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In case-control single-cell RNA-seq studies, sample-level labels are transferred onto individual cells, labeling all case cells as affected, when in reality only a small fraction of them may actually be perturbed. Here, using simulations, we demonstrate that the standard approach to single cell analysis fails to isolate the subset of affected case cells and their markers when either the affected subset is small, or when the strength of the perturbation is mild. To address this fundamental limitation, we introduce HiDDEN, a computational method that refines the case-control labels to accurately reflect the perturbation status of each cell. We show HiDDEN's superior ability to recover biological signals missed by the standard analysis workflow in simulated ground truth datasets of cell type mixtures. When applied to a dataset of human multiple myeloma precursor conditions, HiDDEN recapitulates the expert manual annotation and discovers malignancy in early stage samples missed in the original analysis. When applied to a mouse model of demyelination, HiDDEN identifies an endothelial subpopulation playing a role in early stage blood-brain barrier dysfunction. We anticipate that HiDDEN should find wide usage in contexts that require the detection of subtle transcriptional changes in cell types across conditions., (© 2024. The Author(s).)

Tuberculosis (TB) is a chronic condition that weakens the immune system, causes structural changes in the lungs, and can lead to infections by other bacterial pathogens. Very few studies have been done to understand the magnitude of co-infection with other bacterial pathogens, so this study was conducted to understand the co-infection pattern and burden. A total of 174 microbiologically confirmed pulmonary TB patients' samples, identified by cartridge-based nucleic acid amplification test, were further tested for other bacterial pathogens by culture over a period of five months from May 2023 to September 2023. The isolates' identification and drug susceptibility were performed using the VITEK 2 system (bioMérieux, Marcy-l'Étoile, France). Of the 174 pulmonary samples tested, 19 samples grew a significant amount of other bacterial pathogens, making the prevalence 10.91% (19/174). Among the pulmonary samples tested, 54.59% were sputum, 38.5% were bronchoalveolar lavage, and 6.89% were endotracheal aspirate. Additionally, 70.11% of the patients tested were in the age group of 19-60 years. Of the patients who had co-infection, 94.73% (18/19) were male. The most common bacterial infection was caused by Pseudomonas aeruginosa , which was identified in 36.84% of the co-infection cases (7/19). This was followed by Acinetobacter baumannii in 31.57% (6/19), Klebsiella pneumoniae in 26.31% (5/19), and Stenotrophomonas maltophilia in 5.28% (1/19). Acinetobacter baumannii and Klebsiella pneumoniae showed high drug resistance, ranging from 60% to 100% against various groups of drugs tested. None of the patient samples with co-infection showed rifampicin resistance. Among all the samples with co-infection, the majority (42.10%, or 8/19) had a high load of Mycobacterium tuberculosis complex detected by CBNAAT Ultra (Cepheid, Sunnyvale, California). Pseudomonas aeruginosa , Acinetobacter baumannii , and Klebsiella pneumoniae are unusual pathogens causing infection in community patients and are known to cause illness in hospitalized patients. These organisms' resistance was also similar to the resistance shown by hospital-acquired infections. This indicates that bacterial co-infection in pulmonary TB patients will be similar to the pattern of hospital-acquired infections. The high prevalence of bacterial co-infections (10.91%) in patients with pulmonary TB poses a significant challenge as these bacterial pathogens are not susceptible to anti-tubercular drugs. Therefore, comprehensive screening for other bacterial infections in all pulmonary TB patients is crucial for effective treatment and outcomes., Competing Interests: Human subjects: Consent was obtained or waived by all participants in this study. Institutional Ethics Committee of ESIC MC&H, Faridabad issued approval 134 X/11/13/2024- IEC/DHR/04. Animal subjects: All authors have confirmed that this study did not involve animal subjects or tissue. Conflicts of interest: In compliance with the ICMJE uniform disclosure form, all authors declare the following: Payment/services info: All authors have declared that no financial support was received from any organization for the submitted work. Financial relationships: All authors have declared that they have no financial relationships at present or within the previous three years with any organizations that might have an interest in the submitted work. Other relationships: All authors have declared that there are no other relationships or activities that could appear to have influenced the submitted work., (Copyright © 2024, Bir et al.)

