Detection of Viruses by Multiplex Real-Time Polymerase Chain Reaction in Bronchoalveolar Lavage Fluid of Patients with Nonresponding Community-Acquired Pneumonia

Zhang, Hao; Han, Yinling; Jin, Zhangchu; Ying, Yinghua; Lan, Fang; Huang, Huaqiong; Wang, Shaobin; Zhou, Hongwei; Zhang, Rong; Huang, Wen; Shen, Huahao; Li, Wen; Yan, Fugui

doi:10.1155/2020/8715756

Cited by 5 publications

(7 citation statements)

References 34 publications

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“…A retrospective study investigating the presence of respiratory viruses in bronchoalveolar lavage (BAL) samples of patients with non-responding CAP discovered an underlying viral infection in 47% of these cases, with influenza and adenoviruses as being most frequently identified pathogens. 46 There were no differences regarding clinical and laboratory data between viral or non-viral cases of nonresponding-CAP. However, the presence of ground-glass opacities combined with consolidation on CT scans was specific for viral, non-responding CAP.…”

Section: General Epidemiology and Etiology Of Severe Lvrimentioning

confidence: 81%

“…However, the presence of ground-glass opacities combined with consolidation on CT scans was specific for viral, non-responding CAP. 46 In the study by Shorr et al 45 viral infection was found to be significantly…”

Section: General Epidemiology and Etiology Of Severe Lvrimentioning

confidence: 93%

“…53 Interestingly, a recent study found that 47% of patients with non-responding CAP had a viral etiology, as determined by a study of bronchoalveolar samples, with influenza and adenoviruses being the most frequently identified viruses. 46 In the last decade, multiple studies have investigated the utility of biomarkers in differentiating bacterial and viral infections, including C-reactive protein (CRP), procalcitonin (PCT), interleukin-6, total white cell count, lymphocyte count, and neutrophil count. However, no reliable threshold to distinguish bacterial from viral pneumonia using such biomarkers has been described thus far.…”

Section: Principles Of Lvri Diagnosismentioning

confidence: 99%

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Severe Infections Due to Respiratory Viruses

Cillóniz

Pericàs

Rojas

2022

Semin Respir Crit Care Med

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Severe viral infections may result in severe illnesses capable of causing acute respiratory failure that could progress rapidly to acute respiratory distress syndrome (ARDS), related to worse outcomes, especially in individuals with a higher risk of infection, including the elderly and those with comorbidities such as asthma, diabetes mellitus and chronic respiratory or cardiovascular disease. In addition, in cases of severe viral pneumonia, co-infection with bacteria such as Streptococcus pneumoniae and Staphylococcus aureus is related to worse outcomes. Respiratory viruses like influenza, rhinovirus, parainfluenza, adenovirus, metapneumovirus, respiratory syncytial virus, and coronavirus have increasingly been detected. This trend has become more prevalent, especially in critically ill patients, due to the availability and implementation of molecular assays in clinical practice. Respiratory viruses have been diagnosed as a frequent cause of severe pneumonia, including cases of community-acquired pneumonia, hospital-acquired pneumonia, and ventilator-associated pneumonia. In this review, we will discuss the epidemiology, diagnosis, clinical characteristics, management, and prognosis of patients with severe infections due to respiratory viruses, with a focus on influenza viruses, non-influenza viruses, and coronaviruses.

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Section: General Epidemiology and Etiology Of Severe Lvrimentioning

confidence: 81%

Section: General Epidemiology and Etiology Of Severe Lvrimentioning

confidence: 93%

Section: Principles Of Lvri Diagnosismentioning

confidence: 99%

See 1 more Smart Citation

Severe Infections Due to Respiratory Viruses

Cillóniz

Pericàs

Rojas

2022

Semin Respir Crit Care Med

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“…Molecular methods, such as polymerase chain reaction (PCR), are an alternative method when culture-based microbial detection methods fail. 7 , 8 However, the preselected target pathogens greatly limit the application of multiplex PCR in identifying infections caused by mixed pathogens. 9 PCR-based analyses may fail to detect unexpected, rare, or novel pathogens unless multiplexed PCRs covering all pathogenic microorganisms are employed.…”

Section: Introductionmentioning

confidence: 99%

Clinical Efficacy and Diagnostic Value of Metagenomic Next-Generation Sequencing for Pathogen Detection in Patients with Suspected Infectious Diseases: A Retrospective Study from a Large Tertiary Hospital

