Paeniclostridium sordellii causing liver abscess: A rare case report in India.

Paeniclostridium sordellii, an anaerobic bacterium, causes hepatic infections in alcoholics and post-surgery (liver transplantation). While liver and brain abscesses are rare, drainage procedures and targeted antibiotic therapy assisted by early microbiological diagnosis have reduced mortality rates. We report a rare case of pyogenic liver abscess caused by Paeniclostridium sordellii in India, the early diagnosis of which has led to life saving outcome for the patient. Hence, the microbiological diagnosis and comprehensive medical-surgical treatment are vital for preventing mortality in Paeniclostridium sordellii infections.

Quality assurance of SARS-CoV-2 testing laboratories during the pandemic period in India - An experience from a designated provider laboratory.

PURPOSE: Indian Council of Medical Research (ICMR) initiated an Inter-Laboratory Quality Control testing (ILQC) program for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) testing. Under this program, SARS-CoV-2 testing laboratories across the country submit specimens to the assigned State Quality Control (SQCs) laboratories for ILQC testing. This study aimed to investigate the performance of public and private SARS-CoV-2 testing laboratories in Delhi and highlights the country's effort in ramping up testing facility with close monitoring of the quality of Covid-19 testing results. METHODS: In the present study, two-years of SARS-CoV-2 testing data is included. During July 2020 through February 2022, a total of 1791 anonymised specimens were received from 56 public and private laboratories. These specimens were processed by reverse transcriptase - polymerase chain reaction (RT-PCR) tests as per National Institute of Virology (NIV) protocol and the results were uploaded on the ICMR quality control/quality assurance (QC/QA) portal without directly conveying the results to respective participating laboratories. This portal generated a final report stating concordance and intimate results to individual laboratories. RESULTS: Among the 1791 specimens, 25 were rejected and the remaining 1766 were tested. Among these specimens 1691 (95.75%) revealed concordance, and 75 (4.24%) were discordant. A total of 29 laboratories had 100% concordance, 21 laboratories had over 90% concordance and six laboratories had over 80% concordance. CONCLUSIONS: The study demonstrates that the establishment of an inter-laboratory comparison program for SARS-CoV-2 testing helped in monitoring quality of SARS-CoV-2 testing in the country.

Amplicon-Based Nanopore Sequencing of Patients Infected by the SARS-CoV-2 Omicron (B.1.1.529) Variant in India.

We report the sequencing of SARS-CoV-2 Omicron variants from 75 patients, using nanopore long-read sequencing chemistry. These data show a range of mutations in spike glycoprotein that are both unique and common to other populations.

Clinical characteristic and epidemiological features of SARS CoV -2 disease patients from a COVID 19 designated Hospital in New Delhi.

SARS CoV -2 infection is rapidly evolving as a serious global pandemic. The present study describes the clinical characteristics of SARS CoV-2 infection patients. The Samples were subjected to RT - PCR or Rapid Antigen test for diagnosis of SARS CoV- 2. A cohort of 3745 patients with confirmed diagnosis of SARS CoV -2 infection in a tertiary care center in New Delhi, India were included in this study. Data was collected from offline and online medical records over a period of six months. Amongst 3745 SARS CoV -2 infected patients, 2245 (60%) were symptomatic and 1500 (40%) were asymptomatic. Most common presenting symptom was cough (49.3%) followed febrile episodes (47.1%), breathlessness (42.7%) and sore throat (35.1%). Cough along with breathlessness (24.1) was the most common combination of symptoms followed by fever with cough (22.7). The most common comorbidity found among symptomatic group was diabetes (42.5%) followed by hypertension (21.4%) and chronic kidney disease (18%). Comorbidities like diabetes mellitus, chronic diseases of lungs, heart and kidneys were found to be common in symptomatic group and this was found to be statistically significant (p<0.05). COVID-19 is an evolving disease and data from our study help in understanding the clinic-epidemiological profile of patients. This article is protected by copyright. All rights reserved.

Comparison of two real-time polymerase chain reaction assays for the detection of severe acute respiratory syndrome-CoV-2 from combined nasopharyngeal-throat swabs.

