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Srivastava S, Sharad N, Kiro VV, Ningombam A, Shrivastava S, Farooque K, Mathur P. Utility of a multiplex pathogen detection system directly from respiratory specimens for treatment and diagnostic stewardship. Microbiol Spectr 2024; 12:e0375923. [PMID: 38712971 PMCID: PMC11237763 DOI: 10.1128/spectrum.03759-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 03/29/2024] [Indexed: 05/08/2024] Open
Abstract
The availability of syndrome-based panels for various ailments has widened the scope of diagnostics in many clinical settings. These panels can detect a multitude of pathogens responsible for a particular condition, which can lead to a timely diagnosis and better treatment outcomes. In contrast to traditional identification methods based on pathogen growth on culture, syndrome-based panels offer a quicker diagnosis, which can be especially beneficial in situations requiring urgent care, such as intensive care units. One such panel is the Biofire Filmarray Pneumonia plus Panel (BFP), which we have compared against microbiological culture and identification. The lower respiratory samples from patients were tested with BFP, culture, and identification with culture considered the gold standard. The phenotypic antibiotic susceptibility results (Vitek 2) were compared with the antimicrobial resistance (AMR) genes detected in BFP. Statistical analysis was carried out using GraphPad 7.0 and MS Excel (Microsoft Inc.). The results showed a positive percent agreement of 100% and a negative percent agreement of 47.8% with an overall agreement of 76.72% compared to culture. BFP was better at identifying fastidious bacteria, and the agreement with culture was higher for high bacterial identification numbers (107 and 106). There was also a correlation between the number of pathogens detected and growth in culture. Carbapenemase genes were detected in around 80% of phenotypically resistant samples and correlated with in-house PCR 60% of the time. Hence, BFP results need to be interpreted with caution especially when multiple pathogens are detected. Similarly, the presence or absence of AMR genes should be used to guide the therapy while being watchful of unusual resistance or susceptibility. The cost constraints and low throughput call for patient selection criteria and prioritization in emergency or resource-limited conditions.IMPORTANCEApplication of syndrome-based panels in clinical microbiology is of huge support in infectious conditions requiring urgent interventions, such as pneumonia. Interpreting the results requires caution; hence, we have compared the results obtained from Biofire Filmarray Pneumonia plus Panel with standard microbiological methods.
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Affiliation(s)
| | - Neha Sharad
- Department of Microbiology, AIIMS, New Delhi, India
| | | | - Aparna Ningombam
- Department of Laboratory Medicine, JPNATC, AIIMS, New Delhi, India
| | | | | | - Purva Mathur
- Department of Laboratory Medicine, JPNATC, AIIMS, New Delhi, India
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Walker AM, Timbrook TT, Hommel B, Prinzi AM. Breaking Boundaries in Pneumonia Diagnostics: Transitioning from Tradition to Molecular Frontiers with Multiplex PCR. Diagnostics (Basel) 2024; 14:752. [PMID: 38611665 PMCID: PMC11012095 DOI: 10.3390/diagnostics14070752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 03/24/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
The advent of rapid molecular microbiology testing has revolutionized infectious disease diagnostics and is now impacting pneumonia diagnosis and management. Molecular platforms offer highly multiplexed assays for diverse viral and bacterial detection, alongside antimicrobial resistance markers, providing the potential to significantly shape patient care. Despite the superiority in sensitivity and speed, debates continue regarding the clinical role of multiplex molecular testing, notably in comparison to standard methods and distinguishing colonization from infection. Recent guidelines endorse molecular pneumonia panels for enhanced sensitivity and rapidity, but implementation requires addressing methodological differences and ensuring clinical relevance. Diagnostic stewardship should be leveraged to optimize pneumonia testing, emphasizing pre- and post-analytical strategies. Collaboration between clinical microbiologists and bedside providers is essential in developing implementation strategies to maximize the clinical utility of multiplex molecular diagnostics in pneumonia. This narrative review explores these multifaceted issues, examining the current evidence on the clinical performance of multiplex molecular assays in pneumonia, and reflects on lessons learned from previous microbiological advances. Additionally, given the complexity of pneumonia and the sensitivity of molecular diagnostics, diagnostic stewardship is discussed within the context of current literature, including implementation strategies that consider pre-analytical and post-analytical modifications to optimize the clinical utility of advanced technologies like multiplex PCR.
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Affiliation(s)
| | - Tristan T. Timbrook
- bioMerieux, 69280 Marcy L’etoile, France (A.M.P.)
- Department of Pharmacotherapy, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
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Pickens CI, Gao CA, Morales-Nebreda L, Wunderink RG. Microbiology of Severe Community-Acquired Pneumonia and the Role of Rapid Molecular Techniques. Semin Respir Crit Care Med 2024; 45:158-168. [PMID: 38196061 DOI: 10.1055/s-0043-1777770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
The microbiology of severe community acquired pneumonia (SCAP) has implications on management, clinical outcomes and public health policy. Therefore, knowledge of the etiologies of SCAP and methods to identify these microorganisms is key. Bacteria including Streptococcus pneumoniae, Staphylococcus aureus and Enterobacteriaceae continue to be important causes of SCAP. Viruses remain the most commonly identified etiology of SCAP. Atypical organisms are also important etiologies of SCAP and are critical to identify for public health. With the increased number of immunocompromised individuals, less common pathogens may also be found as the causative agent of SCAP. Traditional diagnostic tests, including semi-quantitative respiratory cultures, blood cultures and urinary antigens continue to hold an important role in the evaluation of patients with SCAP. Many of the limitations of the aforementioned tests are addressed by rapid, molecular diagnostic tests. Molecular diagnostics utilize culture-independent technology to identify species-specific genetic sequences. These tests are often semi-automated and provide results within hours, which provides an opportunity for expedient antibiotic stewardship. The existing literature suggests molecular diagnostic techniques may improve antibiotic stewardship in CAP, and future research should investigate optimal methods for implementation of these assays into clinical practice.
