Early transcriptomic host response signatures in the serum of dengue patients provides insights into clinical pathogenesis and disease severity.

Dengue virus (DENV), known to cause viral infection, belongs to the family Flaviviridae, having four serotypes (DENV1-4) that spreads by the bite of the Aedes aegypti mosquito. India has been suffering from dengue outbreaks annually with widespread epidemics by prevalence of all the four DENV serotypes. The diverse spectrum of clinical manifestations in dengue infection, mild to severe forms, makes the need of timely diagnosis and prompt treatment an essence. The identification of a dengue host response signature in serum can increase the understanding of dengue pathogenesis since most dengue NS1 Ag tests have been developed and evaluated in serum samples. Here, to understand the same, we undertook a dual RNA-sequencing (RNA-Seq) based approach from the serum samples of dengue-infected patients. The results thus yield the early transcriptional signatures that discriminated the high viral reads patients from patients who had low dengue viral reads. We identified a significant upregulation of two sets of genes, key antiviral (IFIT3, RSAD2, SAT1) and vascular dysfunction (TNFS10, CXCL8) related genes in the high viral reads group. Deeper delving of this gene profile revealed a unique two-way response, where the antiviral genes can mediate the disease course to mild, contrarily the increased expression of the other gene set might act as pointers of severe disease course. Further, we explored the hematologic parameters from the complete blood count (CBC), which suggests that lymphocytes (low) and neutrophils (high) might serve as an early predictor of prognosis in dengue infection. Collectively, our findings give insights into the foundation for further investigation of the early host response using the RNA isolated from dengue patients' serum samples and opens the door for careful monitoring of the early clinical and transcriptome profiles for management of the dengue patients.

Epidemiological, clinical and genetic characterization of scrub typhus in patients presenting with acute febrile illness in New Delhi.

PURPOSE: Scrub typhus (ST) is a zoonotic disease, caused by O. tsutsugamushi is a major cause of acute febrile illness (AFI) in India. There is a need to study the prevalence and risk factors in various regions of India. METHODS: A study to estimate the prevalence and study the risk factors of ST in patients presenting with acute febrile illness (AFI) was performed. All patients underwent serology for IgM antibodies to Orientia tsutsugamushi (In Bios International Inc, Seattle, WA) as per the manufacturers' protocol. Following this, Polymerase Chain reaction (PCR) (real time SYBR green based targeting groEL gene and conventional PCR targeting 56 â€‹kDa type specific antigen gene) was performed from stored serum samples. RESULTS: During the study period, 473 patients were admitted. Of these 56 (11.8%) patients were ST positive by IgM serology. The conventional PCR targeting 56 â€‹kDa type specific antigen gene of O. tsutsugamushi was positive in six patients while Ot groEL SYBR green based PCR) was positive in five. PCR was positive in patients who had demonstrated a higher OD value in ELISA. Conventional PCR positive amplicons were sent for Sanger sequencing and confirmed to be O. tsutsugamushi. The mean age of the patients was 49 â€‹± â€‹18.3 years and males constituted a higher number of patients (67.9%, n â€‹= â€‹38). The pathognomonic eschar was present in 7 (12.5%) patients. Phylogenetic analysis revealed that sequences clustered close to Kato-like Hualein-20 strain and Karp-like Linh DT strains. All patients were administered doxycycline in our study. Mortality was recorded in 8.9% of the patients. CONCLUSIONS: In patients presenting with acute febrile illness, ST should be considered as a differential diagnosis, especially in post-monsoon season. Along with serology, serum can also be used as sample for PCR in an intracellular bacterium like O. tsutsugamushi.

Secondary infections modify the overall course of hospitalized patients with COVID-19: a retrospective study from a network of hospitals across North India.