CONTEXT: In the absence of effective treatment or vaccine, the current strategy for the prevention of further transmission of severe acute respiratory syndrome (SARS) CoV-2 (COVID-19) infection is early diagnosis and isolation of cases. The diagnosis of SARS-CoV-2 is done by detecting viral RNA in the nasopharyngeal and throat swabs by real-time polymerase chain reaction (PCR). Many commercial assays are now available for performing the PCR assay. AIMS: The aim was to evaluate the performance of the SD Biosensor nCoV real-time detection kit with the real-time PCR kit provided by the Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune (NIV Protocol). SUBJECTS AND METHODS: A total of 253 pairs of nasopharyngeal-oropharyngeal swabs combined in a single viral transport medium were tested for viral RNA by both the protocols. The sensitivity and specificity of the SD Biosensor were calculated considering the ICMR-NIV kit as the gold standard. Matched pairs of recorded cycle threshold values (Ct values) were compared by Pearson's correlation coefficient. RESULTS: Concordant COVID-19 negative and positive PCR results were reported for 113 and 77 samples, respectively. The SD Biosensor kit additionally detected 62 cases, which were found negative by the NIV protocol. In all discordant positive results by the SD Biosensor kit, the average Ct values were higher than the concordant positive results. A total of forty samples tested positive for E gene by SD Biosensor and having Ct values <25 had 100% concordance with NIV protocol results and 39 samples tested positive for E gene by SD Biosensor having Ct value >32 were all found negative by the NIV protocol. CONCLUSIONS: The results highlight the need for careful evaluation of commercial kits before being deployed for screening of COVID-19 infections.

Association of interleukin-2, -4 and -10 with dengue severity.

BACKGROUND: Dengue is an arboviral disease caused by four distinct serotypes of dengue virus. The pathogenesis of dengue is not very clearly understood. Various pro- and anti-inflammatory cytokines are involved in the immune pathogenesis of dengue. Interleukin (IL)-2/IL-2 receptor interaction is supposed to play a protective role, while IL-4 acts as pro-inflammatory whereas IL-10 acts as anti-inflammatory cytokines. So far, not much information is available regarding the established role of these cytokines with dengue infection and severity. AIMS: our study aimed to show the association of IL-2, -4, and -10 with severity of dengue infection. SETTINGS AND DESIGN: This was a cross-sectional study. MATERIALS AND METHODS: The study was conducted in the year 2015; 150 blood samples from suspected dengue cases were confirmed for dengue and then with an equal number of healthy control samples were tested for cytokines levels (IL-2, -4, and -10) by ELISA. Severity of the dengue infection was determined on the basis of clinical manifestations based on the WHO criteria. STATISTICAL ANALYSIS: for statistical analysis, SPSS version 21 (IBM, New York, United States) was used. RESULTS: Out of 150 samples, 56 samples came to be dengue positive. Thirty-eight (67.85%) cases were classified as nonsevere dengue and 18 (32.15%) were severe dengue. The serum levels of IL-4 and -10 were significantly raised in severe dengue cases as compared to nonsevere dengue cases. No significant association was observed between serum IL-2 levels and the severity of dengue. CONCLUSION: IL-4 and -10 levels can be used as marker of severe dengue and help in early preparedness to start the treatment in the line of severe dengue.

Dengue: Lessons of an Outbreak.

INTRODUCTION: Since 1967 there have been many outbreaks of dengue in Delhi. In the year 2015 Delhi has suffered it's one of the worst dengue outbreaks, with more than 15000 dengue confirmed cases and the highest number of deaths (60) in recent years. AIM: To determine the status of Dengue cases as compared to previous six years, the ratio of primary and secondary dengue cases and to review the effectiveness of the one test strategy (either NS1 antigen or IgM antibody) for the confirmation of Dengue. MATERIALS AND METHODS: A cross-sectional study was performed in the year 2015. A total of 7177 serum samples were tested for the confirmation of suspected cases of dengue at our institute. We performed dengue NS1 antigen and dengue IgM antibody ELISA tests for the confirmation of dengue cases in acute and convalescent fever cases respectively. Hundred random samples negative for NS1 antigen were tested for IgM antibody and 100 random samples negative for IgM antibody were tested for NS1 antigen. For determination of ratio of primary and secondary dengue cases, IgG Avidity ELISA was performed on random 76 dengue positive samples. RESULTS: Out of 7177 samples tested, 2358 were positive either by NS1 antigen or for IgM antibody from January to December. Percentage positivity rates for IgM antibody detection and NS1 antigen detection tests were 24.8% (626) and 37.1% (1732) respectively. Out of 100 NS1 negative samples 8 were positive for IgM antibody and out of 100 IgM negative samples 6 were positive for NS1 antigen. Among the 76 samples tested for dengue IgG Avidity ELISA 52 (68.4%) were found to be of secondary dengue. CONCLUSION: Number of dengue cases is constantly rising in Delhi since 2011 and 2014. IgM antibody detection and NS1 antigen detection both the tests should be performed for each patient. Due to the increased prevalence of past infection of dengue, percentage of secondary dengue cases is also increasing in Delhi.

