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Azad MA, Patel R. Practical Guidance for Clinical Microbiology Laboratories: Microbiologic diagnosis of implant-associated infections. Clin Microbiol Rev 2024; 37:e0010423. [PMID: 38506553 PMCID: PMC11237642 DOI: 10.1128/cmr.00104-23] [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] [Indexed: 03/21/2024] Open
Abstract
SUMMARYImplant-associated infections (IAIs) pose serious threats to patients and can be associated with significant morbidity and mortality. These infections may be difficult to diagnose due, in part, to biofilm formation on device surfaces, and because even when microbes are found, their clinical significance may be unclear. Despite recent advances in laboratory testing, IAIs remain a diagnostic challenge. From a therapeutic standpoint, many IAIs currently require device removal and prolonged courses of antimicrobial therapy to effect a cure. Therefore, making an accurate diagnosis, defining both the presence of infection and the involved microorganisms, is paramount. The sensitivity of standard microbial culture for IAI diagnosis varies depending on the type of IAI, the specimen analyzed, and the culture technique(s) used. Although IAI-specific culture-based diagnostics have been described, the challenge of culture-negative IAIs remains. Given this, molecular assays, including both nucleic acid amplification tests and next-generation sequencing-based assays, have been used. In this review, an overview of these challenging infections is presented, as well as an approach to their diagnosis from a microbiologic perspective.
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Affiliation(s)
- Marisa Ann Azad
- Division of Infectious Diseases, Department of Medicine, The Ottawa Hospital, Ottawa, Canada
- Ottawa Hospital Research Institute, Ottawa, Canada
| | - Robin Patel
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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Gong J, Yang J, Liu L, Chen X, Yang G, He Y, Sun R. Evaluation and clinical practice of pathogens and antimicrobial resistance genes of BioFire FilmArray Pneumonia panel in lower respiratory tract infections. Infection 2024; 52:545-555. [PMID: 38123753 PMCID: PMC10955009 DOI: 10.1007/s15010-023-02144-2] [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: 08/16/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Existing panels for lower respiratory tract infections (LRTIs) are slow and lack quantification of important pathogens and antimicrobial resistance, which are not solely responsible for their complex etiology and antibiotic resistance. BioFire FilmArray Pneumonia (PN) panels may provide rapid information on their etiology. METHODS The bronchoalveolar lavage fluid of 187 patients with LRTIs was simultaneously analyzed using a PN panel and cultivation, and the impact of the PN panel on clinical practice was assessed. The primary endpoint was to compare the consistency between the PN panel and conventional microbiology in terms of etiology and drug resistance, as well as to explore the clinical significance of the PN panel. The secondary endpoint was pathogen detection using the PN panel in patients with community-acquired pneumonia (CAP) or hospital-acquired pneumonia (HAP). RESULTS Fifty-seven patients with HAP and 130 with CAP were included. The most common pathogens of HAP were Acinetobacter baumannii and Klebsiella pneumoniae, with the most prevalent antimicrobial resistance (AMR) genes being CTX-M and KPC. For CAP, the most common pathogens were Haemophilus influenzae and Staphylococcus aureus, with the most frequent AMR genes being CTX-M and VIM. Compared with routine bacterial culture, the PN panel demonstrated an 85% combined positive percent agreement (PPA) and 92% negative percent agreement (NPA) for the qualitative identification of 13 bacterial targets. PN detection of bacteria with higher levels of semi-quantitative bacteria was associated with more positive bacterial cultures. Positive concordance between phenotypic resistance and the presence of corresponding AMR determinants was 85%, with 90% positive agreement between CTX-M-type extended-spectrum beta-lactamase gene type and phenotype and 100% agreement for mecA/C and MREJ. The clinical benefit of the PN panel increased by 25.97% compared with traditional cultural tests. CONCLUSION The bacterial pathogens and AMR identified by the PN panel were in good agreement with conventional cultivation, and the clinical benefit of the PN panel increased by 25.97% compared with traditional detection. Therefore, the PN panel is recommended for patients with CAP or HAP who require prompt pathogen diagnosis and resistance identification.
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Affiliation(s)
- Jinru Gong
- Department of Pulmonary and Critical Care Medicine, Guangdong Second Provincial General Hospital, Guangzhou, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Jiasheng Yang
- Department of Pulmonary and Critical Care Medicine, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Lihong Liu
- Department of Pulmonary and Critical Care Medicine, Guangdong Second Provincial General Hospital, Guangzhou, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Xiaoxuan Chen
- Department of Pulmonary and Critical Care Medicine, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Guangyu Yang
- Department of Pulmonary and Critical Care Medicine, Guangdong Second Provincial General Hospital, Guangzhou, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Yaowei He
- Department of Pulmonary and Critical Care Medicine, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Ruilin Sun
- Department of Pulmonary and Critical Care Medicine, Guangdong Second Provincial General Hospital, Guangzhou, China.
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China.
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Guo Q, Xiao Y, Zhang S. Metagenomic next generation sequencing of bronchoalveolar lavage samples for the diagnosis of lower respiratory tract infections: A systematic review and meta-analysis. Heliyon 2024; 10:e23188. [PMID: 38148812 PMCID: PMC10750151 DOI: 10.1016/j.heliyon.2023.e23188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 10/07/2023] [Accepted: 11/29/2023] [Indexed: 12/28/2023] Open
Abstract
Background Lower respiratory tract infections (LRTI)are known to be diagnosed late or inaccurately. This has fueled the unscrupulous use of antibiotics, as they are often used empirically and clinically, leading to antibiotic abuse and multidrug resistance in patients. Metagenomic next-generation sequencing (mNGS), now widely used in clinical studies, could be a potential intervention to revolutionize microbiology by rapidly identifying unknown species. Methods This review and meta-analysis were conducted on eligible studies with respect to metagenomic sequencing on clinical LRTI diagnostics up to May 01, 2022. QUADAS-2 was employed to assess the methodological bias as well as applicability. After that, a meta-analysis was conducted to analyze the accuracy of mNGS, compared with the composite reference standard (CRS), among the enrolled studies. Results This work collected 1248 samples in 13/21 qualified articles to factor in the accuracy of the diagnostic test. Typically, methods like molecular testing, culture, composite measures, and clinical decision-making were adopted as the reference criteria. With regard to Bronchoalveolar Lavage Samples, their sensitivity was 89% (82-93%) while their specificity was 90% (66-98%), with obvious heterogeneities in these two factors as demonstrated by different studies. The summary receiver operating characteristic (SROC) curve was plotted for mNGS as a function of LRTI, and the area under the curve (AUC) was 0.94. A Funnel plot with a p-value greater than 0.05 indicated the absence of publication bias. Positive and negative likelihood ratios (PLR and NLR) were >10 and > 0.1, respectively. In this pre-test probability-post-probability-likelihood ratio relationship graph, the values were Prior prob (%) = 20, Post-prob-Pos (%) = 77 and Post-prob-Neg (%) = 4. Conclusion The AUC value of SROC suggested a high accuracy of mNGS in diagnosis, with no publication bias and high reliability. The application of mNGS exhibits notable diagnostic efficacy in discerning pathogens present in bronchoalveolar lavage fluid (BALF) among patients afflicted with LRTI. However, mNGS is more meaningful for the definitive diagnosis of the disease rather than the exclusion of the disease. This post-test probability is significantly higher than the pre-test probability.
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Affiliation(s)
- Qiang Guo
- Department of Clinical Laboratory, Anhui Provincial Children’s Hospital, Hefei, 230000, Anhui, China
| | - Yang Xiao
- School of Anesthesiology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Shihai Zhang
- Department of Clinical Laboratory, Anhui Provincial Children’s Hospital, Hefei, 230000, Anhui, China
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Lewinski MA, Alby K, Babady NE, Butler-Wu SM, Bard JD, Greninger AL, Hanson K, Naccache SN, Newton D, Temple-Smolkin RL, Nolte F. Exploring the Utility of Multiplex Infectious Disease Panel Testing for Diagnosis of Infection in Different Body Sites: A Joint Report of the Association for Molecular Pathology, American Society for Microbiology, Infectious Diseases Society of America, and Pan American Society for Clinical Virology. J Mol Diagn 2023; 25:857-875. [PMID: 37757952 DOI: 10.1016/j.jmoldx.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/08/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The use of clinical molecular diagnostic methods for detecting microbial pathogens continues to expand and, in some cases, supplant conventional identification methods in various scenarios. Analytical and clinical benefits of multiplex molecular panels for the detection of respiratory pathogens have been demonstrated in various studies. The use of these panels in managing different patient populations has been incorporated into clinical guidance documents. The Association for Molecular Pathology's Infectious Diseases Multiplex Working Group conducted a review of the current benefits and challenges to using multiplex PCR for the detection of pathogens from gastrointestinal tract, central nervous system, lower respiratory tract, and joint specimens. The Working Group also discusses future directions and novel approaches to detection of pathogens in alternate specimen types, and outlines challenges associated with implementation of these multiplex PCR panels.
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Affiliation(s)
- Michael A Lewinski
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Roche Molecular Systems, San Clemente, California.
| | - Kevin Alby
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - N Esther Babady
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Clinical Microbiology Service, Departments of Laboratory Medicine and Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Susan M Butler-Wu
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Clinical Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jennifer Dien Bard
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Alexander L Greninger
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Kimberly Hanson
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; University of Utah School of Medicine and ARUP Laboratories, Salt Lake City, Utah
| | - Samia N Naccache
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Microbiology, LabCorp Seattle, Seattle, Washington
| | - Duane Newton
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Bio-Rad Laboratories, Irvine, California
| | | | - Frederick Nolte
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
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Alnimr A. Antimicrobial Resistance in Ventilator-Associated Pneumonia: Predictive Microbiology and Evidence-Based Therapy. Infect Dis Ther 2023:10.1007/s40121-023-00820-2. [PMID: 37273072 DOI: 10.1007/s40121-023-00820-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 05/09/2023] [Indexed: 06/06/2023] Open
Abstract
Ventilator-associated pneumonia (VAP) is a serious intensive care unit (ICU)-related infection in mechanically ventilated patients that is frequent, as more than half of antibiotics prescriptions in ICU are due to VAP. Various risk factors and diagnostic criteria for VAP have been referred to in different settings. The estimated attributable mortality of VAP can go up to 50%, which is higher in cases of antimicrobial-resistant VAP. When the diagnosis of pneumonia in a mechanically ventilated patient is made, initiation of effective antimicrobial therapy must be prompt. Microbiological diagnosis of VAP is required to optimize timely therapy since effective early treatment is fundamental for better outcomes, with controversy continuing regarding optimal sampling and testing. Understanding the role of antimicrobial resistance in the context of VAP is crucial in the era of continuously evolving antimicrobial-resistant clones that represent an urgent threat to global health. This review is focused on the risk factors for antimicrobial resistance in adult VAP and its novel microbiological tools. It aims to summarize the current evidence-based knowledge about the mechanisms of resistance in VAP caused by multidrug-resistant bacteria in clinical settings with focus on Gram-negative pathogens. It highlights the evidence-based antimicrobial management and prevention of drug-resistant VAP. It also addresses emerging concepts related to predictive microbiology in VAP and sheds lights on VAP in the context of coronavirus disease 2019 (COVID-19).
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Affiliation(s)
- Amani Alnimr
- Department of Microbiology, College of Medicine, King Fahad Hospital of the University, Imam Abdulrahman Bin Faisal University, Dammam, Kingdom of Saudi Arabia.