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Affiliation(s)
- Chiagozie I Pickens
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Catherine A Gao
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Luisa Morales-Nebreda
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Richard G Wunderink
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
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Søgaard KK, Hinic V, Goldenberger D, Gensch A, Schweitzer M, Bättig V, Siegemund M, Bassetti S, Bingisser R, Tamm M, Battegay M, Weisser M, Stolz D, Khanna N, Egli A. Evaluation of the clinical relevance of the Biofire © FilmArray pneumonia panel among hospitalized patients. Infection 2024; 52:173-181. [PMID: 37572241 PMCID: PMC10810975 DOI: 10.1007/s15010-023-02080-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/27/2023] [Indexed: 08/14/2023]
Abstract
PURPOSE Panel PCR tests provide rapid pathogen identification. However, their diagnostic performance is unclear. We assessed the performance of the Biofire© FilmArray pneumonia (PN)-panel against standard culture in broncho-alveolar lavage (BAL) samples. METHODS Setting: University Hospital Basel (February 2019 to July 2020), including hospitalized patients with a BAL (± pneumonia). We determined sensitivity and specificity of the PN-panel against standard culture. Using univariate logistic regression, we calculated odds ratios (OR) for pneumonia according to PN-panel and culture status, stratifying by chronic pulmonary disease. We calculated ORs for pneumonia for different pathogens to estimate the clinical relevance. RESULTS We included 840 adult patients, 60% were males, median age was 68 years, 35% had chronic pulmonary disease, 21% had pneumonia, and 36% had recent antibiotic use. In 1078 BAL samples, bacterial pathogens were detected in 36% and 16% with PN-panel and culture, respectively. The overall sensitivity and specificity of the PN-panel was high, whereas the positive predictive value was low. The OR of pneumonia was 1.1 (95% CI 0.7-1.6) for PN-panel-positive only; 2.6 (95% CI 1.3-5.3) for culture-positive only, and 1.6 (95% CI 1.0-2.4) for PN-panel and culture-positive. The detection rate of Haemophilus influenzae, Staphylococcus aureus, and Moraxella catarrhalis in the PN-panel was high but not associated with pneumonia. CONCLUSION While sensitivity and specificity of PN-panel are high compared to culture, pathogen detection did not correlate well with a pneumonia diagnosis. Patients with culture-positive BAL had the highest OR for pneumonia-thus the impact of the PN-panel on clinical management needs further evaluation in randomized controlled trials.
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Affiliation(s)
- Kirstine K Søgaard
- Clinical Bacteriology and Mycology, University Hospital Basel, 4031, Basel, Switzerland
- Department of Biomedicine, Applied Microbiology Research, University of Basel, Basel, Switzerland
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
| | - Vladimira Hinic
- Clinical Bacteriology and Mycology, University Hospital Basel, 4031, Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30 8006, Zurich, Switzerland
| | - Daniel Goldenberger
- Clinical Bacteriology and Mycology, University Hospital Basel, 4031, Basel, Switzerland
| | - Alexander Gensch
- Clinical Bacteriology and Mycology, University Hospital Basel, 4031, Basel, Switzerland
- Department of Biomedicine, Applied Microbiology Research, University of Basel, Basel, Switzerland
| | - Michael Schweitzer
- Clinical Bacteriology and Mycology, University Hospital Basel, 4031, Basel, Switzerland
- Department of Biomedicine, Applied Microbiology Research, University of Basel, Basel, Switzerland
| | - Veronika Bättig
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Martin Siegemund
- Intensive Care Medicine, University Hospital Basel, Basel, Switzerland
| | - Stefano Bassetti
- Internal Medicine, University Hospital Basel, Basel, Switzerland
| | - Roland Bingisser
- Emergency Medicine, University Hospital Basel, Basel, Switzerland
| | - Michael Tamm
- Pneumology, University Hospital Basel, Basel, Switzerland
| | - Manuel Battegay
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Maja Weisser
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Daiana Stolz
- Pneumology, University Hospital Basel, Basel, Switzerland
| | - Nina Khanna
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Adrian Egli
- Clinical Bacteriology and Mycology, University Hospital Basel, 4031, Basel, Switzerland.
- Department of Biomedicine, Applied Microbiology Research, University of Basel, Basel, Switzerland.
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30 8006, Zurich, Switzerland.
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Falsey AR, Branche AR, Croft DP, Formica MA, Peasley MR, Walsh EE. Real-life Assessment of BioFire FilmArray Pneumonia Panel in Adults Hospitalized With Respiratory Illness. J Infect Dis 2024; 229:214-222. [PMID: 37369370 PMCID: PMC10786250 DOI: 10.1093/infdis/jiad221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/09/2023] [Accepted: 06/22/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Inability to identify the microbial etiology of lower respiratory tract infection leads to unnecessary antibiotic use. We evaluated the utility of the BioFire FilmArray Pneumonia Panel (BioFire PN) to inform microbiologic diagnosis. METHODS Hospitalized adults with respiratory illness were recruited; sputa and clinical/laboratory data were collected. Sputa were cultured for bacteria and tested with BioFire PN. Microbial etiology was adjudicated by 4 physicians. Bacterial polymerase chain reaction (PCR) was compared with culture and clinical adjudication. RESULTS Of 298 sputa tested, BioFire PN detected significantly more pathogens (350 bacteria, 16 atypicals, and 164 viruses) than sputum culture plus any standard-of-care testing (91% vs 60%, P < .0001). When compared with culture, the sensitivity of BioFire PN for individual bacteria was 46% to 100%; specificity, 61% to 100%; and negative predictive value, 92% to 100%. Cases were adjudicated as viral (n = 58) and bacterial (n = 100). PCR detected bacteria in 55% of viral cases and 95% of bacterial (P < .0001). High serum procalcitonin and bacterial adjudication were more often associated with sputa with 106 or 107 copies detected. CONCLUSIONS Multiplex PCR testing of sputa for bacteria is useful to rule out bacterial infection with added value to detect viruses and atypical bacteria.
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Affiliation(s)
| | | | - Daniel P Croft
- Department of Pulmonary and Critical Medicine, University of Rochester
| | - Maria A Formica
- Infectious Disease Unit, Rochester General Hospital, Rochester, New York, USA
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Moy AC, Kimmoun A, Merkling T, Berçot B, Caméléna F, Poncin T, Deniau B, Mebazaa A, Dudoignon E, Dépret F. Performance evaluation of a PCR panel (FilmArray® Pneumonia Plus) for detection of respiratory bacterial pathogens in respiratory specimens: A systematic review and meta-analysis. Anaesth Crit Care Pain Med 2023; 42:101300. [PMID: 37709201 DOI: 10.1016/j.accpm.2023.101300] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/31/2023] [Accepted: 08/16/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND Accuracy and timing of antibiotic therapy remain a challenge for lower respiratory tract infections. New molecular techniques using Multiplex Polymerase Chain Reaction, including the FilmArray® Pneumonia Plus Panel [FAPP], have been developed to address this. The aim of this study is to evaluate the FAPP diagnostic performance for the detection of the 15 typical bacteria of the panel from respiratory samples in a meta-analysis from a systematic review. METHODS We searched PubMed and EMBASE from January 1, 2010, to December 31, 2022, and selected any study on the FAPP diagnostic performance on respiratory samples compared to the reference standard, bacterial culture. The main outcome was the overall diagnostic accuracy with sensitivity and specificity. We calculated the log Diagnostic Odds Ratio and analyzed performance for separate bacteria, antimicrobial resistance genes, and according to the sample type. We also reported the FAPP turnaround time and the out-of-panel bacteria number and species. This study is registered with PROSPERO (CRD42021226280). RESULTS From 10 317 records, we identified 30 studies including 8 968 samples. Twenty-one were related to intensive care. The overall sensitivity and specificity were 94% [95% Confidence Interval (CI) 91-95] and 98% [95%CI 97-98], respectively. The log Diagnostic Odds Ratio was 6.35 [95%CI 6.05-6.65]. 9.3% [95%CI 9.2-9.5] of bacteria detected in culture were not included in the FAPP panel. CONCLUSION This systematic review reporting the FAPP evaluation revealed a high accuracy. This test may represent an adjunct tool for pulmonary bacterial infection diagnostic and antimicrobial stewardship. Further evidence is needed to assess the impact on clinical outcome.
