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Dung TTN, Phat VV, Vinh C, Lan NPH, Phuong NLN, Ngan LTQ, Thwaites G, Thwaites L, Rabaa M, Nguyen ATK, Duy PT. Development and validation of multiplex real-time PCR for simultaneous detection of six bacterial pathogens causing lower respiratory tract infections and antimicrobial resistance genes. BMC Infect Dis 2024; 24:164. [PMID: 38326753 PMCID: PMC10848345 DOI: 10.1186/s12879-024-09028-2] [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: 06/17/2023] [Accepted: 01/18/2024] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coli, Streptococcus pneumoniae and Staphylococcus aureus are major bacterial causes of lower respiratory tract infections (LRTIs) globally, leading to substantial morbidity and mortality. The rapid increase of antimicrobial resistance (AMR) in these pathogens poses significant challenges for their effective antibiotic therapy. In low-resourced settings, patients with LRTIs are prescribed antibiotics empirically while awaiting several days for culture results. Rapid pathogen and AMR gene detection could prompt optimal antibiotic use and improve outcomes. METHODS Here, we developed multiplex quantitative real-time PCR using EvaGreen dye and melting curve analysis to rapidly identify six major pathogens and fourteen AMR genes directly from respiratory samples. The reproducibility, linearity, limit of detection (LOD) of real-time PCR assays for pathogen detection were evaluated using DNA control mixes and spiked tracheal aspirate. The performance of RT-PCR assays was subsequently compared with the gold standard, conventional culture on 50 tracheal aspirate and sputum specimens of ICU patients. RESULTS The sensitivity of RT-PCR assays was 100% for K. pneumoniae, A. baumannii, P. aeruginosa, E. coli and 63.6% for S. aureus and the specificity ranged from 87.5% to 97.6%. The kappa correlation values of all pathogens between the two methods varied from 0.63 to 0.95. The limit of detection of target bacteria was 1600 CFU/ml. The quantitative results from the PCR assays demonstrated 100% concordance with quantitative culture of tracheal aspirates. Compared to culture, PCR assays exhibited higher sensitivity in detecting mixed infections and S. pneumoniae. There was a high level of concordance between the detection of AMR gene and AMR phenotype in single infections. CONCLUSIONS Our multiplex quantitative RT-PCR assays are fast and simple, but sensitive and specific in detecting six bacterial pathogens of LRTIs and their antimicrobial resistance genes and should be further evaluated for clinical utility.
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Affiliation(s)
- Tran Thi Ngoc Dung
- Molecular Epidemiology Group, Oxford University Clinical Research Unit, 764 Vo Van Kiet Street, Ward 1, District 5, Ho Chi Minh City, Vietnam
| | - Voong Vinh Phat
- Molecular Epidemiology Group, Oxford University Clinical Research Unit, 764 Vo Van Kiet Street, Ward 1, District 5, Ho Chi Minh City, Vietnam
| | - Chau Vinh
- Molecular Epidemiology Group, Oxford University Clinical Research Unit, 764 Vo Van Kiet Street, Ward 1, District 5, Ho Chi Minh City, Vietnam
| | | | | | | | - Guy Thwaites
- Molecular Epidemiology Group, Oxford University Clinical Research Unit, 764 Vo Van Kiet Street, Ward 1, District 5, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Louise Thwaites
- Molecular Epidemiology Group, Oxford University Clinical Research Unit, 764 Vo Van Kiet Street, Ward 1, District 5, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Maia Rabaa
- Molecular Epidemiology Group, Oxford University Clinical Research Unit, 764 Vo Van Kiet Street, Ward 1, District 5, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Anh T K Nguyen
- Molecular Epidemiology Group, Oxford University Clinical Research Unit, 764 Vo Van Kiet Street, Ward 1, District 5, Ho Chi Minh City, Vietnam
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Pham Thanh Duy
- Molecular Epidemiology Group, Oxford University Clinical Research Unit, 764 Vo Van Kiet Street, Ward 1, District 5, Ho Chi Minh City, Vietnam.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK.
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Zheng H, Chen X, Li W, Lu J, Chen X. Establishment of a Fast Diagnostic Method for Sepsis Pathogens Based on M1 Bead Enrichment. Curr Microbiol 2023; 80:166. [PMID: 37022487 DOI: 10.1007/s00284-023-03280-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 03/21/2023] [Indexed: 04/07/2023]
Abstract
Blood culture-based sepsis diagnostic methods usually cannot obtain positive results in a timely manner. Molecular diagnostic methods, such as real-time PCR without blood culture, would be more time-saving and suitable for pathogenic diagnosis of sepsis, while their sensitivities have always been unsatisfactory for the usually low concentration of pathogens in the blood of sepsis patients. In this study, we established a fast diagnostic method using magnetic beads coated with human recombined mannose-binding lectin that makes it possible to concentrate pathogens from human plasma that have low concentrations of pathogens. With subsequent microculture (MC) and real-time PCR, this method allowed the detection of 1-10 CFUs/ml of Staphylococcus aureus, Group A Streptococcus, Escherichia coli, Pseudomonas aeruginosa, Candida tropicalis, or C. albicans from human plasma within 9.5 h, which was 21-80 h earlier than blood culture. The combination of pathogen enrichment and MC made the detection of sepsis-causing pathogens more time-saving and more sensitive than blood culture or real-time PCR alone.
