Metagenomic insights into fungal community composition of the nasopharyngeal region of COVID-19 associated mucormycosis patients from India.

Coronavirus disease 2019 (COVID-19) associated mucormycosis (CAM) was reported predominantly from India during the second wave of COVID-19  and has a high mortality rate. The present study aims to understand the fungal community composition of the nasopharyngeal region of CAM-infected individuals and compare it with severe COVID-19 patients and healthy controls. The fungal community composition was decoded by analyzing the sequence homology of the internal transcribed spacer-2-(ITS-2) region of metagenomic DNA extracted from the upper respiratory samples. The alpha-diversity indices were found to be significantly altered in CAM patients (p < 0.05). Interestingly, a higher abundance of Candida africana, Candida haemuloni, Starmerella floris, and Starmerella lactiscondensi was observed exclusively in CAM patients. The interindividual changes in mycobiome composition were well supported by beta-diversity analysis (p < 0.05). The current study provides insights into the dysbiosis of the nasal mycobiome during CAM infection. In conclusion, our study shows that severe COVID-19 and CAM are associated with alteration in mycobiome as compared to healthy controls. However, the sequential alteration in the fungal flora which ultimately leads to the development of CAM needs to be addressed by future studies.

Utility of an in-house real-time PCR in whole blood samples as a minimally invasive method for early and accurate diagnosis of invasive mould infections.

INTRODUCTION: Invasive mould infections (IMIs) are a leading cause of death in patients with compromised immune systems. Proven invasive mould infection requires detection of a fungus by histopathological analysis of a biopsied specimen, sterile culture, or fungal DNA amplification by PCR in tissue. However, the clinical performance of a PCR assay on blood samples taken from patients suspected of invasive mould disease has not been fully evaluated, particularly for the differential diagnosis of invasive aspergillosis (IA) and invasive Mucormycosis (IM). OBJECTIVES: To assess the diagnostic utility of our previously validated in-house real-time PCR in blood samples for diagnosis of invasive aspergillosis and mucormycosis in patients with suspected invasive mould infection. METHODS: All patients with suspected invasive mould infection were prospectively enrolled from May 2021 to July 2021. Conventional fungal diagnosis was performed using tissue and respiratory samples. In-house PCR was performed on blood samples and its diagnostic performance evaluated. RESULTS: A total of 158 cases of suspected invasive mould infection were enrolled in the study. The sensitivity and specificity of in-house PCR performed on blood samples was found to be 92.5% and 81.4% respectively for diagnosis of probable IA, and 65% and 84.62% respectively for diagnosis of proven and probable IM. It was also able to detect 3 out of 5 cases of possible IM where no other microbiological evidence of IM was obtained. CONCLUSIONS: This assay could be helpful in minimally invasive diagnosis of IMIs for patients in whom invasive sampling is not feasible, especially as a preliminary or screening test. It can help in early diagnosis, anticipating conventional laboratory confirmation by days or weeks. Possible correlation between fungal load and mortality can help in initiating aggressive treatment for patients with high initial fungal load.

Approach towards surveillance-based diagnosis of acute respiratory illness in India: Expert recommendations.

BACKGROUND: Emerging infectious diseases, often zoonotic, demand a collaborative "One-Health" surveillance approach due to human activities. The need for standardized diagnostic and surveillance algorithms is emphasized to address the difficulty in clinical differentiation and curb antimicrobial resistance. OBJECTIVE: The present recommendations are comprehensive diagnostic and surveillance algorithm for ARIs, developed by the Indian Council of Medical Research (ICMR), which aims to enhance early detection and treatment with improved surveillance. This algorithm shall be serving as a blueprint for respiratory infections landscape in the country and early detection of surge of respiratory infections in the country. CONTENT: The ICMR has risen up to the threat of emerging and re-emerging infections. Here, we seek to recommend a structured approach for diagnosing respiratory illnesses. The recommendations emphasize the significance of prioritizing respiratory pathogens based on factors such as the frequency of occurrence (seasonal or geographical), disease severity, ease of diagnosis and public health importance. The proposed surveillance-based diagnostic algorithm for ARI relies on a combination of gold-standard conventional methods, innovative serological and molecular techniques, as well as radiological approaches, which collectively contribute to the detection of various causative agents. The diagnostic part of the integrated algorithm can be dealt at the local microbiology laboratory of the healthcare facility with the few positive and negative specimens shipped to linked viral disease research laboratories (VRDLs) and other ICMR designated laboratories for genome characterisation, cluster identification and identification of novel agents.

