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Open accessJournal ArticleDOI: 10.1007/S10096-021-04195-5

Multinational evaluation of the BioFire® FilmArray® Pneumonia plus Panel as compared to standard of care testing

02 Mar 2021-European Journal of Clinical Microbiology & Infectious Diseases (Springer Berlin Heidelberg)-Vol. 40, Iss: 8, pp 1-14
Abstract: This study compared standard of care testing (SOC) to BioFire® FilmArray® Pneumonia plus Panel (PNplus). PNplus detects 15 bacteria with semiquantitative log bin values, 7 antibiotic resistance markers, three atypical bacteria (AB), and eight viral classes directly from bronchoalveolar lavage-like specimens (BLS) and sputum-like specimens (SLS). Fifty-two laboratories from 13 European countries and Israel tested 1234 BLS and 1242 SLS with PNplus and SOC. Detection rates and number of pathogens/samples were compared for PNplus pathogens. PNplus bin values and SOC quantities were compared. Three thousand two hundred sixty-two bacteria in PNplus were detected by PNplus and/or SOC. SOC detected 57.1% compared to 95.8% for PNplus (p ≤ 0.0001). PNplus semiquantitative bin values were less than SOC, equal to SOC, or greater than SOC in 5.1%, 25.4%, and 69.6% of results, respectively. PNplus bin values were on average ≥ 1 log than SOC values (58.5% 1-2 logs; 11.0% 3-4 logs). PNplus identified 98.2% of MRSA and SOC 55.6%. SOC detected 73/103 AB (70.9%) and 134/631 viruses (21.2%). PNplus detected 93/103 AB (90.3%) and 618/631 viruses (97.9%) (p ≤ 0.0001). PNplus and SOC mean number of pathogens/samples were 1.99 and 1.44, respectively. All gram-negative resistance markers were detected. PNplus and SOC results were fully or partially concordant for 49.1% and 26.4% of specimens, respectively. PNplus was highly sensitive and detected more potential pneumonia pathogens than SOC. Semiquantification may assist in understanding pathogen significance. As PNplus generates results in approximately 1 h, PNplus has potential to direct antimicrobial therapy in near real time and improve antimicrobial stewardship and patient outcomes.

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5 results found

Open accessJournal ArticleDOI: 10.1016/J.DIAGMICROBIO.2021.115476
Abstract: Among critically ill COVID-19 patients, bacterial coinfections may occur, and timely appropriate therapy may be limited with culture-based microbiology due to turnaround time and diagnostic yield challenges (e.g. antibiotic pre-exposure). We performed a systematic review and meta-analysis of the impact of BioFire® FilmArray® Pneumonia Panel in detecting bacteria and clinical management among critically ill COVID-19 patients admitted to the ICU. Seven studies with 558 patients were included. Antibiotic use before respiratory sampling occurred in 28-79% of cases. The panel incidence of detections was 33% (95% CI 0.25 to 0.41, I2=32%) while culture yielded 18% (95% CI 0.02 to 0.45; I2=93%). The panel was associated with approximately a 1 and 2 day decrease in turnaround for identification and common resistance targets, respectively. The panel may be an important tool for clinicians to improve antimicrobial use in critically ill COVID-19 patients.

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Open accessJournal ArticleDOI: 10.1016/J.DIAGMICROBIO.2021.115507
Abstract: The FilmArray Pneumonia Panel has proven to be an effective tool for rapid detection of main respiratory pathogens. However, its rational use needs appropriate knowledge and formation regarding its indication and interpretation. Herein, we provide some advices to help with success of its daily routine use, particularly in critically ill ventilated COVID-19 patients. Clinical Trial registration number: NCT04453540.

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Journal ArticleDOI: 10.1016/J.CLINMICNEWS.2021.08.001
Suong T Nguyen1, Rebecca G Same1Institutions (1)
Abstract: The introduction of rapid diagnostic testing has transformed the practice of infectious diseases, facilitating earlier pathogen identification and optimization of antimicrobial therapy. Rapid diagnostic panels have also created new challenges in the interpretation of increasing numbers of results of unclear clinical significance. We highlight the clinical implications of the increasing use of rapid diagnostic panels in pediatric infectious diseases, focusing on commonly adopted testing for the diagnosis of meningitis and encephalitis, bloodstream infections, gastrointestinal infections, and respiratory infections. Rapid diagnostic panels can be useful adjuncts to conventional culture methods, but results must be interpreted with caution and careful attention to the clinical scenario. They are most likely to be successful when implemented in conjunction with clinical guidance in collaboration between microbiology laboratories and antimicrobial stewardship programs.