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Zhang L, Lu F, Wang Y, Ji J, Xu Y, Huang Y, Zhang M, Li M, Xia J, Wang B. Methodological comparison of bronchoalveolar lavage fluid-based detection of respiratory pathogens in diagnosis of bacterium/fungus-associated pneumonia in critically ill patients. Front Public Health 2023; 11:1168812. [PMID: 37255757 PMCID: PMC10225631 DOI: 10.3389/fpubh.2023.1168812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 04/12/2023] [Indexed: 06/01/2023] Open
Abstract
Background Bacterium/fungus-associated pneumonia (BAP/FAP) is the prominent cause of high mortality and morbidity with important clinical impacts globally. Effective diagnostic methods and proper specimen types hopefully facilitate early diagnosis of pneumonia and prevent spread of drug-resistant bacteria/fungi among critically ill patients. Methods In the present study, 342 bronchoalveolar lavage fluid (BALF) samples were collected from critically ill patients with pulmonary infections between November 2020 and March 2021. The BALF materials were comparatively employed to screen BAP/FAP through microscopy, culture, antigenic marker and PCR-based methods. The limit of detection (LOD) of cultures and PCR for bacteria/fungi was determined by serial dilution assays. Specimen slides were prepared with Gram staining for microscopic examinations. Microbial cultures and identifications underwent routine clinical protocols with the aid of mass spectrometry. (1,3)-β-D-glucan and galactomannan tests with BALF were carried out accordingly. Direct detection of pathogens in BALF was achieved through PCR, followed by sequencing and BLAST in GenBank database for pathogenic identification. The subjects' demographic and clinical characteristics were well evaluated. Results BAP/FAP was identified in approximately 47% of the subjects by the BALF-based PCR. The PCR-based diagnostic methods showed improved detection performance for fungi with good LOD, but performed similarly for bacteria, when compared to the cultures. There was poor agreement among traditional microscopy, culture and PCR assays for bacterial detections (kappa value, 0.184 to 0.277). For overall bacterial/fungal detections, the microscopy showed the lowest detecting rate, followed by the cultures, which displayed a slightly higher sensitivity than the microscopy did. The sensitivity of PCR was much higher than that of the other means of interest. However, the traditional cultures rather than antigenic marker-based approaches were moderately consistent with the PCR-based methods in fungal species identification, particularly for Candida and Aspergillus spp. Our findings further revealed that the age, length of hospital stay, invasive procedures and cerebral diseases were likely considered as main risk factors for BAP/FAP. Conclusion Screening for BALF in critically ill patients with suspected pneumonia pertaining high risk factors using combined PCR-based molecular detection strategies would hopefully contribute to early diagnosis of BAP/FAP and improved prognosis of the patients.
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Affiliation(s)
- Luwen Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Fanbo Lu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Yuerong Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Institute of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Juanjuan Ji
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Yuanhong Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Ying Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Min Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Moyan Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Jinxing Xia
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Bo Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
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Bălan AM, Bodolea C, Trancă SD, Hagău N. Trends in Molecular Diagnosis of Nosocomial Pneumonia Classic PCR vs. Point-of-Care PCR: A Narrative Review. Healthcare (Basel) 2023; 11:healthcare11091345. [PMID: 37174887 PMCID: PMC10177880 DOI: 10.3390/healthcare11091345] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/23/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
Nosocomial pneumonia is one of the most frequent hospital-acquired infections. One of the types of nosocomial pneumonia is ventilator-associated pneumonia, which occurs in endotracheally intubated patients in intensive care units (ICU). Ventilator-associated pneumonia may be caused by multidrug-resistant pathogens, which increase the risk of complications due to the difficulty in treating them. Pneumonia is a respiratory disease that requires targeted antimicrobial treatment initiated as early as possible to have a good outcome. For the therapy to be as specific and started sooner, diagnostic methods have evolved rapidly, becoming quicker and simpler to perform. Polymerase chain reaction (PCR) is a rapid diagnostic technique with numerous advantages compared to classic plate culture-based techniques. Researchers continue to improve diagnostic methods; thus, the newest types of PCR can be performed at the bedside, in the ICU, so-called point of care testing-PCR (POC-PCR). The purpose of this review is to highlight the benefits and drawbacks of PCR-based techniques in managing nosocomial pneumonia.
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Affiliation(s)
- Andrei-Mihai Bălan
- Department of Anaesthesia and Intensive Care 2, "Iuliu Hatieganu", University of Medicine and Pharmacy Cluj-Napoca, 400012 Cluj-Napoca, Romania
- Department of Anaesthesia and Intensive Care, Municipal Clinical Hospital, 400139 Cluj-Napoca, Romania
| | - Constantin Bodolea
- Department of Anaesthesia and Intensive Care 2, "Iuliu Hatieganu", University of Medicine and Pharmacy Cluj-Napoca, 400012 Cluj-Napoca, Romania
- Department of Anaesthesia and Intensive Care, Municipal Clinical Hospital, 400139 Cluj-Napoca, Romania
| | - Sebastian Daniel Trancă
- Department of Anaesthesia and Intensive Care 2, "Iuliu Hatieganu", University of Medicine and Pharmacy Cluj-Napoca, 400012 Cluj-Napoca, Romania
- Emergency Department, The Emergency County Hospital Cluj, 400347 Cluj-Napoca, Romania
| | - Natalia Hagău
- Department of Anaesthesia and Intensive Care 2, "Iuliu Hatieganu", University of Medicine and Pharmacy Cluj-Napoca, 400012 Cluj-Napoca, Romania
- Department of Anaesthesia and Intensive Care, "Regina Maria" Hospital, 400221 Cluj-Napoca, Romania
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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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Argyropoulos CD, Skoulou V, Efthimiou G, Michopoulos AK. Airborne transmission of biological agents within the indoor built environment: a multidisciplinary review. AIR QUALITY, ATMOSPHERE, & HEALTH 2022; 16:477-533. [PMID: 36467894 PMCID: PMC9703444 DOI: 10.1007/s11869-022-01286-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
The nature and airborne dispersion of the underestimated biological agents, monitoring, analysis and transmission among the human occupants into building environment is a major challenge of today. Those agents play a crucial role in ensuring comfortable, healthy and risk-free conditions into indoor working and leaving spaces. It is known that ventilation systems influence strongly the transmission of indoor air pollutants, with scarce information although to have been reported for biological agents until 2019. The biological agents' source release and the trajectory of airborne transmission are both important in terms of optimising the design of the heating, ventilation and air conditioning systems of the future. In addition, modelling via computational fluid dynamics (CFD) will become a more valuable tool in foreseeing risks and tackle hazards when pollutants and biological agents released into closed spaces. Promising results on the prediction of their dispersion routes and concentration levels, as well as the selection of the appropriate ventilation strategy, provide crucial information on risk minimisation of the airborne transmission among humans. Under this context, the present multidisciplinary review considers four interrelated aspects of the dispersion of biological agents in closed spaces, (a) the nature and airborne transmission route of the examined agents, (b) the biological origin and health effects of the major microbial pathogens on the human respiratory system, (c) the role of heating, ventilation and air-conditioning systems in the airborne transmission and (d) the associated computer modelling approaches. This adopted methodology allows the discussion of the existing findings, on-going research, identification of the main research gaps and future directions from a multidisciplinary point of view which will be helpful for substantial innovations in the field.
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Affiliation(s)
| | - Vasiliki Skoulou
- B3 Challenge Group, Chemical Engineering, School of Engineering, University of Hull, Cottingham Road, Hull, HU6 7RX UK
| | - Georgios Efthimiou
- Centre for Biomedicine, Hull York Medical School, University of Hull, Cottingham Road, Hull, HU6 7RX UK
| | - Apostolos K. Michopoulos
- Energy & Environmental Design of Buildings Research Laboratory, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
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Navapurkar V, Bartholdson Scott J, Maes M, Hellyer TP, Higginson E, Forrest S, Pereira-Dias J, Parmar S, Heasman-Hunt E, Polgarova P, Brown J, Titti L, Smith WPW, Scott J, Rostron A, Routledge M, Sapsford D, Török ME, McMullan R, Enoch DA, Wong V, Curran MD, Brown NM, Simpson AJ, Herre J, Dougan G, Conway Morris A. Development and implementation of a customised rapid syndromic diagnostic test for severe pneumonia. Wellcome Open Res 2022; 6:256. [PMID: 36337362 PMCID: PMC9617073 DOI: 10.12688/wellcomeopenres.17099.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2022] [Indexed: 02/02/2023] Open
Abstract
Background: The diagnosis of pneumonia has been hampered by a reliance on bacterial cultures which take several days to return a result, and are frequently negative. In critically ill patients this leads to the use of empiric, broad-spectrum antimicrobials and compromises good antimicrobial stewardship. The objective of this study was to establish the performance of a syndromic molecular diagnostic approach, using a custom TaqMan array card (TAC) covering 52 respiratory pathogens, and assess its impact on antimicrobial prescribing. Methods: The TAC was validated against a retrospective multi-centre cohort of broncho-alveolar lavage samples. The TAC was assessed prospectively in patients undergoing investigation for suspected pneumonia, with a comparator cohort formed of patients investigated when the TAC laboratory team were unavailable. Co-primary outcomes were sensitivity compared to conventional microbiology and, for the prospective study, time to result. Metagenomic sequencing was performed to validate findings in prospective samples. Antibiotic free days (AFD) were compared between the study cohort and comparator group. Results: 128 stored samples were tested, with sensitivity of 97% (95% confidence interval (CI) 88-100%). Prospectively, 95 patients were tested by TAC, with 71 forming the comparator group. TAC returned results 51 hours (interquartile range 41-69 hours) faster than culture and with sensitivity of 92% (95% CI 83-98%) compared to conventional microbiology. 94% of organisms identified by sequencing were detected by TAC. There was a significant difference in the distribution of AFDs with more AFDs in the TAC group (p=0.02). TAC group were more likely to experience antimicrobial de-escalation (odds ratio 2.9 (95%1.5-5.5)). Conclusions: Implementation of a syndromic molecular diagnostic approach to pneumonia led to faster results, with high sensitivity and impact on antibiotic prescribing.
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Affiliation(s)
- Vilas Navapurkar
- John V Farman Intensive Care Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Josefin Bartholdson Scott
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Mailis Maes
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Thomas P Hellyer
- Translational and Clinical Research Institute, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE7 7DN, UK
| | - Ellen Higginson
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Sally Forrest
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Joana Pereira-Dias
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Surendra Parmar
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Emma Heasman-Hunt
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Petra Polgarova
- John V Farman Intensive Care Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Joanne Brown
- John V Farman Intensive Care Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Lissamma Titti
- John V Farman Intensive Care Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - William PW Smith
- School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Jonathan Scott
- Translational and Clinical Research Institute, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK
| | - Anthony Rostron
- Translational and Clinical Research Institute, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK
| | - Matthew Routledge
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - David Sapsford
- Pharmacy Department, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - M. Estée Török
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
- Microbiology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Ronan McMullan
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, BT9 7BL, UK
| | - David A Enoch
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Vanessa Wong
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - VAP-Rapid investigators
- John V Farman Intensive Care Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
- Translational and Clinical Research Institute, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE7 7DN, UK
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
- Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Pharmacy Department, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
- Microbiology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, BT9 7BL, UK
- Respiratory Medicine, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Martin D Curran
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Nicholas M Brown
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - A John Simpson
- Translational and Clinical Research Institute, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE7 7DN, UK
| | - Jurgen Herre
- Respiratory Medicine, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Andrew Conway Morris
- John V Farman Intensive Care Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
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11
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Darie AM, Khanna N, Jahn K, Osthoff M, Bassetti S, Osthoff M, Schumann DM, Albrich WC, Hirsch H, Brutsche M, Grize L, Tamm M, Stolz D. Fast multiplex bacterial PCR of bronchoalveolar lavage for antibiotic stewardship in hospitalised patients with pneumonia at risk of Gram-negative bacterial infection (Flagship II): a multicentre, randomised controlled trial. THE LANCET RESPIRATORY MEDICINE 2022; 10:877-887. [DOI: 10.1016/s2213-2600(22)00086-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 10/18/2022]
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12
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Andrews V, Pinholt M, Schneider UV, Schønning K, Søes LM, Lisby G. Performance of PCR-based syndromic testing compared to bacterial culture in patients with suspected pneumonia applying microscopy for quality assessment. APMIS 2022; 130:417-426. [PMID: 35499302 DOI: 10.1111/apm.13232] [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: 04/22/2022] [Accepted: 04/28/2022] [Indexed: 11/29/2022]
Abstract
Syndromic testing for lower respiratory tract infections with BioFire® FilmArray® Pneumonia Panel Plus (BF) detects 27 pathogens with a turn-around-time of one hour. We compared the performance of BF with culture. Samples from 298 hospitalized patients with suspected pneumonia routinely sent for culture were also analyzed using BF. Retrospectively, patients were clinically categorized as having "pneumonia" or "no pneumonia." BF and culture were compared by analytical performance, which was evaluated by pathogen concordance, and by clinical performance by comparing pathogen detections in patients with and without pneumonia. The BF results for viruses and atypical bacteria were not included in the performance analysis. In 298 patient samples, BF and culture detected 285 and 142 potential pathogens, respectively. Positive percent agreement (PPA) was 88% (125/142). In patients with community-acquired pneumonia (CAP), clinical sensitivity was 70% and 51%, and specificity was 43% and 71% for BF and culture, respectively. In patients with hospital-acquired pneumonia, the corresponding numbers were 55% and 23%, and 47% and 68%. There was no significant improvement of performance, when only high-quality sputum samples were considered. Efficacy of both BF and culture was low. Both tests are best used in CAP patients for whom the diagnosis has already been clinically established. Indiscriminate use may be clinically misleading and a cause of improper use of antibiotics.
