1
|
Rapid Microbiological Diagnostics from Explanted Heart Valves by a Multiplex PCR Assay. J Clin Microbiol 2019; 57:JCM.01575-18. [PMID: 30429258 DOI: 10.1128/jcm.01575-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
2
|
Maugeri G, Lychko I, Sobral R, Roque ACA. Identification and Antibiotic-Susceptibility Profiling of Infectious Bacterial Agents: A Review of Current and Future Trends. Biotechnol J 2019; 14:e1700750. [PMID: 30024110 PMCID: PMC6330097 DOI: 10.1002/biot.201700750] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/06/2018] [Indexed: 12/16/2022]
Abstract
Antimicrobial resistance is one of the most worrying threats to humankind with extremely high healthcare costs associated. The current technologies used in clinical microbiology to identify the bacterial agent and profile antimicrobial susceptibility are time-consuming and frequently expensive. As a result, physicians prescribe empirical antimicrobial therapies. This scenario is often the cause of therapeutic failures, causing higher mortality rates and healthcare costs, as well as the emergence and spread of antibiotic resistant bacteria. As such, new technologies for rapid identification of the pathogen and antimicrobial susceptibility testing are needed. This review summarizes the current technologies, and the promising emerging and future alternatives for the identification and profiling of antimicrobial resistance bacterial agents, which are expected to revolutionize the field of clinical diagnostics.
Collapse
Affiliation(s)
- Gaetano Maugeri
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
| | - Iana Lychko
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
| | - Rita Sobral
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
| | - Ana C A Roque
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
| |
Collapse
|
3
|
Scerbo MH, Kaplan HB, Dua A, Litwin DB, Ambrose CG, Moore LJ, Murray COLCK, Wade CE, Holcomb JB. Beyond Blood Culture and Gram Stain Analysis: A Review of Molecular Techniques for the Early Detection of Bacteremia in Surgical Patients. Surg Infect (Larchmt) 2016; 17:294-302. [PMID: 26918696 PMCID: PMC5118953 DOI: 10.1089/sur.2015.099] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Sepsis from bacteremia occurs in 250,000 cases annually in the United States, has a mortality rate as high as 60%, and is associated with a poorer prognosis than localized infection. Because of these high figures, empiric antibiotic administration for patients with systemic inflammatory response syndrome (SIRS) and suspected infection is the second most common indication for antibiotic administration in intensive care units (ICU)s. However, overuse of empiric antibiotics contributes to the development of opportunistic infections, antibiotic resistance, and the increase in multi-drug-resistant bacterial strains. The current method of diagnosing and ruling out bacteremia is via blood culture (BC) and Gram stain (GS) analysis. METHODS Conventional and molecular methods for diagnosing bacteremia were reviewed and compared. The clinical implications, use, and current clinical trials of polymerase chain reaction (PCR)-based methods to detect bacterial pathogens in the blood stream were detailed. RESULTS BC/GS has several disadvantages. These include: some bacteria do not grow in culture media; others do not GS appropriately; and cultures can require up to 5 d to guide or discontinue antibiotic treatment. PCR-based methods can be potentially applied to detect rapidly, accurately, and directly microbes in human blood samples. CONCLUSIONS Compared with the conventional BC/GS, particular advantages to molecular methods (specifically, PCR-based methods) include faster results, leading to possible improved antibiotic stewardship when bacteremia is not present.