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Affiliation(s)
- Hao Zheng
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xiaoli Chen
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Wenge Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Jinxing Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xiaoping Chen
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
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3
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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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4
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Agerhäll M, Henrikson M, Johansson Söderberg J, Sellin M, Tano K, Gylfe Å, Berggren D. High prevalence of pharyngeal bacterial pathogens among healthy adolescents and young adults. APMIS 2021; 129:711-716. [PMID: 34580908 DOI: 10.1111/apm.13179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/22/2021] [Indexed: 11/28/2022]
Abstract
The pharyngeal mucosa can be colonized with bacteria that have potential to cause pharyngotonsillitis. By the use of culturing techniques and PCR, we aimed to assess the prevalence of bacterial pharyngeal pathogens among healthy adolescents and young adults. We performed a cross-sectional study in a community-based cohort of 217 healthy individuals between 16 and 25 years of age. Samples were analyzed for Group A streptococci (GAS), Group C/G streptococci (SDSE), Fusobacterium necrophorum, and Arcanobacterium haemolyticum. Compared to culturing, the PCR method resulted in more frequent detection, albeit in most cases with low levels of DNA, of GAS (20/217 vs. 5/217; p < 0.01) and F. necrophorum (20/217 vs. 8/217; p < 0.01). Culturing and PCR yielded similar rates of SDSE detection (14/217 vs. 12/217; p = 0.73). Arcanobacterium haemolyticum was rarely detected (3/217), and only by PCR. Overall, in 25.3% (55/217) of these healthy adolescents and young adults at least one of these pathogens was detected, a rate that is higher than previously described. Further studies are needed before clinical adoption of PCR-based detection methods for pharyngeal bacterial pathogens, as our findings suggest a high incidence of asymptomatic carriage among adolescents and young adults without throat infections.
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Affiliation(s)
- Martin Agerhäll
- Department of Clinical Sciences, Otorhinolaryngology, Umeå University, Umeå, Sweden
| | - Martin Henrikson
- Department of Clinical Sciences, Otorhinolaryngology, Umeå University, Umeå, Sweden
| | | | - Mats Sellin
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Krister Tano
- Department of Clinical Sciences, Otorhinolaryngology, Umeå University, Umeå, Sweden
| | - Åsa Gylfe
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Diana Berggren
- Department of Clinical Sciences, Otorhinolaryngology, Umeå University, Umeå, Sweden
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5
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Ewig S, Kolditz M, Pletz M, Altiner A, Albrich W, Drömann D, Flick H, Gatermann S, Krüger S, Nehls W, Panning M, Rademacher J, Rohde G, Rupp J, Schaaf B, Heppner HJ, Krause R, Ott S, Welte T, Witzenrath M. [Management of Adult Community-Acquired Pneumonia and Prevention - Update 2021 - Guideline of the German Respiratory Society (DGP), the Paul-Ehrlich-Society for Chemotherapy (PEG), the German Society for Infectious Diseases (DGI), the German Society of Medical Intensive Care and Emergency Medicine (DGIIN), the German Viological Society (DGV), the Competence Network CAPNETZ, the German College of General Practitioneers and Family Physicians (DEGAM), the German Society for Geriatric Medicine (DGG), the German Palliative Society (DGP), the Austrian Society of Pneumology Society (ÖGP), the Austrian Society for Infectious and Tropical Diseases (ÖGIT), the Swiss Respiratory Society (SGP) and the Swiss Society for Infectious Diseases Society (SSI)]. Pneumologie 2021; 75:665-729. [PMID: 34198346 DOI: 10.1055/a-1497-0693] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The present guideline provides a new and updated concept of the management of adult patients with community-acquired pneumonia. It replaces the previous guideline dating from 2016.The guideline was worked out and agreed on following the standards of methodology of a S3-guideline. This includes a systematic literature search and grading, a structured discussion of recommendations supported by the literature as well as the declaration and assessment of potential conflicts of interests.The guideline has a focus on specific clinical circumstances, an update on severity assessment, and includes recommendations for an individualized selection of antimicrobial treatment.The recommendations aim at the same time at a structured assessment of risk for adverse outcome as well as an early determination of treatment goals in order to reduce mortality in patients with curative treatment goal and to provide palliation for patients with treatment restrictions.