Evaluation of kit-based loop-mediated isothermal amplification (TB-LAMP) assay in the diagnosis of tubercular lymphadenitis.

Background: The rapid and accurate diagnosis of tubercular lymphadenitis remains a challenging task today. The World Health Organization (WHO) endorsed the LoopAMP MTBC kit (TB-LAMP) as a replacement for sputum smear microscopy in the diagnosis of pulmonary tuberculosis (PTB). However, no prospective diagnostic accuracy study of TB-LAMP for tubercular lymphadenitis in adults has been performed yet. The current study evaluated the diagnostic performance of TB-LAMP in tubercular lymphadenitis (LNTB). Methods: In a prospective observational study conducted at a tertiary care hospital in India, 90 subjects (age >18 years) suspected of LNTB were recruited consecutively and followed up for 6 months between January 2019 and December 2020. Samples were processed for microscopy, culture, GeneXpert, histopathology and TB-LAMP. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of TB-LAMP against the composite reference standard (CRS) and culture were determined. Results: TB-LAMP showed a sensitivity of 83.78 % (95 % CI, 73.76-90.47) and a specificity of 81.25 % (95 % CI, 56.99-93.41), respectively, against the CRS. The PPV and NPV were 95.38 % (95 % CI, 87.29-98.42) and 52.00 % (95 % CI, 33.50-69.97), respectively. TB-LAMP showed a sensitivity of 88.89 % (95 % CI, 71.94-96.15) and a specificity of 36.17 % (95 % CI, 23.97-50.46), respectively, against culture. The PPV and NPV were 44.44 % (95 % CI, 32-57.62) and 85 % (95 % CI, 63.96-94.76), respectively. Conclusion: TB-LAMP can be used instead of conventional microscopy for the diagnosis of TB in lymph node specimens at primary healthcare centres. It provides rapid and cost-effective diagnosis of LNTB in resource-limited settings due to good sensitivity and NPV.

Subphenotypes of SARS-CoV-2-Associated ARDS Overlap Each Other: A Retrospective Analysis.

Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus-associated pneumonia and acute respiratory distress syndrome (ARDS) were often associated with hyperinflammation and elevation of several serum inflammatory markers but usually less than what is observed in non-coronavirus disease (COVID) ARDS. Elevated inflammatory markers such as C-reactive protein, interleukin (IL)-6, etc., are associated with severe infection. This study identified subphenotypes of COVID-19 ARDS patients by latent profile analysis in a cohort of Indian patients. Methods Data of n = 233 adult Indian patients with laboratory-confirmed SARS-CoV-2 infection admitted to a tertiary care teaching hospital were analyzed in this retrospective study. Only patients with acute respiratory failure (defined by partial pressure of oxygen/fraction of inspired oxygen ratio < 200 mm Hg) and chest X-ray showing bilateral infiltrates were included. Results The patients' mean (standard deviation) age was 53.3 (14.9) years, and 62% were male. A two subphenotypic model was formulated based on the lowest Bayesian information criterion. Neutrophil-to-lymphocyte ratio and serum IL-6 were latent variables in that model (entropy 0.91). The second phenotype (hyperinflammatory) had lower platelet count ( p = 0.02), higher serum creatinine ( p = 0.004), higher C-reactive protein ( p = 0.001), higher ferritin ( p < 0.001), and serum lactate dehydrogenase ( p = 0.009). Age-adjusted hospital mortality ( p = 0.007), duration of hospital stay ( p < 0.001), and duration of intensive care unit stay ( p < 0.001) were significantly higher in the second subphenotype. Conclusion Two distinct but overlapping subphenotypes were identified in SARS-CoV-2-associated respiratory failure. Hyperinflammatory subphenotype was associated with significantly poor short-term outcomes.

Functional and transcriptional heterogeneity within the massively expanding HLADR+CD38+ CD8 T cell population in acute febrile dengue patients.