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Affiliation(s)
- Anne-Clotilde Moy
- Department of Anesthesiology, Critical Care and Burn Unit, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Antoine Kimmoun
- Intensive Care Medicine Brabois, CHRU de Nancy, INSERM U1116, Université de Lorraine, Nancy, France; INSERM UMR-S 942, MASCOT, Université de Paris, Paris, France
| | - Thomas Merkling
- Nancy Clinical Investigation Centre, INSERM 1433, CHRU Nancy, Université de Lorraine, Nancy, France
| | - Béatrice Berçot
- Department of Microbiology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; University of Paris, INSERM 1137, IAME, Paris, France
| | - François Caméléna
- Department of Microbiology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; University of Paris, INSERM 1137, IAME, Paris, France
| | - Thibaut Poncin
- Department of Microbiology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; University of Paris, INSERM 1137, IAME, Paris, France
| | - Benjamin Deniau
- Department of Anesthesiology, Critical Care and Burn Unit, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; University of Paris, FHU PROMICE, INSERM 942, INI-CRCT Network, Paris, France
| | - Alexandre Mebazaa
- Department of Anesthesiology, Critical Care and Burn Unit, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; University of Paris, FHU PROMICE, INSERM 942, INI-CRCT Network, Paris, France
| | - Emmanuel Dudoignon
- Department of Anesthesiology, Critical Care and Burn Unit, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; University of Paris, FHU PROMICE, INSERM 942, INI-CRCT Network, Paris, France.
| | - François Dépret
- Department of Anesthesiology, Critical Care and Burn Unit, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; University of Paris, FHU PROMICE, INSERM 942, INI-CRCT Network, Paris, France
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Cartuliares MB, Rosenvinge FS, Mogensen CB, Skovsted TA, Andersen SL, Østergaard C, Pedersen AK, Skjøt-arkil H. Evaluation of point-of-care multiplex polymerase chain reaction in guiding antibiotic treatment of patients acutely admitted with suspected community-acquired pneumonia in Denmark: A multicentre randomised controlled trial. PLoS Med 2023; 20:e1004314. [PMID: 38015833 PMCID: PMC10684013 DOI: 10.1371/journal.pmed.1004314] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 10/26/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND Rapid and accurate detection of pathogens is needed in community-acquired pneumonia (CAP) to enable appropriate antibiotics and to slow the development of antibiotic resistance. We aimed to compare the effect of point-of-care (POC) polymerase chain reaction (PCR) detection of respiratory pathogens added to standard care with standard care only (SCO) on antibiotic prescriptions after acute hospital admission. METHODS AND FINDINGS We performed a superiority, parallel-group, open-label, multicentre, randomised controlled trial (RCT) in 3 Danish medical emergency departments (EDs) from March 2021 to February 2022. Adults acutely admitted with suspected CAP during the daytime on weekdays were included and randomly assigned (1:1) to POC-PCR (The Biofire FilmArray Pneumonia Panel plus added to standard care) or SCO (routine culture and, if requested by the attending physician, target-specific PCR) analysis of respiratory samples. We randomly assigned 294 patients with successfully collected samples (tracheal secretion 78.4% or expectorated sputum 21.6%) to POC-PCR (n = 148, 50.4%) or SCO (146, 49.6%). Patients and investigators owning the data were blinded to the allocation and test results. Outcome adjudicators and clinical staff at the ED were not blinded to allocation and test results but were together with the statistician, blinded to data management and analysis. Laboratory staff performing standard care analyses was blinded to allocation. The study coordinator was not blinded. Intention-to-treat and per protocol analysis were performed using logistic regression with Huber-White clustered standard errors for the prescription of antibiotic treatment. Loss to follow-up comprises 3 patients in the POC-PCR (2%) and none in the SCO group. Intention-to-treat analysis showed no difference in the primary outcome of prescriptions of no or narrow-spectrum antibiotics at 4 h after admission for the POC-PCR (n = 91, 62.8%) odds ratio (OR) 1.13; (95% confidence interval (CI) [0.96, 1.34] p = 0.134) and SCO (n = 87, 59.6%). Secondary outcomes showed that prescriptions were significantly more targeted at 4-h OR 5.68; (95% CI [2.49, 12.94] p < 0.001) and 48-h OR 4.20; (95% CI [1.87, 9.40] p < 0.001) and more adequate at 48-h OR 2.11; (95% CI [1.23, 3.61] p = 0.006) and on day 5 in the POC-PCR group OR 1.40; (95% CI [1.18, 1.66] p < 0.001). There was no difference between the groups in relation to intensive care unit (ICU) admissions OR 0.54; (95% CI [0.10, 2.91] p = 0.475), readmission within 30 days OR 0.90; (95% CI [0.43, 1.86] p = 0.787), length of stay (LOS) IRR 0.82; (95% CI [0.63, 1.07] p = 0.164), 30 days mortality OR 1.24; (95% CI [0.32, 4.82] p = 0.749), and in-hospital mortality OR 0.98; (95% CI [0.19, 5.06] p = 0.986). CONCLUSIONS In a setting with an already restrictive use of antibiotics, adding POC-PCR to the diagnostic setup did not increase the number of patients treated with narrow-spectrum or without antibiotics. POC-PCR may result in a more targeted and adequate use of antibiotics. A significant study limitation was the concurrent Coronavirus Disease 2019 (COVID-19) pandemic resulting in an unusually low transmission of respiratory virus. TRIAL REGISTRATION ClinicalTrials.gov (NCT04651712).