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Affiliation(s)
- S Ewig
- Thoraxzentrum Ruhrgebiet, Kliniken für Pneumologie und Infektiologie, EVK Herne und Augusta-Kranken-Anstalt Bochum
| | - M Kolditz
- Universitätsklinikum Carl-Gustav Carus, Klinik für Innere Medizin 1, Bereich Pneumologie, Dresden
| | - M Pletz
- Universitätsklinikum Jena, Institut für Infektionsmedizin und Krankenhaushygiene, Jena
| | - A Altiner
- Universitätsmedizin Rostock, Institut für Allgemeinmedizin, Rostock
| | - W Albrich
- Kantonsspital St. Gallen, Klinik für Infektiologie/Spitalhygiene
| | - D Drömann
- Universitätsklinikum Schleswig-Holstein, Medizinische Klinik III - Pulmologie, Lübeck
| | - H Flick
- Medizinische Universität Graz, Universitätsklinik für Innere Medizin, Klinische Abteilung für Lungenkrankheiten, Graz
| | - S Gatermann
- Ruhr Universität Bochum, Abteilung für Medizinische Mikrobiologie, Bochum
| | - S Krüger
- Kaiserswerther Diakonie, Florence Nightingale Krankenhaus, Klinik für Pneumologie, Kardiologie und internistische Intensivmedizin, Düsseldorf
| | - W Nehls
- Helios Klinikum Erich von Behring, Klinik für Palliativmedizin und Geriatrie, Berlin
| | - M Panning
- Universitätsklinikum Freiburg, Department für Medizinische Mikrobiologie und Hygiene, Freiburg
| | - J Rademacher
- Medizinische Hochschule Hannover, Klinik für Pneumologie, Hannover
| | - G Rohde
- Universitätsklinikum Frankfurt, Medizinische Klinik I, Pneumologie und Allergologie, Frankfurt/Main
| | - J Rupp
- Universitätsklinikum Schleswig-Holstein, Klinik für Infektiologie und Mikrobiologie, Lübeck
| | - B Schaaf
- Klinikum Dortmund, Klinik für Pneumologie, Infektiologie und internistische Intensivmedizin, Dortmund
| | - H-J Heppner
- Lehrstuhl Geriatrie Universität Witten/Herdecke, Helios Klinikum Schwelm, Klinik für Geriatrie, Schwelm
| | - R Krause
- Medizinische Universität Graz, Universitätsklinik für Innere Medizin, Klinische Abteilung für Infektiologie, Graz
| | - S Ott
- St. Claraspital Basel, Pneumologie, Basel, und Universitätsklinik für Pneumologie, Universitätsspital Bern (Inselspital) und Universität Bern
| | - T Welte
- Medizinische Hochschule Hannover, Klinik für Pneumologie, Hannover
| | - M Witzenrath
- Charité, Universitätsmedizin Berlin, Medizinische Klinik mit Schwerpunkt Infektiologie und Pneumologie, Berlin
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6
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Liu K, Jing H, Chen Y, Zheng X, Jiang H, Kong D, Zheng Y, Chen S, Liu P, Jiang Y. Evaluation of TaqMan Array card (TAC) for the detection of 28 respiratory pathogens. BMC Infect Dis 2020; 20:820. [PMID: 33172401 PMCID: PMC7653217 DOI: 10.1186/s12879-020-05562-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 10/30/2020] [Indexed: 12/22/2022] Open
Abstract
Background Respiratory infections are a serious threat to human health. So, rapid detection of all respiratory pathogens can facilitate prompt treatment and prevent the deterioration of respiratory disease. Previously published primers and probes of the TaqMan array card (TAC) for respiratory pathogens are not sensitive to Chinese clinical specimens. This study aimed to develop and improve the TAC assay to detect 28 respiratory viral and bacterial pathogens in a Chinese population. Methods To improve the sensitivity, we redesigned the primers and probes, and labeled the probes with minor groove binders. The amplification efficiency, sensitivity, and specificity of the primers and probes were determined using target-gene containing standard plasmids. The detection performance of the TAC was evaluated on 754 clinical specimens and the results were compared with those from conventional methods. Results The performance of the TAC assay was evaluated using 754 clinical throat swab samples and the results were compared with those from gold-standard methods. The sensitivity and specificity were 95.4 and 96.6%, respectively. The lowest detection limit of the TAC was 10 to 100 copies/μL. Conclusions TAC is an efficient, accurate, and high-throughput approach to detecting multiple respiratory pathogens simultaneously and is a promising tool for the identification of pathogen outbreaks.
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Affiliation(s)
- Keke Liu
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.,Shandong Academy of Clinical Medicine, Shandong Provincial Hospital, Jinan, 250021, China
| | - Hongbo Jing
- Department of Laboratory Medicine, Shunyi District Center for Disease Control and Prevention, Beijing, China
| | - Ying Chen
- School of Food and Chemical Engineering, Beijing Technology and Business University, Beijing, 100048, China
| | - Xin Zheng
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Hua Jiang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Decong Kong
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yvling Zheng
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Shuiping Chen
- Department of Laboratory Medicine, the Fifth Medical Centre, Chinese PLA General Hospital, Beijing, China.
| | - Peng Liu
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.
| | - Yongqiang Jiang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.