We report a rare case of splenic tuberculosis (TB) in a male patient with a competent immune system who had no previous record of pulmonary TB. A 56-year-old male patient came to our outpatient department complaining of upper abdominal pain with a few episodes of vomiting for three days. He had alcoholism, smoked for 15 years, and had no past history of diabetes mellitus, hypertension, TB, or HIV. An abdominal ultrasound and CT scan at admission showed pancreatitis with a splenic abscess. After five days of admission, the patient's vitals deteriorated, and he had severe abdominal pain. CT scan suggested a splenic abscess rupture with hemoperitoneum. An emergency exploratory laparotomy was performed, and a splenectomy was done due to the splenic abscess rupture. A cartridge-based nucleic acid amplification test from splenic intracapsular fluid detected a trace Mycobacterium tuberculosis complex. The patient was discharged after starting first-line antitubercular treatment for six months. After three months of follow-up, the patient was doing well with no complaints., Competing Interests: The authors have declared that no competing interests exist., (Copyright © 2024, Ranjan et al.)

Linking variants from genome-wide association studies (GWAS) to underlying mechanisms of disease remains a challenge 1-3 . For some diseases, a successful strategy has been to look for cases in which multiple GWAS loci contain genes that act in the same biological pathway 1-6 . However, our knowledge of which genes act in which pathways is incomplete, particularly for cell-type-specific pathways or understudied genes. Here we introduce a method to connect GWAS variants to functions. This method links variants to genes using epigenomics data, links genes to pathways de novo using Perturb-seq and integrates these data to identify convergence of GWAS loci onto pathways. We apply this approach to study the role of endothelial cells in genetic risk for coronary artery disease (CAD), and discover 43 CAD GWAS signals that converge on the cerebral cavernous malformation (CCM) signalling pathway. Two regulators of this pathway, CCM2 and TLNRD1, are each linked to a CAD risk variant, regulate other CAD risk genes and affect atheroprotective processes in endothelial cells. These results suggest a model whereby CAD risk is driven in part by the convergence of causal genes onto a particular transcriptional pathway in endothelial cells. They highlight shared genes between common and rare vascular diseases (CAD and CCM), and identify TLNRD1 as a new, previously uncharacterized member of the CCM signalling pathway. This approach will be widely useful for linking variants to functions for other common polygenic diseases., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Population-based association studies have identified many genetic risk loci for coronary artery disease (CAD), but it is often unclear how genes within these loci are linked to CAD. Here, we perform interaction proteomics for 11 CAD-risk genes to map their protein-protein interactions (PPIs) in human vascular cells and elucidate their roles in CAD. The resulting PPI networks contain interactions that are outside of known biology in the vasculature and are enriched for genes involved in immunity-related and arterial-wall-specific mechanisms. Several PPI networks derived from smooth muscle cells are significantly enriched for genetic variants associated with CAD and related vascular phenotypes. Furthermore, the networks identify 61 genes that are found in genetic loci associated with risk of CAD, prioritizing them as the causal candidates within these loci. These findings indicate that the PPI networks we have generated are a rich resource for guiding future research into the molecular pathogenesis of CAD., (© 2024. The Author(s).)

Preeclampsia and gestational hypertension are common pregnancy complications associated with adverse maternal and child outcomes. Current tools for prediction, prevention and treatment are limited. Here we tested the association of maternal DNA sequence variants with preeclampsia in 20,064 cases and 703,117 control individuals and with gestational hypertension in 11,027 cases and 412,788 control individuals across discovery and follow-up cohorts using multi-ancestry meta-analysis. Altogether, we identified 18 independent loci associated with preeclampsia/eclampsia and/or gestational hypertension, 12 of which are new (for example, MTHFR-CLCN6, WNT3A, NPR3, PGR and RGL3), including two loci (PLCE1 and FURIN) identified in the multitrait analysis. Identified loci highlight the role of natriuretic peptide signaling, angiogenesis, renal glomerular function, trophoblast development and immune dysregulation. We derived genome-wide polygenic risk scores that predicted preeclampsia/eclampsia and gestational hypertension in external cohorts, independent of clinical risk factors, and reclassified eligibility for low-dose aspirin to prevent preeclampsia. Collectively, these findings provide mechanistic insights into the hypertensive disorders of pregnancy and have the potential to advance pregnancy risk stratification., (© 2023. The Author(s), under exclusive licence to Springer Nature America, Inc.)