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Affiliation(s)
- Mariana Bichuette Cartuliares
- Department of Emergency Medicine, University Hospital of Southern Denmark, Aabenraa, Denmark
- Department of Regional Health Research, University of Southern Denmark, Aabenraa, Denmark
| | - Flemming Schønning Rosenvinge
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
- Research Unit of Clinical Microbiology, University of Southern Denmark, Odense, Denmark
| | - Christian Backer Mogensen
- Department of Emergency Medicine, University Hospital of Southern Denmark, Aabenraa, Denmark
- Department of Regional Health Research, University of Southern Denmark, Aabenraa, Denmark
| | - Thor Aage Skovsted
- Department of Biochemistry and Immunology, University Hospital of Southern Denmark, Aabenraa, Denmark
| | - Steen Lomborg Andersen
- Department of Clinical Microbiology, University Hospital of Southern Denmark, Aabenraa, Denmark
| | - Claus Østergaard
- Department of Clinical Microbiology, Lillebaelt Hospital, Vejle, Denmark
| | | | - Helene Skjøt-arkil
- Department of Emergency Medicine, University Hospital of Southern Denmark, Aabenraa, Denmark
- Department of Regional Health Research, University of Southern Denmark, Aabenraa, Denmark
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Serigstad S, Knoop ST, Markussen DL, Ulvestad E, Bjørneklett RO, Ebbesen MH, Kommedal Ø, Grewal HMS. Diagnostic utility of oropharyngeal swabs as an alternative to lower respiratory tract samples for PCR-based syndromic testing in patients with community-acquired pneumonia. J Clin Microbiol 2023; 61:e0050523. [PMID: 37585220 PMCID: PMC10512787 DOI: 10.1128/jcm.00505-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/06/2023] [Indexed: 08/17/2023] Open
Abstract
Syndromic PCR-based analysis of lower respiratory tract (LRT) samples in patients with community-acquired pneumonia (CAP) improves the bacterial yield and time-to-results compared to culture-based methods. However, obtaining adequate sputum samples can be challenging and is frequently not prioritized in the emergency department (ED). In this study, we assess the concordance of microbiological detections between oropharyngeal- (OP) and LRT samples from patients presenting to the ED with CAP using a syndromic PCR-based respiratory panel [Biofire FilmArray Pneumonia plus (FAP plus)]. Paired OP- and high-quality LRT samples were collected from 103 patients with confirmed CAP, who had been included in a randomized controlled trial (NCT04660084) or a subsequent observational study at Haukeland University Hospital, and analyzed using the FAP plus. The LRT samples were obtained mainly by sputum induction (88%). Using the LRT samples as a reference standard, the positive percent agreement (PPA), negative percent agreement (NPA), and overall percent agreement for the most common bacterial pathogens in CAP, Streptococcus pneumoniae and Haemophilus influenzae, were 85%, 99% and 95%, and 86%, 98% and 93%, respectively. For Moraxella catarrhalis, the PPA was lower (74%), while the NPA was 100%. For bacteria that are less likely causes of uncomplicated CAP (e.g., Staphylococcus aureus and Enterobacterales) the results were more divergent. In conclusion, the FAP plus detects the most common CAP pathogens S. pneumoniae and H. influenzae from OP samples with high PPAs and excellent NPAs when compared with LRT samples. For these pathogens, the PPAs for OP samples were higher than previous reports for nasopharyngeal samples. This suggests that analysis of OP samples with syndromic PCR panels could represent an alternative approach for rapid microbiological testing in the ED, especially in patients where LRT samples are difficult to obtain. Divergent results for bacteria that are less likely to cause uncomplicated CAP do, however, emphasize the need for clinical evaluation of positive test results.
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Affiliation(s)
- Sondre Serigstad
- Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Siri T. Knoop
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, University of Bergen, Bergen, Norway
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Dagfinn L. Markussen
- Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, University of Bergen, Bergen, Norway
| | - Elling Ulvestad
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, University of Bergen, Bergen, Norway
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Rune O. Bjørneklett
- Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Marit H. Ebbesen
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Øyvind Kommedal
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, University of Bergen, Bergen, Norway
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Harleen M. S. Grewal
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, University of Bergen, Bergen, Norway
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
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Characteristics, Outcomes, and Factors Affecting Mortality in Hospitalized Patients with CAP Due to Different Variants of SARS-CoV-2 and Non-COVID-19 CAP. J Clin Med 2023; 12:jcm12041388. [PMID: 36835923 PMCID: PMC9964315 DOI: 10.3390/jcm12041388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 01/29/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
The study was conducted from October 2020 to March 2022 in a province in southern Thailand. The inpatients with community-acquired pneumonia (CAP) and more than 18 years old were enrolled. Of the 1511 inpatients with CAP, COVID-19 was the leading cause, accounting for 27%. Among the patients with COVID-19 CAP, mortalities, mechanical ventilators, ICU admissions, ICU stay, and hospital costs were significantly higher than of those with non-COVID-19 CAP. Household and workplace contact with COVID-19, co-morbidities, lymphocytopenia and peripheral infiltration in chest imaging were associated with CAP due to COVID-19. The delta variant yielded the most unfavorable clinical and non-clinical outcomes. While COVID-19 CAP due to B.1.113, Alpha and Omicron variants had relatively similar outcomes. Among those with CAP, COVID-19 infection as well as obesity, a higher Charlson comorbidity index (CCI) and APACHE II score were associated with in-hospital mortality. Among those with COVID-19 CAP, obesity, infection due to the Delta variant, a higher CCI and higher APACHE II score were associated with in-hospital mortality. COVID-19 had a great impact on the epidemiology and outcomes of CAP.
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Zhang R, Wu Y, Deng G, Deng J. Value of sputum Gram stain, sputum culture, and bronchoalveolar lavage fluid Gram stain in predicting single bacterial pathogen among children with community-acquired pneumonia. BMC Pulm Med 2022; 22:427. [PMCID: PMC9675245 DOI: 10.1186/s12890-022-02234-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/09/2022] [Indexed: 11/21/2022] Open
Abstract
Background Currently, the microbial etiology of community-acquired pneumonia in children remains challenging. While Gram stain and sputum culture are commonly used to detect bacterial pathogens, it is unclear whether these approaches can predict single pathogen from bronchoalveolar lavage fluid (BALF) culture. Methods A retrospective study involving 287 children hospitalized for pneumonia was conducted. Sputum specimens were collected on admission; and BALF specimens were collected within 24 h after admission. Taking BALF culture as the reference standard, the sensitivity and specificity of Sputum Gram stain (SGS), sputum culture, and BALF Gram stain (BGS) were calculated. The agreement between these approaches and BALF culture was compared using kappa statistics. Results For SGS, the specificity was 23%. The overall sensitivity was 70%, including 87% for Gram-positive (G+) cocci, 56% for Gram-negative (G-) cocci, and 50% for G-bacilli. For sputum culture, the specificity was 70%. The overall sensitivity was 64%, including 71% for Streptococcus pneumoniae, 71% for Moraxella catarrhalis, and 64% for Haemophilus influenzae. For BGS, the specificity was 71%. The overall sensitivity was 60%, including 77% for G+cocci, 38% for G-cocci, and 44% for G-bacilli. While SGS had poor agreement with BALF culture, both sputum culture and BGS had moderate agreement with BALF culture. Conclusions Both sputum culture and BGS are helpful in predicting single bacterial pathogen from BALF culture among children with community-acquired pneumonia. Sputum cultures and BGS can provide early clues for BALF pathogen when BALF culture results are pending or bronchoscopy is not performed.