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7
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Vásquez-Hoyos P, Bernal-Peña LC, Castro-Gómez DA, Jaramillo L, Polo JF, Parra-Medina R. Agreement between the Clinical and Autopsy Results of Children Who Died with Pneumonia in Pediatric Intensive Care. J Pediatr Intensive Care 2020; 11:26-31. [DOI: 10.1055/s-0040-1719032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/23/2020] [Indexed: 10/23/2022] Open
Abstract
AbstractThis study aimed to measure the agreement between the clinical and anatomopathological results of children who died with pneumonia from two pediatric intensive care units. Pediatric patients chosen were those who died between January 2008 and December 2015. The agreement was tested with Kappa. A total of 111 autopsies were included. Upon autopsy, 58 had pneumonia, 33 had it clinically and pathologically, 24 only clinically, and one only in autopsy. The Kappa agreement was 0.5 (95% confidence interval of 0.4 to 0.7). The level of agreement between the clinic and the autopsy is moderate. However, the consistency in cases of clinical pneumonia is low.
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Affiliation(s)
- Pablo Vásquez-Hoyos
- Pediatric Intensive Care, Hospital de San José, University Foundation of Health Sciences, and Universidad Nacional de Colombia, Bogotá, Colombia
| | - Laura C. Bernal-Peña
- Pathology Department, Hospital de San José, Fundación Universitaria de Ciencias de la Salud, Bogotá, Colombia
| | | | - Lina Jaramillo
- Pathology Department at Hospital de San José and Research Institute at Fundación Universitaria de Ciencias de la Salud, Bogotá, Colombia
| | - José F. Polo
- Pathology Department, Hospital de San José, Fundación Universitaria de Ciencias de la Salud, Bogotá, Colombia
| | - Rafael Parra-Medina
- Pathology Department and Research Institute at Fundación Universitaria de Ciencias de la Salud, Bogotá, Colombia
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Multicenter Evaluation of the BioFire FilmArray Pneumonia/Pneumonia Plus Panel for Detection and Quantification of Agents of Lower Respiratory Tract Infection. J Clin Microbiol 2020; 58:JCM.00128-20. [PMID: 32350043 PMCID: PMC7315029 DOI: 10.1128/jcm.00128-20] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/01/2020] [Indexed: 01/05/2023] Open
Abstract
The ability to provide timely identification of the causative agents of lower respiratory tract infections can promote better patient outcomes and support antimicrobial stewardship efforts. Current diagnostic testing options include culture, molecular testing, and antigen detection. These methods may require collection of various specimens, involve extensive sample treatment, and can suffer from low sensitivity and long turnaround times. This study assessed the performance of the BioFire FilmArray Pneumonia Panel (PN panel) and Pneumonia Plus Panel (PNplus panel), an FDA-cleared sample-to-answer assay that enables the detection of viruses, atypical bacteria, bacteria, and antimicrobial resistance marker genes from lower respiratory tract specimens (sputum and bronchoalveolar lavage [BAL] fluid). Semiquantitative results are also provided for the bacterial targets. This paper describes selected analytical and clinical studies that were conducted to evaluate performance of the panel for regulatory clearance. Prospectively collected respiratory specimens (846 BAL and 836 sputum specimens) evaluated with the PN panel were also tested by quantitative reference culture and molecular methods for comparison. The PN panel showed a sensitivity of 100% for 15/22 etiologic targets using BAL specimens and for 10/24 using sputum specimens. All other targets had sensitivities of ≥75% or were unable to be calculated due to low prevalence in the study population. Specificity for all targets was ≥87.2%, with many false-positive results compared to culture that were confirmed by alternative molecular methods. Appropriate adoption of this test could provide actionable diagnostic information that is anticipated to impact patient care and antimicrobial stewardship decisions.
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9
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Lehel J, Yaucat-Guendi R, Darnay L, Palotás P, Laczay P. Possible food safety hazards of ready-to-eat raw fish containing product (sushi, sashimi). Crit Rev Food Sci Nutr 2020; 61:867-888. [PMID: 32270692 DOI: 10.1080/10408398.2020.1749024] [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] [Indexed: 01/30/2023]
Abstract
It is undeniable that with the popularity of sushi and sashimi over the last decade the consumption of raw fish has extremely increased. Raw fish is very appreciated worldwide and has become a major component of human diet because of its fine taste and nutritional properties. Possible hazards concerning fish safety and quality are classified as biological and chemical hazards. They are contaminants that often accumulate in edible tissue of fish and transmit to humans via the food chain affecting the consumer's health. Although their concentration in fish and fishery products are found at non-alarming level of a daily basis period, they induce hazardous outcome on human health due to long and continuous consumption of raw fish. Regular sushi and sashimi eaters have to be aware of the contaminants found in the other components of their dish that often add up to acceptable residue limits found in fish. Hence, there is the urge for effective analytical methods to be developed as well as stricter regulations to be put in force between countries to monitor the safety and quality of fish for the interest of public health.