Frequency of nucleotide sequence variations in the internal ribosome entry site region of hepatitis C virus RNA isolated from responding and non-responding patients with hepatitis C virus genotype 3 infection.

Located within 5' untranslated region of HCV RNA is internal ribosome entry site (IRES) which directs cap-independent translation of viral polyprotein. Mutations in IRES sequence have been shown to cause changes in efficiency of protein translation in vitro in few instances. No study has been done to investigate association between frequency of nucleotide sequence variations in IRES region of HCV-3 RNA and response to pegylated interferon-α plus ribavirin therapy. Hence, this study was planned to analyze relationship between frequency of nucleotide sequence variations of HCV-3 IRES region and response to therapy. Twenty-seven HCV-3 patients were studied, of whom 19 responded to therapy and 8 did not. Alanine aminotransferase and aspartate aminotransferase levels were significantly lower in responders compared to non-responders. HCV RNA detection and genotyping was performed by nested-PCR and RFLP respectively. Viral load quantification in pre and post therapy samples was done by real time PCR. The viral load was significantly lower in the patients after treatment as compared to before treatment. HCV IRES region from pre-treatment sera of 27 HCV-3 infected patients was amplified by nested PCR and sequenced. Secondary structure of IRES region of HCV-3 was predicted using the M fold Web Server. Mutational analysis revealed hot spot of mutations in HCV-3 IRES region from 40-80 and 210-280 nucleotides. Though more mutations were found in non-responders as compared to responders, this difference was statistically insignificant. Therefore, in addition to IRES region of HCV-3, some other host and viral factors may contribute to therapy outcome.

Multi Drug Resistant Klebsiella Isolates in Burn Patients: A Comparative Study.

INTRODUCTION: Infections are the most common complications in the burn patients admitted to the hospitals leading to high morbidity and mortality. Klebsiella is one of the most frequently isolated bacteria from burn wounds. MATERIALS AND METHODS: We studied antimicrobial susceptibility patterns of Klebsiella isolates from burn patients. In this cross- sectional study wound swabs from 1294 patients hospitalized in burnward were collected for bacteriological examination. Antibiotic sensitivity testing of Klebsiella isolates was done by modified Stokes disc diffusion method. RESULTS: Out of 883 isolates from 1294 patients 195 were found to be Klebsiella spp. Based on the biochemical properties 153 isolates were Klebsiella pneumoniae, 37 were Klebsiella oxytoca and 5 were others species. In our study we found that 54% of the Klebsiella isolates were multidrug resistant as they were resistant to at least one antibiotic of three or more different groups of antibiotics. [Table: see text]. CONCLUSION: Rate of isolation of Klebsiella as well as its resistance for commonly used antibiotics is increasing over the time.

Use of dried blood blotted on filter paper to detect dengue IgM antibody and dengue NS1 antigen.

A cross sectional study was conducted at the Department of Microbiology, Maulana Azad Medical College, New Delhi, to determine the efficacy of capillary blood samples collected on filter paper compared with serum samples to detect dengue IgM antibody and dengue NS1 antigen. The serum and capillary blood samples were collected from 104 suspected cases of dengue fever at Lok Nayak Hospital, India. The blood eluted from the filter paper and the serum samples were tested for dengue IgM antibody and dengue NS1 antigen by commercial capture ELISA kits. Of the 104 patients, samples from 61 patients tested positive for dengue IgM antibodies with both the serum and filter paper. Samples from 38 patients were negative for both serum and filter paper. Five samples showed discordant results. The filter paper method had sensitivity of 96.8% and specificity of 97.4% for dengue IgM antibody compared to the serum samples. The positive predictive value (PPV) and negative predictive value (NPV) for the filter paper to detect dengue IgM were 95.31% and 95.0%, respectively. The Kappa value (>0.80) showed agreement between the filter paper and serum results for IgM antibody detection. NS1 antigen was detected 28 serum and 28 filter paper samples and was not detected in 72 serum and 72 filter paper samples. Discordant results were seen in 4 samples. The filter paper method had a sensitivity of 96.5% and a specificity of 96.0% compared to the serum for detecting dengue NS1 antigen. The PPV and NPV for the filter paper samples in detecting dengue NS1 antigen were 90.3% and 98.7%, respectively. The Kappa value showed agreement (>0.80) between the serum and filter paper results for detecting dengue NS1 antigen. The results show filter paper samples are a reasonable alternative to serum for detecting dengue infecting.