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Affiliation(s)
- Vigith Andrews
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
| | - Mette Pinholt
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
| | - Uffe Vest Schneider
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
| | - Kristian Schønning
- Department of Clinical Microbiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Lillian Marie Søes
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
| | - Gorm Lisby
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
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13
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Fanning J, Panigada M, Li Bassi G. Nosocomial Pneumonia in the Mechanically Ventilated Patient. Semin Respir Crit Care Med 2022; 43:426-439. [PMID: 35714627 DOI: 10.1055/s-0042-1749448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Ventilator-associated pneumonia (VAP) is a common complication occurring in critically ill patients who are mechanically ventilated and is the leading cause of nosocomial infection-related death. Etiologic agents for VAP widely differ based on the population of intensive care unit patients, duration of hospital stay, and prior antimicrobial therapy. VAP due to multidrug-resistant pathogens is associated with the highest morbidity and mortality, likely due to delays in appropriate antimicrobial treatment. International guidelines are currently available to guide diagnostic and therapeutic strategies. VAP can be prevented through various pharmacological and non-pharmacological interventions, which are more effective when grouped as bundles. When VAP is clinically suspected, diagnostic strategies should include early collection of respiratory samples to guide antimicrobial therapy. Empirical treatment should be based on the most likely etiologic microorganisms and antibiotics likely to be active against these microorganisms. Response to therapy should be reassessed after 3 to 5 days and antimicrobials adjusted or de-escalated to reduce the burden of the disease. Finally, considering that drug resistance is increasing worldwide, several novel antibiotics are being tested to efficiently treat VAP in the coming decades.
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Affiliation(s)
- Jonathon Fanning
- Critical Care Research Group, The Prince Charles Hospital, Brisbane, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Australia.,Intensive Care Unit, Royal Brisbane and Women's Hospital, Queensland, Australia.,Intensive Care Unit, St Andrew's War Memorial Hospital, Queensland, Australia.,Nuffield Department of Population Health, Oxford University, United Kingdom
| | - Mauro Panigada
- Department of Anaesthesiology, Intensive Care and EmergencyFondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Gianluigi Li Bassi
- Critical Care Research Group, The Prince Charles Hospital, Brisbane, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Australia.,Intensive Care Unit, St Andrew's War Memorial Hospital, Queensland, Australia.,Queensland University of Technology, Brisbane, Australia.,Intensive Care Unit, The Wesley Hospital, Auchenflower, Queensland, Australia.,Wesley Medical Research, The Wesley Hospital, Auchenflower, Australia
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14
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Navapurkar V, Bartholdson Scott J, Maes M, Hellyer TP, Higginson E, Forrest S, Pereira-Dias J, Parmar S, Heasman-Hunt E, Polgarova P, Brown J, Titti L, Smith WPW, Scott J, Rostron A, Routledge M, Sapsford D, Török ME, McMullan R, Enoch DA, Wong V, Curran MD, Brown NM, Simpson AJ, Herre J, Dougan G, Conway Morris A. Development and implementation of a customised rapid syndromic diagnostic test for severe pneumonia. Wellcome Open Res 2022; 6:256. [PMID: 36337362 PMCID: PMC9617073 DOI: 10.12688/wellcomeopenres.17099.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2022] [Indexed: 02/02/2023] Open
Abstract
Background: The diagnosis of pneumonia has been hampered by a reliance on bacterial cultures which take several days to return a result, and are frequently negative. In critically ill patients this leads to the use of empiric, broad-spectrum antimicrobials and compromises good antimicrobial stewardship. The objective of this study was to establish the performance of a syndromic molecular diagnostic approach, using a custom TaqMan array card (TAC) covering 52 respiratory pathogens, and assess its impact on antimicrobial prescribing. Methods: The TAC was validated against a retrospective multi-centre cohort of broncho-alveolar lavage samples. The TAC was assessed prospectively in patients undergoing investigation for suspected pneumonia, with a comparator cohort formed of patients investigated when the TAC laboratory team were unavailable. Co-primary outcomes were sensitivity compared to conventional microbiology and, for the prospective study, time to result. Metagenomic sequencing was performed to validate findings in prospective samples. Antibiotic free days (AFD) were compared between the study cohort and comparator group. Results: 128 stored samples were tested, with sensitivity of 97% (95% confidence interval (CI) 88-100%). Prospectively, 95 patients were tested by TAC, with 71 forming the comparator group. TAC returned results 51 hours (interquartile range 41-69 hours) faster than culture and with sensitivity of 92% (95% CI 83-98%) compared to conventional microbiology. 94% of organisms identified by sequencing were detected by TAC. There was a significant difference in the distribution of AFDs with more AFDs in the TAC group (p=0.02). TAC group were more likely to experience antimicrobial de-escalation (odds ratio 2.9 (95%1.5-5.5)). Conclusions: Implementation of a syndromic molecular diagnostic approach to pneumonia led to faster results, with high sensitivity and impact on antibiotic prescribing.
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Affiliation(s)
- Vilas Navapurkar
- John V Farman Intensive Care Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Josefin Bartholdson Scott
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Mailis Maes
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Thomas P Hellyer
- Translational and Clinical Research Institute, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE7 7DN, UK
| | - Ellen Higginson
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Sally Forrest
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Joana Pereira-Dias
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Surendra Parmar
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Emma Heasman-Hunt
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Petra Polgarova
- John V Farman Intensive Care Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Joanne Brown
- John V Farman Intensive Care Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Lissamma Titti
- John V Farman Intensive Care Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - William PW Smith
- School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Jonathan Scott
- Translational and Clinical Research Institute, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK
| | - Anthony Rostron
- Translational and Clinical Research Institute, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK
| | - Matthew Routledge
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - David Sapsford
- Pharmacy Department, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - M. Estée Török
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
- Microbiology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Ronan McMullan
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, BT9 7BL, UK
| | - David A Enoch
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Vanessa Wong
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - VAP-Rapid investigators
- John V Farman Intensive Care Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
- Translational and Clinical Research Institute, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE7 7DN, UK
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
- Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Pharmacy Department, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
- Microbiology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, BT9 7BL, UK
- Respiratory Medicine, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Martin D Curran
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Nicholas M Brown
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - A John Simpson
- Translational and Clinical Research Institute, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE7 7DN, UK
| | - Jurgen Herre
- Respiratory Medicine, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Andrew Conway Morris
- John V Farman Intensive Care Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
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15
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Boyd S, Nseir S, Rodriguez A, Martin-Loeches I. Ventilator-associated pneumonia in critically ill patients with COVID-19 infection, a narrative review. ERJ Open Res 2022; 8:00046-2022. [PMID: 35891621 PMCID: PMC9080287 DOI: 10.1183/23120541.00046-2022] [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: 01/25/2022] [Accepted: 04/24/2022] [Indexed: 01/08/2023] Open
Abstract
COVID pneumonitis can cause patients to become critically ill. They may require intensive care and mechanical ventilation. Ventilator-associated pneumonia is a concern. This review aims to discuss the topic of ventilator-associated pneumonia in this group. Several reasons have been proposed to explain the elevated rates of VAP in critically ill COVID patients compared to non-COVID patients. Extrinsic factors include understaffing, lack of PPE and use of immunomodulating agents. Intrinsic factors include severe parenchymal damage, immune dysregulation, along with pulmonary vascular endothelial inflammation and thrombosis. The rate of VAP has been reported at 45.4%, with an ICU mortality rate of 42.7%. Multiple challenges to diagnosis exist. Other conditions such as acute respiratory distress syndrome, pulmonary oedema and atelectasis can present with similar features. Frequent growth of gram-negative bacteria has been shown in multiple studies, with particularly high rates of pseudomonas aeruginosa. The rate of invasive pulmonary aspergillosis has been reported at 4–30%. We would recommend the use of invasive techniques when possible. This will enable de-escalation of antibiotics as soon as possible, decreasing overuse. It is also important to keep other possible causes of ventilator-associated pneumonia in mind, such as COVID-19 associated pulmonary aspergillosis, cytomegalovirus, etc. Diagnostic tests such as galactomannan and B-D-glucan should be considered. These patients may face a long treatment course, with risk of re-infection, along with prolonged weaning, which carries its own long-term consequences.
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16
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Abstract
PURPOSE OF REVIEW Ventilator-associated pneumonia (VAP) is a common nosocomial infection in critically ill patients requiring endotracheal intubation and mechanical ventilation. Recently, the emergence of multidrug-resistant Gram-negative bacteria, including carbapenem-resistant Enterobacterales, multidrug-resistant Pseudomonas aeruginosa and Acinetobacter species, has complicated the selection of appropriate antimicrobials and contributed to treatment failure. Although novel antimicrobials are crucial to treating VAP caused by these multidrug-resistant organisms, knowledge of how to optimize their efficacy while minimizing the development of resistance should be a requirement for their use. RECENT FINDINGS Several studies have assessed the efficacy of novel antimicrobials against multidrug-resistant organisms, but high-quality studies focusing on optimal dosing, infusion time and duration of therapy in patients with VAP are still lacking. Antimicrobial and diagnostic stewardship should be combined to optimize the use of these novel agents. SUMMARY Improvements in diagnostic tests, stewardship practices and a better understanding of dosing, infusion time, duration of treatment and the effects of combining various antimicrobials should help optimize the use of novel antimicrobials for VAP and maximize clinical outcomes while minimizing the development of resistance.
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17
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Căpățînă D, Feier B, Hosu O, Tertiș M, Cristea C. Analytical methods for the characterization and diagnosis of infection with Pseudomonas aeruginosa: A critical review. Anal Chim Acta 2022; 1204:339696. [DOI: 10.1016/j.aca.2022.339696] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 02/05/2022] [Accepted: 03/06/2022] [Indexed: 12/11/2022]
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18
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Enne VI, Aydin A, Baldan R, Owen DR, Richardson H, Ricciardi F, Russell C, Nomamiukor-Ikeji BO, Swart AM, High J, Colles A, Barber J, Gant V, Livermore DM, O'Grady J. Multicentre evaluation of two multiplex PCR platforms for the rapid microbiological investigation of nosocomial pneumonia in UK ICUs: the INHALE WP1 study. Thorax 2022; 77:1220-1228. [PMID: 35027473 DOI: 10.1136/thoraxjnl-2021-216990] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 11/29/2021] [Indexed: 01/12/2023]
Abstract
BACKGROUND Culture-based microbiological investigation of hospital-acquired or ventilator-associated pneumonia (HAP or VAP) is insensitive, with aetiological agents often unidentified. This can lead to excess antimicrobial treatment of patients with susceptible pathogens, while those with resistant bacteria are treated inadequately for prolonged periods. Using PCR to seek pathogens and their resistance genes directly from clinical samples may improve therapy and stewardship. METHODS Surplus routine lower respiratory tract samples were collected from intensive care unit patients about to receive new or changed antibiotics for hospital-onset lower respiratory tract infections at 15 UK hospitals. Testing was performed using the BioFire FilmArray Pneumonia Panel (bioMérieux) and Unyvero Pneumonia Panel (Curetis). Concordance analysis compared machine and routine microbiology results, while Bayesian latent class (BLC) analysis estimated the sensitivity and specificity of each test, incorporating information from both PCR panels and routine microbiology. FINDINGS In 652 eligible samples; PCR identified pathogens in considerably more samples compared with routine microbiology: 60.4% and 74.2% for Unyvero and FilmArray respectively vs 44.2% by routine microbiology. PCR tests also detected more pathogens per sample than routine microbiology. For common HAP/VAP pathogens, FilmArray had sensitivity of 91.7%-100.0% and specificity of 87.5%-99.5%; Unyvero had sensitivity of 50.0%-100.0%%, and specificity of 89.4%-99.0%. BLC analysis indicated that, compared with PCR, routine microbiology had low sensitivity, ranging from 27.0% to 69.4%. INTERPRETATION Conventional and BLC analysis demonstrated that both platforms performed similarly and were considerably more sensitive than routine microbiology, detecting potential pathogens in patient samples reported as culture negative. The increased sensitivity of detection realised by PCR offers potential for improved antimicrobial prescribing.