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Affiliation(s)
- József Lehel
- Department of Food Hygiene, University of Veterinary Medicine, Budapest, Hungary
| | | | - Lívia Darnay
- Department of Food Hygiene, University of Veterinary Medicine, Budapest, Hungary
| | | | - Péter Laczay
- Department of Food Hygiene, University of Veterinary Medicine, Budapest, Hungary
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10
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Zhu H, Fohlerová Z, Pekárek J, Basova E, Neužil P. Recent advances in lab-on-a-chip technologies for viral diagnosis. Biosens Bioelectron 2020; 153:112041. [PMID: 31999560 PMCID: PMC7126858 DOI: 10.1016/j.bios.2020.112041] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 01/13/2020] [Accepted: 01/20/2020] [Indexed: 12/12/2022]
Abstract
The global risk of viral disease outbreaks emphasizes the need for rapid, accurate, and sensitive detection techniques to speed up diagnostics allowing early intervention. An emerging field of microfluidics also known as the lab-on-a-chip (LOC) or micro total analysis system includes a wide range of diagnostic devices. This review briefly covers both conventional and microfluidics-based techniques for rapid viral detection. We first describe conventional detection methods such as cell culturing, immunofluorescence or enzyme-linked immunosorbent assay (ELISA), or reverse transcription polymerase chain reaction (RT-PCR). These methods often have limited speed, sensitivity, or specificity and are performed with typically bulky equipment. Here, we discuss some of the LOC technologies that can overcome these demerits, highlighting the latest advances in LOC devices for viral disease diagnosis. We also discuss the fabrication of LOC systems to produce devices for performing either individual steps or virus detection in samples with the sample to answer method. The complete system consists of sample preparation, and ELISA and RT-PCR for viral-antibody and nucleic acid detection, respectively. Finally, we formulate our opinions on these areas for the future development of LOC systems for viral diagnostics.
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Affiliation(s)
- Hanliang Zhu
- Ministry of Education Key Laboratory of Micro/Nano Systems for Aerospace, Department of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Zdenka Fohlerová
- Central European Institute of Technology, Brno University of Technology, 612 00, Brno, Czech Republic; Department of Microelectronics, Faculty of Electrical Engineering and Communication, Brno University of Technology, 616 00, Brno, Czech Republic
| | - Jan Pekárek
- Central European Institute of Technology, Brno University of Technology, 612 00, Brno, Czech Republic; Department of Microelectronics, Faculty of Electrical Engineering and Communication, Brno University of Technology, 616 00, Brno, Czech Republic
| | - Evgenia Basova
- Central European Institute of Technology, Brno University of Technology, 612 00, Brno, Czech Republic
| | - Pavel Neužil
- Ministry of Education Key Laboratory of Micro/Nano Systems for Aerospace, Department of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China; Central European Institute of Technology, Brno University of Technology, 612 00, Brno, Czech Republic; Department of Microelectronics, Faculty of Electrical Engineering and Communication, Brno University of Technology, 616 00, Brno, Czech Republic.
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11
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Comparative Clinical Evaluation of NeoPlex RB-8 with Seeplex PneumoBacter ACE for Simultaneous Detection of Eight Respiratory Bacterial Pathogens. J Clin Microbiol 2020; 58:JCM.01500-19. [PMID: 31748320 DOI: 10.1128/jcm.01500-19] [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: 09/17/2019] [Accepted: 11/06/2019] [Indexed: 11/20/2022] Open
Abstract
There are several convenient and accurate molecular assays to detect respiratory bacterial infection. The NeoPlex RB-8 detection kit (NeoPlex RB-8) is a new multiplex real-time PCR assay that simultaneously detects Streptococcus pneumoniae, Mycoplasma pneumoniae, Chlamydophila pneumoniae, Legionella pneumophila, Haemophilus influenzae, Bordetella pertussis, Bordetella parapertussis, and Moraxella catarrhalis in a single test. This study compared the clinical concordance of NeoPlex RB-8 with another method, Seeplex PneumoBacter ACE detection assay (Seeplex PB ACE), which simultaneously detects S. pneumoniae, M. pneumoniae, C. pneumoniae, L. pneumophila, H. influenzae, and B. pertussis We tested 2,137 nasopharyngeal swab and sputum specimens using both assays. For discordant Bordetella parapertussis and M. catarrhalis specimens, we also performed bidirectional sequencing. For S. pneumoniae, M. pneumoniae, C. pneumoniae, L. pneumophila, H. influenzae, and B. pertussis, which are detected by both NeoPlex RB-8 and Seeplex PB ACE, the positive and negative agreement between the two assays ranged from 91.7 to 100% (κ = 0.918 to 1). S. pneumoniae and H. influenzae were the most discordant targets and measured with higher sensitivity and specificity by NeoPlex RB-8 than Seeplex PB ACE. For Bordetella parapertussis and M. catarrhalis, which are not detected by Seeplex PB ACE, NeoPlex RB-8 sensitivity and specificity were >99%. Overall, NeoPlex RB-8 was highly comparable to Seeplex PB ACE, but NeoPlex RB-8 was more clinically accurate, with higher throughput and more convenience.