Collapse
Affiliation(s)
- Michelle H. Scerbo
- The Center for Translational Injury Research (CeTIR), Department of Surgery, University of Texas Health Science Center, Houston, Texas
| | - Heidi B. Kaplan
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas
| | - Anahita Dua
- Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Douglas B. Litwin
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas
| | - Catherine G. Ambrose
- Department of Orthopedic Surgery, University of Texas Health Science Center, Houston, Texas
| | - Laura J. Moore
- The Center for Translational Injury Research (CeTIR), Department of Surgery, University of Texas Health Science Center, Houston, Texas
| | - COL Clinton K. Murray
- Department of Medicine, Infectious Disease Service, Brooke Army Medical Center, Fort Sam Houston, Texas
| | - Charles E. Wade
- The Center for Translational Injury Research (CeTIR), Department of Surgery, University of Texas Health Science Center, Houston, Texas
| | - John B. Holcomb
- The Center for Translational Injury Research (CeTIR), Department of Surgery, University of Texas Health Science Center, Houston, Texas
| |
Collapse
|
4
|
Baudel JL, Tankovic J, Dahoumane R, Carrat F, Galbois A, Ait-Oufella H, Offenstadt G, Guidet B, Maury E. Multiplex PCR performed of bronchoalveolar lavage fluid increases pathogen identification rate in critically ill patients with pneumonia: a pilot study. Ann Intensive Care 2014; 4:35. [PMID: 25593751 PMCID: PMC4273674 DOI: 10.1186/s13613-014-0035-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 10/31/2014] [Indexed: 12/31/2022] Open
Abstract
Background In critically ill patients with pneumonia, accurate microorganism identification allows appropriate antibiotic treatment. In patients undergoing bronchoalveolar lavage (BAL), direct examination of the fluid using Gram staining provides prompt information but pathogen identification accuracy is low. Culture of BAL fluid is actually the reference, but it is not available before 24 to 48 h. In addition, pathogen identification rate observed with direct examination and culture is decreased when antibiotic therapy has been given prior to sampling. We therefore assessed, in critically ill patients with suspected pneumonia, the performance of a multiplex PCR (MPCR) to identify pathogens in BAL fluid. This study is a prospective pilot observation. Methods We used a MPCR detecting 20 types of microorganisms. Direct examination, culture, and MPCR were performed on BAL fluid of critically ill patients with pneumonia suspicion. The final diagnosis of infective pneumonia was retained after the medical chart was reviewed by two experts. Pathogen identification rate of direct examination, culture, and MPCR in patients with confirmed pneumonia was compared. Results Among the 65 patients with pneumonia suspicion, the diagnosis of pneumonia was finally retained in 53 cases. Twenty nine (55%) were community-acquired pneumonia and 24 (45%) were hospital acquired. Pathogen identification rate with MPCR (66%) was greater than with culture (40%) and direct examination (23%) (p =0.01 and p <0.001, respectively). When considering only the microorganisms included in the MPCR panel, the pathogen identification rate provided by MPCR reached 82% and was still higher than with culture (35%, p <0.001) and direct examination (21%, p <0.001). Pathogen identification rate provided by MPCR was not modified in the case of previous antibiotic treatment (66% vs. 64%, NS) and was still better than with culture (23%, p <0.001). Conclusions The results of this pilot study suggest that in critically ill patients, MPCR performed on BAL fluid could provide higher identification rate of pathogens involved in pneumonia than direct examination and culture, especially in patients having received antimicrobial treatment.
Collapse
Affiliation(s)
- Jean-Luc Baudel
- Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpital Saint-Antoine, Service de Réanimation Médicale, Paris 75012, France
| | - Jacques Tankovic
- AP-HP, Hôpital Saint-Antoine, Service de Microbiologie, Paris 75012, France
| | - Redouane Dahoumane
- AP-HP, Hôpital Saint-Antoine, Service de Microbiologie, Paris 75012, France
| | - Fabrice Carrat
- Inserm, UMR 707, Paris 75012, France ; UPMC - Université Paris 06, Paris 75012, France
| | - Arnaud Galbois
- Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpital Saint-Antoine, Service de Réanimation Médicale, Paris 75012, France
| | - Hafid Ait-Oufella
- Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpital Saint-Antoine, Service de Réanimation Médicale, Paris 75012, France ; UPMC - Université Paris 06, Paris 75012, France
| | - Georges Offenstadt
- Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpital Saint-Antoine, Service de Réanimation Médicale, Paris 75012, France ; Inserm, UMR 707, Paris 75012, France ; UPMC - Université Paris 06, Paris 75012, France
| | - Bertrand Guidet
- Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpital Saint-Antoine, Service de Réanimation Médicale, Paris 75012, France ; Inserm, UMR 707, Paris 75012, France ; UPMC - Université Paris 06, Paris 75012, France
| | - Eric Maury
- Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpital Saint-Antoine, Service de Réanimation Médicale, Paris 75012, France ; Inserm, UMR 707, Paris 75012, France ; UPMC - Université Paris 06, Paris 75012, France
| |
Collapse
|
5
|
Liesenfeld O, Lehman L, Hunfeld KP, Kost G. Molecular diagnosis of sepsis: New aspects and recent developments. Eur J Microbiol Immunol (Bp) 2014; 4:1-25. [PMID: 24678402 DOI: 10.1556/eujmi.4.2014.1.1] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 12/13/2013] [Indexed: 12/29/2022] Open
Abstract
By shortening the time to pathogen identification and allowing for detection of organisms missed by blood culture, new molecular methods may provide clinical benefits for the management of patients with sepsis. While a number of reviews on the diagnosis of sepsis have recently been published we here present up-to-date new developments including multiplex PCR, mass spectrometry and array techniques. We focus on those techniques that are commercially available and for which clinical studies have been performed and published.