Background: Carbapenemase producing gram-negative bacteria (GNB) has become a huge problem in majority of tertiary care centers worldwide. They are associated with very high morbidity and mortality rates, especially when they cause invasive infections. Therefore, rapid detection of these organisms is very important for prompt and adequate antibiotic therapy as well as infection control. The aim of this study was rapid detection of carbapenemase genes and thereby likely carbapenem resistance, 24-48 hours in advance, directly from the positive-flagged blood culture bottles using CHROMagar and Xpert® Carba-R., Methods: Aspirate from positively flagged blood culture bottles was subjected to differential centrifuge. All gram-negative bacilli on gram stain from the deposit were processed in Xpert® Carba-R and inoculated on CHROMagar. The presence of genes and growth on CHROMagar was compared with carbapenem resistance on VITEK-2 Compact., Results: A total of 119 GNB isolates were processed. One or more of the carbapenemase genes were detected in 80 isolates. On comparison with VITEK-2 result, 92 samples showed concordance for carbapenem resistance 48 hours in advance. There was discordance in 21 isolates with 12 major errors and 09 minor errors. The sensitivity of direct Xpert® Carba-R test for rapid detection of carbapenem resistance, 48 hours in advance, was 81.42%. The sensitivity of direct CHROMagar test for accurate detection of carbapenem resistance, 24 hours in advance, was 92.06%., Conclusion: The ability to detect carbapenem resistance with very high accuracy, 48 hours in advance, helps in appropriate antibiotic therapy and implementation of effective infection control practices., Competing Interests: The authors have none to declare., (© 2021 Director General, Armed Forces Medical Services. Published by Elsevier, a division of RELX India Pvt. Ltd.)

Endothelial cells (EC) are an important mediator of atherosclerosis and vascular disease. Their exposure to atherogenic risk factors such as hypertension and serum cholesterol leads to endothelial dysfunction and many disease-associated processes. Identifying which of these multiple EC functions is causally related to disease risk has been challenging. There is evidence from in vivo models and human sequencing studies that dysregulation of nitric oxide production directly affects risk of coronary artery disease. Human genetics can help prioritize the other EC functions with causal relationships because germline mutations are acquired at birth and serve as a randomized test of which pathways affect disease risk. Though several coronary artery disease risk variants have been linked to EC function, this process has been slow and laborious. Unbiased analyses of EC dysfunction using multiomic approaches promise to identify the causal genetic mechanisms responsible for vascular disease. Here, we review the data from genomic, epigenomic, and transcriptomic studies that prioritize EC-specific causal pathways. New methods that CRISPR (clustered regularly interspaced short palindromic repeats) perturbation technology with genomic, epigenomic, and transcriptomic analysis promise to speed up the characterization of disease-associated genetic variation. We summarize several recent studies in ECs which use high-throughput genetic perturbation to identify disease-relevant pathways and novel mechanisms of disease. These genetically validated pathways can accelerate the identification of drug targets for the prevention and treatment of atherosclerosis.