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Pahlow S, Lehniger L, Hentschel S, Seise B, Braun SD, Ehricht R, Berg A, Popp J, Weber K. Rapid Isolation and Identification of Pneumonia-Associated Pathogens from Sputum Samples Combining an Innovative Sample Preparation Strategy and Array-Based Detection. ACS OMEGA 2019; 4:10362-10369. [PMID: 31460130 PMCID: PMC6648014 DOI: 10.1021/acsomega.9b00904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/27/2019] [Indexed: 05/04/2023]
Abstract
With this study, an innovative and convenient enrichment and detection strategy for eight clinically relevant pneumonia pathogens, namely, Acinetobacter baumannii, Escherichia coli, Haemophilus influenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Pseudomonas aeruginosa, Staphylococcus aureus, and Streptococcus pneumoniae is introduced. Bacteria were isolated from sputum samples with amine-modified particles exploiting pH-dependent electrostatic interactions between bacteria and the functionalized particle surface. Following this, an asymmetric polymerase chain reaction as well as subsequent stringent array-based hybridization with specific complementary capture probes were performed. Finally, results were visualized by an enzyme-induced silver nanoparticle deposition, providing stable endpoint signals and consequently an easy detection possibility. The assay was optimized using spiked samples of artificial sputum with different strains of the abovementioned bacterial species. Furthermore, actual patient sputum samples with S. pneumoniae were successfully analyzed. The presented approach offers great potential for the urgent need of a fast, specific, and reliable isolation and identification platform for important pneumonia pathogens, covering the complete process chain from sample preparation up to array-based detection within only 4 h.
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Affiliation(s)
- Susanne Pahlow
- Friedrich
Schiller University Jena, Institute of Physical Chemistry, Abbe Center of Photonics, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics
Research Campus Jena, Centre for Applied
Research, Philosophenweg
7, 07743 Jena, Germany
| | - Lydia Lehniger
- InfectoGnostics
Research Campus Jena, Centre for Applied
Research, Philosophenweg
7, 07743 Jena, Germany
- Leibniz
Institute of Photonic Technology—Member of the Research Alliance
“Leibniz Health Technologies”, Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Stefanie Hentschel
- InfectoGnostics
Research Campus Jena, Centre for Applied
Research, Philosophenweg
7, 07743 Jena, Germany
- Leibniz
Institute of Photonic Technology—Member of the Research Alliance
“Leibniz Health Technologies”, Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Barbara Seise
- InfectoGnostics
Research Campus Jena, Centre for Applied
Research, Philosophenweg
7, 07743 Jena, Germany
- Leibniz
Institute of Photonic Technology—Member of the Research Alliance
“Leibniz Health Technologies”, Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Sascha D. Braun
- InfectoGnostics
Research Campus Jena, Centre for Applied
Research, Philosophenweg
7, 07743 Jena, Germany
- Abbott
(Alere Technologies GmbH), Research and Development, Loebstedter Str. 103-105, 07749 Jena, Germany
| | - Ralf Ehricht
- Friedrich
Schiller University Jena, Institute of Physical Chemistry, Abbe Center of Photonics, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics
Research Campus Jena, Centre for Applied
Research, Philosophenweg
7, 07743 Jena, Germany
- Leibniz
Institute of Photonic Technology—Member of the Research Alliance
“Leibniz Health Technologies”, Albert-Einstein-Straße 9, 07745 Jena, Germany
- Abbott
(Alere Technologies GmbH), Research and Development, Loebstedter Str. 103-105, 07749 Jena, Germany
| | - Albrecht Berg
- INNOVENT
e.V. Jena, Prüssingstraße
27 B, 07745 Jena, Germany
| | - Jürgen Popp
- Friedrich
Schiller University Jena, Institute of Physical Chemistry, Abbe Center of Photonics, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics
Research Campus Jena, Centre for Applied
Research, Philosophenweg
7, 07743 Jena, Germany
- Leibniz
Institute of Photonic Technology—Member of the Research Alliance
“Leibniz Health Technologies”, Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Karina Weber
- Friedrich
Schiller University Jena, Institute of Physical Chemistry, Abbe Center of Photonics, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics
Research Campus Jena, Centre for Applied
Research, Philosophenweg
7, 07743 Jena, Germany
- Leibniz
Institute of Photonic Technology—Member of the Research Alliance
“Leibniz Health Technologies”, Albert-Einstein-Straße 9, 07745 Jena, Germany
- E-mail: . Phone: +49 3641 206102
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Müller DC, Kauppi A, Edin A, Gylfe Å, Sjöstedt AB, Johansson A. Phospholipid levels in blood during community-acquired pneumonia. PLoS One 2019; 14:e0216379. [PMID: 31063483 PMCID: PMC6504044 DOI: 10.1371/journal.pone.0216379] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 04/21/2019] [Indexed: 02/01/2023] Open
Abstract