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Affiliation(s)
- Virve I Enne
- Division of Infection and Immunity, University College London, London, UK
| | - Alp Aydin
- Division of Infection and Immunity, University College London, London, UK
| | - Rossella Baldan
- Centre for Clinical Infection and Diagnostic Research, King's College London, London, UK.,Norwich Medical School, University of East Anglia, Norwich, UK
| | - Dewi R Owen
- Division of Infection and Immunity, University College London, London, UK
| | | | - Federico Ricciardi
- Department of Statistical Science, University College London, London, UK
| | | | | | - Ann-Marie Swart
- Norwich Clinical Trials Unit, University of East Anglia, Norwich, UK
| | - Juliet High
- Norwich Clinical Trials Unit, University of East Anglia, Norwich, UK
| | - Antony Colles
- Norwich Clinical Trials Unit, University of East Anglia, Norwich, UK
| | - Julie Barber
- Department of Statistical Science, University College London, London, UK
| | - Vanya Gant
- Department of Clinical Microbiology, University College London Hospitals NHS Foundation Trust, London, UK.,NIHR Biomedical research Centre, University College London Hospitals, London, UK
| | | | - Justin O'Grady
- Norwich Medical School, University of East Anglia, Norwich, UK.,Quadram Institute Bioscience, Norwich, UK
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19
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Riccobono E, Bussini L, Giannella M, Viale P, Rossolini GM. Rapid diagnostic tests in the management of pneumonia. Expert Rev Mol Diagn 2021; 22:49-60. [PMID: 34894965 DOI: 10.1080/14737159.2022.2018302] [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: 10/19/2022]
Abstract
INTRODUCTION Pneumonia is one of the main causes of mortality associated with infectious diseases worldwide. Several challenges have been identified in the management of patients with pneumonia, ranging from accurate and cost-effective microbiological investigations, prompt and adequate therapeutic management, and optimal treatment duration. AREAS COVERED In this review, an updated summary on the current management of pneumonia patients is provided and the epidemiological issues of infectious respiratory diseases, which in the current pandemic situation are of particular concern, are addressed. The clinical and microbiological approaches to pneumonia diagnosis are reviewed, including discussion about the new molecular assays pointing out both their strengths and limitations. Finally, the current recommendations about antibiotic treatment are examined and discussed depending on the epidemiological contexts, including those with high prevalence of multidrug-resistant bacteria. EXPERT OPINION We claim that rapid diagnostic tests, if well-positioned in the diagnostic workflow and reserved for the subset of patients who could most benefit from these technologies, may represent an interesting and feasible tool to optimize timing of targeted treatments especially in terms of early de-escalation or discontinuation of antibiotic therapy.
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Affiliation(s)
- Eleonora Riccobono
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Linda Bussini
- Infectious Diseases Unit, Department of Medical and Surgical Sciences, Policlinico Sant' Orsola, Bologna, Italy
| | - Maddalena Giannella
- Infectious Diseases Unit, Department of Medical and Surgical Sciences, Policlinico Sant' Orsola, Bologna, Italy
| | - Pierluigi Viale
- Infectious Diseases Unit, Department of Medical and Surgical Sciences, Policlinico Sant' Orsola, Bologna, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Clinical Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
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20
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Fromentin M, Ricard JD, Roux D. Lung Microbiome in Critically Ill Patients. Life (Basel) 2021; 12:life12010007. [PMID: 35054400 PMCID: PMC8778861 DOI: 10.3390/life12010007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 12/11/2022] Open
Abstract
The historical hypothesis of sterility of the lungs was invalidated over a decade ago when studies demonstrated the existence of sparse but very diverse bacterial populations in the normal lung and the association between pulmonary dysbiosis and chronic respiratory diseases. Under mechanical ventilation, dysbiosis occurs rapidly with a gradual decline in diversity over time and the progressive predominance of a bacterial pathogen (mainly Proteobacteria) when lung infection occurs. During acute respiratory distress syndrome, an enrichment in bacteria of intestinal origin, mainly Enterobacteriaceae, is observed. However, the role of this dysbiosis in the pathogenesis of ventilator-associated pneumonia and acute respiratory distress syndrome is not yet fully understood. The lack of exploration of other microbial populations, viruses (eukaryotes and prokaryotes) and fungi is a key issue. Further analysis of the interaction between these microbial kingdoms and a better understanding of the host−microbiome interaction are necessary to fully elucidate the role of the microbiome in the pathogenicity of acute diseases. The validation of a consensual and robust methodology in order to make the comparison of the different studies relevant is also required. Filling these different gaps should help develop preventive and therapeutic strategies for both acute respiratory distress syndrome and ventilator-associated pneumonia.
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Affiliation(s)
- Mélanie Fromentin
- Anesthesiology and Intensive Care Department, AP-HP, Hôpital Cochin, 75014 Paris, France;
- UMR1137 IAME, Université de Paris, INSERM, 75018 Paris, France;
| | - Jean-Damien Ricard
- UMR1137 IAME, Université de Paris, INSERM, 75018 Paris, France;
- Médecine Intensive Réanimation, AP-HP, Hôpital Louis Mourier, DMU ESPRIT, 92700 Colombes, France
| | - Damien Roux
- Médecine Intensive Réanimation, AP-HP, Hôpital Louis Mourier, DMU ESPRIT, 92700 Colombes, France
- Institut Necker-Enfants Malades, Université de Paris, INSERM U1151, CNRS UMR 8253, 75015 Paris, France
- Correspondence: ; Tel.: +33-1-47-60-63-29
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21
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Charalampous T, Alcolea-Medina A, Snell LB, Williams TGS, Batra R, Alder C, Telatin A, Camporota L, Meadows CIS, Wyncoll D, Barrett NA, Hemsley CJ, Bryan L, Newsholme W, Boyd SE, Green A, Mahadeva U, Patel A, Cliff PR, Page AJ, O'Grady J, Edgeworth JD. Evaluating the potential for respiratory metagenomics to improve treatment of secondary infection and detection of nosocomial transmission on expanded COVID-19 intensive care units. Genome Med 2021; 13:182. [PMID: 34784976 PMCID: PMC8594956 DOI: 10.1186/s13073-021-00991-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 10/14/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Clinical metagenomics (CMg) has the potential to be translated from a research tool into routine service to improve antimicrobial treatment and infection control decisions. The SARS-CoV-2 pandemic provides added impetus to realise these benefits, given the increased risk of secondary infection and nosocomial transmission of multi-drug-resistant (MDR) pathogens linked with the expansion of critical care capacity. METHODS CMg using nanopore sequencing was evaluated in a proof-of-concept study on 43 respiratory samples from 34 intubated patients across seven intensive care units (ICUs) over a 9-week period during the first COVID-19 pandemic wave. RESULTS An 8-h CMg workflow was 92% sensitive (95% CI, 75-99%) and 82% specific (95% CI, 57-96%) for bacterial identification based on culture-positive and culture-negative samples, respectively. CMg sequencing reported the presence or absence of β-lactam-resistant genes carried by Enterobacterales that would modify the initial guideline-recommended antibiotics in every case. CMg was also 100% concordant with quantitative PCR for detecting Aspergillus fumigatus from 4 positive and 39 negative samples. Molecular typing using 24-h sequencing data identified an MDR-K. pneumoniae ST307 outbreak involving 4 patients and an MDR-C. striatum outbreak involving 14 patients across three ICUs. CONCLUSION CMg testing provides accurate pathogen detection and antibiotic resistance prediction in a same-day laboratory workflow, with assembled genomes available the next day for genomic surveillance. The provision of this technology in a service setting could fundamentally change the multi-disciplinary team approach to managing ICU infections. The potential to improve the initial targeted treatment and rapidly detect unsuspected outbreaks of MDR-pathogens justifies further expedited clinical assessment of CMg.
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Affiliation(s)
- Themoula Charalampous
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, Kings College London, London, UK
| | - Adela Alcolea-Medina
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, Kings College London, London, UK
- Infection Sciences, Viapath, St Thomas' Hospital, London, UK
| | - Luke B Snell
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, Kings College London, London, UK
- Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Tom G S Williams
- Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Rahul Batra
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, Kings College London, London, UK
- Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Christopher Alder
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, Kings College London, London, UK
- Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Andrea Telatin
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Luigi Camporota
- Critical Care Directorate, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | | | - Duncan Wyncoll
- Critical Care Directorate, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Nicholas A Barrett
- Critical Care Directorate, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Carolyn J Hemsley
- Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Lisa Bryan
- Infection Sciences, Viapath, St Thomas' Hospital, London, UK
| | - William Newsholme
- Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Sara E Boyd
- Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Anna Green
- Department of Cellular Pathology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Ula Mahadeva
- Department of Cellular Pathology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Amita Patel
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, Kings College London, London, UK
- Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | | | - Andrew J Page
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Justin O'Grady
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
| | - Jonathan D Edgeworth
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, Kings College London, London, UK.
- Infection Sciences, Viapath, St Thomas' Hospital, London, UK.
- Department of Infectious Diseases, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK.
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22
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Navapurkar V, Bartholdson Scott J, Maes M, Hellyer TP, Higginson E, Forrest S, Pereira-Dias J, Parmar S, Heasman-Hunt E, Polgarova P, Brown J, Titti L, Smith WPW, Scott J, Rostron A, Routledge M, Sapsford D, Török ME, McMullan R, Enoch DA, Wong V, Curran MD, Brown NM, Simpson AJ, Herre J, Dougan G, Conway Morris A. Development and implementation of a customised rapid syndromic diagnostic test for severe pneumonia. Wellcome Open Res 2021; 6:256. [PMID: 36337362 PMCID: PMC9617073 DOI: 10.12688/wellcomeopenres.17099.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2021] [Indexed: 02/02/2023] Open
Abstract
Background: The diagnosis of pneumonia has been hampered by a reliance on bacterial cultures which take several days to return a result, and are frequently negative. In critically ill patients this leads to the use of empiric, broad-spectrum antimicrobials and compromises good antimicrobial stewardship. The objective of this study was to establish the performance of a syndromic molecular diagnostic approach, using a custom TaqMan array card (TAC) covering 52 respiratory pathogens, and assess its impact on antimicrobial prescribing. Methods: The TAC was validated against a retrospective multi-centre cohort of broncho-alveolar lavage samples. The TAC was assessed prospectively in patients undergoing investigation for suspected pneumonia, with a comparator cohort formed of patients investigated when the TAC laboratory team were unavailable. Co-primary outcomes were sensitivity compared to conventional microbiology and, for the prospective study, time to result. Metagenomic sequencing was performed to validate findings in prospective samples. Antibiotic free days (AFD) were compared between the study cohort and comparator group. Results: 128 stored samples were tested, with sensitivity of 97% (95% confidence interval (CI) 88-100%). Prospectively, 95 patients were tested by TAC, with 71 forming the comparator group. TAC returned results 51 hours (interquartile range 41-69 hours) faster than culture and with sensitivity of 92% (95% CI 83-98%) compared to conventional microbiology. 94% of organisms identified by sequencing were detected by TAC. There was a significant difference in the distribution of AFDs with more AFDs in the TAC group (p=0.02). TAC group were more likely to experience antimicrobial de-escalation (odds ratio 2.9 (95%1.5-5.5)). Conclusions: Implementation of a syndromic molecular diagnostic approach to pneumonia led to faster results, with high sensitivity and impact on antibiotic prescribing.