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Journal ArticleDOI: 10.1016/J.MIMET.2021.106339
Yuying Si, Zhang Tong1, Nianzhen Chen2, Yu Cheng2  +6 moreInstitutions (2)
Abstract: Lower respiratory tract infections (LRTIs) are a leading cause of morbidity and mortality worldwide and lack a rapid diagnostic method. To improve the diagnosis of LRTIs, we established an available loop-mediated isothermal amplification (LAMP) assay for the detection of eight common lower respiratory pathogens, including Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Staphylococcus aureus, Escherichia coli, Haemophilus influenzae, Streptococcus pneumoniae, and Moraxella catarrhalis. The whole process can be achieved within 1 h (sample to results read out). We established an extraction free isothermal system. 528 sputum samples collected from patients suspected to have LRTIs were analyzed by the system (8 tests in each sample, a total of 4224 tests) and compared with the standard culture method (SCM). The samples with inconsistent results were further verified by Sanger sequencing and High-throughput sequencing (NGS). The detection limits of the LAMP assay for the 8 pathogens ranged from 103 to 104 CFU/mL. Upon testing 528 samples, the Kappa coefficients of all pathogens ranged between 0.5 and 0.7 indicated a moderate agreement between the LAMP assay and the SCM. All inconsistent samples were further verified by Sanger sequencing, we found that the developed LAMP assay had a higher consistency level with Sanger sequencing than the SCM for all pathogens. Additionally, when the NGS was set to a diagnostic gold standard, the specificity and sensitivity of the LAMP assay for LRTIs were 94.49% and 75.00%. The present study demonstrated that the developed LAMP has high consistency with the sequencing methods. Meanwhile, the LAMP assay has a higher detection rate compared to the SCM. It may be a powerful tool for rapid and reliable clinical diagnosis of LRTIs in primary hospitals.

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Open accessPosted ContentDOI: 10.1101/2021.02.24.432203
24 Feb 2021-bioRxiv
Abstract: The severe acute respiratory syndrome (SARS)-CoV-2, a newly emerged coronavirus first identified in 2019, is the pathogenetic agent od Corona Virus Induced Disease (COVID)19. The virus enters the human cells after binding to the angiotensin converting enzyme (ACE) 2 receptor in target tissues. ACE2 expression is induced in response to inflammation. The colon expression of ACE2 is upregulated in patients with inflammatory bowel disease (IBD), highlighting a potential risk of intestinal inflammation in promoting viral entry in the human body. Because mechanisms that regulate ACE2 expression in the intestine are poorly understood and there is a need of anti-SARS-CoV2 therapies, we have settled to investigate whether natural flavonoids might regulate the expression of ACE2 in intestinal models of inflammation. The results of these studies demonstrated that pelargonidin, a natural flavonoid bind and activates the Aryl hydrocarbon Receptor (AhR) in vitro and reverses intestinal inflammation caused by chronic exposure to high fat diet or to the intestinal braking-barrier agent DSS in a AhR-dependent manner. In these two models, development of colon inflammation associated with upregulation of ACE2 mRNA expression. Colon levels of ACE2 mRNA were directly correlated with TNF mRNA levels. In contrast to ACE2 the angiotensin 1-7 receptor MAS was downregulated in the inflamed tissues. Molecular docking studies suggested that pelargonidin binds a fatty acid binding pocket on the receptor binding domain of SARS-CoV2 Spike protein. In vitro studies demonstrated that pelargonidin significantly reduces the binding of SARS-CoV2 Spike protein to ACE2 and reduces the SARS-CoV2 replication in a concentration-dependent manner. In summary, we have provided evidence that a natural flavonoid might hold potential in reducing intestinal inflammation and ACE2 induction in the inflamed colon in a AhR-dependent manner.

