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Geslain G, Cointe A, Naudin J, Dauger S, Poey N, Pages J, Le Roux E, Bonacorsi S. Diagnostic Accuracy of Blind Bronchial Sample Testing by BioFire Pneumonia plus Panel in Pediatric Intensive Care Unit Patients and Its Impact in Early Adaptation of Antimicrobial Therapy: A Prospective Observational Study. Pediatr Infect Dis J 2024; 43:725-730. [PMID: 38621162 DOI: 10.1097/inf.0000000000004349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
BACKGROUND Community-acquired and nosocomial lower-respiratory-tract infections in critically ill pediatric patients require early appropriate antibiotic therapy to optimize outcomes. Using blind bronchial samples, we assessed the diagnostic performance of the rapid-multiplex polymerase chain reaction (PCR) assay BioFire Pneumonia plus Panel vs. reference standard culturing with antimicrobial susceptibility testing. METHODS For this prospective observational study in a single pediatric intensive care unit, we included consecutive patients younger than 18 years admitted for suspected community-, hospital- or ventilator-associated pneumonia in 2021-2022. Sensitivity, specificity, positive predictive value and negative predictive value of the multiplex PCR assay were determined. The kappa coefficient was computed to assess agreement, and univariate analyses were done to identify factors associated with discrepancies between the 2 diagnostic methods. RESULTS Of the 36 included patients (median age, 1.4 years; interquartile range, 0.2-9.2), 41.7%, 27.8%, and 30.5% had community-, hospital- and ventilator-associated pneumonia, respectively. The overall κ was 0.74, indicating good agreement. Overall, the sensitivity of the multiplex PCR assay was 92% (95% CI: 77%-98%) and specificity 95% (95% CI: 92%-97%), with variations across microorganisms. The median time from sample collection to antimicrobial susceptibility test results was 3.9 (2.5-15) hours with the multiplex PCR assay and 60.5 (47.6-72.2) hours with the reference technique. CONCLUSION The BioFire Pneumonia plus Panel used to test blind bronchial samples had satisfactory diagnostic performance in critically ill pediatric patients. The rapid results provided by this test may improve the appropriateness of antimicrobial therapy and help minimize the use of antibiotics.
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Affiliation(s)
- Guillaume Geslain
- From the Paediatric Intensive Care Unit, Robert-Debré University Hospital, Assistance Publique - Hôpitaux de Paris (AP-HP), Paris, France
- Paris Cité University, IAME, INSERM UMR 1137, Paris, France
| | - Aurélie Cointe
- Paris Cité University, IAME, INSERM UMR 1137, Paris, France
- Department of Microbiology, Escherichia coli National Reference Center, Robert-Debré University Hospital, Assistance Publique - Hôpitaux de Paris (AP-HP), Paris, France
| | - Jérôme Naudin
- From the Paediatric Intensive Care Unit, Robert-Debré University Hospital, Assistance Publique - Hôpitaux de Paris (AP-HP), Paris, France
| | - Stéphane Dauger
- From the Paediatric Intensive Care Unit, Robert-Debré University Hospital, Assistance Publique - Hôpitaux de Paris (AP-HP), Paris, France
- Paris Cité University, NeuroDiderot, INSERM UMR 1141, Paris, France
| | - Nora Poey
- Department of General Paediatrics, Paediatric Infectious Diseases and Internal Medicine, Robert-Debré University Hospital, Assistance Publique - Hôpitaux de Paris (AP-HP), Paris, France
| | - Justine Pages
- Clinical Epidemiology Unit, INSERM CIC 1426, Robert-Debré University Hospital, Assistance Publique - Hôpitaux de Paris (AP-HP), Paris, France
| | - Enora Le Roux
- Clinical Epidemiology Unit, INSERM CIC 1426, Robert-Debré University Hospital, Assistance Publique - Hôpitaux de Paris (AP-HP), Paris, France
| | - Stéphane Bonacorsi
- Paris Cité University, IAME, INSERM UMR 1137, Paris, France
- Department of Microbiology, Escherichia coli National Reference Center, Robert-Debré University Hospital, Assistance Publique - Hôpitaux de Paris (AP-HP), Paris, France
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Bay P, Fihman V, Woerther PL, Peiffer B, Gendreau S, Arrestier R, Labedade P, Moncomble E, Gaillet A, Carteaux G, de Prost N, Mekontso Dessap A, Razazi K. Performance and impact of rapid multiplex PCR on diagnosis and treatment of ventilated hospital-acquired pneumonia in patients with extended-spectrum β-lactamase-producing Enterobacterales rectal carriage. Ann Intensive Care 2024; 14:118. [PMID: 39073627 PMCID: PMC11286905 DOI: 10.1186/s13613-024-01348-5] [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: 04/16/2024] [Accepted: 06/28/2024] [Indexed: 07/30/2024] Open
Abstract
BACKGROUND Antimicrobial stewardship (AMS) for ventilator-associated pneumonia (VAP) or ventilated hospital-acquired pneumonia (vHAP) in extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) carriers is challenging. BioFire® FilmArray® Pneumonia plus Panel (mPCR) can detect bacteria and antibiotic resistance genes, including blaCTX-M, the most common ESBL-encoding gene. METHODS This monocentric, prospective study was conducted on a group of ESBL-E carriers from March 2020 to August 2022. The primary objective was to evaluate the concordance between the results of mPCR and conventional culture performed on respiratory samples of ESBL-E carriers to investigate suspected VAP/vHAP. The secondary objective was to appraise the impact of performing or not mPCR on initial antibiotic therapy adequacy in ESBL-E carriers with confirmed VAP/vHAP. RESULTS Over the study period, 294 patients with ESBL-E carriage were admitted to the ICU, of who 168 (57%) were mechanically ventilated. (i) Diagnostic performance of mPCR was evaluated in suspected 41 episodes of VAP/vHAP: blaCTX-M gene was detected in 15/41 (37%) episodes, where 9/15 (60%) were confirmed ESBL-E-induced pneumonia. The culture and blaCTX-M were concordant in 35/41 (85%) episodes, and in all episodes where blaCTX-M was negative (n = 26), the culture never detected ESBL-E. (ii) The impact of mPCR on initial antibiotic therapy adequacy was assessed in 95 episodes of confirmed VAP/vHAP (22 episodes were tested with mPCR and 73 without); 47 (49%) episodes were ESBL-E-induced, and 24 (25%) were carbapenem-resistant bacteria-induced. The use of mPCR was significantly associated with higher prescription of adequate empirical antibiotic therapy in the multivariable logistic regression (adjusted odds ratio (aOR) (95% CI) of 7.5 (2.1-35.9), p = 0.004), propensity-weighting (aOR of 5.9 (1.6-22.1), p = 0.008), and matching-cohort models (aOR of 5.8 (1.5-22.1), p = 0.01). CONCLUSION mPCR blaCTX-M showed an excellent diagnostic value to rule out the diagnosis of ESBL-E related pneumonia in ESBL-E carriers with suspected VAP/vHAP. In addition, in patients with confirmed VAP/vHAP, a mPCR-based antibiotic therapy was associated with an increased prescription of adequate empirical antibiotic therapy. Performing mPCR on respiratory samples seems to be a promising tool in ESBL-E carriers with suspected vHAP/VAP. However, if mPCR is used in very low pre-test clinical probability of pneumonia, due to the high sensitivity and the rate of overdiagnosed pneumonia, the risk of overconsumption of carbapenem may prevail. Further studies are warranted.
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Affiliation(s)
- Pierre Bay
- AP-HP (Assistance Publique-Hôpitaux de Paris), Hôpitaux Universitaires Henri Mondor, DMU Médecine, Service de Médecine Intensive Réanimation, CHU Henri Mondor, 51, Av. de Lattre de Tassigny, 94010, Créteil CEDEX, France.
- Faculté de Santé de Créteil, UPEC (Université Paris Est Créteil), IMRB, GRC CARMAS, 94010, Créteil, France.
- UPEC (Université Paris Est), INSERM, Unité U955, Équipe 18, 94010, Créteil, France.
| | - Vincent Fihman
- Département de Virologie, Bactériologie, Parasitologie-Mycologie, AP-HP (Assistance Publique-Hôpitaux de Paris), Hôpitaux Universitaires Henri Mondor, 94010, Créteil, France
- UPEC (Université Paris Est), EA 7380 Dynamic, Ecole Nationale Vétérinaire d'Alfort, USC Anses, Créteil, France
| | - Paul-Louis Woerther
- Département de Virologie, Bactériologie, Parasitologie-Mycologie, AP-HP (Assistance Publique-Hôpitaux de Paris), Hôpitaux Universitaires Henri Mondor, 94010, Créteil, France
- UPEC (Université Paris Est), EA 7380 Dynamic, Ecole Nationale Vétérinaire d'Alfort, USC Anses, Créteil, France
| | - Bastien Peiffer
- Assistance Publique-Hôpitaux de Paris AP-HP, Hôpital Henri Mondor, DMU Médecine, Créteil, France
| | - Ségolène Gendreau
- AP-HP (Assistance Publique-Hôpitaux de Paris), Hôpitaux Universitaires Henri Mondor, DMU Médecine, Service de Médecine Intensive Réanimation, CHU Henri Mondor, 51, Av. de Lattre de Tassigny, 94010, Créteil CEDEX, France
- Faculté de Santé de Créteil, UPEC (Université Paris Est Créteil), IMRB, GRC CARMAS, 94010, Créteil, France
| | - Romain Arrestier
- AP-HP (Assistance Publique-Hôpitaux de Paris), Hôpitaux Universitaires Henri Mondor, DMU Médecine, Service de Médecine Intensive Réanimation, CHU Henri Mondor, 51, Av. de Lattre de Tassigny, 94010, Créteil CEDEX, France
- Faculté de Santé de Créteil, UPEC (Université Paris Est Créteil), IMRB, GRC CARMAS, 94010, Créteil, France
| | - Pascale Labedade
- AP-HP (Assistance Publique-Hôpitaux de Paris), Hôpitaux Universitaires Henri Mondor, DMU Médecine, Service de Médecine Intensive Réanimation, CHU Henri Mondor, 51, Av. de Lattre de Tassigny, 94010, Créteil CEDEX, France
- Faculté de Santé de Créteil, UPEC (Université Paris Est Créteil), IMRB, GRC CARMAS, 94010, Créteil, France
| | - Elsa Moncomble
- AP-HP (Assistance Publique-Hôpitaux de Paris), Hôpitaux Universitaires Henri Mondor, DMU Médecine, Service de Médecine Intensive Réanimation, CHU Henri Mondor, 51, Av. de Lattre de Tassigny, 94010, Créteil CEDEX, France
- Faculté de Santé de Créteil, UPEC (Université Paris Est Créteil), IMRB, GRC CARMAS, 94010, Créteil, France
| | - Antoine Gaillet
- AP-HP (Assistance Publique-Hôpitaux de Paris), Hôpitaux Universitaires Henri Mondor, DMU Médecine, Service de Médecine Intensive Réanimation, CHU Henri Mondor, 51, Av. de Lattre de Tassigny, 94010, Créteil CEDEX, France
- Faculté de Santé de Créteil, UPEC (Université Paris Est Créteil), IMRB, GRC CARMAS, 94010, Créteil, France
| | - Guillaume Carteaux
- AP-HP (Assistance Publique-Hôpitaux de Paris), Hôpitaux Universitaires Henri Mondor, DMU Médecine, Service de Médecine Intensive Réanimation, CHU Henri Mondor, 51, Av. de Lattre de Tassigny, 94010, Créteil CEDEX, France
- Faculté de Santé de Créteil, UPEC (Université Paris Est Créteil), IMRB, GRC CARMAS, 94010, Créteil, France
| | - Nicolas de Prost
- AP-HP (Assistance Publique-Hôpitaux de Paris), Hôpitaux Universitaires Henri Mondor, DMU Médecine, Service de Médecine Intensive Réanimation, CHU Henri Mondor, 51, Av. de Lattre de Tassigny, 94010, Créteil CEDEX, France
- Faculté de Santé de Créteil, UPEC (Université Paris Est Créteil), IMRB, GRC CARMAS, 94010, Créteil, France
| | - Armand Mekontso Dessap
- AP-HP (Assistance Publique-Hôpitaux de Paris), Hôpitaux Universitaires Henri Mondor, DMU Médecine, Service de Médecine Intensive Réanimation, CHU Henri Mondor, 51, Av. de Lattre de Tassigny, 94010, Créteil CEDEX, France