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Affiliation(s)
- Vilas Navapurkar
- John V Farman Intensive Care Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Josefin Bartholdson Scott
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Mailis Maes
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Thomas P Hellyer
- Translational and Clinical Research Institute, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE7 7DN, UK
| | - Ellen Higginson
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Sally Forrest
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Joana Pereira-Dias
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Surendra Parmar
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Emma Heasman-Hunt
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Petra Polgarova
- John V Farman Intensive Care Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Joanne Brown
- John V Farman Intensive Care Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Lissamma Titti
- John V Farman Intensive Care Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - William PW Smith
- School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Jonathan Scott
- Translational and Clinical Research Institute, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK
| | - Anthony Rostron
- Translational and Clinical Research Institute, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK
| | - Matthew Routledge
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - David Sapsford
- Pharmacy Department, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - M. Estée Török
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
- Microbiology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Ronan McMullan
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, BT9 7BL, UK
| | - David A Enoch
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Vanessa Wong
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - VAP-Rapid investigators
- John V Farman Intensive Care Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
- Translational and Clinical Research Institute, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE7 7DN, UK
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
- Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Pharmacy Department, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
- Microbiology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, BT9 7BL, UK
- Respiratory Medicine, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Martin D Curran
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Nicholas M Brown
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - A John Simpson
- Translational and Clinical Research Institute, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE7 7DN, UK
| | - Jurgen Herre
- Respiratory Medicine, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Andrew Conway Morris
- John V Farman Intensive Care Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
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Póvoa P, Coelho L. Which Biomarkers Can Be Used as Diagnostic Tools for Infection in Suspected Sepsis? Semin Respir Crit Care Med 2021; 42:662-671. [PMID: 34544183 DOI: 10.1055/s-0041-1735148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The diagnosis of infection in patients with suspected sepsis is frequently difficult to achieve with a reasonable degree of certainty. Currently, the diagnosis of infection still relies on a combination of systemic manifestations, manifestations of organ dysfunction, and microbiological documentation. In addition, the microbiologic confirmation of infection is obtained only after 2 to 3 days of empiric antibiotic therapy. These criteria are far from perfect being at least in part responsible for the overuse and misuse of antibiotics, in the community and in hospital, and probably the main drive for antibiotic resistance. Biomarkers have been studied and used in several clinical settings as surrogate markers of infection to improve their diagnostic accuracy as well as in the assessment of response to antibiotics and in antibiotic stewardship programs. The aim of this review is to provide a clear overview of the current evidence of usefulness of biomarkers in several clinical scenarios, namely, to diagnose infection to prescribe antibiotics, to exclude infection to withhold antibiotics, and to identify the causative pathogen to target antimicrobial treatment. In recent years, new evidence with "old" biomarkers, like C-reactive protein and procalcitonin, as well as new biomarkers and molecular tests, as breathomics or bacterial DNA identification by polymerase chain reaction, increased markedly in different areas adding useful information for clinical decision making at the bedside when adequately used. The recent evidence shows that the information given by biomarkers can support the suspicion of infection and pathogen identification but also, and not less important, can exclude its diagnosis. Although the ideal biomarker has not yet been found, there are various promising biomarkers that represent true evolutions in the diagnosis of infection in patients with suspected sepsis.
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Affiliation(s)
- Pedro Póvoa
- Polyvalent Intensive Care Unit, Sao Francisco Xavier Hospital, CHLO, Lisbon, Portugal.,Nova Medical School, Clinical Medicine, CHRC, New University of Lisbon, Lisbon, Portugal.,Center for Clinical Epidemiology and Research Unit of Clinical Epidemiology, OUH Odense University Hospital, Odense, Denmark
| | - Luis Coelho
- Polyvalent Intensive Care Unit, Sao Francisco Xavier Hospital, CHLO, Lisbon, Portugal.,Nova Medical School, Clinical Medicine, CHRC, New University of Lisbon, Lisbon, Portugal
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24
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Cintrón M, Sumner R, McMillen T, Mead PA, Babady NE. Evaluation of a Commercial Multiplexed Molecular Lower Respiratory Panel at a Tertiary Care Cancer Center. J Mol Diagn 2021; 23:1741-1748. [PMID: 34438100 DOI: 10.1016/j.jmoldx.2021.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/22/2021] [Accepted: 08/18/2021] [Indexed: 11/30/2022] Open
Abstract
Diagnosis and management of bacterial pneumonia still relies on bacterial culture and antimicrobial susceptibility testing. The Unyvero Lower Respiratory Tract panel (LRT) is a multiplex molecular assay that provides results within approximately 4.5 hours. This study evaluated the analytical performance of the LRT on bronchoalveolar lavage (BAL) fluids and bronchial washings (BW) in a cancer patient population and retrospectively determined clinical impact on therapy. Sensitivity and specificity of LRT on BAL and BW compared with bacterial culture and susceptibilities were calculated. Chart reviews were performed to determine whether antibiotic management would have changed based on the LRT results. A total of 113 BAL and 123 BW respiratory samples from 191 patients were included. The overall sensitivity and specificity were 91.7% (95% CI, 77.5%-98.3%) and 92.0% (95% CI, 87.3%-95.4%), respectively. Staphylococcus aureus was the most common target detected (n = 21) with 89.5% (95% CI, 66.8%-98.7%) sensitivity and 98.2% (95% CI, 95.4%-99.5%) specificity. Based on availability of LRT results, 4.8% of patients could have been de-escalated faster. The LRT demonstrated an overall high accuracy for the detection of common bacteria associated with pneumonia. In this cancer inpatient cohort, treatment adjustment based on LRT results would have occurred in a small number of cases. Larger studies are necessary to understand the real-world impact within specific high-risk populations.
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Affiliation(s)
- Melvilí Cintrón
- Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rawlica Sumner
- Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Hunter College, New York, New York
| | - Tracy McMillen
- Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Peter A Mead
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - N Esther Babady
- Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
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25
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An evaluation of the Unyvero pneumonia system for rapid detection of microorganisms and resistance markers of lower respiratory infections-a multicenter prospective study on ICU patients. Eur J Clin Microbiol Infect Dis 2021; 40:2113-2121. [PMID: 33934275 DOI: 10.1007/s10096-021-04259-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 04/19/2021] [Indexed: 10/21/2022]
Abstract
Rapid diagnosis of microorganisms and antibiotic resistance is vital for the appropriate treatment of patients with lower respiratory infections, especially for patients in Intensive Care Unit. We conducted a multicenter prospective study to evaluate the ability of the Unyvero pneumonia system for rapid detection from bronchoalveolar lavage fluid (BALF) in China. Eighty-four patients with lower respiratory infections were enrolled, and their BALF samples were collected, and Unyvero, a rapid molecular diagnostic sample-to-answer solution based on multiple PCRs, was applied to detect 21 types of pathogens and 19 types of resistance markers, compared to a routine bacterial culture method. The overall concordance of Unyvero and routine culture was 69/84 (82.1%). Unyvero detected more microorganisms than routine culture (38.1% vs 27.4%, P<0.05) and reported multi-pathogens in more patients than routine culture (10.7% vs 2.4%, P=0.01). The overall sensitivity and specificity of Unyvero for bacteria detection were 84.0% and 98.0%. Besides, Unyvero showed a good performance for antibiotic-resistant bacteria, except Pseudomonas aeruginosa. The concordance was 87.5-100% for methicillin-resistant Staphylococcus aureus and carbapenem-resistant isolates but was only 20-33.3% for Pseudomonas aeruginosa. The high-level semi-quantitative signal intensity of microorganisms detected positive by Unyvero correlates well with positive bacterial cultures. For specimens that were exposed to antibiotic treatment, the Unyvero pneumonia system showed a high concordance with routine bacterial culture and performs well for the detection of antibiotic-resistant bacteria, especially, carbapenem-resistant Klebsiella pneumoniae. It shows promise in guiding the clinical use of antibiotics, such as ceftazidime/avibactam. However, the system needs improvement in detecting resistance markers of Pseudomonas aeruginosa.
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26
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Chen H, Yin Y, Gao H, Guo Y, Dong Z, Wang X, Zhang Y, Yang S, Peng Q, Liu Y, Wang H. Clinical Utility of In-house Metagenomic Next-generation Sequencing for the Diagnosis of Lower Respiratory Tract Infections and Analysis of the Host Immune Response. Clin Infect Dis 2021; 71:S416-S426. [PMID: 33367583 DOI: 10.1093/cid/ciaa1516] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Only few pathogens that cause lower respiratory tract infections (LRTIs) can be identified due to limitations of traditional microbiological methods and the complexity of the oropharyngeal normal flora. Metagenomic next-generation sequencing (mNGS) has the potential to solve this problem. METHODS This prospective observational study sequentially enrolled 93 patients with LRTI and 69 patients without LRTI who visited Peking University People's Hospital in 2019. Pathogens in bronchoalveolar lavage fluid (BALF) specimens were detected using mNGS (DNA and RNA) and traditional microbiological assays. Human transcriptomes were compared between LRTI and non-LRTI, bacterial and viral LRTI, and tuberculosis and nontuberculosis groups. RESULTS Among 93 patients with LRTI, 20%, 35%, and 65% of cases were detected as definite or probable pathogens by culture, all microbiological tests, and mNGS, respectively. Our in-house BALF mNGS platform had an approximately 2-working-day turnaround time and detected more viruses and fungi than the other methods. Taking the composite reference standard as a gold standard, it had a sensitivity of 66.7%, specificity of 75.4%, positive-predictive value of 78.5%, and negative-predictive value of 62.7%. LRTI-, viral LRTI-, and tuberculosis-related differentially expressed genes were respectively related to immunity responses to infection, viral transcription and response to interferon-γ pathways, and perforin 1 and T-cell receptor B variable 9. CONCLUSIONS Metagenomic DNA and RNA-seq can identify a wide range of LRTI pathogens, with improved sensitivity for viruses and fungi. Our in-host platform is likely feasible in the clinic. Host transcriptome data are expected to be useful for the diagnosis of LRTIs.
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Affiliation(s)
- Hongbin Chen
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Yuyao Yin
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Hua Gao
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Yifan Guo
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Zhao Dong
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Xiaojuan Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Yawei Zhang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Shuo Yang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Qiusheng Peng
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Yudong Liu
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
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Xu E, Pérez-Torres D, Fragkou PC, Zahar JR, Koulenti D. Nosocomial Pneumonia in the Era of Multidrug-Resistance: Updates in Diagnosis and Management. Microorganisms 2021; 9:534. [PMID: 33807623 PMCID: PMC8001201 DOI: 10.3390/microorganisms9030534] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/25/2021] [Accepted: 03/03/2021] [Indexed: 12/11/2022] Open
Abstract
Nosocomial pneumonia (NP), including hospital-acquired pneumonia in non-intubated patients and ventilator-associated pneumonia, is one of the most frequent hospital-acquired infections, especially in the intensive care unit. NP has a significant impact on morbidity, mortality and health care costs, especially when the implicated pathogens are multidrug-resistant ones. This narrative review aims to critically review what is new in the field of NP, specifically, diagnosis and antibiotic treatment. Regarding novel imaging modalities, the current role of lung ultrasound and low radiation computed tomography are discussed, while regarding etiological diagnosis, recent developments in rapid microbiological confirmation, such as syndromic rapid multiplex Polymerase Chain Reaction panels are presented and compared with conventional cultures. Additionally, the volatile compounds/electronic nose, a promising diagnostic tool for the future is briefly presented. With respect to NP management, antibiotics approved for the indication of NP during the last decade are discussed, namely, ceftobiprole medocaril, telavancin, ceftolozane/tazobactam, ceftazidime/avibactam, and meropenem/vaborbactam.