Objective: To gain better insight into the extent of secondary bacterial and fungal infections in hospitalized patients in India, and to assess how these alter the course of coronavirus disease 2019 (COVID-19) so that control measures can be suggested. Methods: In this retrospective, multicentre study, the data of all patients who tested positive for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) on reverse transcriptase polymerase chain reaction (RT-PCR), admitted to hospital between March 2020 and July 2021, were accessed from the electronic health records of a network of 10 hospitals across five states in North India. Results: Of 19,852 patients testing positive for SARS-CoV-2 on RT-PCR and admitted to the study hospitals during the study period, 1940 (9.8%) patients developed secondary infections (SIs). Patients with SIs were, on average, 8 years older than patients without SIs (median age 62.6 vs 54.3 years; P<0.001). The risk of SIs was significantly (P<0.001) associated with age, severity of disease at admission, diabetes, admission to the intensive care unit (ICU), and ventilator use. The most common site of infection was urine (41.7%), followed by blood (30.8%) and sputum/bronchoalveolar lavage/endotracheal fluid (24.8%); the least common was pus/wound discharge (2.6%). Gram-negative bacilli (GNB) were the most common organisms (63.2%), followed by Gram-positive cocci (GPC) (19.6%) and fungi (17.3%). Most patients with SIs were on multiple antimicrobials. The most commonly used antibiotics against GNB were beta-lactam/beta-lactamase inhibitors (76.9%), carbapenems (57.7%), cephalosporins (53.9%), and antibiotics against carbapenem-resistant Enterobacteriaceae (47.1%). Empirical use of antibiotics against GPC was seen in 58.9% of patients with SIs, and empirical use of antifungals was observed in 56.9% of patients with SIs. The average length of hospital stay for patients with SIs was almost twice as long as that of patients without SIs (median 13 vs 7 days). Overall mortality among patients with SIs (40.3%) was more than eight times higher than that among patients without SIs (4.6%). Only 1.2% of patients with SIs with mild COVID-19 at admission died, compared with 17.5% of those with moderate COVID-19 at admission and 58.5% of those with severe COVID-19 at admission (P<0.001). The mortality rate was highest in patients with bloodstream infections (49.8%), followed by those with hospital-acquired pneumonia (47.9%), urinary tract infections (29.4%), and skin and soft tissue infections (29.4%). The mortality rate in patients with diabetes with SIs was 45.2%, compared with 34.3% in those without diabetes (P<0.001). Conclusions: SIs complicate the course of patients hospitalized with COVID-19. These patients tend to have a much longer hospital stay, a higher requirement for oxygen and ICU care, and a significantly higher mortality rate compared with those without SIs. The groups most vulnerable to SIs are patients with more severe COVID-19, elderly patients and patients with diabetes. Judicious empirical use of combination antimicrobials in these groups of vulnerable patients can save lives. It is desirable to have region- or country-specific guidelines for appropriate use of antibiotics and antifungals to prevent their overuse.

High failure rate of ChAdOx1-nCoV19 immunization against asymptomatic infection in healthcare workers during a Delta variant surge.

Immunization is expected to confer protection against infection and severe disease for vaccines while reducing risks to unimmunized populations by inhibiting transmission. Here, based on serial serological studies of an observational cohort of healthcare workers, we show that during a Severe Acute Respiratory Syndrome -Coronavirus 2 Delta-variant outbreak in Delhi, 25.3% (95% Confidence Interval 16.9-35.2) of previously uninfected, ChAdOx1-nCoV19 double vaccinated, healthcare workers were infected within less than two months, based on serology. Induction of anti-spike response was similar between groups with breakthrough infection (541 U/ml, Inter Quartile Range 374) and without (342 U/ml, Inter Quartile Range 497), as was the induction of neutralization activity to wildtype. This was not vaccine failure since vaccine effectiveness estimate based on infection rates in an unvaccinated cohort were about 70% and most infections were asymptomatic. We find that while ChAdOx1-nCoV19 vaccination remains effective in preventing severe infections, it is unlikely to be completely able to block transmission and provide herd immunity.

COVID-19 Risk Stratification and Mortality Prediction in Hospitalized Indian Patients: Harnessing clinical data for public health benefits.

