Genomic revolution: Transforming tuberculosis diagnosis and treatment with the use of Whole Genome Sequencing - A consensus statement.

Tuberculosis (TB) is a preventable, treatable, and curable disease. However, in 2020, 9∙9 million people were estimated to have developed tuberculosis, and 1.5 million people were estimated to have died from it. Whereas in India, 2.6 million were diagnosed with TB and 436,000 succumbed to TB in 2019. India (26%) is the major contributor to the global drop in TB cases. The COVID-19 pandemic has substantially reduced access to services for the diagnosis and treatment of TB, resulting in an increase in deaths and a reversal in global progress. [1] Presently, TB incidence is falling at a rate of 2% per year, obstructed mainly by the rearing pandemic of drug-resistant tuberculosis (DRTB). Particularly concerning is multi-drug resistant TB (MDRTB), defined as resistance towards isoniazid (INH) and rifampicin (RIF). [2] The World Health Organization (WHO) targeted to reduce worldwide TB incidence by 90% until 2035. (1) Early initiation of effective treatment based on susceptibility patterns of the Mycobacterium tuberculosis complex (MTBC) is considered key to successful TB control in countries with high DRTB incidence. Worldwide MDRTB treatment outcomes are poor, with cure rates less than 60% (2) due to the lack of comprehensive Drug Susceptibility Testing (DST) in most high MDRTB burden countries. This is leading to the inadequate anti-TB activity of the provided regimens (3-5), unlike regimens advised for DST assure optimal results. (6) In addition to resistances to the established regimens, the resistance to the newer DRTB drugs is increasing. On World TB Day 2022, Academy of Advanced Medical Education, Thyrocare Technologies Limited and HyastackAnalytics - IITB along with expert pulmonologist and renowned physicians from India convened for an advisory board meeting in Delhi on 20th March 2022 to discuss the role of Whole Genome Sequencing (WGS) in the diagnosis and management of TB. Objectives and specific topics relating to WGS in MDRTB were discussed, each expert shared their views, which led to a group discussion with a commitment to putting the patient first, and increasing their collective efforts, the organizations recognized that it is possible to make this goal a reality. The organizations involved in the discussion have declared their commitment to engaging in collaborative efforts to tackle DRTB detection efficiently. They advocate for strengthening access to WGS TB services, controlling and preventing TB, improving surveillance and drug resistance management, and investing in research and development. This Round Table serves as a framework to build on and ensure that the goal of ending TB is achievable with WGS services wherever needed. Post discussion, a uniform consensus was said to be arrived if more than 80% board members agreed to the statement. The present paper is the outcome of aspects presented and discussed in the advisory board meeting.

Clinical outcomes of bronchiectasis in India: data from the EMBARC/Respiratory Research Network of India registry.

BACKGROUND: Identifying risk factors for poor outcomes can help with risk stratification and targeting of treatment. Risk factors for mortality and exacerbations have been identified in bronchiectasis but have been almost exclusively studied in European and North American populations. This study investigated the risk factors for poor outcome in a large population of bronchiectasis patients enrolled in India. METHODS: The European Multicentre Bronchiectasis Audit and Research Collaboration (EMBARC) and Respiratory Research Network of India (EMBARC-India) registry is a prospective observational study of adults with computed tomography-confirmed bronchiectasis enrolled at 31 sites across India. Baseline characteristics of patients were used to investigate associations with key clinical outcomes: mortality, severe exacerbations requiring hospital admission, overall exacerbation frequency and decline in forced expiratory volume in 1 s. RESULTS: 1018 patients with at least 12-month follow-up data were enrolled in the follow-up study. Frequent exacerbations (≥3 per year) at baseline were associated with an increased risk of mortality (hazard ratio (HR) 3.23, 95% CI 1.39-7.50), severe exacerbations (HR 2.71, 95% CI 1.92-3.83), future exacerbations (incidence rate ratio (IRR) 3.08, 95% CI 2.36-4.01) and lung function decline. Coexisting COPD, dyspnoea and current cigarette smoking were similarly associated with a worse outcome across all end-points studied. Additional predictors of mortality and severe exacerbations were increasing age and cardiovascular comorbidity. Infection with Gram-negative pathogens (predominantly Klebsiella pneumoniae) was independently associated with increased mortality (HR 3.13, 95% CI 1.62-6.06), while Pseudomonas aeruginosa infection was associated with severe exacerbations (HR 1.41, 95% CI 1.01-1.97) and overall exacerbation rate (IRR 1.47, 95% CI 1.13-1.91). CONCLUSIONS: This study identifies risk factors for morbidity and mortality among bronchiectasis patients in India. Identification of these risk factors may support treatment approaches optimised to an Asian setting.

