Cut-off Ct value of GeneXpert in comparison to gold standard RT-PCR for diagnosis of SARS-CoV-2: A retrospective study

<strong>BACKGROUND</strong> The novel coronavirus disease (COVID-19) has exposed the chinks in the armour of healthcare systems and has single-handedly literally brought the world to a standstill. Diagnostic testing for COVID-19 is critical for understanding epidemiology, contract-tracing, case management, and to control the transmission of the SARS-CoV-2. RT-PCR test, the gold standard test, involves fairly complex steps and take nearly 24–48 h for generating the results. GeneXpert is a rapid nucleic-acid-detection-based test approved by ICMR (Indian Council of Medical Research), which can shorten the turnaround time significantly.AIMThe aim of the study was to compare the performance of GeneXpert against the gold standard RT-PCR for SARS-COV-2. <strong>MATERIALS AND METHODS</strong> This retrospective study was conducted at a tertiary care centre from 25th March 2020 to 8th December 2020. The Nasopharyngeal/Oropharyngeal swabs that were sent to the Covid laboratory for testing of SARS COV-2 by GeneXpert (CBNAAT) were included for the study. The samples that gave a positive result were simultaneously tested for rRT-PCR. According to the manufacturer instructions, the cut-off value for GeneXpert is 45 whereas according to ICMR, cut-off value for RT-PCR to be taken is 35.RESULTSOut of 220 samples positive by GeneXpert , 102 (46%) showed negative results by RT-PCR. Among these 102 samples, 89% (91/102) samples were found to be positive by GeneXpert with Ct value >35 whereas 90% (96/107) positive GeneXpert samples had Ct value <35 which were also positive by RT-PCR. <strong>CONCLUSION</strong> The formulation of certain cut-off Ct values for the uniform results by both GeneXpert and RT-PCR should be implemented.

Ramification of Covid-19 pandemic : Occurrence and impact of fungal Infections in a tertiary care hospital

Coronavirus disease 2019 (Covid-19) pandemic has been prevailing for more than a year associated with increased number of opportunistic invasive fungal infections in patients who have been critically ill or immunocompromised. In this retrospective study, details of various clinical specimens received from suspected patients of fungal infections were processed according to standard protocol were studied. The fungal infections were present in 64% (51/79) COVID-19 positive patients and 43% (163/381) COVID-19 negative patients) during the year 2021 during the second wave of COVID-19. Among Covid infected patients, the fungal infection mostly observed was Candidiasis (63%) followed by Aspergillosis (15% ) and Mucormycosis (6%). The maximum samples positive in Covid patients were urine samples followed by Serum (for Aspergillus Galactomannan). Among the urine and respiratory samples (BAL, Tracheal aspirate, Sputum) in Covid-19 positive patients, maximum positivity of Candida species was seen. Mucormycosis in Covid-19 positive patients was isolated in Nasal samples followed by tissue sample with Rhizopus arrhizus and Rhizopus homothallicus. There has been an increase in fungal co-infections during the COVID-19 pandemic which is a matter of great concern. Early diagnosis is essential for effective management of these patients.

Colonization, Density, and Antibiotic Resistance of Streptococcus pneumoniae, Haemophilus Influenzae, and Moraxella catarrhalis among PCV13-Vaccinated Infants in the First Six Months of Life in Rochester, New York: A Cohort Study.

BACKGROUND: Streptococcus pneumoniae (Spn), Haemophilus influenzae (Hflu), and Moraxella catarrhalis (Mcat) nasopharyngeal colonization precedes disease pathogenesis and varies among settings and countries. We sought to assess colonization prevalence, density, Spn serotypes, and antibiotic resistance in children in the first 6 months of life in pediatric primary care settings. METHODS: Prospective cohort study in Rochester, NY during 2018-2020. Nasopharyngeal swabs were collected from 101 children at age 1, 2, and 3 weeks, then 1, 2, 4, 6, 9, 12, 15, 18, and 24 months. Spn serotypes were determined by Quellung. Oxacillin resistance for Spn and ß-lactamase production by Hflu and Mcat was tested. All children received PCV13 vaccine according to U.S. recommended schedule. RESULTS: Spn, Hflu, and Mcat colonization was detected in only 5% of infants before age 2 months old. Cumulative prevalence was 34% for Spn, 10% for Hflu, and 53% for Mcat in children ≤6 months of age. Nasopharyngeal bacterial density of Spn, Hflu, and Mcat (x = 2.71 log) in children ≤6 months of age was lower than at 7-24 months of age (x = 3.15 log, p < 0.0001). Predominant serotypes detected ≤6 months of age were 23B (16.7%), 22F (12.9%), 15B/C (11%), and 16F (9.2%). In total, 14.8% of Spn isolates were oxacillin resistant and 66.7% of Hflu isolates were ß-lactamase producing. CONCLUSION: Spn, Hflu, and Mcat nasopharyngeal colonization was uncommon and of low density among children ≤6 months old, especially among children <2 months of age. Non-PCV13 serotypes predominated and a different serotype distribution was observed in ≤6-month olds compared to 7- to 24-month olds.

Ulceration by Nocardia Otitidiscaviarum: A case study.

Nocardiosis is an acute, subacute or chronic infectious disease that occurs in cutaneous, pulmonary and disseminated forms. We present a case of Nocardiosis in a post-COVID-19 patient with cutaneous ulceration due to Nocardia otitidiscaviarum, managed with cotrimoxazole and linezolid. Early diagnosis and management proved crucial in preventing dissemination of the organism and improving the patient's outcome.

Outpatient Randomized Crossover Comparison of Zone Model Predictive Control Automated Insulin Delivery with Weekly Data Driven Adaptation Versus Sensor-Augmented Pump: Results from the International Diabetes Closed-Loop Trial 4.