Phospholipids, major constituents of bilayer cell membranes, are present in large amounts in pulmonary surfactant and play key roles in cell signaling. Here, we aim at finding clinically useful disease markers in community-acquired pneumonia (CAP) using comprehensive phospholipid profiling in blood and modeling of changes between sampling time points. Serum samples from 33 patients hospitalized with CAP were collected at admission, three hours after the start of intravenous antibiotics, Day 1 (at 12–24 h), Day 2 (at 36–48 h), and several weeks after recovery. A profile of 75 phospholipid species including quantification of the bioactive lysophosphatidylcholines (LPCs) was determined using liquid chromatography coupled to time-of-flight mass spectrometry. To control for possible enzymatic degradation of LPCs, serum autotaxin levels were examined. Twenty-two of the 33 patients with a clinical diagnosis of CAP received a laboratory-verified CAP diagnosis by microbial culture or microbial DNA detection by qPCR. All major phospholipid species, especially the LPCs, were pronouncedly decreased in the acute stage of illness. Total and individual LPC concentrations increased shortly after the initiation of antibiotic treatment, concentrations were at their lowest 3h after the initiation, and increased after Day 1. The total LPC concentration increased by a change ratio of 1.6–1.7 between acute illness and Day 2, and by a ratio of 3.7 between acute illness and full disease resolution. Autotaxin levels were low in acute illness and showed little changes over time, contradicting a hypothesis of enzymatic degradation causing the low levels of LPCs. In this sample of patients with CAP, the results demonstrate that LPC concentration changes in serum of patients with CAP closely mirrored the early transition from acute illness to recovery after the initiation of antibiotics. LPCs should be further explored as potential disease stage biomarkers in CAP and for their potential physiological role during recovery.
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Affiliation(s)
- Daniel C. Müller
- Department of Clinical Microbiology and the Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Anna Kauppi
- Department of Clinical Microbiology and the Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Alicia Edin
- Department of Clinical Microbiology and the Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Åsa Gylfe
- Department of Clinical Microbiology and the Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Anders B. Sjöstedt
- Department of Clinical Microbiology and the Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Anders Johansson
- Department of Clinical Microbiology and the Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
- * E-mail:
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van den Munckhof EHA, de Koning MNC, Quint WGV, van Doorn LJ, Leverstein-van Hall MA. Evaluation of a stepwise approach using microbiota analysis, species-specific qPCRs and culture for the diagnosis of lower respiratory tract infections. Eur J Clin Microbiol Infect Dis 2019; 38:747-754. [DOI: 10.1007/s10096-019-03511-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 02/11/2019] [Indexed: 01/18/2023]
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Zhang C, Xiu L, Xiao Y, Xie Z, Ren L, Peng J. Simultaneous Detection of Key Bacterial Pathogens Related to Pneumonia and Meningitis Using Multiplex PCR Coupled With Mass Spectrometry. Front Cell Infect Microbiol 2018; 8:107. [PMID: 29675400 PMCID: PMC5895723 DOI: 10.3389/fcimb.2018.00107] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/19/2018] [Indexed: 12/12/2022] Open
Abstract
Pneumonia and meningitis continue to present an enormous public health burden and pose a major threat to young children. Among the causative organisms of pneumonia and meningitis, bacteria are the most common causes of serious disease and deaths. It is challenging to accurately and rapidly identify these agents. To solve this problem, we developed and validated a 12-plex PCR coupled with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) method (bacterial pathogen-mass spectrometry, BP-MS) that can be used to simultaneously screen for 11 key bacterial pathogens related to pneumonia and meningitis. Forty-six nasopharyngeal swabs and 12 isolates were used to determine the specificity of the method. The results showed that, using the BP-MS method, we could accurately identify the expected bacteria without cross-reactivity with other pathogens. For the 11 target bacterial pathogens, the analytical sensitivity of the BP-MS method was as low as 10 copies/reaction. To further evaluate the clinical effectiveness of this method, 204 nasopharyngeal swabs from hospitalized children with suspected pneumonia were tested using this method. In total, 81.9% (167/204) of the samples were positive for at least one of the 11 target pathogens. Among the 167 bacteria-positive samples, the rate of multiple infections was 55.7% (93/167), and the most frequent combination was Streptococcus pneumoniae with Haemophilus influenzae, representing 46.2% (43/93) two-pathogen mixed infections. We used real-time PCR and nested PCR to confirm positive results, with identical results obtained for 81.4% (136/167) of the samples. The BP-MS method is a sensitive and specific molecular detection technique in a multiplex format and with high sample throughput. Therefore, it will be a powerful tool for pathogen screening and antibiotic selection at an early stage of disease.
