers of subclinical atherosclerosis in HIV-infected individuals., Methods: People with HIV (PWH) who were ART naïve (n = 102) or virally suppressed on ART (n = 172) were stratified on nadir CD4 counts and compared to HIV-uninfected controls (n = 64). Determination was made of cardiac function via radial pulse wave and carotid intima thickness (C-IMT) measurements. Plasma biomarkers of inflammation and MT by ELISA or multiplex assays, and immune activation (IA) of T cells based HLA-DR and CD38 expression were investigated by flow cytometry. T-test, Mann-Whitney U test, and Spearman correlation were used to analyze study parameters., Results: Reduction in cardiac function with lower cardiac ejection time (p < 0.001), stroke volume (p < 0.001), cardiac output (p = 0.007), higher arterial stiffness (p < 0.05) were identified in ART-naïve participants, compared to PWH on ART (p < 0.05). No significant difference in C-IMT values were noted. Higher inflammatory and MT markers were found in the ART-naïve group compared to treated group who were comparable to uninfected participants, except for having higher TNF-α (p < 0.001) and sCD14 (p < 0.001). Immune activation of CD4 and CD8 T-cells was greater in ART-naïve participants compared to ART-treated and uninfected controls (p < 0.05). Lower nadir CD4 counts, higher inflammation, and higher MT predicted poor cardiac measures in the ART-naïve with nadir CD4 < 200cells/mm 3 manifesting the highest arterial stiffness, and lowest cardiac function, whereas ART-treated, even with nadir < 200 cells/mm 3 were similar to uninfected in these measures., Conclusions: In HIV-infected individuals, initiation of ART even at nadir of < 200 cells/mm 3 may prevent or reverse cardiovascular disease outcomes that are easily measurable in low income countries., (© 2022. The Author(s).)

Samples of white leg shrimp, Penaeus vannamei, were collected on a monthly basis from freshwater ponds with the salinity of 0 ppt located at Tiruvannamalai and Villupuram districts in Tamil Nadu, India for screening of viral and fungal pathogens. Totally, 130 shrimp samples were collected from 67 freshwater ponds and screened for white spot syndrome virus (WSSV), infectious myonecrosis virus (IMNV), infectious hypodermal and haematopoietic necrosis virus (IHHNV) and Enterocytozoon hepatopenaei (EHP) by PCR and RT-PCR using pathogen-specific primers. Among the samples screened, one sample was found to be positive to WSSV, two samples showed positive to IMNV and two samples positive for EHP. No sample showed positive to IHHNV. The WSSV detected in the sample was found to be a new strain of WSSV and highly virulent. The inoculum prepared from freshwater reared WSSV or IMNV-infected shrimp caused 100% mortality in experimental infection studies. The PCR and RT-PCR results revealed the presence of WSSV and IMNV in different organs of experimentally infected shrimp, respectively. No clinical signs were observed in experimentally EHP-injected shrimp, although the PCR results revealed the presence of EHP in experimentally infected shrimp., (© 2022 John Wiley & Sons Ltd.)

BACKGROUND: Early diagnosis of drug-resistant TB (DR-TB) is crucial in preventing the spread of the disease in the community. Introduction of upfront decentralised drug susceptibility testing to district-level as part of universal drug susceptibility testing (UDST) policy increased the feasibility of rapid and early testing for drug resistance closer to the patient and has resulted in reduced circumstances for transmission. The introduction of the first-line line-probe assay (FL-LPA), GenoType ® MTBDR plus v2, has had an extensive impact on the management of multidrug-resistant TB (MDR-TB) in India. MATERIALS and METHODS: Sputum samples of patients with presumptive TB and DR-TB from selected districts of Tamil Nadu received through National TB Elimination Programme (NTEP) were subjected to FL-LPA as per programme guidelines. In this study, we present trends in genotypic resistance to isoniazid (INH) and rifampicin (RIF) during the 4 years (2016-2019) among these patients. Band patterns were analysed as per the updated GLI (Global Laboratory Initiative) LPA interpretation and reporting guidelines. RESULTS: A total of 26,349 samples were received during the study period. Smear-positive samples ( n = 20231) were directly subjected to FL-LPA; smear-negative samples were cultured in liquid media and M. tuberculosis- positive cultures were tested using FL-LPA. A total of 18,441 were MTB-positive on FL-LPA. INH monoresistance, RIF monoresistance and MDR-TB was observed in respectively 8.7%, 1.1% and 3.3% of the samples. There was a decreasing trend in all types of resistance observed particularly after 2017 ( P < 0.001). MDR-TB showed a steady decrease from 5.6% to 1.8%. S531L (19.5%) and S315T (61.1%) were the most common mutations identified in the rpo B and kat G genes, respectively. The percentage of inh A-c-15t promoter mutation, indicating low-level INH resistance, showed a consistent increase ( P < 0.001). CONCLUSION: The impact of the UDST policy on the NTEP may have led to this decreasing trend in RIF and INH resistance observed in the study period. The increase in low-level INH resistance mutation inh A -c-15t may be associated with ethionamide/prothionamide resistance, and this should be taken into account when designing DR-TB regimen.

