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Era of molecular diagnosis for pathogen identification of unexplained pneumonia, lessons to be learned.

ABSTRACT: Unexplained pneumonia (UP) caused by a novel coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) emerged in China in late December 2019 and has infected more than 9000 cases by 31 January 2020. Shanghai reported the first imported case of COVID-19 (Coronavirus Disease 2019) in 20 January 2020. A combinative approach of real-time RT-PCR, CRISPR-based assay and metagenomic next-generation sequencing (mNGS) were used to diagnose this unexplained pneumonia patient. Real-time RT-PCR and CRISPR-based assay both reported positive. This sample belonged to Betacoronavirus and shared a more than 99% nucleotide (nt) identity with the Wuhan SARS-CoV-2 isolates. We further compared pros and cons of common molecular diagnostics in UP. In this study, we illustrated the importance of combining molecular diagnostics to rule out common pathogens and performed mNGS to obtain unbiased potential pathogen result for the diagnosis of UP.

SUBMITTER: Ai JW

PROVIDER: S-EPMC7144283 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Era of molecular diagnosis for pathogen identification of unexplained pneumonia, lessons to be learned.

Ai Jing-Wen JW Zhang Yi Y Zhang Hao-Cheng HC Xu Teng T Zhang Wen-Hong WH

Emerging microbes & infections 20200316 1

Unexplained pneumonia (UP) caused by a novel coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) emerged in China in late December 2019 and has infected more than 9000 cases by 31 January 2020. Shanghai reported the first imported case of COVID-19 (Coronavirus Disease 2019) in 20 January 2020. A combinative approach of real-time RT-PCR, CRISPR-based assay and metagenomic next-generation sequencing (mNGS) were used to diagnose this unexplained pneumonia patient. Real-time RT- ...[more]

PMID: 32174267

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Project description:IntroductionThe COVID-19 pandemic has dramatically affected the Female and Functional Urology (FFU) practice, leading to massive waiting lists, while patients' quality of life remains severely impaired. The aim of the present study is to develop consensual recommendations to guide clinicians on the management of FFU patients. The present paper focuses on female LUTS.MethodsThe authors used the Delphi methodology to develop a robust survey questionnaire, covering the principal topics in FFU, based on literature review and expert opinions. Regarding female LUTS, a 98-question survey was distributed among FFU specialists to obtain optimized recommendations, under the auspicious of the International Continence Society (TURNOVER, ICS project). A quantitative analysis of the data was performed, categorizing the mean value from 0-10. Consensus achievement was defined as attaining ≥ 70% agreement.Results98 ICS members completed the F-LUTS survey. Recommendations for the diagnosis and management of female LUTS are summarized. Video-consultation should be used for initial assessment, sending questionnaires and bladder diaries in advance to the patient to be filled out before the consultation. However, face-to-face visits are mandatory if POP or continuous incontinence are suspected, and prior to any surgical procedure, regardless of the health alert. Moreover, prescribing medications such as anticholinergics or β 3 agonists in a telemedicine setting is not considered a safe practice. Follow-up teleconsultations can be used to assess the efficacy and treatment-related adverse events.Urodynamic testing should be only performed if consequences on F-LUTS treatment are expected. The study should be postponed until the pandemic local behaviour flattens.Invasive procedures should be postponed during a high alert. In case surgery is scheduled, outpatient clinics and local anaesthesia should be prioritized. Every patient should be screened for SARS-CoV-2 infection before invasive tests or procedures, following local authorities' guidance.ConclusionsDuring a pandemic, telemedicine offers a novel way of communication, maintaining medical care while preventing viral transmission. Non-urgent procedures should be postponed until the pandemic curve flattens. Ambulatory procedures under regional or local anaesthesia should be prioritized, aiming to reduce bed occupancy and risk of transmission.

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Era of molecular diagnosis for pathogen identification of unexplained pneumonia, lessons to be learned.

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Era of molecular diagnosis for pathogen identification of unexplained pneumonia, lessons to be learned.

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