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Affiliation(s)
- Elena Xu
- Burns, Trauma and Critical Care Research Centre, University of Queensland Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia;
| | - David Pérez-Torres
- Servicio de Medicina Intensiva, Hospital Universitario Río Hortega, 47012 Valladolid, Spain;
| | - Paraskevi C. Fragkou
- Fourth Department of Internal Medicine, Attikon University Hospital, 12462 Athens, Greece;
| | - Jean-Ralph Zahar
- Microbiology Department, Infection Control Unit, Hospital Avicenne, 93000 Bobigny, France;
| | - Despoina Koulenti
- Burns, Trauma and Critical Care Research Centre, University of Queensland Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia;
- Second Critical Care Department, Attikon University Hospital, 12462 Athens, Greece
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The Unyvero Hospital-Acquired pneumonia panel for diagnosis of secondary bacterial pneumonia in COVID-19 patients. Eur J Clin Microbiol Infect Dis 2021; 40:2479-2485. [PMID: 33661410 PMCID: PMC7930892 DOI: 10.1007/s10096-021-04194-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/09/2021] [Indexed: 11/03/2022]
Abstract
The study was undertaken to evaluate the performance of Unyvero Hospitalized Pneumonia (HPN) panel application, a multiplex PCR-based method for the detection of bacterial pathogens from lower respiratory tract (LRT) samples, obtained from COVID-19 patients with suspected secondary hospital-acquired pneumonia. Residual LRT samples obtained from critically ill COVID-19 patients with predetermined microbiological culture results were tested using the Unyvero HPN Application. Performance evaluation of the HPN Application was carried out using the standard-of-care (SoC) microbiological culture findings as the reference method. Eighty-three LRT samples were used in the evaluation. The HPN Application had a full concordance with SoC findings in 59/83 (71%) samples. The new method detected additional bacterial species in 21 (25%) and failed at detecting a bacterial species present in lower respiratory culture in 3 (3.6%) samples. Overall the sensitivity, specificity, positive, and negative predictive values of the HPN Application were 95.1% (95%CI 96.5-98.3%), 98.3% (95% CI 97.5-98.9%), 71.6% (95% CI 61.0-80.3%), and 99.8% (95% CI 99.3-99.9%), respectively. In conclusion, the HPN Application demonstrated higher diagnostic yield in comparison with the culture and generated results within 5 h.
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29
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Multicenter Evaluation of the Unyvero Platform for Testing Bronchoalveolar Lavage Fluid. J Clin Microbiol 2021; 59:JCM.02497-20. [PMID: 33328178 DOI: 10.1128/jcm.02497-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 12/10/2020] [Indexed: 01/08/2023] Open
Abstract
Bronchoalveolar lavage (BAL) culture is a standard, though time-consuming, approach for identifying microorganisms in patients with severe lower respiratory tract (LRT) infections. The sensitivity of BAL culture is relatively low, and prior antimicrobial therapy decreases the sensitivity further, leading to overuse of empirical antibiotics. The Unyvero LRT BAL Application (Curetis GmbH, Germany) is a multiplex molecular panel that detects 19 bacteria, 10 antibiotic resistance markers, and a fungus, Pneumocystis jirovecii, in BAL fluid in ∼4.5 h. Its performance was evaluated using 1,016 prospectively collected and 392 archived specimens from 11 clinical trial sites in the United States. Overall positive and negative percent agreements with culture results for identification of bacteria that grow in routine cultures were 93.4% and 98.3%, respectively, with additional potential pathogens identified by Unyvero in 21.7% of prospectively collected specimens. For detection of P. jirovecii, the positive percent agreement with standard testing was 87.5%. Antibiotic resistance marker results were compared to standard antibiotic susceptibility test results to determine positive predictive values (PPVs). PPVs ranged from 80 to 100%, based on the microorganism and specific resistance marker(s). The Unyvero LRT BAL Application provides accurate detection of common agents of bacterial pneumonia and of P. jirovecii The sensitivity and rapidity of this panel suggest significant clinical value for choosing appropriate antibiotics and for antibiotic stewardship.
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Abstract
PURPOSE OF REVIEW Nosocomial pneumonia represents a significant burden even for the most resilient healthcare systems. Timely and reliable diagnosis is critical but remains a deficient field. This review critically revises the latest literature on the diagnosis of nosocomial pneumonia, including advances in imaging techniques, as well as the utility of rapid microbiological tests in establishing the etiological diagnosis. RECENT FINDINGS Studies on low radiation computed tomography (CT) and lung ultrasound (LUS) have shown promising results for early nosocomial pneumonia diagnosis; however, further data on their sensitivity and specificity are needed, especially for picking up subtle and nonspecific radiographic findings. Moreover, data supporting their superiority in pneumonia diagnosis is still limited. As for microbiological diagnosis, several culture-independent molecular diagnostic techniques have been developed, identifying both causative microorganisms as well as determinants of antimicrobial resistance, but more studies are needed to delineate their role in nosocomial pneumonia diagnosis. SUMMARY The development of nonculture dependent tests has launched a new era in microbiological nosocomial pneumonia diagnosis. These modalities along with the use of LUS and/or low radiation CT might improve the sensitivity and specificity of nosocomial pneumonia diagnosis, enhance early detection and guide the antimicrobial therapy but more studies are needed to further evaluate them and determine their role for the routine clinical practice.
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Hanson KE, Azar MM, Banerjee R, Chou A, Colgrove RC, Ginocchio CC, Hayden MK, Holodiny M, Jain S, Koo S, Levy J, Timbrook TT, Caliendo AM. Molecular Testing for Acute Respiratory Tract Infections: Clinical and Diagnostic Recommendations From the IDSA's Diagnostics Committee. Clin Infect Dis 2020; 71:2744-2751. [PMID: 32369578 PMCID: PMC7454374 DOI: 10.1093/cid/ciaa508] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 04/30/2020] [Indexed: 01/08/2023] Open
Abstract
The clinical signs and symptoms of acute respiratory tract infections (RTIs) are not pathogen specific. Highly sensitive and specific nucleic acid amplification tests have become the diagnostic reference standard for viruses, and translation of bacterial assays from basic research to routine clinical practice represents an exciting advance in respiratory medicine. Most recently, molecular diagnostics have played an essential role in the global health response to the novel coronavirus pandemic. How best to use newer molecular tests for RTI in combination with clinical judgment and traditional methods can be bewildering given the plethora of available assays and rapidly evolving technologies. Here, we summarize the current state of the art with respect to the diagnosis of viral and bacterial RTIs, provide a practical framework for diagnostic decision making using selected patient-centered vignettes, and make recommendations for future studies to advance the field.
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Affiliation(s)
- Kimberly E Hanson
- Division of Infectious Diseases, Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
- Section of Clinical Microbiology, Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, Utah, USA
| | - Marwan M Azar
- Department of Medicine, Section of Infectious Diseases, AIDS Program, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Ritu Banerjee
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Andrew Chou
- Michael E. DeBakey VA Medical Center, Baylor College of Medicine, Houston, Texas, USA
| | - Robert C Colgrove
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Christine C Ginocchio
- Global Medical Affairs, bioMérieux/BioFire Diagnostics, Salt Lake City, Utah, USA
- Department of Pathology and Laboratory Medicine, Hofstra North Shore–Long Island Jewish School of Medicine, Hempstead, New York, USA
| | - Mary K Hayden
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, Illinois, USA
- Division of Laboratory Medicine, Department of Pathology, Rush University Medical Center, Chicago, Illinois, USA
| | - Mark Holodiny
- VA Palo Alto Health Care System, Palo Alto, California, USA
- Stanford University, Palo Alto, California, USA
| | - Seema Jain
- Disease Investigations Section, Infectious Diseases Branch, California Department of Public Health, Richmond, California, USA
| | - Sophia Koo
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Jaclyn Levy
- Infectious Diseases Society of America, Arlington, Virginia, USA
| | - Tristan T Timbrook
- Division of Epidemiology, Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah USA
- Department of Pharmacy, University of Utah Health, Salt Lake City, Utah, USA
| | - Angela M Caliendo
- Division of Infectious Diseases, Department of Medicine, Brown University Warren Alpert School of Medicine, Providence, Rhode Island, USA
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Musher DM, Jesudasen SJ, Barwatt JW, Cohen DN, Moss BJ, Rodriguez-Barradas MC. Normal Respiratory Flora as a Cause of Community-Acquired Pneumonia. Open Forum Infect Dis 2020; 7:ofaa307. [PMID: 32968689 PMCID: PMC7491709 DOI: 10.1093/ofid/ofaa307] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 09/11/2020] [Indexed: 12/21/2022] Open
Abstract
Background Intensive studies have failed to identify an etiologic agent in >50% cases of community-acquired pneumonia (CAP). Bacterial pneumonia follows aspiration of recognized bacterial pathogens (RBPs) such as Streptococcus pneumoniae, Haemophilus influenzae, and Staphylococcus aureus after they have colonize the nasopharynx. We hypothesized that aspiration of normal respiratory flora (NRF) might also cause CAP. Methods We studied 120 patients hospitalized for CAP who provided a high-quality sputum specimen at, or soon after admission, using Gram stain, quantitative sputum culture, bacterial speciation by matrix-assisted laser desorption ionization time-of-flight, and viral polymerase chain reaction. Thresholds for diagnosis of bacterial infection were ≥105 colony-forming units (cfu)/mL sputum for RBPs and ≥106 cfu for NRF. Results Recognized bacterial pathogens were found in 68 of 120 (56.7%) patients; 14 (20.1%) of these had a coinfecting respiratory virus. Normal respiratory flora were found in 31 (25.8%) patients; 10 (32.2%) had a coinfecting respiratory virus. Infection by ≥2 RBPs occurred in 10 cases and by NRF together with RBPs in 13 cases. Among NRF, organisms identified as Streptococcus mitis, which share many genetic features of S pneumoniae, predominated. A respiratory virus alone was found in 16 of 120 (13.3%) patients. Overall, an etiologic diagnosis was established in 95.8% of cases. Conclusions Normal respiratory flora, with or without viral coinfection, appear to have caused one quarter of cases of CAP and may have played a contributory role in an additional 10.8% of cases caused by RBPs. An etiology for CAP was identified in >95% of patients who provided a high-quality sputum at, or soon after, the time of admission.
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Affiliation(s)
- Daniel M Musher
- Baylor College of Medicine, Houston, Texas, USA
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas, USA
- Correspondence: Daniel Musher, MD, Infectious Disease Section, Room 4B-370, VA Medical Center, Houston, TX 77030 ()
| | - Sirus J Jesudasen
- Baylor College of Medicine, Houston, Texas, USA
- Massachusetts General Hospital, Boston Massachusetts, USA
| | - Joseph W Barwatt
- Baylor College of Medicine, Houston, Texas, USA
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas, USA
| | - Daniel N Cohen
- Baylor College of Medicine, Houston, Texas, USA
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas, USA
| | - Benjamin J Moss
- Baylor College of Medicine, Houston, Texas, USA
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas, USA
| | - Maria C Rodriguez-Barradas
- Baylor College of Medicine, Houston, Texas, USA
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas, USA
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Mills B, Megia-Fernandez A, Norberg D, Duncan S, Marshall A, Akram AR, Quinn T, Young I, Bruce AM, Scholefield E, Williams GOS, Krstajić N, Choudhary TR, Parker HE, Tanner MG, Harrington K, Wood HAC, Birks TA, Knight JC, Haslett C, Dhaliwal K, Bradley M, Ucuncu M, Stone JM. Molecular detection of Gram-positive bacteria in the human lung through an optical fiber-based endoscope. Eur J Nucl Med Mol Imaging 2020; 48:800-807. [PMID: 32915268 PMCID: PMC7485201 DOI: 10.1007/s00259-020-05021-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 08/31/2020] [Indexed: 12/13/2022]
Abstract
Purpose The relentless rise in antimicrobial resistance is a major societal challenge and requires, as part of its solution, a better understanding of bacterial colonization and infection. To facilitate this, we developed a highly efficient no-wash red optical molecular imaging agent that enables the rapid, selective, and specific visualization of Gram-positive bacteria through a bespoke optical fiber–based delivery/imaging endoscopic device. Methods We rationally designed a no-wash, red, Gram-positive-specific molecular imaging agent (Merocy-Van) based on vancomycin and an environmental merocyanine dye. We demonstrated the specificity and utility of the imaging agent in escalating in vitro and ex vivo whole human lung models (n = 3), utilizing a bespoke fiber–based delivery and imaging device, coupled to a wide-field, two-color endomicroscopy system. Results The imaging agent (Merocy-Van) was specific to Gram-positive bacteria and enabled no-wash imaging of S. aureus within the alveolar space of whole ex vivo human lungs within 60 s of delivery into the field-of-view, using the novel imaging/delivery endomicroscopy device. Conclusion This platform enables the rapid and specific detection of Gram-positive bacteria in the human lung. Electronic supplementary material The online version of this article (10.1007/s00259-020-05021-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bethany Mills
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK.
| | - Alicia Megia-Fernandez
- School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Dominic Norberg
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Sheelagh Duncan
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Adam Marshall
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Ahsan R Akram
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Thomas Quinn
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Irene Young
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Annya M Bruce
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Emma Scholefield
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Gareth O S Williams
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Nikola Krstajić
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Tushar R Choudhary
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK.,The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Helen E Parker
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK.,Department of Applied Physics, Royal Institute of Technology, KTH, SE-106 91, Stockholm, Sweden
| | - Michael G Tanner
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK.,Scottish Universities Physics Alliance (SUPA), Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - Kerrianne Harrington
- Centre for Photonics and Photonic Materials, Department of Physics, University of Bath, Bath, BA2 7AY, UK
| | - Harry A C Wood
- Centre for Photonics and Photonic Materials, Department of Physics, University of Bath, Bath, BA2 7AY, UK
| | - Timothy A Birks
- Centre for Photonics and Photonic Materials, Department of Physics, University of Bath, Bath, BA2 7AY, UK
| | - Jonathan C Knight
- Centre for Photonics and Photonic Materials, Department of Physics, University of Bath, Bath, BA2 7AY, UK
| | - Christopher Haslett
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Kevin Dhaliwal
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Mark Bradley
- School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK.
| | - Muhammed Ucuncu
- School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK. .,Department of Analytical Chemistry, Faculty of Pharmacy, Izmir Katip Celebi University, Izmir, Turkey.
| | - James M Stone
- Centre for Photonics and Photonic Materials, Department of Physics, University of Bath, Bath, BA2 7AY, UK.