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Affiliation(s)
- Ruimu Zhang
- grid.452787.b0000 0004 1806 5224Department of Infectious Diseases, Shenzhen Children’s Hospital, Shenzhen, 518038 China
| | - Yue Wu
- grid.452787.b0000 0004 1806 5224Department of Clinical Pharmacy, Shenzhen Children’s Hospital, Shenzhen, 518038 China
| | - Guangcheng Deng
- grid.1002.30000 0004 1936 7857Faculty of Medicine, Nursing and Health Science, Monash University, Melbourne, Australia
| | - Jikui Deng
- grid.452787.b0000 0004 1806 5224Department of Infectious Diseases, Shenzhen Children’s Hospital, Shenzhen, 518038 China
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11
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Jitmuang A, Puttinad S, Hemvimol S, Pansasiri S, Horthongkham N. A multiplex pneumonia panel for diagnosis of hospital-acquired and ventilator-associated pneumonia in the era of emerging antimicrobial resistance. Front Cell Infect Microbiol 2022; 12:977320. [PMID: 36310855 PMCID: PMC9597303 DOI: 10.3389/fcimb.2022.977320] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/27/2022] [Indexed: 11/24/2022] Open
Abstract
Background Antimicrobial resistance (AMR), including multidrug (MDR) and extensively drug-resistant (XDR) bacteria, is an essential consideration in the prevention and management of hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP). In the AMR era, the clinical utility of the BioFire FilmArray Pneumonia Panel Plus (BFPP) to diagnose HAP/VAP has not been thoroughly evaluated. Methods We enrolled adult hospitalized patients with HAP or VAP at Siriraj Hospital and Saraburi Hospital from July 2019–October 2021. Respiratory samples were collected for standard microbiological assays, antimicrobial susceptibility testing (AST), and the BFPP analysis. Results Of 40 subjects, 21 were men. The median duration of HAP/VAP diagnoses was 10.5 (5, 21.5) days, and 36 endotracheal aspirate and 4 sputum samples were collected. Standard cultures isolated 54 organisms—A. baumannii (37.0%), P. aeruginosa (29.6%), and S. maltophilia (16.7%). 68.6% of Gram Negatives showed an MDR or XDR profile. BFPP detected 77 bacterial targets—A. baumannii 32.5%, P. aeruginosa 26.3%, and K. pneumoniae 17.5%. Of 28 detected AMR gene targets, CTX-M (42.5%), OXA-48-like (25%), and NDM (14.3%) were the most common. Compared with standard testing, the BFPP had an overall sensitivity of 98% (88-100%), specificity of 81% (74-87%), positive predictive value of 60% (47-71%), negative predictive value of 99% (96-100%), and kappa (κ) coefficient of 0.64 (0.53-0.75). The concordance between phenotypic AST and detected AMR genes in Enterobacterales was 0.57. There was no concordance among A. baumannii, P. aeruginosa, and S. aureus Conclusions The BFPP has excellent diagnostic sensitivity to detect HAP/VAP etiology. The absence of S. maltophilia and discordance of AMR gene results limit the test performance.
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Affiliation(s)
- Anupop Jitmuang
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- *Correspondence: Anupop Jitmuang,
| | - Soravit Puttinad
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Siri Pansasiri
- Saraburi Hospital Research Center, Saraburi Hospital, Saraburi, Thailand
| | - Navin Horthongkham
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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12
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Kosai K, Akamatsu N, Ota K, Mitsumoto-Kaseida F, Sakamoto K, Hasegawa H, Izumikawa K, Mukae H, Yanagihara K. BioFire FilmArray Pneumonia Panel enhances detection of pathogens and antimicrobial resistance in lower respiratory tract specimens. Ann Clin Microbiol Antimicrob 2022; 21:24. [PMID: 35659683 PMCID: PMC9166201 DOI: 10.1186/s12941-022-00512-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 05/06/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
This study investigated the diagnostic utility of the BioFire FilmArray Pneumonia Panel (PN panel), an automated and multiplexed nucleic acid detection system that rapidly detects 26 pathogens (18 bacteria and eight viruses) and seven antimicrobial resistance markers in a single assay.
Methods
We analyzed the targets in lower respiratory tract specimens using the PN panel and compared the detection results with those of bacterial culture methods and antimicrobial susceptibility testing.
Results
Of the 57 samples analyzed, the PN panel detected 97 targets (84 bacteria, four viruses, and nine antimicrobial resistance markers). Detection of bacteria and antimicrobial resistance was three times greater than that of the bacterial culture (25 bacteria and two resistant isolates) against the targets available in the panel. The overall positive and negative percent agreements between the PN panel and culture methods for bacterial detection were 100.0% and 92.9%, respectively. Multiple pathogens were detected by the PN panel in 24 samples (42.1%), ranging from two pathogens in 11 samples (19.3%) to six pathogens in one sample (1.8%). The PN panel semiquantitatively detected higher copies (≥ 106 copies/mL) of bacterial targets if the bacteria were positive by the culture method. In contrast, the semiquantitative values obtained by the panel varied (104 to 107 ≤ copies/mL) among bacteria that were negative by the culture method.
Conclusions
The PN panel enhanced the detection of pathogens and antimicrobial resistance markers in lower respiratory tract specimens.