- Faculté de Santé de Créteil, UPEC (Université Paris Est Créteil), IMRB, GRC CARMAS, 94010, Créteil, France
| | - Keyvan Razazi
- AP-HP (Assistance Publique-Hôpitaux de Paris), Hôpitaux Universitaires Henri Mondor, DMU Médecine, Service de Médecine Intensive Réanimation, CHU Henri Mondor, 51, Av. de Lattre de Tassigny, 94010, Créteil CEDEX, France
- Faculté de Santé de Créteil, UPEC (Université Paris Est Créteil), IMRB, GRC CARMAS, 94010, Créteil, France
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Kommedal Ø, Eagan TM, Fløtten Ø, Leegaard TM, Siljan W, Fardal H, Bø B, Grøvan F, Larssen KW, Kildahl-Andersen A, Hjetland R, Tilseth R, Hareide SKØ, Tellevik M, Dyrhovden R. Microbiological diagnosis of pleural infections: a comparative evaluation of a novel syndromic real-time PCR panel. Microbiol Spectr 2024; 12:e0351023. [PMID: 38656204 PMCID: PMC11237507 DOI: 10.1128/spectrum.03510-23] [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: 09/29/2023] [Accepted: 02/19/2024] [Indexed: 04/26/2024] Open
Abstract
Current microbial diagnostics for pleural infections are insufficient. Studies using 16S targeted next-generation sequencing report that only 10%-16% of bacteria present are cultured and that 50%-78% of pleural fluids containing relevant microbial DNA remain culture negative. As a rapid diagnostic alternative suitable for clinical laboratories, we wanted to explore a PCR-based approach. Based on the identification of key pathogens, we developed a syndromic PCR panel for community-acquired pleural infections (CAPIs). This was a pragmatic PCR panel, meaning that it was not designed for detecting all possibly involved bacterial species but for confirming the diagnosis of CAPI, and for detecting bacteria that might influence choice of antimicrobial treatment. We evaluated the PCR panel on 109 confirmed CAPIs previously characterized using culture and 16S targeted next-generation sequencing. The PCR secured the diagnosis of CAPI in 107/109 (98.2%) and detected all present pathogens in 69/109 (63.3%). Culture secured the diagnosis in 54/109 (49.5%) and detected all pathogens in 31/109 (28.4%). Corresponding results for 16S targeted next-generation sequencing were 109/109 (100%) and 98/109 (89.9%). For bacterial species included in the PCR panel, PCR had a sensitivity of 99.5% (184/185), culture of 21.6% (40/185), and 16S targeted next-generation sequencing of 92.4% (171/185). None of the bacterial species present not covered by the PCR panel were judged to impact antimicrobial therapy. A syndromic PCR panel represents a rapid and sensitive alternative to current diagnostic approaches for the microbiological diagnosis of CAPI.IMPORTANCEPleural empyema is a severe infection with high mortality and increasing incidence. Long hospital admissions and long courses of antimicrobial treatment drive healthcare and ecological costs. Current methods for microbiological diagnostics of pleural infections are inadequate. Recent studies using 16S targeted next-generation sequencing as a reference standard find culture to recover only 10%-16% of bacteria present and that 50%-78% of samples containing relevant bacterial DNA remain culture negative. To confirm the diagnosis of pleural infection and define optimal antimicrobial therapy while limiting unnecessary use of broad-spectrum antibiotics, there is a need for rapid and sensitive diagnostic approaches. PCR is a rapid method well suited for clinical laboratories. In this paper we show that a novel syndromic PCR panel can secure the diagnosis of pleural infection and detect all bacteria relevant for choice of antimicrobial treatment with a high sensitivity.
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Affiliation(s)
- Øyvind Kommedal
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Tomas Mikal Eagan
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Øystein Fløtten
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Truls Michael Leegaard
- Division of Medicine and Laboratory Sciences, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Akershus, Norway
| | - William Siljan
- Department of Pulmonary Medicine, Akershus University Hospital, Lorenskog, Akershus, Norway
| | - Hilde Fardal
- Department of Microbiology, Stavanger University Hospital, Stavanger, Norway
| | - Bjørnar Bø
- Department of Pulmonary Medicine, Stavanger University Hospital, Stavanger, Norway
| | - Fredrik Grøvan
- Department of Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway
| | - Kjersti Wik Larssen
- Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Arne Kildahl-Andersen
- Department of Thoracic Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Reidar Hjetland
- Department of Microbiology, Førde Central Hospital, Førde, Norway
| | - Rune Tilseth
- Department of Medicine, Førde Central Hospital, Førde, Norway
| | | | - Marit Tellevik
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Ruben Dyrhovden
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
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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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Cartuliares MB, Mogensen CB, Rosenvinge FS, Skovsted TA, Lorentzen MH, Heltborg A, Hertz MA, Kaldan F, Specht JJ, Skjøt-Arkil H. Community-acquired pneumonia: use of clinical characteristics of acutely admitted patients for the development of a diagnostic model - a cross-sectional multicentre study. BMJ Open 2024; 14:e079123. [PMID: 38816044 PMCID: PMC11141191 DOI: 10.1136/bmjopen-2023-079123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 05/20/2024] [Indexed: 06/01/2024] Open
Abstract
OBJECTIVES This study aimed to describe the clinical characteristics of adults with suspected acute community-acquired pneumonia (CAP) on hospitalisation, evaluate their prediction performance for CAP and compare the performance of the model to the initial assessment of the physician. DESIGN Cross-sectional, multicentre study. SETTING The data originated from the INfectious DisEases in Emergency Departments study and were collected prospectively from patient interviews and medical records. The study included four Danish medical emergency departments (EDs) and was conducted between 1 March 2021 and 28 February 2022. PARTICIPANTS A total of 954 patients admitted with suspected infection were included in the study. PRIMARY AND SECONDARY OUTCOME The primary outcome was CAP diagnosis assessed by an expert panel. RESULTS According to expert evaluation, CAP had a 28% prevalence. 13 diagnostic predictors were identified using least absolute shrinkage and selection operator regression to build the prediction model: dyspnoea, expectoration, cough, common cold, malaise, chest pain, respiratory rate (>20 breaths/min), oxygen saturation (<96%), abnormal chest auscultation, leucocytes (<3.5×109/L or >8.8×109/L) and neutrophils (>7.5×109/L). C reactive protein (<20 mg/L) and having no previous event of CAP contributed negatively to the final model. The predictors yielded good prediction performance for CAP with an area under the receiver-operator characteristic curve (AUC) of 0.85 (CI 0.77 to 0.92). However, the initial diagnosis made by the ED physician performed better, with an AUC of 0.86 (CI 84% to 89%). CONCLUSION Typical respiratory symptoms combined with abnormal vital signs and elevated infection biomarkers were predictors for CAP on admission to an ED. The clinical value of the prediction model is questionable in our setting as it does not outperform the clinician's assessment. Further studies that add novel diagnostic tools and use imaging or serological markers are needed to improve a model that would help diagnose CAP in an ED setting more accurately. TRIAL REGISTRATION NUMBER NCT04681963.
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Affiliation(s)
- Mariana B Cartuliares
- Department of Emergency Medicine, University Hospital of Southern Denmark, Aabenraa, Denmark
- Department of Regional Health Research, 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, Odense, Denmark
| | - Flemming S Rosenvinge
- Department of Clinical Microbiology, Odense Universitetshospital, Odense, Denmark
- Research Unit of Clinical Microbiology, University of Southern Denmark, Odense, Denmark
| | - Thor Aage Skovsted
- Department of Biochemistry and Immunology, University Hospital of Southern Denmark, Aabenraa, Denmark
| | - Morten Hjarnø Lorentzen
- Department of Emergency Medicine, University Hospital of Southern Denmark, Aabenraa, Denmark
- Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Anne Heltborg
- Department of Emergency Medicine, University Hospital of Southern Denmark, Aabenraa, Denmark
- Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Mathias Amdi Hertz
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- Department of Infectious Diseases, Odense University Hospital, Odense, Denmark
| | - Frida Kaldan
- Department of Emergency Medicine, University Hospital of Southern Denmark, Aabenraa, Denmark
| | - Jens Juel Specht
- Department of Emergency Medicine, University Hospital of Southern Denmark, Aabenraa, Denmark
| | - Helene Skjøt-Arkil
- Department of Emergency Medicine, University Hospital of Southern Denmark, Aabenraa, Denmark
- Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
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Nicolau-Guillaumet N, Dortet L, Jacquemin A, Mourvillier B, Muggeo A, Guillard T. Lack of detection of Klebsiella aerogenes sub-species in lung infection by the BioFire® FilmArray® Pneumonia Panel plus. Clin Microbiol Infect 2024; 30:688-690. [PMID: 38368943 DOI: 10.1016/j.cmi.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/12/2024] [Accepted: 02/09/2024] [Indexed: 02/20/2024]
Affiliation(s)
- Nathan Nicolau-Guillaumet
- Université de Reims Champagne-Ardenne, INSERM, CHU de Reims, Laboratoire de bactériologie-Virologie-Hygiène hospitalière-Parasitologie-Mycologie, P3Cell, U 1250, Reims, France
| | - Laurent Dortet
- Team 'Resist', INSERM Unit 1184, Faculty of Medicine, Université Paris-Saclay, Service de Bactériologie-Hygiène, Hôpital Bicêtre, Le Kremlin-Bicêtre, France; Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, AP-HP Paris-Saclay, Bicêtre Hospital, Le Kremlin-Bicêtre, France; Associated French National Reference Center for Antibiotic Resistance, Carbapenemase-Producing Enterobacterales, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Aymeric Jacquemin
- Team 'Resist', INSERM Unit 1184, Faculty of Medicine, Université Paris-Saclay, Service de Bactériologie-Hygiène, Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Bruno Mourvillier
- Medical Intensive Care Unit, University Hospital of Reims, Université de Reims Champagne-Ardenne, CardioVir, France
| | - Anaëlle Muggeo
- Université de Reims Champagne-Ardenne, INSERM, CHU de Reims, Laboratoire de bactériologie-Virologie-Hygiène hospitalière-Parasitologie-Mycologie, P3Cell, U 1250, Reims, France
| | - Thomas Guillard
- Université de Reims Champagne-Ardenne, INSERM, CHU de Reims, Laboratoire de bactériologie-Virologie-Hygiène hospitalière-Parasitologie-Mycologie, P3Cell, U 1250, Reims, France.