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Pickens C, Wunderink RG, Qi C, Mopuru H, Donnelly H, Powell K, Sims MD. A multiplex polymerase chain reaction assay for antibiotic stewardship in suspected pneumonia. Diagn Microbiol Infect Dis 2020; 98:115179. [PMID: 32927409 PMCID: PMC7428672 DOI: 10.1016/j.diagmicrobio.2020.115179] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/07/2020] [Accepted: 08/11/2020] [Indexed: 02/06/2023]
Abstract
Background Multiplexed molecular rapid diagnostic tests (RDTs) may allow for rapid and accurate diagnosis of the microbial etiology of pneumonia. However, little data are available on multiplexed RDTs in pneumonia and their impact on clinical practice. Methods This retrospective study analyzed 659 hospitalized patients for microbiological diagnosis of suspected pneumonia. Results The overall sensitivity of the Unyvero LRT Panel was 85.7% (95% CI 82.3–88.7) and the overall specificity was 98.4% (95% CI 98.2–98.7) with a negative predictive value of 97.9% (95% CI 97.6–98.1). The LRT Panel result predicted no change in antibiotics in 12.4% of cases but antibiotic de-escalation in 65.9% (405/615) of patients, of whom 278/405 (69%) had unnecessary MRSA coverage and 259/405 (64%) had unnecessary P. aeruginosa coverage. Interpretation In hospitalized adults with suspected pneumonia, use of an RDT on respiratory samples can allow for early adjustment of initial antibiotics, most commonly de-escalation.
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Affiliation(s)
- Chiagozie Pickens
- Northwestern University Feinberg School of Medicine, Department of Medicine, Pulmonary and Critical Care Division, Chicago, IL.
| | - Richard G Wunderink
- Northwestern University Feinberg School of Medicine, Department of Medicine, Pulmonary and Critical Care Division, Chicago, IL
| | - Chao Qi
- Northwestern University Feinberg School of Medicine, Department of Pathology, Chicago, IL
| | - Haritha Mopuru
- Beaumont Hospital, Royal Oak, Section of Infectious Diseases and International Medicine, Royal Oak, MI
| | - Helen Donnelly
- Northwestern University Feinberg School of Medicine, Department of Medicine, Pulmonary and Critical Care Division, Chicago, IL
| | - Kimberly Powell
- Beaumont Hospital, Royal Oak, Section of Infectious Diseases and International Medicine, Royal Oak, MI
| | - Matthew D Sims
- Beaumont Hospital, Royal Oak, Section of Infectious Diseases and International Medicine, Royal Oak, MI; Oakland University William Beaumont School of Medicine, Department of Internal Medicine, Rochester, MI
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Luyt CE, Hékimian G, Bonnet I, Bréchot N, Schmidt M, Robert J, Combes A, Aubry A. Usefulness of point-of-care multiplex PCR to rapidly identify pathogens responsible for ventilator-associated pneumonia and their resistance to antibiotics: an observational study. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2020; 24:378. [PMID: 32586347 PMCID: PMC7316635 DOI: 10.1186/s13054-020-03102-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 06/17/2020] [Indexed: 01/07/2023]
Abstract
Background The use of multiplex PCR to shorten time to identification of pathogens and their resistance mechanisms for patients with ventilator-associated pneumonia (VAP) is attractive, but poorly studied. The multiplex PCR–based Unyvero pneumonia cartridge assay can directly identify 20 bacteria and one fungus, amongst the most frequently causing VAP, and 19 of their resistance markers in clinical specimens (bronchoalveolar lavage or tracheal aspirate), with a turnaround time of 4–5 h. We performed this study to evaluate the concordance between the multiplex PCR–based Unyvero pneumonia cartridge assay and conventional microbiological techniques to identify pathogens and their resistance mechanisms in patients with VAP. Methods All patients suspected of having VAP (January 2016 to January 2019), who underwent fiberoptic bronchoscopy with bronchoalveolar lavage fluid (BALF) and whose BALF microscopy examination revealed intracellular bacteria, were included. BALF conventional cultures (gold standard), antimicrobial susceptibility testing and processing for the Unyvero pneumonia cartridge were done. Culture and Unyvero results were compared. Results Compared to cultures of the 93 samples processed for both techniques, Unyvero correctly identified pathogens in 68 (73%) proven VAP episodes, was discordant for 25 (27%), detected no pathogen in 11 and overdetected a not otherwise found pathogen in six. For the eight remaining discordant results, the pathogen responsible for VAP was not included in the Unyvero cartridge panel or it grew at a non-significant level in culture. Amongst the 31 (33%) resistance mechanism discordances observed, 22 were resistance detection failures and 24 concerned Pseudomonas aeruginosa. Conclusions Compared to conventional microbiological cultures, the Unyvero pneumonia cartridge had poor diagnostic performance: it correctly identified pathogens and their resistance mechanisms in 73% and 67% of VAP cases, respectively. The lack of performance on the resistance mechanism was more pronounced when the pathogen detected was a Pseudomonas aeruginosa.
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Affiliation(s)
- Charles-Edouard Luyt
- Service de Médecine Intensive Réanimation, Institut de Cardiologie, Hospital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (APHP), Sorbonne Université, 47-83, Boulevard de l'Hôpital, 75651, Paris Cedex 13, France. .,Sorbonne Université, INSERM, UMRS_1166-ICAN Institute of Cardiometabolism and Nutrition, Paris, France.
| | - Guillaume Hékimian
- Service de Médecine Intensive Réanimation, Institut de Cardiologie, Hospital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (APHP), Sorbonne Université, 47-83, Boulevard de l'Hôpital, 75651, Paris Cedex 13, France
| | - Isabelle Bonnet
- Service de Bactériologie-Hygiène, Hospital Pitié-Salpêtrière, APHP, Sorbonne Université, Paris, France.,Sorbonne Université, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, CIMI-Paris, équipe 2, Paris, France
| | - Nicolas Bréchot
- Service de Médecine Intensive Réanimation, Institut de Cardiologie, Hospital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (APHP), Sorbonne Université, 47-83, Boulevard de l'Hôpital, 75651, Paris Cedex 13, France.,Sorbonne Université, INSERM, UMRS_1166-ICAN Institute of Cardiometabolism and Nutrition, Paris, France
| | - Matthieu Schmidt
- Service de Médecine Intensive Réanimation, Institut de Cardiologie, Hospital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (APHP), Sorbonne Université, 47-83, Boulevard de l'Hôpital, 75651, Paris Cedex 13, France.,Sorbonne Université, INSERM, UMRS_1166-ICAN Institute of Cardiometabolism and Nutrition, Paris, France
| | - Jérôme Robert
- Service de Bactériologie-Hygiène, Hospital Pitié-Salpêtrière, APHP, Sorbonne Université, Paris, France.,Sorbonne Université, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, CIMI-Paris, équipe 2, Paris, France
| | - Alain Combes
- Service de Médecine Intensive Réanimation, Institut de Cardiologie, Hospital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (APHP), Sorbonne Université, 47-83, Boulevard de l'Hôpital, 75651, Paris Cedex 13, France.,Sorbonne Université, INSERM, UMRS_1166-ICAN Institute of Cardiometabolism and Nutrition, Paris, France
| | - Alexandra Aubry
- Service de Bactériologie-Hygiène, Hospital Pitié-Salpêtrière, APHP, Sorbonne Université, Paris, France.,Sorbonne Université, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, CIMI-Paris, équipe 2, Paris, France
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Mizusawa M, Carroll KC. Novel strategies for rapid identification and susceptibility testing of MRSA. Expert Rev Anti Infect Ther 2020; 18:759-778. [PMID: 32329637 DOI: 10.1080/14787210.2020.1760842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION Methicillin-resistant Staphylococcus aureus (MRSA) is associated with adverse clinical outcomes and increased morbidity, mortality, length of hospital stay, and health-care costs. Rapid diagnosis of MRSA infections has been associated with positive impact on clinical outcomes. AREAS COVERED We searched relevant papers in PubMed for the last 10 years. In major papers, we scanned the bibliographies to ensure that important articles were included. This review describes screening and diagnostic test methods for MRSA and their analytical performances with a focus on rapid molecular-based assays including those that are on the horizon. Future novel technologies will allow more rapid detection of phenotypic resistance. In the case of whole-genome sequencing, detection of mutations may predict resistance, transmission, and virulence. EXPERT OPINION Currently there are many diagnostic options for the detection of MRSA in surveillance and clinical samples. In general, these are highly accurate and have resulted in improvements in targeted management and reduction in hospital or intensive care unit length of stay for both MSSA and MRSA. Impact on mortality has been variable. Promising novel technologies will not only accurately identify pathogens and detect their resistance markers but will allow discovery of virulence determinants that might further affect patient management.
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Affiliation(s)
- Masako Mizusawa
- Section of Infectious Diseases, Department of Internal Medicine, University of Missouri , Kansas, MO, USA
| | - Karen C Carroll
- Department of Pathology, Division of Medical Microbiology, The Johns Hopkins University School of Medicine , Baltimore, MD, USA
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Dhesi Z, Enne VI, O'Grady J, Gant V, Livermore DM. Rapid and Point-of-Care Testing in Respiratory Tract Infections: An Antibiotic Guardian? ACS Pharmacol Transl Sci 2020; 3:401-417. [PMID: 32551433 PMCID: PMC7233852 DOI: 10.1021/acsptsci.0c00027] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Indexed: 12/15/2022]
Abstract
![]()
This
is a narrative review on the potential of rapid and point-of-care
microbiological testing in pneumonia patients, focusing particularly
on hospital-acquired and ventilator-associated pneumonia, which have
substantial mortality and diverse microbiology. This work is written
from a United Kingdom perspective, but much of it is generalizable
internationally. In a world where antimicrobial resistance is a major
international threat, the use of rapid molecular diagnostics has great
potential to improve both the management of pneumonia patients and
the stewardship of antibiotics. Rapid tests potentially can distinguish
patients with bacterial versus viral infection and can swiftly identify
bacterial pathogens and their resistances. We seek to answer the question:
“Can such tests be used as an antibiotic guardian?”
Their availability at the bedside rather than in the laboratory should
best ensure that results are swiftly used to optimize patient management
but will raise new challenges, not the least with respect to maintaining
quality control and microbiology/infection control input. A further
challenge lies in assessing the degree of trust that treating clinicians
will place in these molecular diagnostic tests, particularly when
early de-escalation of antibiotic therapy is indicated.