IMPORTANCE: CD8 T cells play a crucial role in protecting against intracellular pathogens such as viruses by eliminating infected cells and releasing anti-viral cytokines such as interferon gamma (IFNγ). Consequently, there is significant interest in comprehensively characterizing CD8 T cell responses in acute dengue febrile patients. Previous studies, including our own, have demonstrated that a discrete population of CD8 T cells with HLADR+ CD38+ phenotype undergoes massive expansion during the acute febrile phase of natural dengue virus infection. Although about a third of these massively expanding HLADR+ CD38+ CD8 T cells were also CD69high when examined ex vivo, only a small fraction of them produced IFNγ upon in vitro peptide stimulation. Therefore, to better understand such functional diversity of CD8 T cells responding to dengue virus infection, it is important to know the cytokines/chemokines expressed by these peptide-stimulated HLADR+CD38+ CD8 T cells and the transcriptional profiles that distinguish the CD69+IFNγ+, CD69+IFNγ-, and CD69-IFNγ- subsets.

Baroreflex sensitivity is impaired in survivors of mild COVID-19 at 3-6 months of clinical recovery; association with carotid artery stiffness.

The association between the stiffening of barosensitive regions of central arteries and the derangements in baroreflex functions remains unexplored in COVID-19 survivors. Fifty-seven survivors of mild COVID-19 (defined as presence of upper respiratory tract symptoms and/or fever without shortness of breath or hypoxia; SpO2 > 93%), with an age range of 22-66 years (27 females) participated at 3-6 months of recovering from the acute phase of RT-PCR positive COVID-19. Healthy volunteers whose baroreflex sensitivity (BRS) and arterial stiffness data were acquired prior to the onset of the pandemic constituted the control group. BRS was found to be significantly lower in the COVID survivor group for the systolic blood pressure-based sequences (BRSSBP ) [9.78 (7.16-17.74) ms/mmHg vs 16.5 (11.25-23.78) ms/mmHg; p = 0.0253]. The COVID survivor group showed significantly higher carotid ß stiffness index [7.16 (5.75-8.18) vs 5.64 (4.34-6.96); (p = 0.0004)], and pulse wave velocity ß (PWVß ) [5.67 (4.96-6.32) m/s vs 5.12 (4.37-5.41) m/s; p = 0.0002]. BRS quantified by both the sequence and spectral methods showed an inverse correlation with PWVß in the male survivors. Impairment of BRS in the male survivors of mild COVID-19 at 3-6 months of clinical recovery shows association with carotid artery stiffness.

Transfusion trigger in the critically ill with sepsis or septic shock: A prospective study.

Background & objectives: Current practice around transfusion trigger in critically ill sepsis patients is not clear. Moreover, any association of haemoglobin trigger and other transfusion parameters such as age of red blood cells (RBCs) at transfusion and number of units of RBCs transfused with mortality and other adverse outcomes need further assessment. Methods: In this prospective study, patients aged 18-70 yr and admitted to intensive care with a diagnosis of sepsis were included (n=108). Baseline demographic, clinical and laboratory parameters were noted and various transfusion data, i.e., haemoglobin trigger, number of units of RBCs and the age of RBCs were recorded. Following outcome data were collected: 28 and 90 day mortality, duration of mechanical ventilation, vasopressor therapy, intensive care unit (ICU) and hospital stay and requirement of renal replacement therapy. Results: Of the total 108 participants, 78 (72.2%) survived till 28 days and 66 (61.1%) survived till 90 days. Transfusion trigger was 6.9 (6.7-7.1) g/dl [median (interquartile range)]. On multivariable logistic regression analysis, acute physiology and chronic health evaluation (APACHE) II [adjusted odds ratio (aOR) (95% confidence interval {CI}): 0.86 (0.78, 0.96); P=0.005], cumulative fluid balance (CFB) [aOR (95% CI): 0.99 (0.99, 0.99); P=0.005] and admission platelet count [aOR (95% CI): 1.69 (1.01, 2.84); P=0.043] were the predictors of 28 day mortality [model area under the receiver operating characteristics (AUROC) 0.81]. APACHE II [aOR (95% CI): 0.88 (0.81, 0.97); P=0.013], CFB [a OR (95% CI): 0.99977 (0.99962, 0.99993); P=0.044] and transfusion trigger [aOR (95% CI): 3 (1.07, 8.34); P=0.035] were the predictors of 90 day mortality (model AUROC: 0.82). Interpretation & conclusions: In sepsis, patients admitted to the ICU, current practice suggests transfusion trigger is below 7 g/dl and it does not affect any adverse outcome including 28 day mortality.