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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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Gavalda M, Fullana MI, Ferre A, Peña RR, Armendariz J, Torrallardona O, Magraner A, Lorenzo A, García C, Mut G, Planas L, Iglesias C, Fraile-Ribot P, Macia Romero MD, Riera M, García-Gasalla M. Clinical Characteristics and Microorganisms Isolated in Community-Acquired Pneumonia in the COVID-19 Period. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2024; 2024:5948747. [PMID: 38532828 PMCID: PMC10965275 DOI: 10.1155/2024/5948747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 01/15/2024] [Accepted: 02/28/2024] [Indexed: 03/28/2024]
Abstract
Introduction Community-acquired pneumonia is a leading cause of mortality and hospital admissions. The aetiology remains unknown in 30-65% of the cases. Molecular tests are available for multiple pathogen detection and are under research to improve the causal diagnosis. Methods We carried out a prospective study to describe the clinical characteristics and aetiology of community-acquired pneumonia during the COVID-19 pandemic and to assess the diagnostic effectivity of the microbiological tests, including a molecular test of respiratory pathogens (FilmArray™ bioMérieux). Results From the 1st of February 2021 until the 31st of March 2022, 225 patients were included. Failure in microorganism identification occurred in approximately 70% of patients. Streptococcus pneumoniae was the most common isolate. There were 5 cases of viral pneumonia. The tested FilmArray exhibited a low positivity rate of 7% and mainly aided in the diagnosis of viral coinfections. Conclusions Despite our extensive diagnostic protocol, there is still a low rate of microorganism identification. We have observed a reduction in influenza and other viral pneumoniae during the COVID-19 pandemic. Having a high NEWS2 score on arrival at the emergency department, an active oncohematological disease or chronic neurological conditions and a positive microbiological test result were related to worse outcomes. Further research is needed to determine the role of molecular tests in the microbiological diagnosis of pneumonia.
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Affiliation(s)
- Meritxell Gavalda
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Maria Isabel Fullana
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Adrià Ferre
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Rebecca Rowena Peña
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Julen Armendariz
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Orla Torrallardona
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Aina Magraner
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Alejandro Lorenzo
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Carles García
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Gemma Mut
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Lluís Planas
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Carla Iglesias
- Microbiology Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
| | - Pablo Fraile-Ribot
- Microbiology Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
- Fundació Institut d'Investigació Sanitària Illes Balears (IdISBa), Illes Balears, Palma, Spain
| | - Maria Dolores Macia Romero
- Microbiology Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
- Fundació Institut d'Investigació Sanitària Illes Balears (IdISBa), Illes Balears, Palma, Spain
- Universitat de les Illes Balears, Illes Balears, Palma, Spain
| | - Melchor Riera
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
- Fundació Institut d'Investigació Sanitària Illes Balears (IdISBa), Illes Balears, Palma, Spain
- Universitat de les Illes Balears, Illes Balears, Palma, Spain
| | - Mercedes García-Gasalla
- Internal Medicine Department, Hospital Universitari Son Espases, Illes Balears, Palma, Spain
- Fundació Institut d'Investigació Sanitària Illes Balears (IdISBa), Illes Balears, Palma, Spain
- Universitat de les Illes Balears, Illes Balears, Palma, Spain
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9
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Matsuura H, Arimoto K, Takahashi Y, Kishimoto M. Combination of a multiplex pneumonia panel and Gram staining for antimicrobial selection to treat lower respiratory tract infection. Pneumonia (Nathan) 2024; 16:4. [PMID: 38438932 PMCID: PMC10913398 DOI: 10.1186/s41479-024-00125-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 01/09/2024] [Indexed: 03/06/2024] Open
Abstract
AIM This study aimed to examine the utility of simultaneously performed the Film Array pneumonia panels (pneumonia panels) and Gram staining with the same specimens and evaluate their effect on antimicrobial selection. METHODS This prospective study, conducted from April 2022 to January 2023, enrolled adult patients with pneumonia, including those with ventilator-associated pneumonia (VAP). Specimens obtained at the time of sputum culture were tested using Gram staining and the pneumonia panel. The patients' characteristics and pneumonia panel results were assessed. We also evaluated the selection of antimicrobial agents for drug-resistant bacteria detected by the pneumonia panel. RESULTS This study comprised 39 patients: 25 patients (64.1%) underwent intubation, including 7 (17.9%) patients with VAP. Most tests were performed at the time of admission, while some were performed during hospitalization. Good quality sputum was obtained from intubated patients. The pneumonia panel detected drug-resistant bacteria in 12 cases. Six patients required antimicrobial escalation, while the antimicrobial regimen remained unchanged for 2 patients in whom Pseudomonas aeruginosa was detected and had already received meropenem. The attending physician did not change the antimicrobials, considering the results of Gram staining and the patient's general condition in 4 patients. CONCLUSIONS The pneumonia panel might be useful for detecting drug-resistant organisms at an early stage. It may be important to take the Gram staining results and the patient's condition into account with pneumonia panel for appropriate antibiotic prescription.
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Affiliation(s)
- Hiroshi Matsuura
- Osaka Prefectural Nakakawachi Emergency and Critical Care Center, 3-4-13 Nishiiwata, Higashiosaka, Osaka, 578-0947, Japan.
| | - Koudai Arimoto
- Osaka Prefectural Nakakawachi Emergency and Critical Care Center, 3-4-13 Nishiiwata, Higashiosaka, Osaka, 578-0947, Japan
| | - Yoshihito Takahashi
- Osaka Prefectural Nakakawachi Emergency and Critical Care Center, 3-4-13 Nishiiwata, Higashiosaka, Osaka, 578-0947, Japan
| | - Masafumi Kishimoto
- Osaka Prefectural Nakakawachi Emergency and Critical Care Center, 3-4-13 Nishiiwata, Higashiosaka, Osaka, 578-0947, Japan
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10
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Jose Lucar, Rebecca Yee. Diagnostic Stewardship for Multiplex Respiratory Testing: What We Know and What Needs to Be Done. Clin Lab Med 2024; 44:45-61. [PMID: 38280797 DOI: 10.1016/j.cll.2023.10.001] [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] [Indexed: 01/29/2024]
Abstract
Syndromic respiratory panels are now widely available in clinical microbiology laboratories and health care institutions. These panels can rapidly diagnose infections and detect antimicrobial resistance genes allowing for more rapid therapeutic optimization compared to standard microbiology approaches. However, given reimbursement concerns and limitations of multiplex molecular testing and results interpretation, maximum clinical utility and positive clinical outcomes depend on active diagnostic stewardship. Here, the authors review clinical outcomes of both upper and lower respiratory panels and present diagnostic stewardship strategies for optimal use of respiratory panels.
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Affiliation(s)
- Jose Lucar
- Division of Infectious Diseases, George Washington University School of Medicine and Health Sciences, 2150 Pennsylvania Avenue Northeast, Washington, DC 20037, USA
| | - Rebecca Yee
- Department of Pathology, George Washington University School of Medicine and Health Sciences, 900 23rd Street Northwest, Washington, DC 20037, USA.
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11
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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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12
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Dessajan J, Timsit JF. Impact of Multiplex PCR in the Therapeutic Management of Severe Bacterial Pneumonia. Antibiotics (Basel) 2024; 13:95. [PMID: 38247654 PMCID: PMC10812737 DOI: 10.3390/antibiotics13010095] [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: 12/26/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 01/23/2024] Open
Abstract
Pneumonia is a common and severe illness that requires prompt and effective management. Advanced, rapid, and accurate tools are needed to diagnose patients with severe bacterial pneumonia, and to rapidly select appropriate antimicrobial therapy, which must be initiated within the first few hours of care. Two multiplex molecular tests, Unyvero HPN and FilmArray Pneumonia+ Panel, have been developed using the multiplex polymerase chain reaction (mPCR) technique to rapidly identify pathogens and their main antibiotic resistance mechanisms from patient respiratory specimens. Performance evaluation of these tests showed strong correlations with reference techniques. However, good knowledge of their indications, targets, and limitations is essential. Collaboration with microbiologists is, therefore, crucial for their appropriate use. Under these conditions, and with standardized management, these rapid tests can improve the therapeutic management of severe pneumonia faster, more precisely, and with narrow-spectrum antibiotic therapy. Further randomized controlled trials are needed to address the many unanswered questions about multiplex rapid molecular testing during the diagnosis and the management of severe pneumonia. This narrative review will address the current knowledge, advantages, and disadvantages of these tests, and propose solutions for their routine use.
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Affiliation(s)
- Julien Dessajan
- Assistance Publique Hôpitaux de Paris (AP-HP), Medical and Infectious Diseases Intensive Care Unit, Bichat Claude-Bernard Hospital, Paris Cité University, 46 Rue Henri Huchard, 75018 Paris, France;
| | - Jean-François Timsit
- Assistance Publique Hôpitaux de Paris (AP-HP), Medical and Infectious Diseases Intensive Care Unit, Bichat Claude-Bernard Hospital, Paris Cité University, 46 Rue Henri Huchard, 75018 Paris, France;
- Mixt Research Unit (UMR) 1137, Infection, Antimicrobials, Modelization, Epidemiology (IAME), Institut National de la Recherche Médicale (INSERM), Paris Cité University, 75018 Paris, France
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13
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Verroken A, Favresse J, Anantharajah A, Rodriguez-Villalobos H, Wittebole X, Laterre PF. Optimized Antibiotic Management of Critically Ill Patients with Severe Pneumonia Following Multiplex Polymerase Chain Reaction Testing: A Prospective Clinical Exploratory Trial. Antibiotics (Basel) 2024; 13:67. [PMID: 38247626 PMCID: PMC10812711 DOI: 10.3390/antibiotics13010067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/24/2023] [Accepted: 01/04/2024] [Indexed: 01/23/2024] Open
Abstract
Molecular diagnostic testing is assumed to enable fast respiratory pathogen identification and contribute to improved pneumonia management. We set up a prospective clinical trial at a tertiary hospital intensive care unit including adult patients suspected of severe pneumonia from whom a lower respiratory tract sample could be obtained. During control periods (CPs), routine testing was performed, and during intervention periods (IPs), this testing was completed with the FilmArray Pneumonia Panel plus test (FA-PNEU) executed 24/7. The main objective was to measure the impact of FA-PNEU results in terms of reduced time to targeted antimicrobial treatment administration. Over a 10-month period, analysis was performed on 35 CP and 50 IP patients. The median time to targeted antimicrobial treatment administration was reduced to 4.3 h in IPs compared to 26.4 h in CPs, with 54% of IP patients having FA-PNEU results that led to a treatment modification, of which all but one were targeted. Modifications included 10 (37%) de-escalations, 7 (25.9%) escalations, 3 (11.1%) regimen switches, and 7 (25.9%) complete antimicrobial discontinuations. FA-PNEU results were available with a 42.3 h gain compared to routine identification. This prospective study confirmed retrospective data demonstrating the benefit of FA-PNEU testing in severe pneumonia management of critically ill patients through improved antimicrobial use.
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Affiliation(s)
- Alexia Verroken
- Department of Microbiology, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Avenue Hippocrate 10, 1200 Brussels, Belgium
| | - Julien Favresse
- Department of Microbiology, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Avenue Hippocrate 10, 1200 Brussels, Belgium
| | - Ahalieyah Anantharajah
- Department of Microbiology, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Avenue Hippocrate 10, 1200 Brussels, Belgium
| | - Hector Rodriguez-Villalobos
- Department of Microbiology, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Avenue Hippocrate 10, 1200 Brussels, Belgium
| | - Xavier Wittebole
- Department of Critical Care Medecine, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Avenue Hippocrate 10, 1200 Brussels, Belgium;
| | - Pierre-François Laterre
- Department of Critical Care Medecine, Centres Hospitaliers Universitaires HELORA, 1200 Brussels, Belgium
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14
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Clark JA, Curran MD, Gouliouris T, Conway Morris A, Bousfield R, Navapurkar V, Kean IRL, Daubney E, White D, Baker S, Pathan N. Rapid Detection of Antimicrobial Resistance Genes in Critically Ill Children Using a Custom TaqMan Array Card. Antibiotics (Basel) 2023; 12:1701. [PMID: 38136735 PMCID: PMC10740637 DOI: 10.3390/antibiotics12121701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Bacteria are identified in only 22% of critically ill children with respiratory infections treated with antimicrobial therapy. Once an organism is isolated, antimicrobial susceptibility results (phenotypic testing) can take another day. A rapid diagnostic test identifying antimicrobial resistance (AMR) genes could help clinicians make earlier, informed antimicrobial decisions. Here we aimed to validate a custom AMR gene TaqMan Array Card (AMR-TAC) for the first time and assess its feasibility as a screening tool in critically ill children. An AMR-TAC was developed using a combination of commercial and bespoke targets capable of detecting 23 AMR genes. This was validated using isolates with known phenotypic resistance. The card was then tested on lower respiratory tract and faecal samples obtained from mechanically ventilated children in a single-centre observational study of respiratory infection. There were 82 children with samples available, with a median age of 1.2 years. Major comorbidity was present in 29 (35%) children. A bacterial respiratory pathogen was identified in 13/82 (16%) of children, of which 4/13 (31%) had phenotypic AMR. One AMR gene was detected in 49/82 (60%), and multiple AMR genes were detected in 14/82 (17%) children. Most AMR gene detections were not associated with the identification of phenotypic AMR. AMR genes are commonly detected in samples collected from mechanically ventilated children with suspected respiratory infections. AMR-TAC may have a role as an adjunct test in selected children in whom there is a high suspicion of antimicrobial treatment failure.