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13
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El-Nawawy AA, Antonios MA, Tawfik ME, Meheissen MA. Comparison of a Point-of-Care FilmArray Test to Standard-of-Care Microbiology Test in Diagnosis of Healthcare Associated Infections in a Tertiary Care Pediatric Intensive Care Unit. Antibiotics (Basel) 2022; 11:antibiotics11040453. [PMID: 35453205 PMCID: PMC9029956 DOI: 10.3390/antibiotics11040453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/04/2022] [Accepted: 03/08/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Rapid and accurate identification of healthcare associated pathogens is crucial for early diagnosis and treatment of infections. This study aimed to assess the performance of a point-of-care multiplex polymerase chain reaction (PCR) in diagnosis of pathogens and their antibiotic resistance genes in bloodstream infections, pneumonia and meningitis/encephalitis in a pediatric intensive care unit (PICU). Methods: A retrospective cross-sectional study was conducted on pediatric patients diagnosed with healthcare associated infections at Alexandria University PICU, Egypt. A total of 111 samples from 98 patients were subjected simultaneously to standard-of-care microbiology testing (SOCMT) and molecular testing by BioFire multiplex PCR. Results: In comparison to SOCMT, the BioFire FilmArray® had a better diagnostic yield with broncho-alveolar lavage (BAL) (45 vs. 21) and cerebrospinal fluid (CSF) samples (five vs. none) (p ≤ 0.0001). Klebsiella pneumoniae was the most common pathogen in BAL (n = 19 by BioFire, n = 9 by SOCMT) and blood (n = 7, by SOCMT and BioFire) samples, while Streptococcus pneumoniae was the most common in CSF samples. BioFire showed 95.8% overall percent agreement, 100% positive percent agreement and 95.6% negative percent agreement with SOCMT. All phenotypically confirmed resistant isolates had resistance genes by the BioFire FilmArray® (100%). The turnaround time (TAT) of positive results by the FilmArray panels was 1–1.5 h in comparison to 48–72 h by SOCMT (p ≤ 0.001). Conclusions: The results of the current study confirm the utility of the BioFire FilmArray® in making early decisions regarding patients’ diagnosis and management of infection in the PICU, in terms of rapid TAT and appropriate antimicrobial use.
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Affiliation(s)
- Ahmed A. El-Nawawy
- Department of Pediatrics, Faculty of Medicine, Alexandria University, Alexandria 21512, Egypt; (A.A.E.-N.); (M.A.A.); (M.E.T.)
| | - Manal A. Antonios
- Department of Pediatrics, Faculty of Medicine, Alexandria University, Alexandria 21512, Egypt; (A.A.E.-N.); (M.A.A.); (M.E.T.)
| | - Medhat E. Tawfik
- Department of Pediatrics, Faculty of Medicine, Alexandria University, Alexandria 21512, Egypt; (A.A.E.-N.); (M.A.A.); (M.E.T.)
| | - Marwa A. Meheissen
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Alexandria University, Alexandria 21512, Egypt
- Correspondence:
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14
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Kamel NA, Alshahrani MY, Aboshanab KM, El Borhamy MI. Evaluation of the BioFire FilmArray Pneumonia Panel Plus to the Conventional Diagnostic Methods in Determining the Microbiological Etiology of Hospital-Acquired Pneumonia. BIOLOGY 2022; 11:biology11030377. [PMID: 35336751 PMCID: PMC8945136 DOI: 10.3390/biology11030377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/18/2022] [Accepted: 02/23/2022] [Indexed: 01/13/2023]
Abstract
Hospital-acquired pneumonia (HAP) is a substantial public health issue that is associated with high mortality rates and is complicated by an arsenal of microbial etiologies, expressing multidrug-resistant phenotypes, rendering relatively limited therapeutic options. BioFire FilmArray Pneumonia Panel plus (BFPP) is a simple multiplexed PCR system that integrates sample preparation, nucleic acid extraction, amplification, and analysis of microbial etiology, with a turnaround time of about one hour. In comparison to standard culture methods, BFPP is simpler, easier to perform, and can simultaneously detect the most common pathogens involved in lower respiratory tract infections (34 targets). Accordingly, we evaluated the diagnostic performance of the multiplexed BFPP for the rapid detection of 27 clinically relevant respiratory pathogens and 7 genetic markers among 50 HAP cases admitted to the intensive care unit (ICU), who submitted mini-bronchoalveolar (mBAL) specimens. In comparison to standard culture methods, BFPP showed an overall sensitivity of 100% [95% CI; 90-100] and overall specificity of 90% [95% CI; 87.4-92.5] among all the tested bacterial targets. BFPP identified 11 viral targets (22%) among the tested specimens. The BFPP semi-quantitative analysis showed a concordance rate of 47.4% among positive culture specimens. For the investigation of the antibiotic resistance genes, BFPP showed a positive percent agreement (PPA), a negative percent agreement (NPA), and an overall percent agreement (OPA), reaching 97% [95% CI; 90-100], 95% [95% CI; 91.5-97], and 95% [95% CI; 93-97], respectively, with standard antibiotic sensitivity testing. In conclusion, BFPP has the potential to enhance the rapid microbiological diagnosis of HAP cases, and could aid in tailoring appropriate antibiotic therapies.
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Affiliation(s)
- Noha A. Kamel
- Department of Microbiology, Faculty of Pharmacy, Misr International University (MIU), Cairo P.O. Box 19648, Egypt; (N.A.K.); (M.I.E.B.)
| | - Mohammad Y. Alshahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, P.O. Box 61413, Abha 9088, Saudi Arabia;
| | - Khaled M. Aboshanab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity St., Abbassia, Cairo P.O. Box 11566, Egypt
- Correspondence: ; Tel.:+20-1007582620
| | - Mervat I. El Borhamy
- Department of Microbiology, Faculty of Pharmacy, Misr International University (MIU), Cairo P.O. Box 19648, Egypt; (N.A.K.); (M.I.E.B.)
- International Medical Center, Clinical Microbiology Laboratory, Cairo P.O. Box 11451, Egypt
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15
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Fireizen Y, Babbitt CJ, Adams S, Morphew T, Ferro ET, Randhawa I. The Impact of Pneumonia PCR Panel Testing in the PICU: A Quality Improvement Study. J Pediatr Intensive Care 2022. [DOI: 10.1055/s-0042-1743178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
AbstractInappropriate antibiotic usage can contribute to the promotion of resistant bacteria. In an effort to reduce antibiotic length of therapy (LOT), we initiated a performance improvement project utilizing pneumonia polymerase chain reaction (PCR) testing in ventilated pediatric intensive care unit (PICU) patients suspected of tracheitis or pneumonia. This is a single-center cohort intervention study that compared pre- and postimplementation patients. The intervention was the use of a pneumonia PCR panel on all PICU patients undergoing an evaluation for acute tracheitis or pneumonia during the postimplementation period. The inclusion criteria were either acute or acute on chronic respiratory failure. After an 8-month period, the charts were reviewed from both cohorts and baseline data, and outcome data were compared by statistical analysis. A total of 41 preimplementation and 30 postimplementation patients were compared, and no baseline differences were found except postimplementation patients being slightly older (133 vs. 56 months, p-value = 0.040). Analysis of the primary outcome measures found that the time to identification of organism (5 vs. 67 hours) and LOT (5 vs. 9 days, p < 0.001) were shorter in postimplementation patients compared with preimplementation patients. Antibiotics were changed based on the results of the pneumonia PCR on 18 of 30 patients (60%). There was no difference in ventilator-free days, PICU length of stay, or mortality. In conclusion, pneumonia PCR panel testing leads to more rapid results and is associated with reduced antibiotic LOT.