Utility of in-house and commercial PCR assay in diagnosis of Covid-19 associated mucormycoss in an emergency setting in a tertiary care center.

Introduction. Invasive mucormycosis (IM) is a potentially fatal infection caused by fungi of the order Mucorales. Histopathology, culture, and radiology are the mainstays of diagnosis, but they are not sufficiently sensitive, resulting in delayed diagnosis and intervention. Recent studies have shown that PCR-based techniques can be a promising way to diagnose IM.Hypothesis/Gap Statement. Early diagnosis of fungal infections using molecular diagnostic techniques can improve patient outcomes, especially in invasive mucormycosis.Aim. The aim of this study was to evaluate the utility of our in-house mould-specific real time PCR assay (qPCR) in comparison with the commercially available real time PCR (MucorGenius PCR), for the early diagnosis of mucormycosis in tissue samples from patients with suspicion of invasive mucormycosis (IM). This in-house assay can detect and distinguish three clinically relevant mould species, e.g. Aspergillus spp., Mucorales and Fusarium spp. in a single reaction with only one pair of primers, without the need for sequencing.Methodology. We enrolled 313 tissue samples from 193 patients with suspected IM in this prospective study. All cases were classified using EORTC/MSGERC guidelines. All samples were tested using traditional methods, in-house qPCR, and MucorGenius PCR.Results. Using direct microscopy as a gold standard, the overall sensitivity and specificity of in-house qPCR for detection of IM was 92.46% and 80% respectively, while that of the MucorGenius PCR was 66.67% and 90% respectively. However, co-infection of IM and IA adversely affected the performance of MucorGenius PCR in detection of IM.The in-house PCR detected Aspergillus spp. in 14 cases and Fusarium spp. in 4 cases which showed clinical and radiological features of fungal sinusitis. The in-house qPCR also performed better in detecting possible cases of IM. This aids early diagnosis and appropriate treatment to improve patient outcomes.Conclusion. Because the in-house PCR is not only sensitive and specific, but also entirely based on SYBR Green for detection of targets, it is less expensive than probe-based assays and can be used on a regular basis for the diagnosis of IM in resource-constrained settings. It can be used to distinguish between mucormycosis and fungal sinusitis caused by Aspergillus and Fusarium in high-risk patients, as well as to accurately detect Mucorales in fungal co-infection cases.

Th17 overexpression in severe COVID-19: a prospective observational study.

INTRODUCTION: The objective of the study was to determine T-cell subtypes, Natural Killer cell activity and cytokines in COVID-19 patients with mild to moderate disease and compare them between patients who had recovered and those who had progressed to severe disease. METHODS: Peripheral blood samples of COVID-19 patients were collected at the time of hospital admission and after one week. These samples were analysed for interleukins (IL-6, IL-17a) using chemiluminescence ELISA. The T-cell subsets (T naïve, T regulatory, Th17, Th1, Th2, CD8+ T cells] were studied using flow cytometry. Mild, moderate and severe COVID-19 are defined as per CDC guidelines. RESULTS: Nineteen COVID-19-positive patients were enrolled between June 2020 to December 2021. Nine had mild COVID-19 and 10 had moderate COVID-19 at recruitment. All mild cases recovered without progression to severe disease, while five patients from the moderate group progressed to severe disease. Overall, there is a decrease in lymphocyte count in patients with moderate-severe disease, but the ratio of Th17 [5.91 (2.69-12.01)] was higher compared to Th1 [1.12 (0.27-3.13)] and Th2[2.34 (2-3.5)]. The high baseline level of IL-6 observed in patients with moderate disease leads to the proliferation of more Th17 type of CD4+ T-cells(p=0.002) and suppression of Treg cells. A higher Th17 subset leads to neutrophilic inflammation in patients with severe COVID-19. CONCLUSION: Interpretation conclusions: Higher baseline IL-6 leads to depletion of regulatory T-cells, Th1 Th2 CD4 cells. IL-6 leads to the proliferation of Th17 type of CD4+ subsets in moderate COVID-19. Higher Th17 cells in moderate COVID-19 patients lead to the production of IL-17a, which may result in intense neutrophilic inflammatory response and cytokine storm.