Indian Guidelines on Nebulization Therapy.

Inhalational therapy, today, happens to be the mainstay of treatment in obstructive airway diseases (OADs), such as asthma, chronic obstructive pulmonary disease (COPD), and is also in the present, used in a variety of other pulmonary and even non-pulmonary disorders. Hand-held inhalation devices may often be difficult to use, particularly for children, elderly, debilitated or distressed patients. Nebulization therapy emerges as a good option in these cases besides being useful in the home care, emergency room and critical care settings. With so many advancements taking place in nebulizer technology; availability of a plethora of drug formulations for its use, and the widening scope of this therapy; medical practitioners, respiratory therapists, and other health care personnel face the challenge of choosing appropriate inhalation devices and drug formulations, besides their rational application and use in different clinical situations. Adequate maintenance of nebulizer equipment including their disinfection and storage are the other relevant issues requiring guidance. Injudicious and improper use of nebulizers and their poor maintenance can sometimes lead to serious health hazards, nosocomial infections, transmission of infection, and other adverse outcomes. Thus, it is imperative to have a proper national guideline on nebulization practices to bridge the knowledge gaps amongst various health care personnel involved in this practice. It will also serve as an educational and scientific resource for healthcare professionals, as well as promote future research by identifying neglected and ignored areas in this field. Such comprehensive guidelines on this subject have not been available in the country and the only available proper international guidelines were released in 1997 which have not been updated for a noticeably long period of over two decades, though many changes and advancements have taken place in this technology in the recent past. Much of nebulization practices in the present may not be evidence-based and even some of these, the way they are currently used, may be ineffective or even harmful. Recognizing the knowledge deficit and paucity of guidelines on the usage of nebulizers in various settings such as inpatient, out-patient, emergency room, critical care, and domiciliary use in India in a wide variety of indications to standardize nebulization practices and to address many other related issues; National College of Chest Physicians (India), commissioned a National task force consisting of eminent experts in the field of Pulmonary Medicine from different backgrounds and different parts of the country to review the available evidence from the medical literature on the scientific principles and clinical practices of nebulization therapy and to formulate evidence-based guidelines on it. The guideline is based on all possible literature that could be explored with the best available evidence and incorporating expert opinions. To support the guideline with high-quality evidence, a systematic search of the electronic databases was performed to identify the relevant studies, position papers, consensus reports, and recommendations published. Rating of the level of the quality of evidence and the strength of recommendation was done using the GRADE system. Six topics were identified, each given to one group of experts comprising of advisors, chairpersons, convenor and members, and such six groups (A-F) were formed and the consensus recommendations of each group was included as a section in the guidelines (Sections I to VI). The topics included were: A. Introduction, basic principles and technical aspects of nebulization, types of equipment, their choice, use, and maintenance B. Nebulization therapy in obstructive airway diseases C. Nebulization therapy in the intensive care unit D. Use of various drugs (other than bronchodilators and inhaled corticosteroids) by nebulized route and miscellaneous uses of nebulization therapy E. Domiciliary/Home/Maintenance nebulization therapy; public & health care workers education, and F. Nebulization therapy in COVID-19 pandemic and in patients of other contagious viral respiratory infections (included later considering the crisis created due to COVID-19 pandemic). Various issues in different sections have been discussed in the form of questions, followed by point-wise evidence statements based on the existing knowledge, and recommendations have been formulated.

Expert recommendations on the role of macrolides in chronic respiratory diseases.