Background: Leber's Hereditary Optic Neuropathy (LHON) is a rare mitochondriopathy causing retinal ganglion cell degeneration resulting in central vision loss. It is caused by mitochondrial DNA (mtDNA) mutations and thus follows maternal inheritance pattern., Methods: We analysed the whole mitochondrial genome in 100 South Indian LHON patients by utilizing Sanger and Next Generation Sequencing approaches. Haplogroup analysis was performed using HaploGrep2 to predict the risk group. Methylation changes in the mtDNA D-loop region were investigated by performing methylation-specific polymerase chain reaction (MSP)., Results: LHON associated mutations were detected in 55% of the patients of which 42% harboured the primary mutations and 13% harboured potentially pathogenic variants that were previously reported to cause LHON. The candidate mutations identified with confirmed pathogenicity are: m.11778G > A (38%), m.14484 T > C (3%), m.4171C > A (1%) and m.11696G > A (1%). MSP results demonstrated that the D-loop region was unmethylated in all the study subjects including mutation-positive patients, mutation-negative patients, asymptomatic carriers, and controls. Haplogroup-M was prevalent (69%) in the study cohort followed by R (14%), U (9%), N (3%), HV (2%), G (2%), and W (1%). The frequency of the predominant mutation m.11778G > A was found lower (̴ 11%) in haplogroup-U., Conclusions: South Indian LHON cohort shows a unique profile of mtDNA mutations and haplogroup association presumably with no role of D-loop methylation. MT-ND4, MT-ND5, and MT-ND1 serve as the hotspot genes in this cohort. The presence of LHON associated mutations in patients lacking the common primary mutations insists on the necessity of mitochondrial genome sequencing in individuals suspected with LHON., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Thamirabarani river acquires large untreated sewage effluents from the Tirunelveli and Thoothukudi districts of South Tamil Nadu. This study examined the concentration of trace elements in water, sediment, and phytoaccumulation potential of aquatic weeds viz., A. cristata, E. crassipes, S. natans, and P. stratiotes, growing along Srivaikundam dam of Thamirabarani river. The Pb, As, Hg, Cd, and Ni concentrations in water were slightly higher than the US Food and Drug Administration (USFDA) drinking water guidelines; however, their accumulation in sediment was below WHO's sediment quality guideline. This study concludes that the phytoaccumulation factor (PAF) and translocation factor (TF) was >1 in E. crassipes and A. cristata, representing them as hyperaccumulators, suitable for phytoremediation in polluted localities. E. crassipes, A. cristata, and S. natans accumulated (100-500 fold) higher trace elements concentrations than that present in the water. Also, the concentrations of trace elements found in the aquatic weeds were below the recommended levels for the critical plant range (CRP). These selected aquatic weeds are more suitable for plant hybridization to be modified as superbug plants., (Copyright © 2021 Elsevier Inc. All rights reserved.)

With increasing use of Xpert MTB/RIF a point of care molecular test for simultaneous detection of TB and resistance to rifampicin, a growing number of rifampicin resistant cases are being detected and notified. Insights into the variation and frequencies in the probe mutations obtained through Xpert testing in the RRTB case will form the baseline information for further investigation on drug resistance. In this study we did a retrospective analysis of the GeneXpert data obtained from patient samples received at a National reference laboratory in Chennai between the years 2014 and 2020 to look at the probe distribution, the variation in the mutation and explore its significance. Probe E mutation was most commonly identified followed by Probe D, Probe A, Probe B and Probe C. Coexistence of multiple probe mutations in low bacillary load samples could be related to prolonged amplification cycle leading to delayed hybridization of probes. In such instances reporting false RR in xpert testing is possible. The probe mutations of RR should be monitored in depth with inclusion of codon specific targets for management of drug sensitive TB. In addition, heteroresistance needs to be further tested by alternative genotypic methods to avoid false resistance., (Copyright © 2022. Published by Elsevier Ltd.)