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Topics: Aryl hydrocarbon receptor (54%), Inflammation (54%), Fatty acid binding (53%) ... read more

42 results found

Open accessJournal ArticleDOI: 10.1093/CID/CIW353
Andre C. Kalil1, Mark L. Metersky2, Michael Klompas3, John Muscedere4  +17 moreInstitutions (18)
Abstract: It is important to realize that guidelines cannot always account for individual variation among patients. They are not intended to supplant physician judgment with respect to particular patients or special clinical situations. IDSA considers adherence to these guidelines to be voluntary, with the ultimate determination regarding their application to be made by the physician in the light of each patient's individual circumstances.These guidelines are intended for use by healthcare professionals who care for patients at risk for hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP), including specialists in infectious diseases, pulmonary diseases, critical care, and surgeons, anesthesiologists, hospitalists, and any clinicians and healthcare providers caring for hospitalized patients with nosocomial pneumonia. The panel's recommendations for the diagnosis and treatment of HAP and VAP are based upon evidence derived from topic-specific systematic literature reviews.

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1,637 Citations

Open accessJournal ArticleDOI: 10.1056/NEJMOA1500245
Seema Jain1, Derek J. Williams2, Sandra R. Arnold3, Krow Ampofo4  +28 moreInstitutions (5)
Abstract: Background Incidence estimates of hospitalizations for community-acquired pneumonia among children in the United States that are based on prospective data collection are limited. Updated estimates of pneumonia that has been confirmed radiographically and with the use of current laboratory diagnostic tests are needed. Methods We conducted active population-based surveillance for community-acquired pneumonia requiring hospitalization among children younger than 18 years of age in three hospitals in Memphis, Nashville, and Salt Lake City. We excluded children with recent hospitalization or severe immunosuppression. Blood and respiratory specimens were systematically collected for pathogen detection with the use of multiple methods. Chest radiographs were reviewed independently by study radiologists. Results From January 2010 through June 2012, we enrolled 2638 of 3803 eligible children (69%), 2358 of whom (89%) had radiographic evidence of pneumonia. The median age of the children was 2 years (interquartile ...

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Topics: Pneumonia (58%), Community-acquired pneumonia (58%), Population (52%)

1,630 Citations

Open accessJournal ArticleDOI: 10.1164/RCCM.201908-1581ST
Joshua P. Metlay1, Grant W. Waterer2, Ann C. Long3, Antonio Anzueto4  +14 moreInstitutions (14)
Abstract: Background: This document provides evidence-based clinical practice guidelines on the management of adult patients with community-acquired pneumonia.Methods: A multidisciplinary panel conducted pra...

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Topics: Guideline (57%)

955 Citations

Open accessJournal ArticleDOI: 10.1183/09031936.05.00055705
Mark Woodhead1Institutions (1)
Abstract: Guidelines for the management of adult lower respiratory tract infections (LRTIs) were first published by a Task Force of the European Respiratory Society (ERS) in 1998 [1]. In 2005, a completely revised version was produced, this time by a joint Task Force of the ERS and the European Society for Clinical Microbiology and Infectious Diseases (ESCMID) [2]. They used up-to-date methodology for guideline development, including a transparent and objective systematic literature search strategy, and evidence and recommendation grading [2]. Now, 6 yrs later, a joint Task Force of the two Societies, using the same methodology as in 2005, has produced a further update of these guidelines incorporating publications through to May 2010. The Task Force included an epidemiologist with expertise in guideline methodology and experts in the specialty areas relevant to LRTI management, including general practice, microbiology, infectious diseases, respiratory medicine, intensive care and public health. A short version of the guidelines containing only the recommendations has now been published in Clinical Microbiology and Infection [3], with more detailed versions available on each Society’s website. The guidelines cover the breadth of adult community-acquired respiratory infection, including prevention (both vaccine- and nonvaccine-related), infections in the community and infections in those admitted to hospital, including pneumonia, exacerbations of chronic obstructive pulmonary disease (COPD) and exacerbations of bronchiectasis. The …

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Topics: Respiratory infection (61%), Respiratory tract infections (58%), Guideline (54%) ... read more

879 Citations

Open accessJournal ArticleDOI: 10.1111/J.1469-0691.2011.03672.X
Mark Woodhead1, Francesco Blasi2, Santiago Ewig, Javier Garau3  +8 moreInstitutions (6)
Abstract: This document is an update of Guidelines published in 2005 and now includes scientific publications through to May 2010. It provides evidence-based recommendations for the most common management questions occurring in routine clinical practice in the management of adult patients with LRTI. Topics include management outside hospital, management inside hospital (including community-acquired pneumonia (CAP), acute exacerbations of COPD (AECOPD), acute exacerbations of bronchiectasis) and prevention. Background sections and graded evidence tables are also included. The target audience for the Guideline is thus all those whose routine practice includes the management of adult LRTI.

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Topics: Guideline (53%), Evidence-based medicine (50%)

669 Citations

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