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Affiliation(s)
- John A. Clark
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK; (I.R.L.K.); (E.D.); (D.W.); (N.P.)
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
| | - Martin D. Curran
- Clinical Microbiology and Public Health Laboratory, United Kingdom Health Security Agency, Cambridge CB2 0QQ, UK;
| | - Theodore Gouliouris
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
- Clinical Microbiology and Public Health Laboratory, United Kingdom Health Security Agency, Cambridge CB2 0QQ, UK;
| | - Andrew Conway Morris
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge CB2 2QQ, UK
- Division of Immunology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Rachel Bousfield
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
- Clinical Microbiology and Public Health Laboratory, United Kingdom Health Security Agency, Cambridge CB2 0QQ, UK;
| | - Vilas Navapurkar
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
| | - Iain R. L. Kean
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK; (I.R.L.K.); (E.D.); (D.W.); (N.P.)
| | - Esther Daubney
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK; (I.R.L.K.); (E.D.); (D.W.); (N.P.)
| | - Deborah White
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK; (I.R.L.K.); (E.D.); (D.W.); (N.P.)
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge CB2 0AW, UK;
| | - Nazima Pathan
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK; (I.R.L.K.); (E.D.); (D.W.); (N.P.)
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
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15
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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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16
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Heitz M, Levrat A, Lazarevic V, Barraud O, Bland S, Santiago-Allexant E, Louis K, Schrenzel J, Hauser S. Metagenomics for the microbiological diagnosis of hospital-acquired pneumonia and ventilator-associated pneumonia (HAP/VAP) in intensive care unit (ICU): a proof-of-concept study. Respir Res 2023; 24:285. [PMID: 37968636 PMCID: PMC10648381 DOI: 10.1186/s12931-023-02597-x] [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: 05/16/2023] [Accepted: 11/07/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND Hospital-acquired and ventilator-associated-pneumonia (HAP/VAP) are one of the most prevalent health-care associated infections in the intensive care unit (ICU). Culture-independent methods were therefore developed to provide faster route to diagnosis and treatment. Among these, metagenomic next-generation sequencing (mNGS) has shown considerable promise. METHODS This proof-of-concept study describes the technical feasibility and evaluates the clinical validity of the mNGS for the detection and characterization of the etiologic agents causing hospital-acquired and ventilator-associated pneumonia. We performed a prospective study of all patients with HAP/VAP hospitalized in our intensive care unit for whom a bronchoalveolar lavage (BAL) was performed between July 2017 and November 2018. We compared BAL fluid culture and mNGS results of these patients. RESULTS A total of 32 BAL fluids were fully analyzed. Of these, 22 (69%) were positive by culture and all pathogens identified were also reported by mNGS. Among the culture-positive BAL samples, additional bacterial species were revealed by mNGS for 12 patients, raising the issue of their pathogenic role (colonization versus coinfection). Among BALF with culture-negative test, 5 were positive in mNGS test. CONCLUSIONS This study revealed concordant results for pneumonia panel pathogens between mNGS and culture-positive tests and identified additional pathogens potentially implicated in pneumonia without etiologic diagnosis by culture. mNGS has emerged as a promising methodology for infectious disease diagnoses to support conventional methods. Prospective studies with real-time mNGS are warranted to examine the impact on antimicrobial decision-making and clinical outcome.
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Affiliation(s)
- Morgane Heitz
- Intensive Care Unit, Annecy-Genevois Hospital, Site d'Annecy, 1 Avenue de L'hôpital, 74370, Metz Tessy, France.
| | - Albrice Levrat
- Intensive Care Unit, Annecy-Genevois Hospital, Site d'Annecy, 1 Avenue de L'hôpital, 74370, Metz Tessy, France
| | - Vladimir Lazarevic
- Genomic Research Laboratory, Geneva University Hospitals and Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Olivier Barraud
- Genomic Research Laboratory, Geneva University Hospitals and Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Stéphane Bland
- Bacteriology Laboratory, Annecy-Genevois Hospital, Metz Tessy, France
| | | | - Karen Louis
- BIOASTER Microbiology Technology Institute, 40 Avenue Tony Garnier, 69007, Lyon, France
| | - Jacques Schrenzel
- Genomic Research Laboratory, Geneva University Hospitals and Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Bacteriology Laboratory, Geneva University Hospitals and Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Sébastien Hauser
- bioMérieux Grenoble, Centre Christophe Mérieux, 5 Rue Des Berges, 38024, Grenoble Cedex 01, France
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17
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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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18
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Markussen DL, Ebbesen M, Serigstad S, Knoop ST, Ritz C, Bjørneklett R, Kommedal Ø, Jenum S, Ulvestad E, Grewal HMS. The diagnostic utility of microscopic quality assessment of sputum samples in the era of rapid syndromic PCR testing. Microbiol Spectr 2023; 11:e0300223. [PMID: 37772853 PMCID: PMC10581175 DOI: 10.1128/spectrum.03002-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 08/11/2023] [Indexed: 09/30/2023] Open
Abstract
This prospective study assessed the value of initial microscopy evaluation of sputum samples submitted for rapid syndromic PCR-based testing. Bacterial detections by the BioFire FilmArray Pneumonia Panel plus in 126 high- and 108 low-quality sputum samples, based on initial microscopy evaluation in samples from patients with lower respiratory tract infections were compared. We found that high-quality samples had a higher proportion of bacterial detections compared to low-quality samples (P = 0.013). This included a higher proportion of detections of bacteria deemed clinically relevant by predefined criteria (70% and 55%, P = 0.016), as well as a higher proportion of detections of Haemophilus influenzae (36% and 20%, P = 0.010). High-quality samples also had more detections of bacteria with high semi-quantitative values. The study found no significant difference between high- and low-quality samples in the proportions of samples with a single species of bacteria detected, samples with a bacteria treated by the clinician, samples with detection of a proven etiology of community-acquired pneumonia by predefined criteria, the number of bacterial species detected, or the detection of Streptococcus pneumoniae, Moraxella catarrhalis, or Staphylococcus aureus. The results showed that 40% (95% CI 35%-47%) of the bacterial detections would have been missed if only high-quality samples were analyzed. This included 41% (27%-56%) of detections of S. pneumoniae, 33% (23%-45%) of detections of H. influenzae, 42% (28%-58%) of detections of S. aureus, and 37% (23%-54%) of detections of M. catarrhalis. These findings suggest that all sputum samples submitted for rapid syndromic PCR testing should be analyzed, regardless of initial microscopy quality assessment. (This study has been registered at ClinicalTrials.gov under registration no. NCT04660084.) IMPORTANCE Microscopic quality assessment of sputum samples was originally designed for sputum culture, and its applicability in today's workflow, which includes syndromic PCR testing, may differ. Addressing this crucial gap, our study emphasizes the need to optimize the use and workflow of syndromic PCR panels, like the BioFire FilmArray Pneumonia plus (FAP plus), in microbiology laboratories. These advanced PCR-based tests offer rapid and comprehensive pathogen detection for respiratory infections, yet their full potential remains uncertain. By comparing bacterial detections in high- and low-quality sputum samples, we underscore the importance of including low-quality samples in testing. Our findings reveal a significant proportion of potentially clinically relevant bacterial detections that would have been missed if only high-quality samples were analyzed. These insights support the efficient implementation of syndromic PCR panels, ultimately enhancing patient care and outcomes.
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Affiliation(s)
- Dagfinn Lunde Markussen
- Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Marit Ebbesen
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Sondre Serigstad
- Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine, University of Bergen, Bergen, Norway
- Department of Clinical Medicine, Faculty of Medicine, University of Bergen, Bergen, Norway
| | | | - Christian Ritz
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine, University of Bergen, Bergen, Norway
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
| | - Rune Bjørneklett
- Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Øyvind Kommedal
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine, University of Bergen, Bergen, Norway
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Synne Jenum
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine, University of Bergen, Bergen, Norway
- Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
| | - Elling Ulvestad
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine, 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, Faculty of Medicine, University of Bergen, Bergen, Norway
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
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19
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Mizusawa M, Carroll KC. Recent updates in the development of molecular assays for the rapid identification and susceptibility testing of MRSA. Expert Rev Mol Diagn 2023; 23:679-699. [PMID: 37419696 DOI: 10.1080/14737159.2023.2234823] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/22/2023] [Accepted: 07/06/2023] [Indexed: 07/09/2023]
Abstract
INTRODUCTION Methicillin-resistant Staphylococcus aureus (MRSA) is a frequent cause of healthcare- and community-associated infections. Nasal carriage of MRSA is a risk factor for subsequent MRSA infections. Increased morbidity and mortality are associated with MRSA infections and screening and diagnostic tests for MRSA play an important role in clinical management. AREAS COVERED A literature search was conducted in PubMed and supplemented by citation searching. In this article, we provide a comprehensive review of molecular-based methods for MRSA screening and diagnostic tests including individual nucleic acid detection assays, syndromic panels, and sequencing technologies with a focus on their analytical performance. EXPERT OPINION Molecular based-assays for the detection of MRSA have improved in terms of accuracy and availability. Rapid turnaround enables earlier contact isolation and decolonization for MRSA. The availability of syndromic panel tests that include MRSA as a target has expanded from positive blood cultures to pneumonia and osteoarticular infections. Sequencing technologies allow detailed characterizations of novel methicillin-resistance mechanisms that can be incorporated into future assays. Next generation sequencing is capable of diagnosing MRSA infections that cannot be identified by conventional methods and metagenomic next-generation sequencing (mNGS) assays will likely move closer to implementation as front-line diagnostics in the near future.
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Affiliation(s)
- Masako Mizusawa
- Monmouth Medical Center, Rutgers University Robert Wood Johnson Medical School, Long Branch, NJ, USA
| | - Karen C Carroll
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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20
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Hayotte A, Mariani-Kurkdjian P, Boizeau P, Dauger S, Riaud C, Lacarra B, Bourmaud A, Levy M. Viral Identification Using Multiplex Polymerase Chain Reaction Testing Does Not Reduce Antibiotic Prescribing in Paediatric Intensive Care Units. Microorganisms 2023; 11:microorganisms11040884. [PMID: 37110306 PMCID: PMC10143589 DOI: 10.3390/microorganisms11040884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/07/2023] [Accepted: 03/28/2023] [Indexed: 03/31/2023] Open
Abstract
PCR tests for viral identification, performed on nasopharyngeal secretions, have experienced a major boom in the last few years. Their use is very frequent, but their indications are still not well defined, especially in Paediatric Intensive Care Units (PICU). These tests are used for the microbiological diagnosis of lower respiratory infections but can be used in other situations. The aim of the study was to investigate the effect of viral identification on antibiotic therapy management. We conducted a single-centre retrospective study from 1 October 2017 to 31 December 2019. This study included all consecutive FilmArray® Respiratory Panel tests performed in patients hospitalised in a PICU. Patients were identified using the microbiology laboratory prospective database and data were extracted from the medical record. 544 tests corresponding to 408 patients were included. The main reasons for testing were pneumonia (34%) and bronchiolitis (24%). In 70% of cases, at least one virus was identified, with Human Rhinovirus (56%) and Respiratory Syncytial Virus (28%) being the two predominant. Bacterial co-infection was present in 25% of cases. Viral identification was not associated with reduced antibiotic therapy. On multivariate analysis, antibiotic management was significantly associated with clinical gravity, CRP value or radiology findings regardless of virus identification. Viral identification has an epidemiological value, but antibiotic prescription relies on other factors.