In this study, we reported Shiga toxin-producing Escherichia coli (STEC) in 847 samples, including those in coastal waters, sediments, and fish samples in the Southeast Coast of India. A total of 3742 E. coli strains were identified using conventional and molecular identification methods. Of these, 1518 isolates expressed virulent genes Stx1, Stx2, and Eae; effects on these genes on toxicity were examined. Furthermore, 2224 non-STEC isolates caused hemolytic uremic syndrome and played a key role in the persistence of STEC contamination. We conclude that toxin production is not adequate to cause disease, and the pathogenic mechanism of STEC remains poorly defined. Therefore, the present study indicates the status of pollution, highlighting the need for sanitation in public health., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Background: Marine organisms are the potential contributors of novel bioactive molecules. Nevertheless, their biodiversity and the versatility of bioactive metabolites have not been fully explored. Hence, the aim of the present study was to investigate the potentials of gut associated bacteria from a marine crab for the production of novel antibacterial compound., Methods: Aerobic gut autochthonous bacteria isolated from marine crab (Lissocarinus orbicularis) collected from Pazhayar coastal area in Nagapattinam district of Tamil Nadu, India were screened for antibacterial activity. Optimization for bacterial growth and antimicrobial compound production, extraction, purification and characterization were studied., Results: In the present study, eight morphologically distinct colonies of L. orbicularis gut associated aerobic bacterial isolates (Iso1-Iso8) on Zobell marine agar plate were selected. Isolates were screened for antimicrobial activity against human bacterial pathogens such as Salmonella paratyphi, Vibrio cholera, Vibrio parahaemolyticus, Aeromonas hydrophila and Listeria monocytogenes. On the basis of screening results, isolate 5 (Iso5) was selected as the most potential strain and identified as Paenibacillus polymyxa using biochemical and 16S rRNA sequencing methods. The sequence data was submitted to NCBI (Gene bank Accession No: MK583465). Optimization of P. polymyxa for growth and antimicrobial compound production revealed incubation period (36 h), agitation (150 rpm), pH 8.0, 35 °C, 2.5% salinity, 2% glucose and 1% yeast extract as carbon and nitrogen sources respectively were the ideal conditions and mass culture was done with these parameters. Antimicrobial compound from the cell free supernatant of mass culture medium was extracted using ethanol. The lowest minimum inhibitory concentration (MIC) of 16 μg/ml was observed against of both V. parahaemolyticus and V. cholerae. GC-MS analysis of the active ethanol fraction showed the presence of different components such as dodecane (96.72%), Tridecane (1.69%), Undecane, 2,6-dimethyl- (1.69%), Tetradecane (1.12%) and Dodecane, 2,6,11-trimethyl- (1.12%)., Conclusion: The present study showed that the gut associated autochthonous bacteria of marine crabs are one of the potential sources of antibacterial compound. However, further studies are needed for the identification of the antimicrobial compound., (Copyright © 2021 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Objective: To describe the characteristics of contacts of patients with COVID-19 case in terms of time, place and person, to calculate the secondary attack rate (SAR) and factors associated with COVID-19 infection among contacts., Design: A retrospective cohort study SETTING AND PARTICIPANTS: Contacts of cases identified by the health department from 14 March 2020to 30 May 2020, in 9 of 38 administrative districts of Tamil Nadu. Significant proportion of cases attended a religious congregation., Outcome Measure: Attack rate among the contacts and factors associated with COVID-19 positivity., Results: We listed 15 702 contacts of 931 primary cases. Of the contacts, 89% (n: 14 002) were tested for COVID-19. The overall SAR was 4% (599/14 002), with higher among the household contacts (13%) than the community contacts (1%). SAR among the contacts of primary cases with congregation exposure were 5 times higher than the contacts of non-congregation primary cases (10% vs 2%). Being a household contact of a primary case with congregation exposure had a fourfold increased risk of getting COVID-19 (relative risk (RR): 16.4; 95% CI: 13 to 20) than contact of primary case without congregation exposure. Among the symptomatic primary cases, household contacts of congregation primaries had higher RR than household contacts of other cases ((RR: 25.3; 95% CI: 10.2 to 63) vs (RR: 14.6; 95% CI: 5.7 to 37.7)). Among asymptomatic primary case, RR was increased among household contacts (RR: 16.5; 95% CI: 13.2 to 20.7) of congregation primaries compared with others., Conclusion: Our study showed an increase in disease transmission among household contacts than community contacts. Also, symptomatic primary cases and primary cases with exposure to the congregation had more secondary cases than others., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2021. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Background: Plasma chemokines are biomarkers of greater disease severity, higher bacterial burden, and delayed sputum culture conversion in pulmonary tuberculosis (PTB). Whether plasma chemokines could also serve as biomarkers of unfavorable treatment outcomes in PTB is not known., Methods: A cohort of newly diagnosed, sputum smear- and culture-positive adults with drug-sensitive PTB were recruited under the Effect of Diabetes on Tuberculosis Severity study in Chennai, India. Plasma chemokine levels measured before treatment initiation were compared between 68 cases with unfavorable outcomes (treatment failure, death, or recurrence) and 136 control individuals who had recurrence-free cure. A second validation cohort comprising newly diagnosed, culture-positive adults with drug-sensitive TB was used to measure plasma chemokine levels in 20 cases and 40 controls., Results: Six chemokines (CCL2, CCL3, CCL4, CXCL8, CXCL10, and CX3CL1) were associated with increased risk, while CXCL1 was associated with decreased risk of unfavorable outcomes in unadjusted and adjusted analyses in the test cohort. Similarly, CCL3, CXCL8, and CXCL10 were associated with increased risk of unfavorable treatment outcomes in the validation cohort. Receiver operating characteristic analysis revealed that combinations of CCL3, CXCL8, and CXCL10 exhibited very high sensitivity and specificity in differentiating cases vs controls., Conclusions: Our study reveals a plasma chemokine signature that can be used as a novel biomarker for predicting adverse treatment outcomes in PTB., (© The Author(s) 2020. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.)

In this study, we have analyzed the metagenomic DNA from the pooled sediment sample of the river Ganges to explore the abundance and diversity of phages, microbial community, and antibiotic resistance genes (ARGs). Utilizing data from Illumina platform, 4,174 (∼0.0013%) reads were classified for the 285 different DNA viruses largely dominated by the group of 260 distinctive phages (3,602 reads, ∼86.3%). Among all, Microcystis (782 hits), Haemophilus (403), Synechococcus (386), Pseudomonas (279), Enterococcus (232), Bacillus (196), Rhodococcus (166), Caulobacter (163), Salmonella (146), Enterobacteria (143), Mycobacterium and (128) phages show the highest abundance and account for ∼90% of the total identified phages. In addition, we have also identified corresponding host pertaining to these phages. Mainly, Proteobacteria (∼69.3%) dominates the microbial population structure. Primarily, orders such as Caulobacterales (∼28%), Burkholderiales (∼13.9%), Actinomycetales (∼13.7%), and Pseudomonadales (∼7.5%) signify the core section. Furthermore, 21,869 (∼0.00695%) reads were classified in 20 ARG types (classes) and 240 ARGs (subtypes), among which 4 ARG types, namely multidrug resistance (12,041 reads, ∼55%), bacitracin (3,202 reads, ∼15%), macrolide-lincosamide-streptogramin (1,744 reads, ∼7.98%), and fosmidomycin (990 reads, ∼4.53%), have the highest abundance. Simultaneously, six resistance mechanisms were also recognized with the dominance of antibiotic efflux (72.8%, 15,919 reads). The results unveil the distribution of (pro)-phages; microbial community; and various ARGs in the Ganges river sediments.

Background and Aims: Implementing effective interventions for HCV requires a detailed understanding of local transmission dynamics and geospatial spread. Little is known about HCV phylodynamics, particularly among high-burden populations, such as people who inject drugs (PWID)., Approach and Results: We used 483 HCV sequences and detailed individual-level data from PWID across four Indian cities. Bayesian phylogeographic analyses were used to evaluate transmission hotspots and geospatial diffusion of the virus. Phylogenetic cluster analysis was performed to infer epidemiologic links and factors associated with clustering. A total of 492 HIV sequences were used to draw comparisons within the same population and, in the case of coinfections, evaluate molecular evidence for shared transmission pathways. Overall, 139/483 (28.8%) of HCV sequences clustered with a median cluster size of 3 individuals. Genetically linked participants with HCV were significantly younger and more likely to be infected with HCV subtype 3b as well as to live and inject close to one another. Phylogenetic evidence suggests likely ongoing HCV infection/reinfection with limited support for shared HIV/HCV transmission pathways. Phylogeographic analyses trace historic HCV spread back to Northeastern India and show diffusion patterns consistent with drug trafficking routes., Conclusions: This study characterizes HCV phylodynamics among PWID in a low and middle-income country setting. Heterogeneity and recent genetic linkage of HCV across geographically disparate Indian states suggest that targeted interventions could help prevent reimportation of virus through drug trafficking routes., (© 2021 The Authors. Hepatology published by Wiley Periodicals LLC on behalf of American Association for the Study of Liver Diseases.)