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Affiliation(s)
- Zaneeta Dhesi
- University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Virve I Enne
- University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Justin O'Grady
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UA, United Kingdom
| | - Vanya Gant
- University College London Hospitals NHS Foundation Trust, London NW1 2PG, United Kingdom
| | - David M Livermore
- University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
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39
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Evaluation of a Novel Multiplex PCR Panel Compared to Quantitative Bacterial Culture for Diagnosis of Lower Respiratory Tract Infections. J Clin Microbiol 2020; 58:JCM.02013-19. [PMID: 32075901 DOI: 10.1128/jcm.02013-19] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/11/2020] [Indexed: 11/20/2022] Open
Abstract
Quantitative bacterial culture of bronchoalveolar lavage fluids (BALF) is labor-intensive, and the delay involved in performing culture, definitive identification, and susceptibility testing often results in prolonged use of broad-spectrum antibiotics. The Unyvero lower respiratory tract (LRT) panel (Curetis, Holzgerlingen, Germany) allows the multiplexed rapid detection and identification of 20 potential etiologic agents of pneumonia within 5 h of collection. In addition, the assay includes detection of gene sequences that confer antimicrobial resistance. We retrospectively compared the performance of the molecular panel to routine quantitative bacterial culture methods on remnant BALF. Upon testing 175 BALF, we were able to analyze positive agreement of 181 targets from 129 samples, and 46 samples were negative. The positive percent agreement (PPA) among the microbial targets was 96.5%, and the negative percent agreement (NPA) was 99.6%. The targets with a PPA of <100% were Staphylococcus aureus (34/37 [91.9%]), Streptococcus pneumoniae (10/11 [90.9%]), and Enterobacter cloacae complex (2/4 [50%]). For the analyzable resistance targets, concordance with phenotypic susceptibility testing was 79% (14/18). This study found the Unyvero LRT panel largely concordant with culture results; however, no outcome or clinical impact studies were performed.
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Edin A, Eilers H, Allard A. Evaluation of the Biofire Filmarray Pneumonia panel plus for lower respiratory tract infections. Infect Dis (Lond) 2020; 52:479-488. [PMID: 32319831 DOI: 10.1080/23744235.2020.1755053] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Background: Standard diagnostic methods for lower respiratory tract infections are currently too slow and insensitive to guide early clinical decisions concerning treatment and isolation. Syndrome-specific, diagnostic panels have potential to provide information about aetiology quickly. Available panels have been of limited use in lower respiratory tract infections due to slow turn-around-time, lack of quantification of important pathogens and lack of detection of resistance genes.Materials/methods: We evaluated the newly developed Biofire® Filmarray® Pneumonia Panel plus (Biomérieux). Eighty-eight consecutive lower respiratory tract samples were analyzed by both standard microbiological methods, as requested by the referring clinician, and by the panel. The agreement with standard methods, empirical treatment coverage and possible impact on isolation practices were assessed by comparing the results from standard diagnostic methods with the panel results in relation to clinical data and information of antimicrobial therapy.Results: Both qualitative and semi-quantitative results from the panel generally displayed good agreement with standard methods and by combining methods, a possible aetiology was detected in 73% of patients. Due to the panel approach, the panel detected viruses more frequently. In 25% of the 60 patients assessed for empirical treatment coverage, a pathogen not covered by current therapy was detected and in 30% of in-house patients the panel results were found to potentially influence clinical decisions related to isolation care.Conclusions: The new diagnostic panel shows promise in improving aetiological diagnostics of lower respiratory tract infections. Correctly applied it has potential to offer support in clinical decision-making within hours of sampling.
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Affiliation(s)
- Alicia Edin
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden.,Anesthesiology and Intensive Care Medicine, Department of Surgical and Perioperative Sciences, Umeå University, Umeå, Sweden
| | - Hinnerk Eilers
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Annika Allard
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
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Yoo IY, Huh K, Shim HJ, Yun SA, Chung YN, Kang OK, Huh HJ, Lee NY. Evaluation of the BioFire FilmArray Pneumonia Panel for rapid detection of respiratory bacterial pathogens and antibiotic resistance genes in sputum and endotracheal aspirate specimens. Int J Infect Dis 2020; 95:326-331. [PMID: 32179139 DOI: 10.1016/j.ijid.2020.03.024] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 03/06/2020] [Accepted: 03/06/2020] [Indexed: 10/24/2022] Open
Abstract
OBJECTIVES The performance of the investigational-use-only version of the BioFire FilmArray Pneumonia Panel (FA-Pneumo), a high-order nested multiplex PCR, was evaluated for the detection of typical respiratory bacterial pathogens and antibiotic resistance genes in sputa and endotracheal aspirate (ETA) specimens. METHODS Thirty-one sputa and 69 ETA specimens were analyzed. The diagnostic performance of FA-Pneumo was assessed using routine microbiological methods as the reference standard. RESULTS Overall sensitivity and specificity for organism detection using FA-Pneumo were 98.5% and 76.5%, respectively. The sensitivity for each pathogen was 100%, except for Klebsiella aerogenes, and the range of specificity was 83.3-99.0%. FA-Pneumo detected antimicrobial resistance genes in 17 out of 18 specimens (94.4%) that were resistant by antimicrobial susceptibility testing. FA-Pneumo additionally detected 25 resistance genes in 22 specimens, and sequencing for the presence of resistance genes confirmed the majority of these results (20/25, 80%). Semi-quantitative analysis of bacterial nucleic acid amounts by FA-Pneumo revealed that 88.2% of the identified bacteria (67/76) with ≥106 copies/ml also gave culture-positive results with significant amounts of bacteria. CONCLUSIONS FA-Pneumo is a rapid test with high sensitivity for the detection of bacteria and antimicrobial resistance genes in sputum and ETA specimens and could aid in determining antibiotic therapy.
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Affiliation(s)
- In Young Yoo
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kyungmin Huh
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea; Asia Pacific Foundation for Infectious Diseases, Seoul, Republic of Korea
| | - Hyang Jin Shim
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Sun Ae Yun
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Yoo Na Chung
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - On Kyun Kang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
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Papazian L, Klompas M, Luyt CE. Ventilator-associated pneumonia in adults: a narrative review. Intensive Care Med 2020; 46:888-906. [PMID: 32157357 PMCID: PMC7095206 DOI: 10.1007/s00134-020-05980-0] [Citation(s) in RCA: 316] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/19/2020] [Indexed: 12/15/2022]
Abstract
Ventilator-associated pneumonia (VAP) is one of the most frequent ICU-acquired infections. Reported incidences vary widely from 5 to 40% depending on the setting and diagnostic criteria. VAP is associated with prolonged duration of mechanical ventilation and ICU stay. The estimated attributable mortality of VAP is around 10%, with higher mortality rates in surgical ICU patients and in patients with mid-range severity scores at admission. Microbiological confirmation of infection is strongly encouraged. Which sampling method to use is still a matter of controversy. Emerging microbiological tools will likely modify our routine approach to diagnosing and treating VAP in the next future. Prevention of VAP is based on minimizing the exposure to mechanical ventilation and encouraging early liberation. Bundles that combine multiple prevention strategies may improve outcomes, but large randomized trials are needed to confirm this. Treatment should be limited to 7 days in the vast majority of the cases. Patients should be reassessed daily to confirm ongoing suspicion of disease, antibiotics should be narrowed as soon as antibiotic susceptibility results are available, and clinicians should consider stopping antibiotics if cultures are negative.
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Affiliation(s)
- Laurent Papazian
- Médecine Intensive Réanimation, Hôpital Nord, Hôpitaux de Marseille, Chemin des Bourrely, 13015, Marseille, France. .,Centre d'Etudes et de Recherches sur les Services de Santé et qualité de vie EA 3279, Groupe de recherche en Réanimation et Anesthésie de Marseille pluridisciplinaire (GRAM +), Faculté de médecine, Aix-Marseille Université, 13005, Marseille, France.
| | - Michael Klompas
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, USA.,Department of Medicine, Brigham and Women's Hospital, Boston, USA
| | - Charles-Edouard Luyt
- Médecine Intensive Réanimation, Institut de Cardiologie, Assistance Publique-Hôpitaux de Paris, Paris, France.,INSERM, UMRS 1166, ICAN Institute of Cardiometabolism and Nutrition, Sorbonne Université, Paris, France
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43
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Innovative and rapid antimicrobial susceptibility testing systems. Nat Rev Microbiol 2020; 18:299-311. [PMID: 32055026 DOI: 10.1038/s41579-020-0327-x] [Citation(s) in RCA: 163] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2020] [Indexed: 12/21/2022]
Abstract
Antimicrobial resistance (AMR) is a major threat to human health worldwide, and the rapid detection and quantification of resistance, combined with antimicrobial stewardship, are key interventions to combat the spread and emergence of AMR. Antimicrobial susceptibility testing (AST) systems are the collective set of diagnostic processes that facilitate the phenotypic and genotypic assessment of AMR and antibiotic susceptibility. Over the past 30 years, only a few high-throughput AST methods have been developed and widely implemented. By contrast, several studies have established proof of principle for various innovative AST methods, including both molecular-based and genome-based methods, which await clinical trials and regulatory review. In this Review, we discuss the current state of AST systems in the broadest technical, translational and implementation-related scope.
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Poole S, Clark TW. Rapid syndromic molecular testing in pneumonia: The current landscape and future potential. J Infect 2020; 80:1-7. [PMID: 31809764 PMCID: PMC7132381 DOI: 10.1016/j.jinf.2019.11.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 12/18/2022]
Abstract
Community acquired pneumonia (CAP), hospital-acquired pneumonia (HAP) and ventilator associated pneumonia (VAP) are all associated with significant mortality and cause huge expense to health care services around the world. Early, appropriate antimicrobial therapy is crucial for effective treatment. Syndromic diagnostic testing using novel, rapid multiplexed molecular platforms represents a new opportunity for rapidly targeted antimicrobial therapy to improve patient outcomes and facilitate antibiotic stewardship. In this article we review the currently available testing platforms and discuss the potential benefits and pitfalls of rapid testing in pneumonia.
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Affiliation(s)
- Stephen Poole
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust Southampton, United Kingdom.
| | - Tristan W Clark
- School of Clinical and Experimental Sciences, University of Southampton and NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
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Lee SH, Ruan SY, Pan SC, Lee TF, Chien JY, Hsueh PR. Performance of a multiplex PCR pneumonia panel for the identification of respiratory pathogens and the main determinants of resistance from the lower respiratory tract specimens of adult patients in intensive care units. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2019; 52:920-928. [PMID: 31806539 PMCID: PMC7185395 DOI: 10.1016/j.jmii.2019.10.009] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/27/2019] [Accepted: 10/27/2019] [Indexed: 11/16/2022]
Abstract
Background Timely diagnostic investigation to establish the microbial etiology of pneumonia is essential to ensure the administration of effective antibiotic therapy to individual patients. Methods We evaluated a multiplex PCR assay panel, the FilmArray® pneumonia panel (FilmArray PP, BioFire Diagnostics), for detection of 35 respiratory pathogens and resistance determinants and compared the performance of the standard-of-care test in intensive care unit patients with lower respiratory tract infections. Results Among the 59 endotracheal aspirates and bronchoalveolar lavage specimens obtained from 51 adult patients, FilmArray PP was effective in detecting respiratory bacterial pathogens with an overall positive percent agreement of 90% (95% confidence interval [CI], 73.5–97.9%) and negative percent agreement of 97.4% (95% CI, 96.0–98.4%). FilmArray PP semi-quantitative reporting demonstrated a concordance rate of 53.6% for the culture-positive specimens and 86.3% for the culture-negative specimens. FilmArray PP detected 16 viral targets, whereas the conventional viral isolation failed, except influenza A, which showed 100% concordance with PCR. Coinfections were detected in 42.3% of the specimens. Substantial discrepancies were observed in identifying antimicrobial resistance gene targets and in the susceptibility testing. However, FilmArray PP may still be useful at the early stage of pneumonia before culture and susceptibility test reports are available. Consequently, the results of FilmArray PP might alter the antibiotic prescription in 40.7% of the patients. Conclusions FilmArray PP offers a rapid and sensitive diagnostic method for lower respiratory tract infections. However, clinical correlation is advised to determine its significance in interpreting multiple pathogens and detection of genes involved in antimicrobial resistance.
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Affiliation(s)
- Sze Hwei Lee
- Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Sheng-Yuan Ruan
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Sung-Ching Pan
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Tai-Fen Lee
- Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Jung-Yien Chien
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan.
| | - Po-Ren Hsueh
- Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan.
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