Background: All four dengue serotypes cause infection, with one of them predominantly reported from a particular geographical region. Coinfection by more than one serotype is reported from hyperendemic regions. These coinfections are clinically more severe than infection with a single serotype. This study was carried out to detect the predominant dengue serotype and presence of coinfections., Methods: Acute-phase serum samples of patients suffering from dengue infection were collected. They were screened for the presence of IgM, IgG and NS1Ag by a rapid test. Conventional multiplex reverse transcriptase polymerase chain reaction (RT-PCR) and multiplex real-time RT-PCR assays were carried out for detection and serotyping of the dengue virus., Results: A total of 196 samples were positive by the rapid card test. Of these, 139 were NS1Ag positive, 40 were positive only for IgM, 5 were positive only for IgG and 12 samples were positive for different combinations of antigen and antibodies. All four serotypes were detected in these samples by PCR. DENV-3 was found to be most common circulating serotype. A total of 22 cases were found to have coinfection with more than one dengue serotypes. Samples having only antibodies and no antigen on rapid card test were also positive for virus by PCR., Conclusion: Prevalence of dengue co-infections is increasing. Moreover, it is important to screen for dengue virus in those samples also which do not show NS1Ag on rapid tests and have either one or both the antibodies. Real-time multiplex RT-PCR is found to be more sensitive in detecting coinfection than conventional multiplex RT-PCR., Competing Interests: The authors have none to declare., (© 2021 Director General, Armed Forces Medical Services. Published by Elsevier, a division of RELX India Pvt. Ltd.)

Background: Early case detection is a crucial step in the control of tuberculosis (TB). Sputum smear microscopy is the primary method of TB diagnosis in developing countries. The modified Petroff's method using sodium hydroxide at concentrations ranging between 2% and 4% to digest the specimen is widely used in developing countries. A novel ReaSLR (ReaMetrix's Sputum Liquefying Reagent) methodology has been proposed as a simple, easy, low-cost, and better alternative to conventional methods for sputum processing. This study was undertaken to evaluate the performance of the ReaSLR method of sputum processing in comparison with that of the modified Petroff's method., Methods: Early-morning sputum samples were collected. After preparing a direct smear, each sample was divided into two equal halves and processed by both the methods, i.e., modified Petroff's method and ReaSLR method. Direct smears were graded according to Revised National Tuberculosis Control Program grading, and smears prepared after processing by the two different methods were graded according to Center for Disease Control and Prevention grading. Smear microscopy results were compared taking culture results of samples processed by the modified Petroff's method as the gold standard., Results: The rate of smear positivity with the modified Petroff's method (22.22%) was found to be higher than that with direct smear microscopy (13.56%; p = 0.0002) and the ReaSLR method (17.32%; p = 0.04). The modified Petroff's method was found to be 26.76% more sensitive than direct microscopy and 15.59% more sensitive than the ReaSLR method., Conclusion: The ReaSLR method was not superior to the modified Petroff's method for smear microscopy. Although this method was more sensitive than the direct method in smear microscopy, the modified Petroff's method performed much better than the ReaSLR method., Competing Interests: The authors have none to declare., (© 2020 Director General, Armed Forces Medical Services. Published by Elsevier, a division of RELX India Pvt. Ltd.)

Background: Device-associated infections (DAIs) such as ventilator associated pneumonia (VAP), central line-associated blood stream infection (CLABSI), and catheter-related urinary tract infection (CAUTI) are principal contributors to health hazard and a major preventable threat to patient safety. Robust surveillance of DAI delineates infections, pathogens, resistograms, and facilitates antimicrobial therapy, infection-control, antimicrobial stewardship, and improvement in quality of care., Methods: This prospective outcome surveillance study was conducted amongst 2067 ICU patients in a 1000-bedded teaching hospital. Clinical, laboratory, and environmental surveillance, as well as screening of health care professionals (HCPs) were conducted using the modified US Centers for Disease Control and Prevention-National Healthcare Safety Network definitions and methods. Morbidity, mortality, and health-care indices were analyzed and two-tier infection prevention and control was promulgated., Results: Mean occupancy was 95.34% for 2061 patients of 7381 patients/bed/ICU days. One hundred seventeen episodes of DAI occurred in 1258 patients of 12,882 device-days with mean device utilization ratio of 1.79. Mean rate of DAI was 7.40 per 1000 device days. Multiresistant Pseudomonas aeruginosa was most commonly followed by Acinetobacter. Mean all-cause mortality in ICU was 24.85%, whereas all-cause mortality after DAI was 9.79%. Methicillin-resistant Staphylococcus aureus prevalence was 38.46% amongst health-care professionals., Conclusion: Mean rates of VAP, CLABSI, and CAUTI were 20.69, 2.53, and 2.23 per 1000 device days comparable with Indian and global ICUs. Resolute conviction and sustained momentum in infection prevention and control is an essential step toward patient safety., Competing Interests: The authors have none to declare., (© 2022 Director General, Armed Forces Medical Services. Published by Elsevier, a division of RELX India Pvt. Ltd.)