Background: Population-level prevalence of detectable HIV viraemia (PDV) has been proposed as a metric for monitoring the population-level effectiveness of HIV treatment as prevention. We aimed to characterise temporal changes in PDV in people who inject drugs (PWID) and men who have sex with men (MSM) in India and evaluate community-level and individual-level associations with cross-sectional HIV incidence., Methods: We did a serial cross-sectional study in which baseline (from Oct 1, 2012, to Dec 19, 2013) and follow-up (from Aug 1, 2016, to May 28, 2017) respondent-driven sampling (RDS) surveys were done in MSM (ten community sites) and PWID (12 community sites) across 21 cities in India. Eligible participants were those aged 18 years or older who provided informed consent and possessed a valid RDS referral coupon. Annualised HIV incidence was estimated with validated multiple-assay algorithms. PDV was calculated as the percentage of people with detectable HIV RNA (>150 copies per mL) in a community site. Community-level associations were determined by linear regression. Multivariable, multilevel Poisson regression was used to assess associations with recent HIV infection., Findings: We recruited 21 990 individuals in the baseline survey and 21 726 individuals in the follow-up survey. The median community-level HIV incidence estimate increased from 0·9% (range 0·0-2·2) at baseline to 1·5% (0·5-3·0) at follow-up in MSM and from 1·6% (0·5-12·4) to 3·6% (0·0-18·4) in PWID. At the community-level, every 1 percentage point increase in baseline PDV and temporal change in PDV between surveys was associated with higher annualised HIV incidence at follow-up: for baseline PDV β=0·41 (95% CI 0·18-0·63) and for change in PDV β=0·52 (0·38-0·66). After accounting for individual-level risk factors, every 10 percentage point increase in baseline PDV and temporal change in PDV was associated with higher individual-level risk of recent HIV infection at follow-up: adjusted risk ratio 1·85 (95% CI 1·44-2·37) for baseline PDV and 1·81 (1·43-2·29) for change in PDV., Interpretation: PDV was temporally associated with community-level and individual-level HIV incidence. These data support scale-up of treatment as prevention programmes to reduce HIV incidence and the programmatic use of PDV to monitor community HIV risk potential., Funding: US National Institutes of Health, Elton John AIDS Foundation., Competing Interests: Declaration of interests SSS reports grants from National Institutes of Health (USA) during the conduct of the study, grants, personal fees, and non-financial support from Gilead Sciences, and grants and non-financial support from Abbott Laboratories, outside the submitted work. SHM reports personal fees from Gilead Sciences, outside the submitted work. All other authors declare no competing interests., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Background: People who inject drugs (PWID) account for some of the most explosive human immunodeficiency virus (HIV) and hepatitis C virus (HCV) epidemics globally. While individual drivers of infection are well understood, less is known about network factors, with minimal data beyond direct ties., Methods: 2512 PWID in New Delhi, India were recruited in 2017-19 using a sociometric network design. Sampling was initiated with 10 indexes who recruited named injection partners (people who they injected with in the prior month). Each recruit then recruited their named injection partners following the same process with cross-network linkages established by biometric data. Participants responded to a survey, including information on injection venues, and provided a blood sample. Factors associated with HIV/HCV infection were identified using logistic regression., Results: The median age was 26; 99% were male. Baseline HIV prevalence was 37.0% and 46.8% were actively infected with HCV (HCV RNA positive). The odds of prevalent HIV and active HCV infection decreased with each additional degree of separation from an infected alter (HIV AOR: 0.87; HCV AOR: 0.90) and increased among those who injected at a specific venue (HIV AOR: 1.50; HCV AOR: 1.69) independent of individual-level factors (p<0.001). In addition, sociometric factors, for example, network distance to an infected alter, were statistically significant predictors even when considering immediate egocentric ties., Conclusions: These data demonstrate an extremely high burden of HIV and HCV infection and a highly interconnected injection and spatial network structure. Incorporating network and spatial data into the design/implementation of interventions may help interrupt transmission while improving efficiency., Funding: National Institute on Drug Abuse and the Johns Hopkins University Center for AIDS Research., Competing Interests: SC, AS, KZ, PD, SM, SS, PN, MK, EO, GL, CL No competing interests declared, SM reports personal fees from Gilead Sciences, outside the submitted work. SS reports grants/products and advisory board fees from Gilead Sciences and grants/products from Abbott Diagnostics, outside the submitted work., (© 2021, Clipman et al.)