BACKGROUND: India contributes to 32% of the total global disability-adjusted life years, due to chronic respiratory diseases. This has led to a high rate of health loss from these diseases. Antibiotics are commonly used in the management of respiratory disorders. With excellent tissue penetration, prolonged tissue persistence, and favorable side effect profile, macrolides are one of the best treatment options being recommended for respiratory, urogenital, dermal, and other bacterial infections. Still, there is a lack of clinical trial data on the use of macrolides in the management of respiratory chronic disease, and hence, there is a need for clinical guidance on their use in Indian setting. METHODS: A systematic review of the literature was conducted on PubMed, Cochrane database, and Google Scholar. Existing guidelines, meta-analyses, systematic reviews, randomized controlled trials (RCTs), non-RCTs, landmark studies, and key-cited articles were selected. Recommendations were based on available evidence and expert panel's logical empiricism and consensus. RESULTS AND DISCUSSION: This article discusses evidence-based and clinical practice based management of chronic respiratory conditions including chronic obstructive pulmonary disease, asthma, bronchiectasis, diffusive panbronchiolitis, and organizing pneumonia. The authors reviewed different respiratory conditions, role of macrolides in their management, adverse events and antimicrobial resistance associated with macrolides, evidence review of various clinical trials, guideline recommendations, and clinical recommendations.

Live birth rate from euploid blastocysts is not associated with infertility etiology or oocyte source following frozen-thawed embryo transfer (FET): analysis of 4148 cycles reported to SART CORS.

PURPOSE: To investigate whether live birth rates from euploid blastocyst frozen-thawed embryo transfer (FET) cycles are associated with infertility diagnosis or oocyte source. DESIGN: Retrospective analysis of FET cycles reported to SART CORS in 2014. METHODS: Data from fresh IVF cycles with preimplantation genetic testing for aneuploidy (PGT-A), linked to the first FET cycles, were collected from the 2014 SART CORS database for autologous and donor oocyte cycles. Inclusion criteria were patients undergoing FET with euploid embryos (n = 4148). Demographic data including age, BMI, prior fertility, and etiology of infertility were collected from the retrieval cycle and analyzed. Patients with uterine anomalies, preimplantation genetic testing-mutation (PGT-M) for genetic diseases, gender selection, HLA determination, or systemic and immunologic disorders were excluded. The primary outcome measure was live birth (LB) rate. Potential confounders such as age, prior fertility, and maximum baseline FSH values were analyzed with regression models as indicated. RESULTS: Though age, maximum baseline FSH, and infertility diagnosis were significantly different, LB was similar between patients undergoing autologous or donor oocyte FET cycles. Etiology of infertility was not significantly associated with LB in autologous cycles (p = 0.95). Potential confounders such as maternal age, prior fertility, and maximum baseline FSH were not associated with outcomes; however, maternal BMI was inversely related to LB in autologous cycles, with an odds ratio of 0.97 (95% CI: 0.96-0.98 (rho = - 0.08, p < 0.01)). CONCLUSIONS: After controlling for confounding variables, a euploid embryo derived from a donor or autologous oocyte results in similar LB in women with different infertility diagnoses.

COPD exacerbation rates are higher in non-smoker patients in India.

BACKGROUND: Chronic obstructive pulmonary disease (COPD) is common among non-smokers exposed to solid fuel combustion at home. Different clinical characteristics in these patients may have significant therapeutic and prognostic implications.METHODS: We used medical record review and a questionnaire among COPD patients at 15 centres across India to capture data on demographic details, different types of exposures and clinical characteristics. Chest radiography and pulmonary function testing were performed in all 1984 cases; C-reactive protein and exhaled breath nitric oxide were measured wherever available.RESULTS: There were 1388 current or ex-smokers and 596 (30.0%) non-smokers who included 259 (43.5%) male and 337 (56.5%) female patients. Sputum production was significantly more common in smokers with COPD (P < 0.05). The frequency of acute symptomatic worsening, emergency visits and hospitalisation were significantly higher (P < 0.05) in non-smokers with COPD; however, intensive care unit admissions were similar in the two groups. There was no significant difference with respect to the use of bronchodilators, inhalational steroids or home nebulisation among smoker and non-smoker patients. The mean predicted forced expiratory volume in 1 sec in smokers (43.1%) was significantly lower than in non-smokers (46.5%).CONCLUSION: Non-smoker COPD, more commonly observed in women exposed to biomass fuels, was characterised by higher rate of exacerbations and higher healthcare resource utilisation.