Background: Hepatitis B (HepB) is an important vaccine preventable infection among healthcare workers (HCWs). Vaccination against Hep B virus, remains the foremost preventive approach. This study aims to measure the antibody titres to Hep B surface antigen (anti-HBs) in a mixed cohort of HCWs. It also aims to study the association between time since vaccination and the anti-HBs titres thus evaluating the duration of seroprotection., Methods: A total of 200 HCWs, including nursing students (n = 112), nursing staff (n = 49), laboratory technicians (n = 30) and doctors (n = 9) who had received all three doses of the Hep B vaccine and met the inclusion criteria of having taken all three doses of vaccine were included in this study. Anti-HBs titres were estimated by bioMérieux mini VIDAS® automated immunoassay based on the principle of enzyme-linked fluorescence assay., Results: Two hundred subjects aged 19 to 52 years were included in the study; mean age was 27.29 ± 0.568 years. Duration since vaccination in the study cohort was ≤ 5 years in 149 (74.5.0%), 6-10 years in 20 (10.0%) and >10 years in 31 (15.5%) subjects. Postvaccination antibody titres were > 100 mIU/ml in 85.0%, 10-100 mIU/ml in 11.0% and ≤ 10 mIU/ml in 3.5%. There was a decline noted in antibody titres as duration after vaccination increased. Increasing age was associated with falling protective titres., Conclusion: The study revealed that majority of the HCWs had adequate anti-HBs titres and were protected after vaccination., Competing Interests: The authors have none to declare., (© 2022 Director General, Armed Forces Medical Services. Published by Elsevier, a division of RELX India Pvt. Ltd.)

Background: Corin is a protease expressed in cardiomyocytes that plays a key role in salt handling and intravascular volume homeostasis via activation of natriuretic peptides. It is unknown if Corin loss-of-function (LOF) is causally associated with risk of coronary artery disease (CAD)., Methods: We analyzed all coding CORIN variants in an Italian case-control study of CAD. We functionally tested all 64 rare missense mutations in Western Blot and Mass Spectroscopy assays for proatrial natriuretic peptide cleavage. An expanded rare variant association analysis for Corin LOF mutations was conducted in whole exome sequencing data from 37 799 CAD cases and 212 184 controls., Results: We observed LOF variants in CORIN in 8 of 1803 (0.4%) CAD cases versus 0 of 1725 controls ( P , 0.007). Of 64 rare missense variants profiled, 21 (33%) demonstrated <30% of wild-type activity and were deemed damaging in the 2 functional assays for Corin activity. In a rare variant association study that aggregated rare LOF and functionally validated damaging missense variants from the Italian study, we observed no association with CAD-21 of 1803 CAD cases versus 12 of 1725 controls with adjusted odds ratio of 1.61 ([95% CI, 0.79-3.29]; P =0.17). In the expanded sequencing dataset, there was no relationship between rare LOF variants with CAD was also observed (odds ratio, 1.15 [95% CI, 0.89-1.49]; P =0.30). Consistent with the genetic analysis, we observed no relationship between circulating Corin concentrations with incident CAD events among 4744 participants of a prospective cohort study-sex-stratified hazard ratio per SD increment of 0.96 ([95% CI, 0.87-1.07], P =0.48)., Conclusions: Functional testing of missense mutations improved the accuracy of rare variant association analysis. Despite compelling pathophysiology and a preliminary observation suggesting association, we observed no relationship between rare damaging variants in CORIN or circulating Corin concentrations with risk of CAD.