Covid-19 Nationwide lockdown for social containment was implemented on the 23rd of March 2020. The objective of this study was to look at the impact of lockdown on STEMI (<24hrs window period). This study was done in 2 phases, 43 days before (phase1) and 43 days during lockdown (phase 2). During the lockdown, there was a 31% decrease in hospital admission rates, 11.5% and 9.38% proportional increase in diabetics and hypertensive patients presenting with STEMI. The public must be educated about the existing important health problems in the community along with the pandemic warnings., Competing Interests: Declaration of competing interest All the authors have no conflicts of interests and financial disclosure., (Copyright © 2021 Cardiological Society of India. Published by Elsevier B.V. All rights reserved.)

Background: The association of BAX -248 G>A and BCL2 -938 C>A with different cancers created conflicts.  We studied the correlation and the effect of these polymorphisms in patients with Nasopharyngeal Carcinoma (NPC).  Methods: PCR-RFLP and Sanger sequencing were used to detect polymorphisms. Statistical analysis including forest plot and Kaplan-Meier Log-rank test was conducted to investigate the association and effect of these SNPs on the NPC patients' survival. The computational study was performed to investigate the possible regulatory role between these polymorphisms and the poor survival of NPC patients. Meta-analysis was executed to check the tissue-specific association of these polymorphisms in the context of global cancer prognosis., Results: We observed an increased and significant association of BAX -248 G>A [GA:OR=5.29, 95%CI=1.67,16.67, P=0.004; GA+AA:OR=5.71, 95%CI=1.82,17.90, P =0.002; A:OR=5.33, 95%CI=1.76,16.13, P=0.003], and BCL2 -938 C>A [CA:OR=2.26, 95%CI=1.03,4.96, P=0.04; AA:OR=3.56, 95%CI=0.97,13.05, P=0.05; CA+AA:OR=3.10, 95%CI=1.51,6.35, P=0.002; A:OR=2.90, 95% CI=1.59,5.29, P=0.0005] with the risk of NPC. Also, these SNPs were strongly correlated with poor survival in NPC patients (lower estimated survival mean, lower estimated proportion surviving at 5 years with p <0.05). The computational study showed that these SNPs altered the binding affinity of transcription factors HIF1, SP1, PAX3, PAX9 and CREB towards promoter (Lower p indicates strong affinity). The meta-analysis revealed the tissue-specific association of these polymorphisms. BAX -248 G>A showed a significant correlation with carcinomas [A vs G:OR=1.60, 95%CI=1.09,2.34, P=0.01; AA vs GG:OR=2.61, 95%CI=1.68,4.06, p <0.001; AA+GA vs GG:OR=1.53,95%CI=1.04,2.25, P=0.02); AA vs GG+GA:OR=2.53, 95%CI=1.65,3.87, p <0.001], and BCL2 -938 C>A with other malignancies [A vs C:OR=1.45, 95%CI=1.26,1.66, p <0.001; AA vs CC:OR=2.07, 95%CI: 1.15,3.72, P=0.01; AA+CA vs CC:OR=1.42, 95%CI=1.18,1.72, p <0.001; AA vs CC+CA:OR=1.89, 95%CI=1.02,3.50, P=0.04]., Conclusions: BAX -248 G>A and BCL2 -938 C>A was associated with poor survival in NPC patients. It may increase cancer susceptibility through transcriptional regulation. Moreover, these SNPs' effects could be tissue-specific., .

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome corona virus-2 (SARS-CoV-2), is the most important health issue, internationally. With no specific and effective antiviral therapy for COVID-19, new or repurposed antiviral are urgently needed. Phytochemicals pose a ray of hope for human health during this pandemic, and a great deal of research is concentrated on it. Phytochemicals have been used as antiviral agents against several viruses since they could inhibit several viruses via different mechanisms of direct inhibition either at the viral entry point or the replication stages and via immunomodulation potentials. Recent evidence also suggests that some plants and its components have shown promising antiviral properties against SARS-CoV-2. This review summarizes certain phytochemical agents along with their mode of actions and potential antiviral activities against important viral pathogens. A special focus has been given on medicinal plants and their extracts as well as herbs which have shown promising results to combat SARS-CoV-2 infection and can be useful in treating patients with COVID-19 as alternatives for treatment under phytotherapy approaches during this devastating pandemic situation.