Diagnoses and management of adult cough: An Indian Environmental Medical Association (EMA) position paper.

BACKGROUND: Cough is a common yet distressing symptom that results in significant health care costs from outpatient visits and related consultations. OBJECTIVE: The understanding of the pathobiology of cough in recent times has undergone an evolution with Cough hypersensitivity syndrome (CHS) being suggested in most cases of dry cough. However, in the case of productive cough, ancillary mechanisms including impaired Mucociliary clearance, in addition to hypermucosecretory bronchospastic conditions of Smoker's cough, asthma-COPD overlap, bronchiectasis, and allergic bronchopulmonary aspergillosis, need to be critically addressed while optimizing patient care with symptomatic therapy in outpatient settings of India. METHODS: In this review, evidence-based graded recommendations on use of antitussives - & protussives as a Position Paper were developed based on the Level and Quality of Scientific evidence as per Agency for Health Care and Quality (AHRQ) criteria listing and Expert opinions offered by a multidisciplinary EMA panel in India. RESULTS: Management of acute or chronic cough involves addressing common issues of environmental exposures and patient concerns before instituting supportive therapy with antitussives or bronchodilatory cough formulations containing mucoactives, anti-inflammatory, or short-acting beta-2 agonist agents. CONCLUSION: The analyses provides a real world approach to the management of acute or chronic cough in various clinical conditions with pro- or antitussive agents while avoiding their misuse in empirical settings.

Joint Indian Chest Society-National College of Chest Physicians (India) guidelines for spirometry.

Although a simple and useful pulmonary function test, spirometry remains underutilized in India. The Indian Chest Society and National College of Chest Physicians (India) jointly supported an expert group to provide recommendations for spirometry in India. Based on a scientific grading of available published evidence, as well as other international recommendations, we propose a consensus statement for planning, performing and interpreting spirometry in a systematic manner across all levels of healthcare in India. We stress the use of standard equipment, and the need for quality control, to optimize testing. Important technical requirements for patient selection, and proper conduct of the vital capacity maneuver, are outlined. A brief algorithm to interpret and report spirometric data using minimal and most important variables is presented. The use of statistically valid lower limits of normality during interpretation is emphasized, and a listing of Indian reference equations is provided for this purpose. Other important issues such as peak expiratory flow, bronchodilator reversibility testing, and technician training are also discussed. We hope that this document will improve use of spirometry in a standardized fashion across diverse settings in India.

Symptom profile as assessed on delirium rating scale-revised-98 of delirium in respiratory intensive care unit: A study from India.

AIM: This study aimed to evaluate the phenomenology of delirium in patients admitted in a Respiratory Intensive Care Unit (RICU). METHODS: Consecutive patients admitted to RICU were screened for delirium using Richmond Agitation-Sedation Scale (RASS), Confusion Assessment Method for ICU (CAM-ICU) assessment tool and those found positive for delirium were evaluated by a psychiatrist to confirm the diagnosis. Those with a diagnosis of delirium as per the psychiatrist were evaluated on Delirium Rating Scale-Revised-98 (DRS-R-98) to study phenomenology. RESULTS: All the 75 patients fulfilled the criteria of "acute onset of symptoms" and "presence of an underlying physical disorder" as per the DRS-R-98. Commonly seen symptoms of delirium included disturbances in attention (100%), thought process abnormality (100%), fluctuation in symptoms (97.33%) disturbance in, sleep-wake cycle, language disturbance (94.7%), disorientation (81.33%), and short-term memory impairments (73.33%). No patient had delusions and very few (5.3%) reported perceptual disturbances. According to RASS subtyping, hypoactive delirium was the most common subtype (n = 34; 45.33%), followed by hyperactive subtype (n = 28; 37.33%) and a few patients had mixed subtype of delirium (n = 13; 17.33%). Factor structure of DRS-R-98 symptoms yielded 3 factors (Factor-1: cognitive factor; Factor-2: motoric factor; Factor-3; thought, language, and fluctuation factor). CONCLUSION: The phenomenology of delirium in ICU patients is similar to non-ICU patients, but hypoactive delirium is the most common subtype.