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21
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Tran-Dinh A, Tir I, Tanaka S, Atchade E, Lortat-Jacob B, Jean-Baptiste S, Zappella N, Boudinet S, Castier Y, Mal H, Mordant P, Ben Abdallah I, Bunel V, Messika J, Armand-Lefèvre L, Grall N, Montravers P. Impact of Culture-Positive Preservation Fluid on Early Morbidity and Mortality After Lung Transplantation. Transpl Int 2023; 36:10826. [PMID: 36846604 PMCID: PMC9945515 DOI: 10.3389/ti.2023.10826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/24/2023] [Indexed: 02/11/2023]
Abstract
The prevalence, risk factors and outcomes associated with culture-positive preservation fluid (PF) after lung transplantation (LT) are unknown. From January 2015 to December 2020, the microbiologic analyses of PF used to store the cold ischaemia-placed lung graft(s) of 271 lung transplant patients were retrospectively studied. Culture-positive PF was defined as the growth of any microorganism. Eighty-three (30.6%) patients were transplanted with lung grafts stored in a culture-positive PF. One-third of culture-positive PF were polymicrobial. Staphylococcus aureus and Escherichia coli were the most frequently isolated microorganisms. No risk factors for culture-positive PF based on donor characteristics were identified. Forty (40/83; 48.2%) patients had postoperative pneumonia on Day 0 and 2 (2/83; 2.4%) patients had pleural empyema with at least one identical bacteria isolated in culture-positive PF. The 30-day survival rate was lower for patients with culture-positive PF compared with patients with culture-negative PF (85.5% vs. 94.7%, p = 0.01). Culture-positive PF has a high prevalence and may decrease lung transplant recipient survival. Further studies are required to confirm these results and improve understanding of the pathogenesis of culture-positive PF and their management.
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Affiliation(s)
- Alexy Tran-Dinh
- Université Paris Cité, AP-HP, Hôpital Bichat Claude Bernard, Département d'Anesthésie-Réanimation, Paris, France
- INSERM UMR 1148 LVTS, Université de Paris, Paris, France
| | - Imane Tir
- Université Paris Cité, AP-HP, Hôpital Bichat Claude Bernard, Département d'Anesthésie-Réanimation, Paris, France
| | - Sébastien Tanaka
- Université Paris Cité, AP-HP, Hôpital Bichat Claude Bernard, Département d'Anesthésie-Réanimation, Paris, France
- Réunion Island University, INSERM U1188 Diabetes Atherothrombosis Réunion Indian Ocean (DéTROI), CYROI Plateform, Saint-Denis de la Réunion, France
| | - Enora Atchade
- Université Paris Cité, AP-HP, Hôpital Bichat Claude Bernard, Département d'Anesthésie-Réanimation, Paris, France
| | - Brice Lortat-Jacob
- Université Paris Cité, AP-HP, Hôpital Bichat Claude Bernard, Département d'Anesthésie-Réanimation, Paris, France
| | - Sylvain Jean-Baptiste
- Université Paris Cité, AP-HP, Hôpital Bichat Claude Bernard, Département d'Anesthésie-Réanimation, Paris, France
| | - Nathalie Zappella
- Université Paris Cité, AP-HP, Hôpital Bichat Claude Bernard, Département d'Anesthésie-Réanimation, Paris, France
| | - Sandrine Boudinet
- Université Paris Cité, AP-HP, Hôpital Bichat Claude Bernard, Département d'Anesthésie-Réanimation, Paris, France
| | - Yves Castier
- Université Paris Cité, AP-HP, Hôpital Bichat Claude Bernard, Service de Chirurgie Vasculaire, Thoracique et Transplantation Pulmonaire, Paris, France
- INSERM UMR 1152 PHERE, Université de Paris, Paris, France
| | - Hervé Mal
- INSERM UMR 1152 PHERE, Université de Paris, Paris, France
- Université Paris Cité, AP-HP, Hôpital Bichat Claude Bernard, Pneumologie B et Transplantation Pulmonaire, Paris, France
| | - Pierre Mordant
- Université Paris Cité, AP-HP, Hôpital Bichat Claude Bernard, Service de Chirurgie Vasculaire, Thoracique et Transplantation Pulmonaire, Paris, France
- INSERM UMR 1152 PHERE, Université de Paris, Paris, France
- Paris Transplant Group, Paris, France
| | - Iannis Ben Abdallah
- Université Paris Cité, AP-HP, Hôpital Bichat Claude Bernard, Service de Chirurgie Vasculaire, Thoracique et Transplantation Pulmonaire, Paris, France
- INSERM UMR 1152 PHERE, Université de Paris, Paris, France
| | - Vincent Bunel
- INSERM UMR 1152 PHERE, Université de Paris, Paris, France
- Université Paris Cité, AP-HP, Hôpital Bichat Claude Bernard, Pneumologie B et Transplantation Pulmonaire, Paris, France
| | - Jonathan Messika
- INSERM UMR 1152 PHERE, Université de Paris, Paris, France
- Université Paris Cité, AP-HP, Hôpital Bichat Claude Bernard, Pneumologie B et Transplantation Pulmonaire, Paris, France
- Paris Transplant Group, Paris, France
| | - Laurence Armand-Lefèvre
- Université Paris Cité, AP-HP, Hôpital Bichat Claude Bernard, Service de Bactériologie, Paris, France
- INSERM UMR 1137 IAME, Université de Paris, Paris, France
| | - Nathalie Grall
- Université Paris Cité, AP-HP, Hôpital Bichat Claude Bernard, Service de Bactériologie, Paris, France
- INSERM UMR 1137 IAME, Université de Paris, Paris, France
| | - Philippe Montravers
- Université Paris Cité, AP-HP, Hôpital Bichat Claude Bernard, Département d'Anesthésie-Réanimation, Paris, France
- INSERM UMR 1152 PHERE, Université de Paris, Paris, France
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22
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Barreto JV, Dias CC, Cardoso T. Does etiological investigation have an impact on the outcomes of community-acquired pneumonia? - A prospective cohort study. Eur J Intern Med 2023; 108:85-92. [PMID: 36494307 DOI: 10.1016/j.ejim.2022.11.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 12/12/2022]
Abstract
INTRODUCTION There is lack of evidence that etiological investigation influences outcomes in community-acquired pneumonia (CAP). Guidelines recommend diverse approaches to this matter. Our aim was to find if etiological investigation has an impact on CAP management and outcomes. METHODS Prospective cohort study, conducted over a two years' period, in a community-based hospital, including all adult patients with CAP. Univariate and multivariate logistic regression modeling were performed to understand the association of etiological identification with CAP outcomes, particularly hospital mortality. RESULTS A total of 660 cases of CAP were included, with a mean±sd age of 74±15 years and 58.9% of males. Etiology was documented in 33% of cases. Antibiotic (ATB) was modified in 148 patients, in 51 (34%) motivated by microbiological results. There was no significant impact on hospital mortality of microbiological documentation (35.5% vs 31.2%, p=0.352), or the fact that ATB was modified due to microbiological findings (27.0% vs 36.9%, p=0.272). When stratified by 3 subgroups of risk for drug-resistant pathogens (zero, one or two risk factors: being bed-ridden and/or ATB use within 90 days), etiology identification still did not influence mortality. When adjusted for CURB-65, Charlson's index, being bed-ridden, having had ATB or hospitalization within 90 days or coming from long-term care facilities, microbial identification was not associated with lower mortality. CONCLUSION Etiological investigation of patients with CAP does not have an association with hospital mortality, irrespective of the risk for drug-resistant pathogens.
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Affiliation(s)
- J Vasco Barreto
- Medicine Department, Hospital Pedro Hispano, Matosinhos Local Health Unit, Internal Medicine Service, Rua Dr. Eduardo Torres, Senhora da Hora 4464-513, Portugal; ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Rua Jorge de Viterbo Ferreira 228, Porto 4050-313, Portugal.
| | - Cláudia Camila Dias
- Knowledge Management Unit and Department of Community Medicine, Information and Health Decision Sciences, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, Porto 4200-319, Portugal; CINTESIS@RISE - Health Research Netwok - From Lab to the Community, Alameda Prof. Hernâni Monteiro, Porto 4200-319, Portugal
| | - Teresa Cardoso
- ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Rua Jorge de Viterbo Ferreira 228, Porto 4050-313, Portugal; Intensive Care Unit (UCIP) and Hospital Infection Control Committee, Hospital de Santo António, Oporto University Hospital Center, University of Porto, Largo Prof. Abel Salazar, Porto 4099-001, Portugal
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23
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Van Der Westhuyzen M, Samodien N, Brink AJ, Moodley C. Utility of the BioFire ® FilmArray ® Pneumonia Panel plus assay for syndromic testing of lower respiratory tract infections in a low/middle-income setting. JAC Antimicrob Resist 2023; 5:dlac139. [PMID: 36628341 PMCID: PMC9825243 DOI: 10.1093/jacamr/dlac139] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/15/2022] [Indexed: 01/09/2023] Open
Abstract
Background Determining lower respiratory tract infection (LRTI) aetiology is complex. Culture-based methods are laborious with poor sensitivity. Molecular assays improve detection of potential pathogens, but incorrect interpretation of results may lead to inappropriate antimicrobial therapy. Methods The utility of the BioFire® FilmArray® Pneumonia Panel plus (FA-PP) to detect LRTI pathogens, and the potential impact on antimicrobial stewardship in a low-resource setting, were assessed. Routine LRT samples were included from adult patients with clinically suspected LRTI or with a concomitant blood culture at Groote Schuur Hospital and referring facilities. Culture and FA-PP results were compared, and pharmacy data analysed to determine appropriateness of antibiotic therapy. Results There was an 80% correlation between cultured LRTI pathogens and the FA-PP bin ≥107 results. Compared with culture, the FA-PP detected substantially more pathogens (86.6% versus 17.9%) and produced a combined 100% positive percent agreement, and 88% negative percent agreement. The FA-PP detected bacterial/viral coinfections in 27% of samples. Correlation of FA-PP results with pharmacy data (n = 69) indicated a potential antibiotic change in 75% of cases, but this is difficult to accurately characterize without a 'gold standard' for treatment or complete clinical data. Conclusions The FA-PP increased the number of positive samples with typical bacteria, but the semi-quantitative reporting algorithm does not describe the correlation between the different bin values and colonization versus infection. This complicates result interpretation and may lead to inappropriate antimicrobial treatment. This study highlights the potential positive impact of rapid molecular assays for routine care in lower-income settings, but also underscores the interpretive challenges associated with these tests.