Diabetes is a chronic metabolic disorder that results in distorted insulin signaling and microvascular complications. Current antidiabetic drugs possess harmful long term side effects, necessitating the need for alternate or compliment therapy with lesser issues. Medicinal plants such as ginger have been reported to possess several beneficial activities including antidiabetic activity. The antidiabetic efficacy of microwave-assisted polyphenolic extracts of Indian ginger cultivars from Odisha (MPO) and Tamil Nadu (MPT) is reported here. MPT and MPO showed insulin stimulated glucose uptake of 1.74 ± 0.25 and 1.47 ± 0.15 fold at 6.25 µg/ml of concentrations in C2C12 cells respectively when compared to control. MPT possessed α-amylase, α-glucosidase inhibitory and anti-glycation properties. It also showed DPPH radical scavenging activity (7.69 ± 0.001%), inhibited LPS-induced nitric oxide production (1.06 ± 0.004 fold) than the latter and increased the GLUT4 protein expression by 1.4 fold. Major active compounds such as shogaol and gingerol derivatives, curcumene, zingiberone were identified through GC-ESI/MS analysis and D-pinitol (cyclitol) was identified through HPLC analysis in this variety. This is the first paper to report the presence of an antidiabetic compound, D-pinitol, in the ginger variety. Polyphenol rich, biologically potent ginger extracts can be a good food and nutraceutical supplement to address diabetes and related complications. PRACTICAL APPLICATIONS: Ginger is a native spice of South Asian Countries including India. Ginger extracts possess several medicinal properties such as anti-inflammatory, antidiabetic and antioxidant activities. It is used to treat nausea, vomiting and commonly used as a food flavouring agent and dietary food supplement. Our study shows the antidiabetic, anti-glycation and antioxidant efficacy of polyphenol rich Indian ginger cultivars grown in different geographical regions. Variations in the biological activities between the MPT and MPO ginger variety was observed. Different environmental conditions and their corresponding metabolite accumulation can be correlated with the better activity shown by MPT variety. It showed an increased GLUT4 expression even at a lower dose of 6.25 µg/ml. Ginger cultivar, especially MPT variety can be used as an adjuvant therapy for treating diabetes. Therefore, our study indicates that polyphenols rich ginger cultivar has major application in functional food product development., (© 2021 Wiley Periodicals LLC.)

Importance: Identifying biomarkers of treatment response is an urgent need in the treatment of tuberculosis (TB). Matrix metalloproteinases (MMPs) and tissue inhibitors of matrix metalloproteinases (TIMPs) are potential diagnostic biomarkers in pulmonary TB (PTB)., Objective: To assess whether baseline plasma levels of MMPs and TIMPs are also prognostic biomarkers for adverse treatment outcomes in patients with PTB., Design, Setting, and Participants: Two different cohorts (test and validation) of individuals with PTB were recruited from 2 different sets of primary care centers in Chennai, India, and were followed up for treatment outcomes. Participants were individuals with newly diagnosed TB that was sputum smear and culture positive and drug sensitive. A total of 68 cases and 133 controls were in the test cohort and 20 cases and 40 controls were in the validation cohort. A nested case-control study was performed by matching case patients to control participants in a 1:2 ratio for age, sex, and body mass index. Data for the test cohort was taken from a study performed from 2014 to 2019, and data for the validation cohort, from a study performed from 2008 to 2012. The data analysis was performed from November 2019 to May 2020., Interventions: Individuals with PTB were treated with antituberculosis chemotherapy for 6 months and followed up for 1 year after completion of treatment., Main Outcomes and Measures: Individuals with PTB with adverse outcomes (treatment failure, all-cause mortality, or recurrent TB) were defined as cases and those with favorable outcomes (recurrence-free cure) were defined as controls. Plasma levels of MMPs and TIMPs were measured before treatment as potential biomarkers., Results: In all, 68 cases and 133 matched controls were enrolled in the study (170 [85%] males and 31 [15%] females; median age, 45 years [range, 23-73 