Background: Automated insulin delivery (AID) systems have proven effective in increasing time-in-range during both clinical trials and real-world use. Further improvements in outcomes for single-hormone (insulin only) AID may be limited by suboptimal insulin delivery settings. Methods: Adults (≥18 years of age) with type 1 diabetes were randomized to either sensor-augmented pump (SAP) (inclusive of predictive low-glucose suspend) or adaptive zone model predictive control AID for 13 weeks, then crossed over to the other arm. Each week, the AID insulin delivery settings were sequentially and automatically updated by an adaptation system running on the study phone. Primary outcome was sensor glucose time-in-range 70-180 mg/dL, with noninferiority in percent time below 54 mg/dL as a hierarchical outcome. Results: Thirty-five participants completed the trial (mean age 39 ± 16 years, HbA1c at enrollment 6.9% ± 1.0%). Mean time-in-range 70-180 mg/dL was 66% with SAP versus 69% with AID (mean adjusted difference +2% [95% confidence interval: -1% to +6%], P = 0.22). Median time <70 mg/dL improved from 3.0% with SAP to 1.6% with AID (-1.5% [-2.4% to -0.5%], P = 0.002). The adaptation system decreased initial basal rates by a median of 4% (-8%, 16%) and increased initial carbohydrate ratios by a median of 45% (32%, 59%) after 13 weeks. Conclusions: Automated adaptation of insulin delivery settings with AID use did not significantly improve time-in-range in this very well-controlled population. Additional study and further refinement of the adaptation system are needed, especially in populations with differing degrees of baseline glycemic control, who may show larger benefits from adaptation.

The laboratory diagnostic profile of SARS-CoV-2 (COVID-19) patients & associated factors

Background: Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) is the novel corona virus first detected in Wuhan in 2019. nCOV belongs to the beta-corona virus cluster. As the third most highly pathogenic corona virus, the clinical presentations of 2019-nCoV infection resemble those of the other two corona viruses, Severe Acute Respiratory Syndrome Corona Virus (SARS-CoV) and Middle East Respiratory Syndrome Corona Virus (MERS-CoV). The abnormalities in the laboratory indices particularly the Blood Biochemical parameters may be associated with the severity of multiple organ dysfunction seen in COVID-19. The aim of the present project was to analyze the laboratory diagnostic profile of sars-cov-2 (covid-19) patients & to study the associated factors.

COVID-19 Pandemic Impact on Respiratory Infectious Diseases in Primary Care Practice in Children.

Background: The coronavirus disease 2019 (COVID-19) pandemic led to day care and school closures and children staying home for several months. When they gradually returned, aggressive regulations were implemented in New York State to reduce viral transmission. Method: An ongoing prospective study occurring in the Rochester, NY region, focused on early childhood respiratory infectious diseases, afforded an opportunity to assess the impact of the pandemic on the incidence of these illnesses in a primary care outpatient setting. Physician-diagnosed, medically attended infection visits were assessed in two child cohorts, age 6-36 months old: from March 15 to December 31, 2020 (the pandemic period) compared to the same months in 2019 (prepandemic). Nasopharyngeal colonization by potential otopathogens during healthy/well-child and acute otitis media (AOM) visits was evaluated. Results: One hundred and forty-four children were included in the pandemic cohort and 215 in the prepandemic cohort. The pandemic cohort of children experienced 1.8-fold less frequent infectious disease visits during the pandemic (p < 0.0001). Specifically, visits for AOM were 3.7-fold lower (p < 0.0001), viral upper respiratory infections (URI) 3.8-fold lower (p < 0.0001), croup 27.5-fold lower (p < 0.0001), and bronchiolitis 7.4-fold lower (p = 0.04) than the prepandemic cohort. Streptococcus pneumoniae (p = 0.03), Haemophilus influenzae (p < 0.0001), and Moraxella catarrhalis (p < 0.0001) nasopharyngeal colonization occurred less frequently among children during the pandemic. Conclusion: In primary care pediatric practice, during the first 9 months of the COVID-19 pandemic, significant decreases in the frequency of multiple respiratory infections and nasopharyngeal colonization by potential bacterial respiratory pathogens occurred in children age 6-36 months old.

The Syndromic Spectrum of COVID-19 and Correlates of Admission Parameters with Severity-outcome Gradients: A Retrospective Study.

BACKGROUND: Clinical and laboratory features of COVID-19 may have regional variations. This study aimed to discern their association with severity of illness and mortality in tertiary setup of Delhi, India. METHODS: Retrospective data of hospitalised COVID-19 patients over 3 months (end March to June 2020) were evaluated for symptom profile, blood investigations and chest radiograph data and classified according to COVID-19 severity and as survivors and non-survivors. RESULTS: Average age (n=182) was 46.1 years, male to female ratio 1.4:1. Fever (51.1%), cough (49.4%) and breathlessness (48.3%) were the commonest symptoms, and frequency of all the three increased with severity of COVID-19. Fever duration, leucocytosis, neutrophilia, elevated blood urea, transaminitis and higher Brixia score on chest X-ray were also more in severe COVID-19 compared to mild and moderate categories. Higher age, more comorbidities, fever, breathlessness and chest pain; longer duration of fever, leucocytosis, neutrophilia, lymphopenia, high neutrophil to lymphocyte ratio, elevated serum urea, creatinine, transaminases and hyperglycemia, and higher radiographic Brixia score were observed in non-survivors compared to survivors. CONCLUSION: Greater prevalence of symptoms (alone and in combination) and derangements in blood biochemistry are seen in severe COVID-19 compared to mild or moderate cases, and also in non-survivors compared to survivors.