Introduction and Background: Both human papillomavirus (HPV) and the human immunodeficiency virus (HIV) are sexually transmitted. High-risk (HR) HPV types are a causal factor in cervical cancer. Persistent HPV infection in this subset of immunocompromised women results in faster disease progression. The study determined the prevalence of HPV genotypes in cervicovaginal secretions of HIV seropositive women and the correlation with CD4 counts and cytology. Method: One hundred, non-pregnant, HIV-positive women of 18 years of age and above were enrolled in this cross-sectional study following approval by the institutional ethical committee. A written consent, questionnaire, followed by sample collection including a Papanicolaou (Pap) smear for cytology was undertaken. Cervicovaginal secretion samples were collected in the Digene ® specimen transport medium (STM) (Qiagen Gaithersburg Inc., MD, USA). HPV genotyping was carried out with PCR amplification of a 65-base pair (bp) fragment in the L1 region of the HPV genome using the short PCR fragment (SPF10) primers followed by reverse hybridization by line probe assay (LPA) using the INNOLiPA HPV Genotyping Extra kit (Fujirebio, Belgium). Quantitation of HPV-16 and-18 viral loads (VLs) was done by real-time PCR. Results of Pap smear cytology were correlated with CD4 counts and HPV-16 and-18 VLs. Results: Mean age of the subjects was 34.9 years ± 7.2 years (median 33.0 years, range 24-60 years). HPV was detected in 62 of 93 (66.6%) samples. Twenty (32.25%) of these 62 samples harbored a single HPV genotype. Multiple genotypes (more than two) were detected in 38 (61.3%) samples. HPV-16 was the commonest genotype detected in 26 (27.9%) of all samples and 41.9% of HPV positive samples. Pap smear cytology was reported for 93 women included in the study. Women who had normal cytology were reported as negative for intraepithelial malignancy or lesion (NILM; n = 62; 71.36%), two women had a high-grade squamous intraepithelial lesion (HSIL), low-grade squamous intraepithelial lesion (LSIL; n = 11), atypical squamous cells of undetermined significance (ASCUS; n = 12). Those smears with inadequate material were reported as scant ( n = 6). The median CD4 count was 363/cu.mm (range 39-787) in HPV-positive women compared to 423/cu.mm (range 141-996) in those HPV-negative women. Quantitation of HPV-16 and-18 VL was done in duplicate for samples positive by PCR reverse hybridization (INNOLiPA). Of these 20 samples (65%), 12 samples were positive by real-time PCR. The normalized HPV-16 VL ranged between 18 and 240,000 copies/cell. The normalized HPV-18 VL in cervical samples ranged between ~24 and 60,000 copies/cell. Conclusion: HIV-positive women may be infected with multiple genotypes other than HPV-16 and-18. This may have implications on the vaccines available currently which target few specific genotypes only. Studies are required to determine the predictive role of HR HPV genotypes, in significant copy numbers especially in HIV seropositive women. It would be clinically relevant if the HPV VLs, cervical cytology, and CD4 counts are considered into cervical cancer screening programs for triage and follow-up of these women., 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 © 2021 Lall, Dar, Bhatla, Kumar, Choudhary, Mathur and Gupta.)

Background: Antibody response to SARS-CoV may be estimated to give trends and patterns emerging in a population during an evolving epidemic. The novel coronavirus has opened a new chapter in the history of pandemics and understanding the disease epidemiology., Methods: The study was a cross-sectional descriptive study. Institutional Ethical clearance and informed consent were taken for participation in the study. The study population included all personnel reporting to the institute for training courses, permanent posting or joining back from leave during the study period of 2 months (16 June to 16 August 2020). The sample size was calculated assuming the prevalence of COVID-19 to be 1% with the absolute precision of 0.5% and 5% level of significance, and finite correction for population size of 500, and the calculated sample size was 377. Inclusion criteria were all personnel reporting to the institute from different states and districts. Exclusion criteria-Any personnel reported for a short visit of lesser than 14 days. Demographic details and details of any likely exposure to a confirmed COVID-19 case were noted. A blood sample was collected, and serological tests were done using ErbaLisa COVID-19 IgG kit by Calbiotech, as per the manufacturer's instructions., Results: Overall seropositivity of IgG COVID-19 antibodies was 7.5% (31/413) (95% CI: 5.3-10.4%). Study population (n = 413) comprised of an adult population in the age range of 21 years-53 years, and the mean age was 31.4 years (SD = 6.2 years)., Conclusion: As the personnel joining the institute have come from various parts of the country the study provides an estimation of antibodies against COVID-19., Competing Interests: The authors have none to declare., (© 2021 Director General, Armed Forces Medical Services. Published by Elsevier, a division of RELX India Pvt. Ltd.)