The variability of clinical course and prognosis of COVID-19 highlights the necessity of patient sub-group risk stratification based on clinical data. In this study, clinical data from a cohort of Indian COVID-19 hospitalized patients is used to develop risk stratification and mortality prediction models. We analyzed a set of 70 clinical parameters including physiological and hematological for developing machine learning models to identify biomarkers. We also compared the Indian and Wuhan cohort, and analyzed the role of steroids. A bootstrap averaged ensemble of Bayesian networks was also learned to construct an explainable model for discovering actionable influences on mortality and days to outcome. We discovered blood parameters, diabetes, co-morbidity and SpO2 levels as important risk stratification features, whereas mortality prediction is dependent only on blood parameters. XGboost and logistic regression model yielded the best performance on risk stratification and mortality prediction, respectively (AUC score 0.83, AUC score 0.92). Blood coagulation parameters (ferritin, D-Dimer and INR), immune and inflammation parameters IL6, LDH and Neutrophil (%) are common features for both risk and mortality prediction. Compared with Wuhan patients, Indian patients with extreme blood parameters indicated higher survival rate. Analyses of medications suggest that a higher proportion of survivors and mild patients who were administered steroids had extreme neutrophil and lymphocyte percentages. The ensemble averaged Bayesian network structure revealed serum ferritin to be the most important predictor for mortality and Vitamin D to influence severity independent of days to outcome. The findings are important for effective triage during strains on healthcare infrastructure.

Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations?

Vaccine development against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been of primary importance to contain the ongoing global pandemic. However, studies have demonstrated that vaccine effectiveness is reduced and the immune response is evaded by variants of concern (VOCs), which include Alpha, Beta, Delta, and, the most recent, Omicron. Subsequently, several vaccine breakthrough (VBT) infections have been reported among healthcare workers (HCWs) due to their prolonged exposure to viruses at healthcare facilities. We conducted a clinico-genomic study of ChAdOx1 (Covishield) VBT cases in HCWs after complete vaccination. Based on the clinical data analysis, most of the cases were categorized as mild, with minimal healthcare support requirements. These patients were divided into two sub-phenotypes based on symptoms: mild and mild plus. Statistical analysis showed a significant correlation of specific clinical parameters with VBT sub-phenotypes. Viral genomic sequence analysis of VBT cases revealed a spectrum of high- and low-frequency mutations. More in-depth analysis revealed the presence of low-frequency mutations within the functionally important regions of SARS-CoV-2 genomes. Emphasizing the potential benefits of surveillance, low-frequency mutations, D144H in the N gene and D138Y in the S gene, were observed to potentially alter the protein secondary structure with possible influence on viral characteristics. Substantiated by the literature, our study highlights the importance of integrative analysis of pathogen genomic and clinical data to offer insights into low-frequency mutations that could be a modulator of VBT infections.

Respiratory Co-Infections: Modulators of SARS-CoV-2 Patients' Clinical Sub-Phenotype.

Co-infection with ancillary pathogens is a significant modulator of morbidity and mortality in infectious diseases. There have been limited reports of co-infections accompanying SARS-CoV-2 infections, albeit lacking India specific study. The present study has made an effort toward elucidating the prevalence, diversity and characterization of co-infecting respiratory pathogens in the nasopharyngeal tract of SARS-CoV-2 positive patients. Two complementary metagenomics based sequencing approaches, Respiratory Virus Oligo Panel (RVOP) and Holo-seq, were utilized for unbiased detection of co-infecting viruses and bacteria. The limited SARS-CoV-2 clade diversity along with differential clinical phenotype seems to be partially explained by the observed spectrum of co-infections. We found a total of 43 bacteria and 29 viruses amongst the patients, with 18 viruses commonly captured by both the approaches. In addition to SARS-CoV-2, Human Mastadenovirus, known to cause respiratory distress, was present in a majority of the samples. We also found significant differences of bacterial reads based on clinical phenotype. Of all the bacterial species identified, ∼60% have been known to be involved in respiratory distress. Among the co-pathogens present in our sample cohort, anaerobic bacteria accounted for a preponderance of bacterial diversity with possible role in respiratory distress. Clostridium botulinum, Bacillus cereus and Halomonas sp. are anaerobes found abundantly across the samples. Our findings highlight the significance of metagenomics based diagnosis and detection of SARS-CoV-2 and other respiratory co-infections in the current pandemic to enable efficient treatment administration and better clinical management. To our knowledge this is the first study from India with a focus on the role of co-infections in SARS-CoV-2 clinical sub-phenotype.

FilmArray® meningitis/encephalitis (ME) panel, a rapid molecular platform for diagnosis of CNS infections in a tertiary care hospital in North India: one-and-half-year review.