years]) in the test cohort and 20 cases with 40 matched controls (51 [85%] males and 9 [15%] females; median age, 45 years [range, 19-61 years]) in the validation cohort. Baseline plasma levels of 5 MMPs and 2 TIMPs in the test cohort and 5 MMPs and all 4 TIMPS in the validation cohort were significantly higher in cases vs controls. In the test cohort, the geometric means (GMs), cases vs controls, were as follows: for MMP-1, 3680 vs 2484 pg/mL (P = .008); for MMP-2, 6523 vs 4762 pg/mL (P < .001); for MMP-7, 3346 vs 2100 pg/mL (P < .001); for MMP-8, 1915 vs 1066 pg/mL (P < .001); for MMP-9, 2774 vs 2336 pg/mL (P = .009); for TIMP-1, 4491 vs 2910 pg/mL (P < .001); and for TIMP-2, 3082 vs 2115 pg/mL (P < .001). In the validation cohort, the GMs, cases vs controls were as follows: for MMP-1, 3680 vs 2484 pg/mL (P < .001); for MMP-2, 6523 vs 4762 pg/mL (P < .001); for MMP-7, 3346 vs 2100 pg/mL (P < .001); for MMP-9, 1915 vs 1066 pg/mL (P < .001); for MMP-13, 2774 vs 2336 pg/mL (P < .001); for TIMP-1, 4491 vs 2910 pg/mL (P = .003); for TIMP-2, 3082 vs 2115 pg/mL (P = .003); for TIMP-3, 2066 vs 1020 pg/mL (P < .001); and for TIMP-4, 2130 vs 694 pg/mL (P < .001). Plasma levels of MMPs and TIMPs were associated with increased risk of adverse outcomes according to both univariate and multivariable analysis in the test cohort (eg, univariate analysis: odds ratio [OR] for MMP-8, 2.04; 95% CI, 1.33-3.14; P = .001; multivariable analysis: OR for MMP-8, 2.16; 95% CI, 1.34-3.47; P = .001). Combined receiver operating characteristic analysis revealed significant area under the curve (AUC), with high sensitivity and specificity in both cohorts (eg, for a combination of MMP-2, MMP-7, and TIMP-1 in the test cohort: sensitivity, 84%; specificity, 83%; and AUC, 0.886; for a combination of MMP-2, MMP-7, TIMP-1, and TIMP-2 in the validation cohort: sensitivity, 85%; specificity, 95%; and AUC, 0.944)., Conclusions and Relevance: Baseline plasma MMP and TIMP levels may be correlates of risk and prognostic biomarkers for treatment failure, relapse, and death in individuals with PTB and merit further evaluation as predictive biomarkers for stratification of patients to shortened or intensified treatment regimens.

Background: Tuberculosis (TB) though primarily affects the lungs it may also affect the other parts of the body and referred as extra pulmonary (EPTB). This study is focused on understanding the genetic diversity and molecular epidemiology of Mycobacterium tuberculosis (M.tb) among tuberculous lymphadenitis (TBL), a form of EPTB patients identified in Chennai, Tamil Nadu., Methods: The genetic diversity was identified by performing spoligotyping on the M.tb clinical isolates that were recovered from lymph node samples. A total of 71 M.tb isolates were recovered from extra pulmonary lymph node samples and subjected to Drug susceptibility testing and spoligotyping was carried out. In addition, immunological characterization from blood of same individuals from whom M.tb was isolated was carried out between the two major lineages groups East African Indian 3 (EAI3) and non-EAI3 strains by ELISA. The results of spoligotyping patterns were compared with the world Spoligotyping Database of Institute Pasteur de Guadeloupe (SpolDB4)., Results: We found 41 spoligotype patterns and their associated lineages. Out of 41 spoligotype pattern, only 22 patterns are available in the spoldB4 database with Spoligotype international Type (SIT) number and remaining patterns were orphan strains without SIT number. The most predominant spoligotype lineage that was found in lymph node sample in this region of India was EAI (36), followed by central Asian strain (CAS) (6), T1 (5), Beijing (3), Latin American & Mediterranean (LAM) (2), U (1), X2 (1) and orphan (22). In addition to EAI, CAS and Beijing, our study identified the presence of orphan and unique spoligotyping patterns in Chennai region. We observed six drug resistant isolates. Out of six drug resistant isolates, four were resistant to isoniazid drug and associated with EAI family. Moreover, we observed increased levels of type 2 and type 17 cytokine profiles between EAI3 and non-EAI family, infected individuals., Conclusions: The study confirms that EAI lineage to be the most predominant lineages in EPTB patients with lymphadenitis and were found to have increased type 1 and type 17 proinflammatory cytokine profiles.