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Affiliation(s)
- Yaron Fireizen
- Department of Pediatric Pulmonology, Miller Children's and Women's Hospital of Long Beach, University of California, Irvine School of Medicine, Irvine, California, United States
| | - Christopher J. Babbitt
- Department of Pediatric Critical Care, Miller Children's and Women's Hospital of Long Beach, Long Beach, California, United States
| | - Susan Adams
- Department of Pediatric Pharmacy, Miller Children's and Women's Hospital of Long Beach, Long Beach, California, United States
| | - Tricia Morphew
- Morphew Consulting LLC, Bothell, Washington, United States
- MemorialCare Health System, Fountain Valley, California, United States
| | - Emanuel T. Ferro
- Department of Pathology, Long Beach Memorial Medical Center, Long Beach, California, United States
| | - Inderpal Randhawa
- Department of Pediatric Pulmonology, Miller Children's and Women's Hospital of Long Beach, University of California, Irvine School of Medicine, Irvine, California, United States
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16
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Serigstad S, Markussen D, Grewal HMS, Ebbesen M, Kommedal Ø, Heggelund L, van Werkhoven CH, Faurholt-Jepsen D, Clark TW, Ritz C, Ulvestad E, Bjørneklett R, Knoop ST. Rapid syndromic PCR testing in patients with respiratory tract infections reduces time to results and improves microbial yield. Sci Rep 2022; 12:326. [PMID: 35013351 PMCID: PMC8748978 DOI: 10.1038/s41598-021-03741-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/29/2021] [Indexed: 12/16/2022] Open
Abstract
Lack of rapid and comprehensive microbiological diagnosis in patients with community acquired pneumonia (CAP) hampers appropriate antimicrobial therapy. This study evaluates the real-world performance of the BioFire FilmArray Pneumonia panel plus (FAP plus) and explores the feasibility of evaluation in a randomised controlled trial. Patients presenting to hospital with suspected CAP were recruited in a prospective feasibility study. An induced sputum or an endotracheal aspirate was obtained from all participants. The FAP plus turnaround time (TAT) and microbiological yield were compared with standard diagnostic methods (SDs). 96/104 (92%) enrolled patients had a respiratory tract infection (RTI); 72 CAP and 24 other RTIs. Median TAT was shorter for the FAP plus, compared with in-house PCR (2.6 vs 24.1 h, p < 0.001) and sputum cultures (2.6 vs 57.5 h, p < 0.001). The total microbiological yield by the FAP plus was higher compared to SDs (91% (162/179) vs 55% (99/179), p < 0.0001). Haemophilus influenzae, Streptococcus pneumoniae and influenza A virus were the most frequent pathogens. In conclusion, molecular panel testing in adults with CAP was associated with a significant reduction in time to actionable results and increased microbiological yield. The impact on antibiotic use and patient outcome should be assessed in randomised controlled trials.
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Affiliation(s)
- S Serigstad
- Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Medicine, University of Bergen, Bergen, Norway.,Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine and Dentistry, University of Bergen, The New Lab. Building, NO-5021, Bergen, Norway
| | - D Markussen
- Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway
| | - H M S Grewal
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine and Dentistry, University of Bergen, The New Lab. Building, NO-5021, Bergen, Norway. .,Department of Microbiology, Haukeland University Hospital, Bergen, Norway.
| | - M Ebbesen
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Ø Kommedal
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine and Dentistry, University of Bergen, The New Lab. Building, NO-5021, Bergen, Norway.,Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - L Heggelund
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine and Dentistry, University of Bergen, The New Lab. Building, NO-5021, Bergen, Norway.,Department of Internal Medicine, Vestre Viken Hospital Trust, Drammen, Norway
| | - C H van Werkhoven
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - D Faurholt-Jepsen
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine and Dentistry, University of Bergen, The New Lab. Building, NO-5021, Bergen, Norway.,Department of Infectious Diseases, Rigshospitalet, Copenhagen, Denmark
| | - T W Clark
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - C Ritz
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine and Dentistry, University of Bergen, The New Lab. Building, NO-5021, Bergen, Norway.,National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
| | - E Ulvestad
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine and Dentistry, University of Bergen, The New Lab. Building, NO-5021, Bergen, Norway.,Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - R Bjørneklett
- Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - S T Knoop
- Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway.,Department of Microbiology, Haukeland University Hospital, Bergen, Norway
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17
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Kayser MZ, Seeliger B, Valtin C, Fuge J, Ziesing S, Welte T, Pletz MW, Chhatwal P, Gottlieb J. Clinical decision making is improved by BioFire Pneumonia Plus in suspected lower respiratory tract infection after lung transplantation: Results of the prospective DBATE-IT * study. Transpl Infect Dis 2021; 24:e13725. [PMID: 34542213 DOI: 10.1111/tid.13725] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/20/2021] [Accepted: 08/29/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND Lower respiratory tract infections (LRTIs) are a significant cause of morbidity and mortality in lung transplant (LTx) recipients. Timely and precise pathogen detection is vital to successful treatment. Multiplex PCR kits with short turnover times like the BioFire Pneumonia Plus (BFPPp) (manufactured by bioMérieux) may be a valuable addition to conventional tests. METHODS We performed a prospective observational cohort study in 60 LTx recipients with suspected LRTI. All patients received BFPPp testing of bronchoalveolar lavage fluid in addition to conventional tests including microbiological cultures and conventional diagnostics for respiratory viruses. Primary outcome was time-to-test-result; secondary outcomes included time-to-clinical-decision and BFPPp test accuracy compared to conventional tests. RESULTS BFPPp provided results faster than conventional tests (2.3 h [2-2.8] vs. 23.4 h [21-62], p < 0.001), allowing for faster clinical decisions (2.8 [2.2-44] vs. virology 28.1 h [23.1-70.6] and microbiology 32.6 h [4.6-70.9], both p < 0.001). Based on all available diagnostic modalities, 26 (43%) patients were diagnosed with viral LRTI, nine (15 %) with non-viral LRTI, and five (8 %) with combined viral and non-viral LRTI. These diagnoses were established by BFPPp in 92%, 78%, and 100%, respectively. The remaining 20 patients (33 %) received a diagnosis other than LRTI. Preliminary therapies based on BFPPp results were upheld in 90% of cases. There were six treatment modifications based on pathogen-isolation by conventional testing missed by BFPPp, including three due to fungal pathogens not covered by the BFPPp. CONCLUSION BFPPp offered faster test results compared to conventional tests with good concordance. The absence of fungal pathogens from the panel is a potential weakness in a severely immunosuppressed population.