Competing Interests: The authors have none to declare.

Background: With virtually dried out new antibiotic discovery pipeline, emergence and spread of antimicrobial resistance is a cause for global concern. Colistin, a cyclic polypeptide antibiotic, often regarded as last resort for multi drug resistance gram-negative bacteria, is also rendered ineffective by horizontal transfer of resistance genes. Surveillance of colistin resistance in GNB is essential to ascertain molecular epidemiology., Methods: Whole genome sequencing (WGS) of an unusual colistin resistant urinary isolate of Escherichia coli was performed using Illumina MiSeq platform using 2x250bp V2 chemistry by following the manufactures protocol (Illumina Inc. USA). Multiple web-based bio-informatic tools were utilized to ascertain antibiotic resistant genes., Results: An approximate 5.4 Mb of genome of the urinary isolate AFMC&#95;UC19 was sequenced successfully. Mobile colistin resistance gene (mcr) on the plasmid responsible for horizontal spread was absent in the isolate., Conclusion: Colistin resistance has been reported previously in Klebsiella pneumoniae and it is a rare occurrence in Escherichia coli in Indian setting. Although the isolate lack mcr mediated colistin resistance, emergence and spread of colistin resistant in gram-negative bacteria pose a threat., Competing Interests: The authors have none to declare., (© 2020 Director General, Armed Forces Medical Services. Published by Elsevier, a division of RELX India Pvt. Ltd.)

COVID-19, which is caused by SARS-CoV-2, can result in acute respiratory distress syndrome and multiple organ failure 1-4 , but little is known about its pathophysiology. Here we generated single-cell atlases of 24 lung, 16 kidney, 16 liver and 19 heart autopsy tissue samples and spatial atlases of 14 lung samples from donors who died of COVID-19. Integrated computational analysis uncovered substantial remodelling in the lung epithelial, immune and stromal compartments, with evidence of multiple paths of failed tissue regeneration, including defective alveolar type 2 differentiation and expansion of fibroblasts and putative TP63 + intrapulmonary basal-like progenitor cells. Viral RNAs were enriched in mononuclear phagocytic and endothelial lung cells, which induced specific host programs. Spatial analysis in lung distinguished inflammatory host responses in lung regions with and without viral RNA. Analysis of the other tissue atlases showed transcriptional alterations in multiple cell types in heart tissue from donors with COVID-19, and mapped cell types and genes implicated with disease severity based on COVID-19 genome-wide association studies. Our foundational dataset elucidates the biological effect of severe SARS-CoV-2 infection across the body, a key step towards new treatments.

Background: Currently CD4+ T lymphocyte counts and HIV-1 RNA levels are being utilized to predict outcome of human immunodeficiency virus (HIV) disease. Recently, the role of immune activation in HIV disease progression and response to treatment is being investigated. This study focused on the expression of CD38 and HLA-DR on lymphocyte subsets in various groups of HIV-infected individuals and to determine their association with HIV-1 disease progression., Methods: Ninety-eight cases of patients with HIV/AIDS in different disease stages and twenty-four healthy HIV-negative individuals were included in the cross-sectional study. Their immune function and abnormal immune activation markers (CD38 & HLA-DR) were detected using a flowcytometer, and HIV-1 RNA levels in individuals receiving antiretroviral drugs were estimated., Results: The immune activation marker levels were significantly different between patients with different disease stages (P < 0.001). A significant negative correlation was observed between peripheral blood CD4+ T cell counts and immune activation markers. Also, a significant positive correlation was observed between HIV-1 RNA levels and CD38+CD8+ T lymphocyte., Conclusion: Immune activation markers (CD38 & HLA-DR) increase with disease progression. CD38+ on CD8+ T lymphocyte correlates well with HIV1 RNA levels in individuals failing on antiretroviral therapy., (© 2019 Director General, Armed Forces Medical Services. Published by Elsevier, a division of RELX India Pvt. Ltd.)