Thermal stability of diagnostic targets plasmodium falciparum histidine rich protein II and plasmodium lactate dehydrogenase in rapid detection.

During the COVID-19 epidemic, blood samples are usually processed at 56 to attenuate the virus before pathogen detection. 71 blood samples of malaria patients reported by Shanghai Center for Disease Control and Prevention in 2017-2019 were collected, including 38 with Plasmodium falciparum infection, 8 P. malariae, 11 P. ovale and 14 P. vivax. The effect of inactivation on the thermal stability of P. falciparum histidine rich protein II (PfHRPII) and Plasmodium lactate dehydrogenase (pLDH) in blood samples was assessed before and after incubation at 56 for 30 min using the rapid diagnostic test (RDT) kit. The results showed that among the 38 P. falciparum T1-positive (PfHRPII) blood samples before heat treatment, 35 samples remained to be T1-positive (92.11%, 35/38, chi2=3.123, P>0.05) after heat treatment;while 54 blood samples (26 P. falciparum, 6 P. vivax, 10 P. ovale and 12 P. vivax) that were T2-positive (pLDH) before heat treatment turned to be T2-negative (positive rate 0, 0/54, chi2=87.755, P<0.01) after heat treatment. It was demonstrated that PfHRPII is stable during incubation at 56 for 30 min, while pLDH is unstable and degraded or inactivated during the heating. Therefore, the detection results of P. falciparum will not be affected by RDT, but diagnosis of the parasites other than P. falciparum in blood samples may be missed.Copyright © 2021, National Institute of Parasitic Diseases. All rights reserved.

AMR Enzymatic inactivation mechanism attributed to fosA Gene antibiotic resistance among Covid 19 hospitalized patients

Introduction: The prevalence of antimicrobial resistance genes ARGs and their resistance genetic mechanisms among Covid- 19 patients are yet to be identified. The human microbiome is a significant reservoir of antimicrobial resistance genes. The overprescription of antimicrobials can select multi-resistant bacteria and modify the repertoire of ARGs in the gut. The World Health Organization has reported 148 million hospitalized cases worldwide. Objective(s): The purpose of the current study is to explore the genetic mechanisms of antimicrobial resistance among hospitalized COVID-19 patients, furthermore, to review their antibiotic resistance gene occurrence. Methodology 438 Microbiome of clinical hospitalized COVID-19 positive cases with 11 129 isolates were downloaded from the EMBL's European Bioinformatics Institute and the NCBI Pathogen Detection using the following keywords AMR, mechanism of resistance, and COVID-19 SARS CoV 2 bacterial Infection.We also have used the Comprehensive Antibiotic Resistance Database Card, and RESfinder are used for the metagenomics analysis based on programming languages JavaScript and R (v. 4) for data analysis. Result(s): We explored the AMR diversity among prevalent microbes(n = 410), including Klebsiella pneumoniae, Acinetobacter baumannii E. coli, Salmonella, Enterobacter and Pseudomonas aeruginosa.We found that Enzyme activation (72.7%) was the most prevalent mechanism due to the fosA gene 54.5%. Then the aadA2 gene (18%) and catA1 gene(9%). Moreover, the Increased efflux mechanisms were detected in Escherichia coli towards Quinolone using the oqxA gene (17.3%). FosA was also intermittently found in Salmonella (9.8%), and Pseudomonas aeruginosa (7.8%). Conclusion(s): We anticipate that FosA homologous is prevalent in Gram-negative bacterial infections among hospitalized COVID-19 patients, and it encodes for Fosfomycin resistance. The findings might shed light on controlling Fosfomycin resistance among hospitalized patients with COVID-19.Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.

Present status of microfluidic PCR chip in nucleic acid detection and future perspective

Polymerase chain reaction (PCR) amplifies specific fragment of DNA molecules and has been extensively applied in fields of pathogens and gene mutation detection, food safety and clinical diagnosis which on the other hand, holds the drawbacks of large size instrument, high heat dissipation etc. It has been demonstrated that microfluidics technique coupling with PCR reaction exhibits characteristics of integration, automatization, miniaturization, and portability. Meanwhile, various designed fabrication of microchip could contribute to diverse applications. In this review, we summarized major works about a variety of microfluidic chips equipped with several kinds of PCR techniques (PCR, RT-PCR, mPCR, dPCR) and detection methods like fluorescence, electrochemistry, and electrophoresis detection. The development and application of PCR-based microfluidic chip in pathogen and gene mutation detection, diseases prevention and diagnosis, DNA hybridization and low-volume sample treatment were also discussed. Copyright © 2022 Elsevier B.V.

Evaluation of Features for Ground Glass Opacities in Lung Cancer Patients Positive with Covid-19

Objective: To evaluate radiological features of Covid-19 and early lung cancer through High-resolution computed tomography (HRCT) and demonstrate the disparity between them. Study Design: A retrospective study Place and Duration of Study: This study was conducted at the Covid-19 ward, Oncology, Radiology Ward of Nishtar Medical University & Hospital Multan from 12th Nov 2019 to 12th Nov 2020. Materials and Methods: A total of 100 Covid-19 patients and 300 patients with pulmonary ground-glass opacities undergoing lung surgery (control group) were included in the study. After propensity score-matched analysis, patients were divided into two groups with 80 matched pairs each. The clinical, pathological, epidemiological, and radiological characteristics (evaluated through HRCT) of both groups were compared. Results: It was observed that Covid-19 patients presented more definite symptoms, were mostly younger men, and had higher BMI (body-mass index). After the radiological analysis of the matched patients, it was revealed that single lesion patients constituted 17% of Covid-19 cases and 89% of lung cancer cases. Patients in both groups mostly presented peripheral lesions. Covid-19 lesions had more lobes, segments and had various types with patchy forms. On the other hand, lung cancer tended to have only one type and had an oval form. Conclusion: Both Covid-19 and lung cancer showed ground-glass opacities with similar but independent characteristics. These characteristics combined with pathogen detection, short-term CT examination, and laboratory tests will aid in improved diagnosis.