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Affiliation(s)
| | - N Samodien
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa,National Health Laboratory Service, Microbiology, Groote Schuur Hospital, Cape Town, South Africa
| | - A J Brink
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa,National Health Laboratory Service, Microbiology, Groote Schuur Hospital, Cape Town, South Africa
| | - C Moodley
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa,National Health Laboratory Service, Microbiology, Groote Schuur Hospital, Cape Town, South Africa
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Yen TY, Chen JF, Lu CY, Wu ET, Wang CC, Lu FL, Huang LM, Chang LY. Application of nested multiplex polymerase chain reaction respiratory and pneumonia panels in children with severe community-acquired pneumonia. J Med Virol 2023; 95:e28334. [PMID: 36418155 PMCID: PMC10108056 DOI: 10.1002/jmv.28334] [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: 08/13/2022] [Revised: 09/22/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022]
Abstract
Community-acquired pneumonia (CAP) is a serious clinical concern. A lack of accurate diagnosis could hinder pathogen-directed therapeutic strategies. To solve this problem, we evaluated clinical application of nested multiplex polymerase chain reaction (PCR) in children with severe CAP. We prospectively enrolled 60 children with severe CAP requiring intensive care between December 2019 and November 2021 at a tertiary medical center. Nested multiplex PCR respiratory panel (RP) and pneumonia panel (PP) were performed on upper and lower respiratory tract specimens. We integrated standard-of-care tests and quantitative PCR for validation. The combination of RP, PP, and standard-of-care tests could detect at least one pathogen in 98% of cases and the mixed viral-bacterial detection rate was 65%. The positive percent agreement (PPA), and negative percent agreement (NPA) for RP were 94% and 99%; the PPA and NPA for PP were 89% and 98%. The distribution of pathogens was similar in the upper and lower respiratory tracts, and the DNA or RNA copies of pathogens in the lower respiratory tract were equal to or higher than those in the upper respiratory tract. PP detected bacterial pathogens in 40 (67%) cases, and clinicians tended to increase bacterial diagnosis and escalate antimicrobial therapy for them. RP and PP had satisfactory performance to help pediatricians make pathogenic diagnoses and establish therapy earlier. The pathogens in the upper respiratory tract had predictive diagnostic values for lower respiratory tract infections in children with severe CAP.
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Affiliation(s)
- Ting-Yu Yen
- Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Jian-Fu Chen
- Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chun-Yi Lu
- Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - En-Ting Wu
- Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ching-Chia Wang
- Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Frank Leigh Lu
- Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Li-Min Huang
- Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Luan-Yin Chang
- Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
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Gadsby NJ, Musher DM. The Microbial Etiology of Community-Acquired Pneumonia in Adults: from Classical Bacteriology to Host Transcriptional Signatures. Clin Microbiol Rev 2022; 35:e0001522. [PMID: 36165783 PMCID: PMC9769922 DOI: 10.1128/cmr.00015-22] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
All modern advances notwithstanding, pneumonia remains a common infection with substantial morbidity and mortality. Understanding of the etiology of pneumonia continues to evolve as new techniques enable identification of already known organisms and as new organisms emerge. We now review the etiology of pneumonia (at present often called "community-acquired pneumonia") beginning with classic bacteriologic techniques, which identified Streptococcus pneumoniae as the overwhelmingly common cause, to more modern bacteriologic studies, which emphasize Haemophilus influenzae, Staphylococcus aureus, Moraxella catarrhalis, Enterobacteriaceae, Pseudomonas, and normal respiratory flora. Urine antigen detection is useful in identifying Legionella and pneumococcus. The low yield of bacteria in recent studies is due to the failure to obtain valid sputum samples before antibiotics are administered. The use of high-quality sputum specimens enables identification of recognized ("typical") bacterial pathogens as well as a role for commensal bacteria ("normal respiratory flora"). Nucleic acid amplification technology for viruses has revolutionized diagnosis, showing the importance of viral pneumonia leading to hospitalization with or without coinfecting bacterial organisms. Quantitative PCR study of sputum is in its early stages of application, but regular detection of high counts of bacterial DNA from organisms that are not seen on Gram stain or grown in quantitative culture presents a therapeutic dilemma. This finding may reflect the host microbiome of the respiratory tract, in which case treatment may not need to be given for them. Finally, host transcriptional signatures might enable clinicians to distinguish between viral and bacterial pneumonia, an important practical consideration.
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Affiliation(s)
- Naomi J. Gadsby
- Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Daniel M. Musher
- Michael E. DeBakey Veterans Administration Medical Center, Houston, Texas, USA
- Baylor College of Medicine, Houston, Texas, USA
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Evaluation and Clinical Impact of Biofire FilmArray Pneumonia Panel Plus in ICU-Hospitalized COVID-19 Patients. Diagnostics (Basel) 2022; 12:diagnostics12123134. [PMID: 36553141 PMCID: PMC9777407 DOI: 10.3390/diagnostics12123134] [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: 10/20/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Microbiological diagnosis by using commercial multiplex quantitative PCR systems provides great advantages over the conventional culture. In this work, the Biofire FilmArray Pneumonia Panel Plus (FAPP+) was used to test 144 low respiratory tract samples from 105 COVID-19 patients admitted to an Intensive Care Unit (ICU), detecting 78 pathogens in 59 (41%) samples. The molecular panel was evaluated by using the conventional culture (CC) as comparator, which isolated 42 pathogens in 40 (27.7%) samples. The overall percentage of agreement was 82.6%. Values of sensitivity (93%), specificity (62%), positive predictive value (50%), and negative predictive value (96%) were obtained. The mean time elapsed from sample extraction to modification of antibiotic treatment was 7.6 h. A change in antimicrobial treatment after the FAPP+ results was performed in 27% of patients. The FAPP+ is a highly sensitive diagnostic method that can be used to significantly reduce diagnostic time and that allows an early optimization of antimicrobial treatment.
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Empirical antibiotic therapy for difficult-to-treat Gram-negative infections: when, how, and how long? Curr Opin Infect Dis 2022; 35:568-574. [PMID: 36206149 DOI: 10.1097/qco.0000000000000884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
PURPOSE OF REVIEW To discuss empirical therapy for severe infections due to Gram-negative bacteria with difficult-to-treat resistance (GNB-DTR) in current clinical practice, focusing in particular on the positioning of novel therapeutic agents and rapid diagnostic tests. RECENT FINDINGS The current era of novel agents active against GNB-DTR and showing differential activity against specific determinants of resistance is an unprecedented scenario, in which the clinical reasoning leading to the choice of the empirical therapy for treating severe GNB-DTR infections is becoming more complex, but it also allows for enhanced treatment precision. SUMMARY Novel agents should be used in line with antimicrobial stewardship principles, aimed at reducing selective pressure for antimicrobial resistance. However, this does not mean that they should not be used. Indeed, excesses in restrictive uses may be unethical by precluding access to the most effective and less toxic treatments for patients with severe GNB-DTR infections. Given these premises (the 'how'), empirical treatment with novel agents should be considered in all patients with risk factors for GNB-DTR and severe clinical presentation of acute infection (the 'when'). Furthermore, empirical novel agents should preferably be continued only for a few hours, until de-escalation, modification, or confirmation (as targeted therapy) is made possible by the results of rapid diagnostic tests (the 'how long').
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Schmitz JE, Stratton CW, Persing DH, Tang YW. Forty Years of Molecular Diagnostics for Infectious Diseases. J Clin Microbiol 2022; 60:e0244621. [PMID: 35852340 PMCID: PMC9580468 DOI: 10.1128/jcm.02446-21] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Nearly 40 years have elapsed since the invention of the PCR, with its extremely sensitive and specific ability to detect nucleic acids via in vitro enzyme-mediated amplification. In turn, more than 2 years have passed since the onset of the coronavirus disease 2019 (COVID-19) pandemic, during which time molecular diagnostics for infectious diseases have assumed a larger global role than ever before. In this context, we review broadly the progression of molecular techniques in clinical microbiology, to their current prominence. Notably, these methods now entail both the detection and quantification of microbial nucleic acids, along with their sequence-based characterization. Overall, we seek to provide a combined perspective on the techniques themselves, as well as how they have come to shape health care at the intersection of technologic innovation, pathophysiologic knowledge, clinical/laboratory logistics, and even financial/regulatory factors.
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Affiliation(s)
- Jonathan E. Schmitz
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Charles W. Stratton
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - David H. Persing
- Medical and Scientific Affairs, Cepheid, Sunnyvale, California, USA
| | - Yi-Wei Tang
- Medical Affairs, Danaher Diagnostic Platform/Cepheid, Shanghai, China
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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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Potential of Multiplex Polymerase Chain Reaction Performed on Protected Telescope Catheter Samples for Early Adaptation of Antimicrobial Therapy in ARDS Patients. J Clin Med 2022; 11:jcm11154366. [PMID: 35955983 PMCID: PMC9369416 DOI: 10.3390/jcm11154366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/20/2022] [Accepted: 07/23/2022] [Indexed: 02/04/2023] Open
Abstract
Background: Diagnosis of co/superinfection in patients with Acute Respiratory Distress Syndrome (ARDS) is challenging. The FilmArray Pneumonia plus Panel (bioMérieux, France), a new rapid multiplex Polymerase Chain Reaction (mPCR), has never been assessed on a blinded protected telescope catheter (PTC) samples, a very common diagnostic tool in patients under mechanical ventilation. We evaluated the performance of mPCR on PTC samples compared with conventional culture and its impact on antibiotic stewardship. Methods: Observational study in two intensive care units, conducted between March and July 2020, during the first wave of the COVID-19 pandemic in France. Results: We performed 125 mPCR on blinded PTC samples of 95 ARDS patients, including 73 (77%) SARS-CoV-2 cases and 28 (29%) requiring extracorporeal membrane oxygenation. Respiratory samples were drawn from mechanically ventilated patients either just after intubation (n = 48; 38%) or later for suspected ventilator-associated pneumonia (VAP) (n = 77; 62%). The sensitivity, specificity, positive, and negative predictive values of mPCR were 93% (95% CI 84–100), 99% (95% CI 99–100), 68% (95% CI 54–83), and 100% (95% CI 100–100), respectively. The overall coefficient of agreement between mPCR and standard culture was 0.80 (95% CI 0.68–0.89). Intensivists changed empirical antimicrobial therapy in only 14% (18/125) of cases. No new antibiotic was initiated in more than half of the CAP/HAP pneumonia-suspected cases (n = 29; 60%) and in more than one-third of those suspected to have VAP without affecting or delaying their antimicrobial therapy. Conclusions: Rapid mPCR was feasible on blinded PTC with good sensitivity and specificity. New antibiotics were not initiated in more than half of patients and more than one-third of VAP-suspected cases. Further studies are needed to assess mPCR potential in improving antibiotic stewardship.
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Gerace E, Mancuso G, Midiri A, Poidomani S, Zummo S, Biondo C. Recent Advances in the Use of Molecular Methods for the Diagnosis of Bacterial Infections. Pathogens 2022; 11:pathogens11060663. [PMID: 35745518 PMCID: PMC9229729 DOI: 10.3390/pathogens11060663] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/31/2022] [Accepted: 06/05/2022] [Indexed: 12/14/2022] Open
Abstract
Infections caused by bacteria have a major impact on public health-related morbidity and mortality. Despite major advances in the prevention and treatment of bacterial infections, the latter continue to represent a significant economic and social burden worldwide. The WHO compiled a list of six highly virulent multidrug-resistant bacteria named ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) responsible for life-threatening diseases. Taken together with Clostridioides difficile, Escherichia coli, Campylobacter spp., (C. jejuni and C. coli), Legionella spp., Salmonella spp., and Neisseria gonorrhoeae, all of these microorganisms are the leading causes of nosocomial infections. The rapid and accurate detection of these pathogens is not only important for the early initiation of appropriate antibiotic therapy, but also for resolving outbreaks and minimizing subsequent antimicrobial resistance. The need for ever-improving molecular diagnostic techniques is also of fundamental importance for improving epidemiological surveillance of bacterial infections. In this review, we aim to discuss the recent advances on the use of molecular techniques based on genomic and proteomic approaches for the diagnosis of bacterial infections. The advantages and limitations of each of the techniques considered are also discussed.