Xiao¹,

Liu²,

Wu³

et al. 2023

IDR

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Purpose Metagenomic next-generation sequencing (mNGS) is a powerful yet unbiased method to identify pathogens in suspected infections. However, little is known about its clinical effectiveness. The present study aimed to assess the efficacy of mNGS in routine clinical practice. Patients and Methods In this single-center retrospective cohort study, 518 patients with suspected infectious diseases were assessed for inclusion. Among them, each patient had undergone mNGS testing; 407 patients had undergone both microbial culture and mNGS testing. The result of mNGS testing was compared to microbial culture performed concurrently. The diagnostic performance of mNGS was evaluated using the comprehensive clinical diagnosis as the reference standard. Results There was a significant difference in the positive detection rates of pathogens between mNGS and culture (331/407, 81.3% vs 79/407, 19.4%, P < 0.001). The sensitivity of mNGS was much higher than the culture method (79.5% vs 21.3%, P < 0.001), especially in sample types of sputum and bronchoalveolar lavage fluid (BALF). Notably, the sensitivity of blood mNGS was relatively lower than other sample types (67.4% vs 88.9–93.8%). Pathogen cfDNA load based on standardized stringently mapped read number at the species level of microorganisms (SDSMRN) was significantly lower in blood than in other sample types from the same patient ( P = 0.0003). Importantly, mNGS directly led to a change of treatment regimen in 142 (27.4%) cases, including antibiotic escalation (15.3%), antibiotic de-escalation (9.1%), and early definitive diagnosis to initiate appropriate treatment (3.1%). Conclusion Our in-house mNGS platform significantly improved the sensitivity for the diagnosis of infectious diseases. mNGS has the potential to improve clinical outcomes by optimizing antimicrobial therapy.

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“…Although widely used in the clinical practice, the specificity of viruses detected in the upper respiratory airways for the etiologic diagnosis of CAP remains a challenge, mostly because about 7.1% healthy people are asymptomatic carriers. 8 , 9 , 10 In addition, diagnostic samples with high specificity from lower respiratory tract (LRT) are difficult to obtain or need invasive procedures. 9 …”

Section: Introductionmentioning

confidence: 99%

Prepandemic viral community‐acquired pneumonia: Diagnostic sensitivity and specificity of nasopharyngeal swabs and performance of clinical severity scores

Berastegui‐Cabrera

Aguilar‐Guisado

Crespo‐Rivas

et al. 2022

Journal of Medical Virology

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The objectives of this work were to assess the diagnostic sensitivity and specificity of nasopharyngeal (NP) swabs for viral community‐acquired pneumonia (CAP) and the performance of pneumonia severity index (PSI) and CURB‐65 severity scores in the viral CAP in adults. A prospective observational cohort study of consecutive 341 hospitalized adults with CAP was performed between January 2018 and March 2020. Demographics, comorbidities, symptoms/signs, analytical data, severity scores, antimicrobials, and outcomes were recorded. Blood, NP swabs, sputum, and urine samples were collected at admission and assayed by multiplex real time‐PCR, bacterial cultures, and Streptococcus pneumoniae and Legionella pneumophila antigens detection, to determine the etiologies and quantify the viral load. The etiology was identified in 174 (51.0%) patients, and in 85 (24.9%) it was viral, the most frequent rhinovirus and influenza virus. The sensitivity of viral detection in sputum (50.7%) was higher than in NP swabs (20.9%). Compared with sputum, the positive predictive value and specificity of NP swabs for viral diagnosis were 95.8% and 96.9%, respectively. Performance of PSI and CURB‐65 scores in all CAP with etiologic diagnosis were as expected, with mortality associated with higher values, but they were not associated with mortality in patients with viral pneumonia. NP swabs have lower sensitivity but high specificity for the diagnosis of viral CAP in adults compared with sputum, reinforcing the use NP swabs for the diagnostic etiology work‐up. The PSI and CURB‐65 scores did not predict mortality in the viral CAP, suggesting that they need to be updated scores based on the identification of the etiological agent.

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Detection of Viruses by Multiplex Real-Time Polymerase Chain Reaction in Bronchoalveolar Lavage Fluid of Patients with Nonresponding Community-Acquired Pneumonia

Cited by 5 publications

References 34 publications

Severe Infections Due to Respiratory Viruses

Severe Infections Due to Respiratory Viruses

Clinical Efficacy and Diagnostic Value of Metagenomic Next-Generation Sequencing for Pathogen Detection in Patients with Suspected Infectious Diseases: A Retrospective Study from a Large Tertiary Hospital

Prepandemic viral community‐acquired pneumonia: Diagnostic sensitivity and specificity of nasopharyngeal swabs and performance of clinical severity scores

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