An evaluation of Composite Reference Standard (CRS) for diagnosis of Female Genital Tuberculosis.

BACKGROUND: Female genital tuberculosis (FGTB) is a common cause of infertility in developing countries. Its diagnosis is difficult due to its paucibacillary nature, with no single test having high sensitivity and specificity. This study is to share the experience of using Composite Reference Standard (CRS) for the diagnosis of FGTB. METHODS: This is a prospective study conducted between September 2017 to June 2019, over 100 infertile females found to have FGTB on composite reference standard which consisted of acid-fast bacilli on microscopy or culture, histopathological evidence of epithelioid granuloma, positive gene Xpert on endometrial sample or definite or probable finding of FGTB on laparoscopy. RESULTS: A total of 100 infertile women (78% primary, 22% secondary) found to have FGTB on CRS were enrolled in this study. Mean age, body mass index, parity and duration of infertility were 28.2 years, 23.17 kg/m2, 0.24 ± 0.12 and 2.41 years respectively. Various symptoms were scanty menses (16%), irregular cycle (7%), dysmenorrhea (11%), pelvic pain (11%). Various signs were vaginal discharge (65%), adnexal mass (6%), tubo-ovarian mass on ultrasound (15%), abnormal hysterosalpingography findings (57.14%), positive polymerase chain reaction test (65%) and abnormal hysteroscopy (82.2%). The positive findings on CRS were positive AFB on microscopy or culture (3%), positive gene Xpert (28%) (done in some cases), epithelioid granuloma on histopathology (13%), definite findings on laparoscopy like tubercles, caseous nodules and beaded tubes in (57.19%) patients while probable findings of FGTB like straw colored fluid in POD, extensive dense pelvic, peri-tubal, peri-ovarian adhesions; hydrosalpinx; tubo-ovarian mass; thick fibrosed tubes; mid tubal block; peri hepatic adhesions (Fitz Hugh Curtis Syndrome); hyperemia of tubes/blue uterus on chromotubation were seen in (48.8%) patients. All patients found to be positive on CRS were given 6 months of anti-tubercular therapy. CONCLUSION: This study demonstrates the high reliability of use of composite reference standard for diagnosis of FGTB.

Acanthamoeba meningoencephalitis causing secondary hemophagocytic lymphohistiocytosis in an immunocompetent patient: A first case report.

Acanthamoeba is a rare cause of granulomatous amoebic encephalitis (GAE) associated with high mortality. There have been few case reports of Acanthamoeba meningoencephalitis worldwide. Hemophagocytic lymphohistiocytosis (HLH) is a severe hyperinflammatory condition caused by abnormally active macrophages and cytotoxic T lymphocytes; its secondary form is due to infections or malignancies. However, HLH is rather an unknown complication of GAE. We describe an unusual and previously unreported case of Acanthamoeba meningoencephalitis in a young immunocompetent female culminating in secondary HLH.

Cryptococcal antigenemia in people living with HIV and AIDS.

AIM: To assess the prevalence of cryptococcal antigenemia among people living with HIV/AIDS (PLHA) with CD4 ≤100/mm3. DESIGN: This observational study was performed on PLHA with laboratory-confirmed CD4 ≤100/mm3. All PLHA were recruited irrespective of their duration of HIV diagnosis, antiretroviral therapy (ART) naïve, or ART failure. METHODS: The prevalence of cryptococcal antigen (CrAg) was assessed in 102 PLHA, with CD4 ≤100/mm3, using a latex agglutination test on serum samples. All the subjects were followed up for 3 months. RESULTS: Amongst 102 PLHA, 62 (60.8%) and 40 (39.2%) patients were ART-naïve and ART failures, respectively, with 2.9% (n = 3) having clinical features of meningitis and 6.8% (n = 7) patients being asymptomatic CrAg-positive. At the 3 month follow-up, total mortality was 10.8%, of which 33.3% and 8.8% were among CrAg-positive and negative patients (p = 0.05). Mortality in asymptomatic and meningitis symptomatic CrAg-positive patients was 1.03% (n = 1) and 2.06% (n = 2), respectively. Of note, five patients were lost to follow-up. CONCLUSION: Cryptococcal antigenemia is common among patients with CD4 ≤100/mm3 who were either ART naïve or had treatment failure. Asymptomatic patients who underwent pre-emptive therapy demonstrated good clinical outcomes.