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Affiliation(s)
- Chi Zhang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Leshan Xiu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yan Xiao
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhengde Xie
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics, National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Virology Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Lili Ren
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Junping Peng
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Barkallah M, Gharbi Y, Slima AB, Elleuch F, Mallek Z, Saad RB, Gautier M, Gdoura R, Fendri I. Simultaneous detection of Waddlia chondrophila and Listeria monocytogenes in aborted ruminant samples by real-time quantitative PCR. J Microbiol Methods 2016; 125:64-9. [DOI: 10.1016/j.mimet.2016.04.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 03/26/2016] [Accepted: 04/01/2016] [Indexed: 11/26/2022]
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Loens K, Ieven M. Mycoplasma pneumoniae: Current Knowledge on Nucleic Acid Amplification Techniques and Serological Diagnostics. Front Microbiol 2016; 7:448. [PMID: 27064893 PMCID: PMC4814781 DOI: 10.3389/fmicb.2016.00448] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 03/18/2016] [Indexed: 12/12/2022] Open
Abstract
Mycoplasma pneumoniae (M. pneumoniae) belongs to the class Mollicutes and has been recognized as a common cause of respiratory tract infections (RTIs), including community-acquired pneumonia (CAP), that occur worldwide and in all age groups. In addition, M. pneumoniae can simultaneously or sequentially lead to damage in the nervous system and has been associated with a wide variety of other acute and chronic diseases. During the past 10 years, the proportion of LRTI in children and adults, associated with M. pneumoniae infection has ranged from 0 to more than 50%. This variation is due to the age and the geographic location of the population examined but also due to the diagnostic methods used. The true role of M. pneumoniae in RTIs remains a challenge given the many limitations and lack of standardization of the applied diagnostic tool in most cases, with resultant wide variations in data from different studies. Correct and rapid diagnosis and/or management of M. pneumoniae infections is, however, critical to initiate appropriate antibiotic treatment and is nowadays usually done by PCR and/or serology. Several recent reviews, have summarized current methods for the detection and identification of M. pneumoniae. This review will therefore provide a look at the general principles, advantages, diagnostic value, and limitations of the most currently used detection techniques for the etiological diagnosis of a M. pneumoniae infection as they evolve from research to daily practice.
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Affiliation(s)
- Katherine Loens
- Department of Microbiology, National Reference Centre for Respiratory Pathogens, University Hospital Antwerp Antwerp, Belgium
| | - Margareta Ieven
- Department of Microbiology, National Reference Centre for Respiratory Pathogens, University Hospital Antwerp Antwerp, Belgium
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Gadsby NJ, Russell CD, McHugh MP, Mark H, Conway Morris A, Laurenson IF, Hill AT, Templeton KE. Comprehensive Molecular Testing for Respiratory Pathogens in Community-Acquired Pneumonia. Clin Infect Dis 2016; 62:817-823. [PMID: 26747825 PMCID: PMC4787606 DOI: 10.1093/cid/civ1214] [Citation(s) in RCA: 266] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 11/24/2015] [Indexed: 01/22/2023] Open
Abstract
Background. The frequent lack of a microbiological diagnosis in community-acquired pneumonia (CAP) impairs pathogen-directed antimicrobial therapy. This study assessed the use of comprehensive multibacterial, multiviral molecular testing, including quantification, in adults hospitalized with CAP. Methods. Clinical and laboratory data were collected for 323 adults with radiologically-confirmed CAP admitted to 2 UK tertiary care hospitals. Sputum (96%) or endotracheal aspirate (4%) specimens were cultured as per routine practice and also tested with fast multiplex real-time polymerase-chain reaction (PCR) assays for 26 respiratory bacteria and viruses. Bacterial loads were also calculated for 8 bacterial pathogens. Appropriate pathogen-directed therapy was retrospectively assessed using national guidelines adapted for local antimicrobial susceptibility patterns. Results. Comprehensive molecular testing of single lower respiratory tract (LRT) specimens achieved pathogen detection in 87% of CAP patients compared with 39% with culture-based methods. Haemophilus influenzae and Streptococcus pneumoniae were the main agents detected, along with a wide variety of typical and atypical pathogens. Viruses were present in 30% of cases; 82% of these were codetections with bacteria. Most (85%) patients had received antimicrobials in the 72 hours before admission. Of these, 78% had a bacterial pathogen detected by PCR but only 32% were culture-positive (P < .0001). Molecular testing had the potential to enable de-escalation in number and/or spectrum of antimicrobials in 77% of patients. Conclusions. Comprehensive molecular testing significantly improves pathogen detection in CAP, particularly in antimicrobial-exposed patients, and requires only a single LRT specimen. It also has the potential to enable early de-escalation from broad-spectrum empirical antimicrobials to pathogen-directed therapy.
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Affiliation(s)
- Naomi J Gadsby
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh
| | - Clark D Russell
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh.,College of Medicine and Veterinary Medicine, University of Edinburgh
| | - Martin P McHugh
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh
| | - Harriet Mark
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh
| | | | - Ian F Laurenson
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh
| | - Adam T Hill
- Respiratory Medicine, Royal Infirmary of Edinburgh, United Kingdom
| | - Kate E Templeton
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh
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