Sharp Decline in Rates of Community Respiratory Viral Infections among NIH Clinical Center Patients during the COVID-19 Pandemic

Background. During the first year of the COVID-19 pandemic, nonpharmaceutical interventions had a broad impact on viral transmission apart from SARS-CoV-2. The NIH Clinical Center has used the BioFire FilmArray multiplex PCR respiratory pathogen panel (RPP) for evaluation of upper respiratory symptoms since 2014. Beginning in 3/20, respiratory samples from symptomatic patients were tested by SARS-CoV-2 PCR and the RPP. We performed a retrospective study comparing frequency and rates of community respiratory viruses detected by RPP from 1/14 through 3/21. Methods. Results of RPPs from nasopharyngeal swabs/washes, bronchoalveolar lavages, and bronchial washes were included. Results from viral challenge studies were excluded. Charts were reviewed to determine whether repeat positives for the same virus within 12 months represented new infections;repeats from the same infection were excluded. A quantitative data analysis was completed using cross tabulations;comparisons were done using mixed models, applying Dunnett's correction for multiplicity. Results. A total of 3,329 patients underwent 8,122 RPPs from 1/14 through 3/21. Frequency of all respiratory pathogens declined from an annual range of 0.88-1.97% from 1/14-3/20 to 0.29% in 4/20-3/21 (p < 0.001). Individual viral pathogens declined sharply in frequency during the pandemic, with zero cases of influenza A/B, parainfluenza, or metapneumovirus detected from 4/20-3/21. One case each of adenovirus, RSV, CoV OC43, and CoV HKU1 were detected in 4/20-3/21. Rhino/enterovirus detection continued, but with a substantially lower frequency of 4.27% in 4/20-3/21, compared with an annual range of 8.65-18.28% from 1/14-3/20 (p < 0.001). Frequency of detection of all respiratory pathogens tested using the Biofire FilmArray multiplex PCR respiratory pathogen panel from January 2014 through March 2021. The frequency of pathogen detection from April 2020 through March 2021 declined substantially in comparison with previous years. Frequency of detection of influenza A, influenza B, rhinovirus/enterovirus, parainfluenza (1, 2, 3, 4), and respiratory syncytial virus from January 2014 through March 2021. The frequency of detection of these pathogens declined sharply starting in April 2020. Conclusion. During the pandemic, the burden of viral respiratory infections detected among patients at the NIH Clinical Center improved considerably. This reprieve was likely thanks to the layered COVID-19 prevention and mitigation measures implemented in the community and the hospital: masking, distancing, symptom screening, isolation and testing symptomatic persons. As COVID-19 vaccination allows relaxation of masking, community transmission of respiratory viruses will likely resume;continued mask-wearing in the hospital may provide an enduring benefit by preventing nosocomial transmission.

Before and After: The Impact of the COVID-19 Pandemic on Influenza-Like Illness Trends in PAIVED

Background. The Pragmatic Assessment of Influenza Vaccine Effectiveness in the DoD (PAIVED) is a multicenter study assessing influenza vaccine effectiveness in active duty service members, retirees, and dependents. PAIVED recently completed its third year and offers a unique opportunity to examine influenza-like illness (ILI) trends prior to and during the COVID-19 pandemic in a prospective, well-defined cohort. Methods. During the 2018-19, 2019-20, and 2020-21 influenza seasons, PAIVED enrolled DoD beneficiaries presenting for annual influenza vaccination. After collecting baseline demographic data, participants were randomized to receive egg-based, cell-based, or recombinant-derived influenza vaccine. Weekly throughout the influenza season of enrollment, participants were surveyed electronically for ILI, defined as (1) having cough or sore throat, plus (2) feeling feverish/having chills or having body aches/fatigue. Participants with ILI completed a daily symptom diary for seven days and submitted a nasal swab for pathogen detection. Results. Over the three seasons, there were 10,656 PAIVED participants: 1514 (14.2%) in 2018-19, 5876 (55.1%) in 2019-20, and 3266 (30.6%) in 2020-21. The majority were male (68-73% per year) with a mean age of 34±14.8 years at enrollment. 2266 participants reported a total of 2673 unique ILIs. The highest percentage of participants with ILI was in 2019-20 (28.2%), versus 19.6% in 2018-19 and 9.6% in 2020-21. Figure 1 depicts the percent of individuals reporting ILI by week of the season for each of the PAIVED seasons. Notably, after March 21, 2020, the weekly incidence of participants reporting ILI never exceeded 1%. Figure 1. Percent of PAIVED participants reporting ILI by week of season. Conclusion. The low incidence of reported ILI in PAIVED participants during the COVID-19 pandemic is consistent with national influenza surveillance reports of influenza and outpatient ILI activity, suggesting that mitigation measures taken to reduce transmission of SARS-CoV-2 reduced the spread of other respiratory viruses.