A study on the morbid histopathological changes in COVID-19 patients with or without comorbidities using minimally invasive tissue sampling.

COVID-19 causes morbid pathological changes in different organs including lungs, kidneys, liver, and so on, especially in those who succumb. Though clinical outcomes in those with comorbidities are known to be different from those without-not much is known about the differences at the histopathological level. To compare the morbid histopathological changes in COVID-19 patients between those who were immunocompromised (Gr 1), had a malignancy (Gr 2), or had cardiometabolic conditions (hypertension, diabetes, or coronary artery disease) (Gr 3), postmortem tissue sampling (minimally invasive tissue sampling [MITS]) was done from the lungs, kidney, heart, and liver using a biopsy gun within 2 hours of death. Routine (hematoxylin and eosin) and special staining (acid fast bacilli, silver methanamine, periodic acid schiff) was done besides immunohistochemistry. A total of 100 patients underwent MITS and data of 92 patients were included (immunocompromised: 27, malignancy: 18, cardiometabolic conditions: 71). In lung histopathology, capillary congestion was more in those with malignancy, while others like diffuse alveolar damage, microthrombi, pneumocyte hyperplasia, and so on, were equally distributed. In liver histopathology, architectural distortion was significantly different in immunocompromised; while steatosis, portal inflammation, Kupffer cell hypertrophy, and confluent necrosis were equally distributed. There was a trend towards higher acute tubular injury in those with cardiometabolic conditions as compared to the other groups. No significant histopathological difference in the heart was discerned. Certain histopathological features were markedly different in different groups (Gr 1, 2, and 3) of COVID-19 patients with fatal outcomes.

Chronic active Epstein-Barr virus infection mimicking tuberculosis - A diagnostic enigma.

ABSTRACT: Chronic active EBV infection is a rare disorder prone for misdiagnosis. They present with a wide range of symptoms from indolent to aggressive clinical course. Clinico-pathological correlation with confirmation by ancillary techniques is inevitable to diagnose this disease. We present a case of a 29-year-old male with fever, weight loss, and lymphadenopathy for 6 months. Lymph node biopsy showed occasional granuloma with preserved architecture. Suspected to have tuberculosis, he received antitubercular treatment (ATT) with no response for 3 months. Subsequently, additional workup showed many EBV-positive cells in sinusoids with high serum EBV titer, confirming the difficult diagnosis of CAEBV. The present case highlights the difficulty in the diagnosis of this entity and also emphasizes the necessity to recognize this disorder in countries endemic for tuberculosis, as it is no longer bound by ethnicity and geographical boundaries.

Seroprevalence of Strongyloides infection among steroid recipients in a tertiary care centre in North India.

Background: Strongyloides stercoralis (S. stercoralis), a unique parasite, can cause mortal disease even years after the exposure. Iatrogenic use of steroids can complicate asymptomatic infections to a life-threatening hyperinfection and/or disseminated infection. Data regarding seroprevalence of strongyloidiasis remains scarce and this knowledge gap needs due attention in many endemic countries including India. Aim: The present study is aimed at assessing the seroprevalence of Strongyloides infection and the need for routine screening among individuals receiving steroid therapy. Methodology: Eighty patients receiving steroid therapy and thirty healthy volunteers who had not received any immunosuppressive drugs and/or anthelminthic therapy in last six months were enrolled as cases and controls respectively and they were screened by Strongyloides IgG ELISA. Results: Among the 80 patients on steroids, the mean cumulative prednisolone equivalent dose received was 8.2 g (±11.2 g) for a mean duration of 184 days, 16 patients (20%, 95% CI 11.9-30) had a positive Strongyloides IgG serology. Only 4 controls (4/30, 13.3%, CI 3.8-30.7) tested positive (p=0.4). Conclusions: Our study demonstrated a Strongyloides seroprevalence of 20% in the study population emphasizing the need for screening for Strongyloides infection prior to immunosuppressive therapy in order to prevent hyperinfection or possible dissemination.