BACKGROUND: Acute meningitis and encephalitis (AME) is a syndrome of central nervous system (CNS) infections, which could lead to neurological damage and fatality. This study evaluates the multiplex FilmArray® ME Panel which is aimed to diagnose agents causing suspect CNS infections in north India. METHODS: A total number of 969 cerebrospinal fluid (CSF) samples collected between August 2016 and January 2018 from patients who showed clinical symptoms of CNS infections were analyzed using the FilmArray® ME Panel. Also a comparison of molecular diagnosis and various laboratory and radiological findings for Streptococcus pneumoniae, Enterovirus and Cryptococcus neoformans positive cases was done. RESULT: Out of the 969 CSF samples, 101 cases were found to be positive for viral (n = 55), bacterial (n = 38), fungal (n = 7), and poly-microbial (n = 1) agents. Out of the 55 viral positive cases, the most detected pathogen was Enterovirus (n = 23) with predominance in the age group of 2-17 years, followed by Varicella Zoster virus (n = 14) and HSV1(n = 9) cases. Streptococcus pneumoniae (n = 26) was found to be the predominant bacterial pathogen, of which 17 were detected in the age group above 35 years. Cryptococcus neoformans was found in 7 cases. CONCLUSION: The FilmArray® ME Panel aids in rapid detection of 14 pathogens directly from CSF. When compared to gram stain, culture, antigen detection, and CSF biochemical analysis, the FilmArray® ME Panel has detected more cases, some of which are difficult to diagnose by conventional methods. This rapid technology will help the clinicians in case of early patient management, outcomes and provide aid in antimicrobial stewardship.

Evaluation of mean monocyte volume in septicemia caused by Salmonella species.

OBJECTIVE: The objective was to study the significance of volume, conductivity, and scatter (VCS) parameters of monocytes in Salmonella infection. MATERIALS AND METHODS: We selected peripheral blood samples of 52 patients whose blood culture was positive for Salmonella species (Salmonella typhi and Salmonella paratyphi A) and analyzed VCS parameters by subjecting them to differential count in hematology analyzer LH750 (Beckman Coulter). Out of these, we studied VCS parameters of monocytes in Salmonella infection and compared with two control groups (control 1: other infections and control 2: normal subjects). RESULTS: Mean monocyte volume (MMV), standard deviation (SD) of MMV, and SD of mean channel monocyte conductivity were found to be significantly increased in Salmonella infection (P < 0.05) when compared with both controls. We propose a cutoff value of 185 for MMV with sensitivity and specificity of 80% and 73%, respectively, to predict Salmonella infection. CONCLUSIONS: MMV can be a useful tool for predicting Salmonella infection under appropriate clinical settings.

Paired blood cultures increase the sensitivity for detecting pathogens in both inpatients and outpatients.

The objective of this study was to show the differences between paired blood cultures (PBC) versus single blood cultures (SBC) in the microbiologic yield, the sensitivity to detect pathogens and the time to positivity (TTP). We performed a retrospective study examining 112,570 blood culture samples over a 5-year period from July 2011 to May 2016 in the BacT/ALERT® 3D automated blood culture system (bioMérieux, Marcy l'Etoile, France). Bacteria and yeasts were identified using the VITEK® 2 Compact system (bioMérieux, Marcy l'Etoile, France). True-positives and contaminated bottles were defined and analysed separately. We analysed TTP and adherence to blood volume guidelines for a convenience sample of 510 and 999 sequential positive cultures, respectively. Out of 49,438 PBC samples, 5810 (11.7%) were positive. In 63,132 SBC samples, 4552 (7.2%) were positive (p < 0.0001). In PBC, 5371 (10.9%) were true-positives and 439 (0.9%) contaminants. In SBC, 4095 (6.5%) were true-positives and 457 (0.7%) contaminants. In the inpatient departments (IPD), the most common isolate was Escherichia coli (n = 1373), followed by Klebsiella pneumoniae (n = 1206), whereas in the outpatient departments (OPD), the most common isolates were Salmonella typhi (n = 612) and S. paratyphi A (n = 278). In the analysis of TTP, 98% grew within 72 h, 91% within 48 h and 89% within 36 h. In the blood volume analysis, 90% of the cultures had optimal blood volume. A significantly higher positivity rate was seen in PBC compared with SBC. Our study adds to the increasing evidence of improved microbial yield of clinically significant bacteria and fungi by performing PBC instead of SBC and adhering to blood volume collection guidelines.