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Affiliation(s)
| | - Giuseppe Mancuso
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
| | - Angelina Midiri
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
| | - Stefano Poidomani
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
| | - Sebastiana Zummo
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
| | - Carmelo Biondo
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
- Correspondence: ; Tel.: +39-090-2213322
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Zhuo X, Zhao J, Wang L, Sun B, Sun L, Wang C, Li B, Fan Y, Liu Y, Cao B. Development and evaluation of a multiplex quantitative polymerase chain reaction assay for detecting bacteria associated with lower respiratory tract infection. Int J Infect Dis 2022; 122:202-211. [PMID: 35644352 DOI: 10.1016/j.ijid.2022.05.052] [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: 02/22/2022] [Revised: 05/06/2022] [Accepted: 05/23/2022] [Indexed: 10/18/2022] Open
Abstract
OBJECTIVES This study aimed to establish a multiplex quantitative polymerase chain reaction (MQ-PCR) assay for 12 bacterial pathogens found in lower respiratory tract infection (LRTI) and to evaluate its performance in a cohort of 211 patients with LRTI. METHODS The study was divided into two stages: a pilot study to establish the methodology and a clinical validation study to evaluate its performance. In the pilot study, we established the MQ-PCR and analyzed its performance regarding limits of detection, reproducibility, specificity, and efficiency. In the clinical validation study, we obtained 211 sputum and/or bronchoalveolar lavage fluid (BALF) samples and detected pathogens by MQ-PCR. The MQ-PCR time was 3 h from sample collection to complete pathogen detection. RESULTS The limit of detection was 1000 copies/ml, and the maximum efficiency was >95%. When cutoffs of ≥105 copies/ml in sputum and ≥104 copies/ml in BALF were applied, the sensitivity, specificity, and positive and negative predictive values of the MQ-PCR were 77% (95% confidence interval [CI] 67-88%), 94% (95% CI 93-95%), 25% (95% CI 19-31%), and 99% (95% CI 99-100%), respectively. CONCLUSIONS This study demonstrates that the new MQ-PCR assay is time-saving, more effective and sensitive, and brings us closer to mainstream adoption of quantitative molecular detection of bacteria.
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Affiliation(s)
- Xianxia Zhuo
- Department of Pulmonary and Critical Care Medicine, Capital Medical University, Beijing, China; Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China; Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science; National Clinical Research Center of Respiratory Diseases, Beijing, China
| | - Jiankang Zhao
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China; Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science; National Clinical Research Center of Respiratory Diseases, Beijing, China
| | - Lei Wang
- Beijing Applied Biological Technologies Co., Ltd
| | - Bin Sun
- Beijing Applied Biological Technologies Co., Ltd
| | - Lanhua Sun
- Beijing Applied Biological Technologies Co., Ltd
| | - Chunlei Wang
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China; Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science; National Clinical Research Center of Respiratory Diseases, Beijing, China
| | - Binbin Li
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China; Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science; National Clinical Research Center of Respiratory Diseases, Beijing, China
| | - Yanyan Fan
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China; Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science; National Clinical Research Center of Respiratory Diseases, Beijing, China
| | - Yingmei Liu
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China; Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science; National Clinical Research Center of Respiratory Diseases, Beijing, China
| | - Bin Cao
- Department of Pulmonary and Critical Care Medicine, Capital Medical University, Beijing, China; Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China; Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science; National Clinical Research Center of Respiratory Diseases, Beijing, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, China.
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M. Patil S. Hospital-Acquired Pneumonia. Infect Dis (Lond) 2022. [DOI: 10.5772/intechopen.101236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Pneumonia acquired during hospitalization is called nosocomial pneumonia (NP). Nosocomial pneumonia is divided into two types. Hospital-acquired pneumonia (HAP) refers to hospital-acquired pneumonia, whereas ventilator-associated pneumonia (VAP) refers to ventilator-associated pneumonia. Most clinical literature stresses VAP’s importance and associated mortality and morbidity, whereas HAP is not given enough attention even while being the most common cause of NP. HAP, like VAP, carries a high mortality and morbidity. HAP is the commonest cause of mortality from hospital-acquired infections. HAP is a common determinant for intensive care unit (ICU) admits with respiratory failure. Recent research has identified definite risk factors responsible for HAP. If these are prevented or modified, the HAP incidence can be significantly decreased with improved clinical outcomes and lesser utilization of the health care resources. The prevention approach will need multiple strategies to address the issues. Precise epidemiological data on HAP is deficient due to limitations of the commonly used diagnostic measures. The diagnostic modalities available in HAP are less invasive than VAP. Recent infectious disease society guidelines have stressed the importance of HAP by removing healthcare-associated pneumonia as a diagnosis. Specific differences exist between HAP and VAP, which are gleaned over in this chapter.
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Ruppé E, d'Humières C, Armand-Lefèvre L. Inferring antibiotic susceptibility from metagenomic data: dream or reality? Clin Microbiol Infect 2022; 28:1225-1229. [PMID: 35551982 DOI: 10.1016/j.cmi.2022.04.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND The diagnosis of bacterial infections continues to rely on culture, a slow process in which antibiotic susceptibility profiles of potential pathogens are made available to clinicians 48h after sampling, at best. Recently, clinical metagenomics (CMg), the metagenomic sequencing of samples with the purpose of identifying microorganisms and determining their susceptibility to antimicrobials, has emerged as a potential diagnostic tool that could prove faster than culture. CMg indeed has the potential to detect antibiotic resistance genes (ARGs) and mutations associated with resistance. Nevertheless, many challenges have yet to be overcome in order to make rapid phenotypic inference of antibiotic susceptibility from metagenomic data a reality. OBJECTIVES The objective of this narrative review is to discuss the challenges underlying the phenotypic inference of antibiotic susceptibility from metagenomic data. SOURCES We conducted a narrative review using published articles available in the NCBI Pubmed database. CONTENT We review the current ARG databases with a specific emphasis on those which now provide associations with phenotypic data. Next, we discuss the bioinformatic tools designed to identify ARGs in metagenomes. We then report on the performance of phenotypic inference from genomic data and the issue predicting the expression of ARGs. Finally, we address the challenge of linking an ARG to this host. IMPLICATIONS Significant improvements have recently been made in associating ARG and phenotype, and the inference of susceptibility from genomic data has been demonstrated in pathogenic bacteria such as Staphylococci and Enterobacterales. Resistance involving gene expression is more challenging however, and inferring susceptibility from species such as Pseudomonas aeruginosa remains difficult. Future research directions include the consideration of gene expression via RNA sequencing and machine learning.
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Affiliation(s)
- Etienne Ruppé
- Université de Paris Cité, INSERM UMR1137 IAME, F-75018 Paris, France; AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, F-75018 Paris, France.
| | - Camille d'Humières
- Université de Paris Cité, INSERM UMR1137 IAME, F-75018 Paris, France; AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, F-75018 Paris, France
| | - Laurence Armand-Lefèvre
- Université de Paris Cité, INSERM UMR1137 IAME, F-75018 Paris, France; AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, F-75018 Paris, France
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Empiric Treatment in HAP/VAP: “Don’t You Want to Take a Leap of Faith?”. Antibiotics (Basel) 2022; 11:antibiotics11030359. [PMID: 35326822 PMCID: PMC8944836 DOI: 10.3390/antibiotics11030359] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/04/2022] [Accepted: 03/06/2022] [Indexed: 12/26/2022] Open
Abstract
Ventilator-associated pneumonia is a frequent cause of ICU-acquired infections. These infections are associated with high morbidity and mortality. The increase in antibiotic resistance, particularly among Gram-negative bacilli, makes the choice of empiric antibiotic therapy complex for physicians. Multidrug-resistant organisms (MDROs) related infections are associated with a high risk of initial therapeutic inadequacy. It is, therefore, necessary to quickly identify the bacterial species involved and their susceptibility to antibiotics. New diagnostic tools have recently been commercialized to assist in the management of these infections. Moreover, the recent enrichment of the therapeutic arsenal effective on Gram-negative bacilli raises the question of their place in the therapeutic management of these infections. Most national and international guidelines recommend limiting their use to microbiologically documented infections. However, many clinical situations and, in particular, the knowledge of digestive or respiratory carriage by MDROs should lead to the discussion of the use of these new molecules, especially the new combinations with beta-lactamase inhibitors in empirical therapy. In this review, we present the current epidemiological data, particularly in terms of MDRO, as well as the clinical and microbiological elements that may be taken into account in the discussion of empirical antibiotic therapy for patients managed for ventilator-associated pneumonia.
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Wicky PH, Martin-Loeches I, Timsit JF. "HAP and VAP after Guidelines". Semin Respir Crit Care Med 2022; 43:248-254. [PMID: 35042265 DOI: 10.1055/s-0041-1740246] [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]
Abstract
Nosocomial pneumonia is associated with worsened prognosis when diagnosed in intensive care unit (ICU), ranging from 12 to 48% mortality. The incidence rate of ventilation-acquired pneumonia tends to decrease below 15/1,000 intubation-day. Still, international guidelines are heterogeneous about diagnostic criteria because of inaccuracy of available methods. New entities have thus emerged concerning lower respiratory tract infection, namely ventilation-acquired tracheobronchitis (VAT), or ICU-acquired pneumonia (ICUAP), eventually requiring invasive ventilation (v-ICUAP), according to the type of ventilation support. The potential discrepancy with non-invasive methods could finally lead to underdiagnosis in almost two-thirds of non-intubated patients. Delayed diagnostic could explain in part the 2-fold increase in mortality of penumonia when invasive ventilation is initiated. Here we discuss the rationale underlying this new classification.Many situations can lead to misdiagnosis, even more when the invasive mechanical ventilation is initiated. The chest radiography lacks sntivity and specificity for diagnosing pneumonia. The place of chest computed tomography and lung ultrasonography for routine diagnostic of new plumonary infiltrate remain to be evaluated.Microbiological methods used to confirm the diagnostic can be heterogeneous. The development of molecular diagnostic tools may improve the adequacy of antimicrobial therapies of ventilated patients with pneumonia, but we need to further assess its impact in non-ventilated pneumonia.In this review we introduce distinction between hospital-acquired pneumonia according to the localization in the hospital and the oxygenation/ventilation mode. A clarification of definition is the first step to develop more accurate diagnostic strategies and to improve the patients' prognosis.
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Affiliation(s)
- Paul-Henri Wicky
- Medical and Infectious Diseases Intensive Care Unit, AP-HP, Bichat Hospital, Paris Diderot University, Paris, France
| | - Ignacio Martin-Loeches
- Department of Anaesthesia and Critical Care Medicine, St. James's Hospital, Dublin, Ireland.,Multidisciplinary Intensive Care Research Organization (MICRO), St James's Hospital, Dublin, Ireland
| | - Jean-François Timsit
- Medical and Infectious Diseases Intensive Care Unit, AP-HP, Bichat Hospital, Paris Diderot University, Paris, France.,UMR 1137, IAME, Université Paris Diderot, Paris, France
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37
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Renaud C, Kollef MH. Classical and Molecular Techniques to Diagnose HAP/VAP. Semin Respir Crit Care Med 2022; 43:219-228. [PMID: 35042263 DOI: 10.1055/s-0041-1739359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Nosocomial pneumonia, including hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP), are the most common nosocomial infections occurring in critically ill patients requiring intensive care. However, challenges exist in making a timely and accurate diagnosis of HAP and VAP. Under diagnosis of HAP and VAP can result in greater mortality risk, especially if accompanied by delays in the administration of appropriate antimicrobial treatment. Over diagnosis of HAP and VAP results in the unnecessary administration of broad spectrum antibiotics that can lead to further escalation of antibiotic resistance. Optimal diagnosis and management of HAP and VAP require a systematic approach that combines clinical and radiographic assessments along with proper microbiologic techniques. The use of more invasive sampling methods (bronchoalveolar lavage and protected specimen brush) may enhance specimen collection resulting in more specific diagnoses to limit unnecessary antibiotic exposure. Molecular techniques, currently in use and investigational technique, may improve the diagnosis of HAP and VAP by allowing more rapid identification of offending pathogens, if present, thus increasing both appropriate antibiotic treatment and avoiding unnecessary drug exposure.