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Affiliation(s)
- Moritz Z Kayser
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany
| | - Benjamin Seeliger
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany.,Biomedical Research in End-Stage and Obstructive Lung Disease (BREATH), German Centre for Lung Research (DZL), Hannover, Germany
| | - Christina Valtin
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany
| | - Jan Fuge
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany.,Biomedical Research in End-Stage and Obstructive Lung Disease (BREATH), German Centre for Lung Research (DZL), Hannover, Germany
| | - Stefan Ziesing
- Department of Microbiology and Hospital Hygiene, Hannover Medical School, Hannover, Germany
| | - Tobias Welte
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany.,Biomedical Research in End-Stage and Obstructive Lung Disease (BREATH), German Centre for Lung Research (DZL), Hannover, Germany
| | - Mathias W Pletz
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Patrick Chhatwal
- Department of Microbiology and Hospital Hygiene, Hannover Medical School, Hannover, Germany.,Department of Microbiology, MVZ Medical Laboratory Hannover, Hannover, Germany
| | - Jens Gottlieb
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany.,Biomedical Research in End-Stage and Obstructive Lung Disease (BREATH), German Centre for Lung Research (DZL), Hannover, Germany
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18
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Rand KH, Beal SG, Cherabuddi K, Houck H, Lessard K, Tremblay EE, Couturier B, Lingenfelter B, Rindlisbacher C, Jones J. Relationship of Multiplex Molecular Pneumonia Panel Results With Hospital Outcomes and Clinical Variables. Open Forum Infect Dis 2021; 8:ofab368. [PMID: 34458392 DOI: 10.1093/ofid/ofab368] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/07/2021] [Indexed: 11/12/2022] Open
Abstract
Background Antibiotic treatment decisions in severely ill patients must often be made in the absence of microbiologic results. The recently Food and Drug Administration-cleared BioFire FilmArray Pneumonia Panel (PN) detects 15 bacteria semiquantitatively, 3 atypical pneumonia bacteria, 8 viruses, and 7 antimicrobial resistance markers by multiplex PCR in ~1 hour in the laboratory. Previous reports have shown that the PN Panel bacterial detections are highly accurate, even when routine culture had no growth. Methods Consecutive bronchoalveolar lavage and endotracheal specimens submitted for culture between June and September 2018 from 270 patients with sufficient clinical and laboratory data were tested with the PN Panel. Patients were divided into 3 groups: (1) both culture and PN Panel positive, (2) PN Panel positive but culture uninformative (no growth or normal flora), and (3) patients with no PN Panel detections. Results Groups 1 and 2 had significantly higher maximum temperatures on the day of culture (P = .00036, analysis of variance [ANOVA] with Bonferroni correction), higher levels of an inflammatory response as measured by percent polymorphonuclear leukocytes in bronchoalveolar lavage (P = .00025, ANOVA with Bonferroni correction), and gram stain report of white blood cells, as previously reported [1]. Conclusions Both group 1 (culture and PN Panel positive), and group 2 (PN Panel positive but culture uninformative) had higher levels of host response inflammatory responses compared with group 3, which had no targets detected, suggesting that PN Panel detections need to be interpreted in the clinical context, even if cultures are discordant. Depending on laboratory turnaround time, there could be opportunities for improved diagnosis and antibiotic stewardship.
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Affiliation(s)
- K H Rand
- University of Florida, Gainesville, Florida, USA
| | - S G Beal
- University of Florida, Gainesville, Florida, USA
| | - K Cherabuddi
- University of Florida, Gainesville, Florida, USA
| | - H Houck
- University of Florida, Gainesville, Florida, USA
| | - K Lessard
- University of Florida, Gainesville, Florida, USA
| | - E E Tremblay
- University of Florida, Gainesville, Florida, USA
| | - B Couturier
- BioFire Diagnostics, LLC, Salt Lake City, Utah, USA
| | | | | | - J Jones
- BioFire Diagnostics, LLC, Salt Lake City, Utah, USA
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19
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Fernández-Barat L, Alcaraz-Serrano V, Amaro R, Torres A. Pseudomonas aeruginosa in Bronchiectasis. Semin Respir Crit Care Med 2021; 42:587-594. [PMID: 34261182 DOI: 10.1055/s-0041-1730921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Pseudomonas aeruginosa (PA) in patients with bronchiectasis (BE) is associated with a poor outcome and quality of life, and its presence is considered a marker of disease severity. This opportunistic pathogen is known for its ability to produce biofilms on biotic or abiotic surfaces and to survive environmental stress exerted by antimicrobials, inflammation, and nutrient or oxygen depletion. The presence of PA biofilms has been linked to chronic respiratory infection in cystic fibrosis but not in BE. There is considerable inconsistency in the reported infection/eradication rates of PA and chronic PA. In addition, inadequate antimicrobial treatment may potentiate the progression from intermittent to chronic infection and also the emergence of antibiotic resistance. A better comprehension of the pathophysiology of PA infections and its implications for BE is urgently needed. This can drive improvements in diagnostic accuracy, can move us toward a new consensus definition of chronic infection, can better define the follow-up of patients at risk of PA, and can achieve more successful eradication rates. In addition, the new technological advances regarding molecular diagnostics, -omics, and biomarkers require us to reconsider our traditional concepts.
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Affiliation(s)
- Laia Fernández-Barat
- Cellex Laboratory, CibeRes (Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, 06/06/0028), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,School of Medicine, University of Barcelona, Barcelona, Spain.,Department of Pneumology, Respiratory Institute, Hospital Clinic of Barcelona, Spain
| | - Victoria Alcaraz-Serrano
- Cellex Laboratory, CibeRes (Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, 06/06/0028), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,School of Medicine, University of Barcelona, Barcelona, Spain.,Department of Pneumology, Respiratory Institute, Hospital Clinic of Barcelona, Spain
| | - Rosanel Amaro
- Cellex Laboratory, CibeRes (Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, 06/06/0028), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,School of Medicine, University of Barcelona, Barcelona, Spain.,Department of Pneumology, Respiratory Institute, Hospital Clinic of Barcelona, Spain
| | - Antoni Torres
- Cellex Laboratory, CibeRes (Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, 06/06/0028), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,School of Medicine, University of Barcelona, Barcelona, Spain.,Department of Pneumology, Respiratory Institute, Hospital Clinic of Barcelona, Spain
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Identification of bacterial co-detections in COVID-19 critically Ill patients by BioFire® FilmArray® pneumonia panel: a systematic review and meta-analysis. Diagn Microbiol Infect Dis 2021; 101:115476. [PMID: 34303085 PMCID: PMC8245667 DOI: 10.1016/j.diagmicrobio.2021.115476] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/24/2021] [Accepted: 06/26/2021] [Indexed: 12/14/2022]
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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