Recurrent Challenges for Clinicians: Emergence of Methicillin-Resistant Staphylococcus aureus, Vancomycin Resistance, and Current Treatment Options.

Gram-positive pathogens mainly, Staphylococcus aureus, Enterococcus and coagulase-negative Staphylococcus, are developing increasing resistance to glycopeptides that pose a problem in treating infections caused by these pathogens. Vancomycin is the treatment of choice in treating methicillin-resistant S. aureus (MRSA). Community-acquired MRSA is associated with infections in patients without recent history of hospital admission and without the classical risk factors for MRSA carriage (including healthcare personnel). MRSA poses new threats and challenges beyond the hospital with the emergence of community-acquired MRSA. Indiscriminate use of vancomycin leads to the emergence and spread of vancomycin resistance in multidrug resistant strains is of growing concern in the recent years. Minimum Inhibitory concentration (MIC) remains an important determinant in choosing the right antibiotics. Infections caused by MRSA strains with vancomycin MIC > 4 µg/mL leads to the vancomycin treatment failure. The Clinical Laboratory Standards Institute had also lowered the cut-off susceptibility and resistance breakpoints for vancomycin. Despite the availability of newer antimicrobial agents (Linezolid, Daptomycin, Tigecycline) for drug-resistant Gram-positive pathogens, clinicians and patients still need options for treatment of MRSA infection. There is a need to reduce the global burden of infections caused by Gram-positive pathogens and its resistant strains (mainly MRSA). Continuous efforts should be made to prevent the spread and the emergence of glycopeptide resistance by early detection of the resistant strains and using the proper infection control measures in the hospital setting.

Medical tourism in India.

The term 'medical tourism' is under debate because health care is a serious business and rarely do patients combine the two. India is uniquely placed by virtue of its skilled manpower, common language, diverse medical conditions that doctors deal with, the volume of patients, and a large nonresident Indian population overseas. Medical tourism requires dedicated services to alleviate the anxiety of foreign patients. These include translation, currency conversion, travel, visa, posttreatment care system,and accommodation of patient relatives during and after treatment.

Cervical ectopic thymic cyst: a rare preoperative diagnosis.

We present a case of a 5-year-old child with a painless swelling on the neck. Imaging revealed a multilocular cystic lesion lying in close proximity to carotid vessels. Based on imaging a possibility of ectopic thymic cyst was considered, which was confirmed on histopathology. Ectopic cervical cyst is an infrequent cause of neck cyst in a child which is rarely diagnosed preoperatively.

Juvenile psammomatoid ossifying fibroma: a rare cause of unilateral proptosis.

This is case of a young girl who presented with unilateral proptosis. Imaging (CT & MRI) revealed an expansile lytic bony tumour involving the left frontal bone and orbital roof. The globe was displaced but uninvolved. Complete surgical resection was done and histopathology revealed psammomatoid bodies diagnostic of juvenile psammomatoid ossifying fibroma (JPOF). JPOF is a rare bone tumour characterised by a predilection for the sino-nasal tract and orbit, a tendency to affect younger patients, a potential for aggressive growth and a high recurrence rate of 30-50%. It warrants a complete surgical resection to avoid recurrence.

Salivary flow rate in patients with schizophrenia on clozapine.

AIMS: To assess the change in salivary flow rate in patients with schizophrenia on clozapine and whether the change in salivary flow rate was dose related. METHODS: Twenty male inpatients with a diagnosis of schizophrenia according to the International Statistical Classification of Diseases, 10th Revision diagnostic criteria for research who were started on clozapine were recruited for the study. Unstimulated salivary flow rate was assessed at baseline and then weekly for 4 weeks using cotton swab method in 17 patients. RESULTS: Repeated-measures analysis of variance showed a significant increase in salivary flow rate over time (F [2.37/37.94] = 3.134, P = 0.047, Greenhouse-Geisser correction, eta = 0.16). Also, there was a significant increase in salivary flow rate between weeks 2 and 3 (P < 0.05). There was no correlation between salivary flow rate and mean clozapine dose. CONCLUSIONS: There was a significant increase in salivary flow rate from baseline after starting clozapine, with a significant increase from the second to the third week followed by a "plateau."