Estrogen receptor gene 1 expression in caprine and its effect on fertility.

The present study was undertaken to analyze the expression pattern of estrogen receptor 1 gene (ESR1) in Barbari bucks (fertile and non-fertile) identified on the basis of seminal quality traits and fertility trials. RNA was extracted from the spleen by Trizol method. The expression pattern of ESR1 gene was analyzed using real time polymerase chain reaction (RT-PCR). The expression pattern of ESR1 gene was analyzed by RT-PCR (Roche LC-480). Relative quantification by RT-PCR indicated that the ESR1 gene expression showed more fold in fertile bucks as compared to non-fertile.

Molecular expression of caprine estrogen receptor gene 1 in reproductive and non-reproductive tissues.

During the last decades, physiological effects of oestrogens have been increasingly explored by scientists and biotechnologists. Estrogens exert a wide range of effects on a large variety of cell types. Oestrogen and its receptors are essential for sexual development and reproduction. Estrogen receptor alpha is a nuclear receptor activated by the hormone oestrogen. In male, ERα is encoded by the gene estrogen receptor gene 1 (ESR1), responsible for better fertility. The ESR1 is involved in the reabsorption of luminal fluid during the transit of spermatozoa from the testis to the head of the epididymis which is important for their survival and maturation during epididymal storage. The absence of ESR1 leads to reduced epididymal sperm content, reduced sperm motility and fertilizing ability. Therefore, this is a good startby to study the expression pattern of estrogen receptor 1 gene in high-fertile (G1) and low-fertile (G2) bucks of Jamunapari and Barbari breeds identified on the basis of seminal quality traits and fertility trials. RNA was extracted from the tissues by TRIzol method. The identification and expression pattern of caprine ESR1 gene was analysed by real-time PCR (Roche LC-480). Our work shows that the relative quantification by RT-PCR indicates more fold in head of epididymis as compared to spleen of caprine ESR1 gene. Furthermore, the RT-PCR indicated that fertile bucks of Jamunapari breed have more fold value as compared to Barbari breed in respect of reproductive organ.

Effect of management system and season on semen freezability in Jakhrana bucks.

AIM: The objective of the study was to determine the effect of the management system (intensive and semi-intensive) and season (autumn and winter) on semen freezability in Jakhrana bucks. MATERIALS AND METHODS: A total of 24 Jakhrana bucks of same body weight and age (BW=30 kg, age=1 year) were randomly allotted into two groups, viz., Group I (intensive system, 12 bucks) and Group II (semi-intensive system, 12 bucks). These two groups were statistically tested for their homogeneity with respect to age and BW. Semen was collected twice weekly using an artificial vagina during two seasons: autumn (September-November) and winter (December-February). A total of 240 semen samples (120 from each group and season) were evaluated for post-thaw motility (PTM), viability, abnormality, functional membrane integrity (hypo-osmotic swelling [HOS]) response and acrosomal integrity. RESULTS: The mean values of PTM and acrosomal integrity of spermatozoa were significantly (p<0.01) higher in Group II as compared to Group I. The mean values of viability and abnormality were also differed significant (p<0.05) between groups. However, the mean values of HOS response were found non-significant (p>0.05) between groups. The season showed a significant effect on all parameters except viability and HOS response. The PTM and acrosomal integrity of spermatozoa were significantly (p<0.01) higher in winter as compared to autumn season. Abnormality of spermatozoa was significantly (p<0.05) lower in winter season. CONCLUSIONS: This study indicates that both management system and season influence semen freezability. The semen collected from bucks reared under the semi-intensive system and winter season showed better semen freezability characteristics.

Association of growth related seedling traits in Acacia senegal under arid environment of western Rajasthan.