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Affiliation(s)
- Cherie Renaud
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Marin H Kollef
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri
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38
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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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Barraud O, Guichard E, Chainier D, Postil D, Chimot L, Mercier E, Frat JP, Desachy A, Lacherade JC, Mathonnet A, Bellec F, Giraudeau B, Ploy MC, François B. Integrons, a predictive biomarker for antibiotic resistance in acute sepsis: the IRIS study. J Antimicrob Chemother 2021; 77:213-217. [PMID: 34557914 DOI: 10.1093/jac/dkab348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/15/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Considering the increase in MDR Gram-negative bacteria (GNB), the choice of empirical antibiotic therapy is challenging. In parallel, use of broad-spectrum antibiotics should be avoided to decrease antibiotic selection pressure. Accordingly, clinicians need rapid diagnostic tools to narrow antibiotic therapy. Class 1-3 integrons, identified by intI1-3 genes, are genetic elements that play a major role in antibiotic resistance in GNB. OBJECTIVES The objective of the IRIS study was to evaluate the negative and positive predictive values (NPVs and PPVs, respectively) of intI1-3 as markers of antibiotic resistance. METHODS The IRIS study was an observational cross-sectional multicentre study that enrolled adult subjects with suspected urinary tract or intra-abdominal infections. intI1-3 were detected directly from routinely collected biological samples (blood, urine or intra-abdominal fluid) using real-time PCR. A patient was considered 'MDR positive' if at least one GNB, expressing acquired resistance to at least two antibiotic families among β-lactams, aminoglycosides, fluoroquinolones and/or co-trimoxazole, was isolated from at least one biological sample. RESULTS Over a 2 year period, 513 subjects were enrolled and 409 had GNB documentation, mostly Enterobacterales. intI1 and/or intI2 were detected in 31.8% of patients and 24.4% of patients were considered 'MDR positive'. The NPV of intI1 and/or intI2 as a marker of acquired antibiotic resistances was estimated at 92.8% (89.1%-95.5%). The NPVs for first-line antibiotics were all above 92%, notably >96% for resistance to third-generation cephalosporins. CONCLUSIONS The IRIS study strongly suggests that the absence of intI1 and intI2 in biological samples from patients with GNB-related infections is predictive of the absence of acquired resistances.
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Affiliation(s)
- Olivier Barraud
- Université Limoges, INSERM, CHU Limoges, UMR 1092, Limoges, France.,INSERM, CIC1435, CHU Limoges, Limoges, France
| | | | | | | | - Loïc Chimot
- CH Périgueux, Réanimation, Périgueux, France
| | | | - Jean-Pierre Frat
- CHU Poitiers, Réanimation médicale et médecine interne, Poitiers, France
| | - Arnaud Desachy
- CH Angoulême, Réanimation Polyvalente, Angoulême, France
| | | | | | - Frédéric Bellec
- CH Montauban, Réanimation-Surveillance continue, Montauban, France
| | | | | | - Bruno François
- Université Limoges, INSERM, CHU Limoges, UMR 1092, Limoges, France.,INSERM, CIC1435, CHU Limoges, Limoges, France.,CHU Limoges, Réanimation Polyvalente, Limoges, France
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40
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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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41
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Ghosh C, Leon A, Koshy S, Aloum O, Al-Jabawi Y, Ismail N, Weiss ZF, Koo S. Breath-Based Diagnosis of Infectious Diseases: A Review of the Current Landscape. Clin Lab Med 2021; 41:185-202. [PMID: 34020759 DOI: 10.1016/j.cll.2021.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Various analytical methods can be applied to concentrate, separate, and examine trace volatile organic metabolites in the breath, with the potential for noninvasive, rapid, real-time identification of various disease processes, including an array of microbial infections. Although biomarker discovery and validation in microbial infections can be technically challenging, it is an approach that has shown great promise, especially for infections that are particularly difficult to identify with standard culture and molecular amplification-based approaches. This article discusses the current state of breath analysis for the diagnosis of infectious diseases.
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Affiliation(s)
- Chiranjit Ghosh
- Division of Infectious Diseases, Brigham and Women's Hospital, 181 Longwood Avenue, MCP642, Boston, MA 02115, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Armando Leon
- Division of Infectious Diseases, Brigham and Women's Hospital, 181 Longwood Avenue, MCP642, Boston, MA 02115, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Seena Koshy
- Division of Infectious Diseases, Brigham and Women's Hospital, 181 Longwood Avenue, MCP642, Boston, MA 02115, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Obadah Aloum
- Division of Infectious Diseases, Brigham and Women's Hospital, 181 Longwood Avenue, MCP642, Boston, MA 02115, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Yazan Al-Jabawi
- Division of Infectious Diseases, Brigham and Women's Hospital, 181 Longwood Avenue, MCP642, Boston, MA 02115, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Nour Ismail
- Division of Infectious Diseases, Brigham and Women's Hospital, 181 Longwood Avenue, MCP642, Boston, MA 02115, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Zoe Freeman Weiss
- Division of Infectious Diseases, Brigham and Women's Hospital, 181 Longwood Avenue, MCP642, Boston, MA 02115, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sophia Koo
- Division of Infectious Diseases, Brigham and Women's Hospital, 181 Longwood Avenue, MCP642, Boston, MA 02115, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA; Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
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42
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Jacobs MR, Colson JD, Rhoads DD. Recent advances in rapid antimicrobial susceptibility testing systems. Expert Rev Mol Diagn 2021; 21:563-578. [PMID: 33926351 DOI: 10.1080/14737159.2021.1924679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
INTRODUCTION Until recently antimicrobial susceptibility testing (AST) methods based on the demonstration of phenotypic susceptibility in 16-24 h remained largely unchanged. AREAS COVERED Advances in rapid phenotypic and molecular-based AST systems. EXPERT OPINION AST has changed over the past decade, with many rapid phenotypic and molecular methods developed to demonstrate phenotypic or genotypic resistance, or biochemical markers of resistance such as β-lactamases associated with carbapenem resistance. Most methods still require isolation of bacteria from specimens before both legacy and newer methods can be used. Bacterial identification by MALDI-TOF mass spectroscopy is now widely used and is often key to the interpretation of rapid AST results. Several PCR arrays are available to detect the most frequent pathogens associated with bloodstream infections and their major antimicrobial resistance genes. Many advances in whole-genome sequencing of bacteria and fungi isolated by culture as well as directly from clinical specimens have been made but are not yet widely available. High cost and limited throughput are the major obstacles to uptake of rapid methods, but targeted use, continued development and decreasing costs are expected to result in more extensive use of these increasingly useful methods.
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Affiliation(s)
- Michael R Jacobs
- Emeritus Professor of Pathology and Emeritus Medical Director, Clinical Microbiology, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Jordan D Colson
- Microbiology Fellow, Department of Pathology, Cleveland Clinic, Cleveland, OH, USA
| | - Daniel D Rhoads
- Section Head of Microbiology, Robert J. Tomsich Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
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43
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Abstract
Pneumonia is a common acute respiratory infection that affects the alveoli and distal airways; it is a major health problem and associated with high morbidity and short-term and long-term mortality in all age groups worldwide. Pneumonia is broadly divided into community-acquired pneumonia or hospital-acquired pneumonia. A large variety of microorganisms can cause pneumonia, including bacteria, respiratory viruses and fungi, and there are great geographical variations in their prevalence. Pneumonia occurs more commonly in susceptible individuals, including children of <5 years of age and older adults with prior chronic conditions. Development of the disease largely depends on the host immune response, with pathogen characteristics having a less prominent role. Individuals with pneumonia often present with respiratory and systemic symptoms, and diagnosis is based on both clinical presentation and radiological findings. It is crucial to identify the causative pathogens, as delayed and inadequate antimicrobial therapy can lead to poor outcomes. New antibiotic and non-antibiotic therapies, in addition to rapid and accurate diagnostic tests that can detect pathogens and antibiotic resistance will improve the management of pneumonia.
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44
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Maataoui N, Chemali L, Patrier J, Tran Dinh A, Le Fèvre L, Lortat-Jacob B, Marzouk M, d'Humières C, Rondinaud E, Ruppé E, Montravers P, Timsit JF, Armand-Lefèvre L. Impact of rapid multiplex PCR on management of antibiotic therapy in COVID-19-positive patients hospitalized in intensive care unit. Eur J Clin Microbiol Infect Dis 2021; 40:2227-2234. [PMID: 33733394 PMCID: PMC7968559 DOI: 10.1007/s10096-021-04213-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/25/2021] [Indexed: 12/27/2022]
Abstract
Because the diagnosis of co/superinfection in COVID-19 patients is challenging, empirical antibiotic therapy is frequently initiated until microbiological analysis results. We evaluated the performance and the impact of the BioFire® FilmArray® Pneumonia plus Panel on 112 respiratory samples from 67 COVID-19 ICU patients suspected of co/superinfections. Globally, the sensitivity and specificity of the test were 89.3% and 99.1%, respectively. Positive tests led to antibiotic initiation or adaptation in 15% of episodes and de-escalation in 4%. When negative, 28% of episodes remained antibiotic-free (14% no initiation, 14% withdrawal). Rapid multiplex PCRs can help to improve antibiotic stewardship by administering appropriate antibiotics earlier and avoiding unnecessary prescriptions.
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Affiliation(s)
- Naouale Maataoui
- Université de Paris, INSERM, IAME, F-75006, Paris, France. .,Service de Bactériologie, Hôpital Bichat Claude Bernard, AP-HP Nord, Université de Paris, 46 rue Henri Huchard, 75877, Paris Cedex 18, France.
| | - Lotfi Chemali
- Service de Bactériologie, Hôpital Bichat Claude Bernard, AP-HP Nord, Université de Paris, 46 rue Henri Huchard, 75877, Paris Cedex 18, France
| | - Juliette Patrier
- Medical and Infectious Diseases ICU (MI2), Hôpital Bichat, AP-HP, F-75018, Paris, France
| | - Alexy Tran Dinh
- Department of Anesthesiology and Surgical Critical Care, Hôpital Bichat, AP-HP, F-75018, Paris, France.,Université de Paris, INSERM U 1148, F-75006, Paris, France
| | - Lucie Le Fèvre
- Medical and Infectious Diseases ICU (MI2), Hôpital Bichat, AP-HP, F-75018, Paris, France
| | - Brice Lortat-Jacob
- Department of Anesthesiology and Surgical Critical Care, Hôpital Bichat, AP-HP, F-75018, Paris, France
| | - Mehdi Marzouk
- Medical and Infectious Diseases ICU (MI2), Hôpital Bichat, AP-HP, F-75018, Paris, France
| | - Camille d'Humières
- Université de Paris, INSERM, IAME, F-75006, Paris, France.,Service de Bactériologie, Hôpital Bichat Claude Bernard, AP-HP Nord, Université de Paris, 46 rue Henri Huchard, 75877, Paris Cedex 18, France
| | - Emilie Rondinaud
- Université de Paris, INSERM, IAME, F-75006, Paris, France.,Service de Bactériologie, Hôpital Bichat Claude Bernard, AP-HP Nord, Université de Paris, 46 rue Henri Huchard, 75877, Paris Cedex 18, France
| | - Etienne Ruppé
- Université de Paris, INSERM, IAME, F-75006, Paris, France.,Service de Bactériologie, Hôpital Bichat Claude Bernard, AP-HP Nord, Université de Paris, 46 rue Henri Huchard, 75877, Paris Cedex 18, France
| | - Philippe Montravers
- Department of Anesthesiology and Surgical Critical Care, Hôpital Bichat, AP-HP, F-75018, Paris, France.,Université de Paris, INSERM U 1148, F-75006, Paris, France
| | - Jean-François Timsit
- Université de Paris, INSERM, IAME, F-75006, Paris, France.,Medical and Infectious Diseases ICU (MI2), Hôpital Bichat, AP-HP, F-75018, Paris, France
| | - Laurence Armand-Lefèvre
- Université de Paris, INSERM, IAME, F-75006, Paris, France.,Service de Bactériologie, Hôpital Bichat Claude Bernard, AP-HP Nord, Université de Paris, 46 rue Henri Huchard, 75877, Paris Cedex 18, France
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