Collapse
|
6
|
Abstract
Sepsis is among the most common causes of death in hospitals. It arises from the host response to infection. Currently, diagnosis relies on nonspecific physiological criteria and culture-based pathogen detection. This results in diagnostic uncertainty, therapeutic delays, the mis- and overuse of antibiotics, and the failure to identify patients who might benefit from immunomodulatory therapies. There is a need for new sepsis biomarkers that can aid in therapeutic decision making and add information about screening, diagnosis, risk stratification, and monitoring of the response to therapy. The host response involves hundreds of mediators and single molecules, many of which have been proposed as biomarkers. It is, however, unlikely that one single biomarker is able to satisfy all the needs and expectations for sepsis research and management. Among biomarkers that are measurable by assays approved for clinical use, procalcitonin (PCT) has shown some usefulness as an infection marker and for antibiotic stewardship. Other possible new approaches consist of molecular strategies to improve pathogen detection and molecular diagnostics and prognostics based on transcriptomic, proteomic, or metabolic profiling. Novel approaches to sepsis promise to transform sepsis from a physiologic syndrome into a group of distinct biochemical disorders and help in the development of better diagnostic tools and effective adjunctive sepsis therapies.
Collapse
|
7
|
Mencacci A, Leli C, Montagna P, Cardaccia A, Meucci M, Bietolini C, Cenci E, Pasticci MB, Bistoni F. Diagnosis of infective endocarditis: comparison of the LightCycler SeptiFast real-time PCR with blood culture. J Med Microbiol 2012; 61:881-883. [DOI: 10.1099/jmm.0.040113-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Antonella Mencacci
- Microbiology Section, Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Italy
| | - Christian Leli
- Microbiology Section, Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Italy
| | - Paolo Montagna
- Microbiology Section, Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Italy
| | - Angela Cardaccia
- Clinic of Infectious Diseases, Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Italy
| | - Marta Meucci
- Microbiology Section, Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Italy
| | - Cristiana Bietolini
- Microbiology Section, Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Italy
| | - Elio Cenci
- Microbiology Section, Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Italy
| | - Maria Bruna Pasticci
- Clinic of Infectious Diseases, Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Italy
| | - Francesco Bistoni
- Microbiology Section, Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Italy
| |
Collapse
|
8
|
Afshari A, Schrenzel J, Ieven M, Harbarth S. Bench-to-bedside review: Rapid molecular diagnostics for bloodstream infection--a new frontier? CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2012; 16:222. [PMID: 22647543 PMCID: PMC3580598 DOI: 10.1186/cc11202] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Among critically ill patients, the diagnosis of bloodstream infection poses a major challenge. Current standard bacterial identification based on blood culture platforms is intrinsically time-consuming and slow. The continuous evolvement of molecular techniques has the potential of providing a faster, more sensitive and direct identification of causative pathogens without prior need for cultivation. This may ultimately impact clinical decision-making and antimicrobial treatment. This review summarises the currently available technologies, their strengths and limitations and the obstacles that have to be overcome in order to develop a satisfactory bedside point-of-care diagnostic tool for detection of bloodstream infection.
Collapse
|
9
|
Comparison of conventional culture with SeptiFast real-time PCR for microbial pathogen detection in clinical specimens other than blood. J Med Microbiol 2011; 60:1774-1778. [DOI: 10.1099/jmm.0.034280-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|