Climatic models and predictions indicate increase in aridity world over due to global warming. Arid environments occupy about one third land area of the world. A. senegal is the most important dryland resource of western Rajasthan desert ecosystem. The seeds of 13 low and high seed yielding exotic and indigenous provenances were evaluated for diversity and interrelationship among growth related seedling traits targeting establishment and end use of this species. Under the present study most of the growth related seedling traits varied within and amongst provenances. Highly significant correlation of dry biomass per plant of more than 72% with root length (73.3%), collar diameter (72.2%), shoot dryweight (99.7%), root dry weight (95.7%) and seedling length (79.9%) under the present study may be used for early selection. Similarly, highly significant positive correlation of seedling length with seven out of 12 growth related seedling traits validate strong inherent association of these traits under strong genetic control and are amenable for selection. Significant negative correlation in number of nodules per plant with root/shoot length ratio (-57.6%) and no correlation with 10 out of 12 growth related seedling traits tested advocate emphasis on other growth related seedling traits in selection of elite A. senegal genotypes for afforestation. The non significant associations suggest that per cent germination was independent of other characters and could be selected separately.

Effect of different activators on development of activated in vitro matured caprine oocytes.

This study was designed to compare the effectiveness of different activation treatments for activation of in vitro matured oocytes and their developmental potency in mCR2aa medium so as to obtain maximum number of embryos. A total of 1090 cumulus oocyte complexes (COC's) were collected from 480 ovaries. In vitro matured oocytes were randomly divided into four groups. Group 1 in vitro matured oocytes (n=226) were exposed to 7% ethanol for 5 min followed by treatment with 2.0 mM DMAP for 4 h in mCR2aa medium. Group 2 in vitro matured oocytes (n=294) were exposed to 7% ethanol for 5 min followed by treatment with 10 µg/ml CHX for 4 h in mCR2aa medium. Group 3 in vitro matured oocytes (n=325) were exposed to 7% ethanol for 5 min followed by treatment with 2.0 mM DMAP and 10 µg/ml CHX for 4 h in mCR2aa medium. Group 4 in vitro matured oocytes (n=108) were cultured for 4 h without any chemical treatment in mCR2aa medium (control). The cleavage rate in groups 1, 2, 3 and 4 was 54.42%, 44.55%, 51.69% and 0.00%, respectively. The percentage of morula and blastocyst production in group 1, group 2 and group 3 was 26.01%, 29.77% and 29.76% and 2.43%, 1.52% and 1.78%, respectively. These results suggest that the activation of in vitro matured oocytes by 7% ethanol for 5 min followed by treatment with 2.0 mM DMAP for 4 h in mCR2aa is most favorable for parthenogenetic caprine embryos production.

Role of TLR4 C>1196T (Thr399Ile) and TLR4 A>896G (Asp299Gly) polymorphisms in a North Indian population with asthma: a case-control study.

Toll-like receptor 4 (TLR4) is the most important TLR among the pattern recognition receptors which recognizes lipopolysaccharide of gram-negative bacteria. They identify a highly conserved structure of microbes called pathogen-associated molecular patterns and activate immune and inflammatory responses that have been shown to be involved in the pathogenesis of asthma. The role of TLR4 gene polymorphisms in asthma was detected in a total of 964 individuals, including 483 healthy controls and 481 asthma patients from a North Indian population. The genotyping was carried out using polymerase chain reaction-restriction fragment length polymorphism method. Statistical analysis revealed that the heterozygous genotype as well as the mutant (T) allele of the TLR4 C>1196T (Thr399Ile) polymorphism shows resistance towards asthma with OR = 0.70, 95% CI (0.49-0.99), P corrected value = 0.046 and OR = 0.72, 95% CI (0.52-0.98), P corrected value = 0.039, respectively. However, no association was found between the TLR4 A>896G (Asp299Gly) polymorphism and asthma patients (P > 0.05). This is the first study conducted in India conferring TLR4 (Thr399Ile) polymorphism resistance towards asthma, while lack of association was found between TLR4 (Asp299Gly) polymorphism and asthma in the studied North Indian population.