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Schwarz C, Bend J, Hebestreit H, Hogardt M, Hügel C, Illing S, Mainz JG, Rietschel E, Schmidt S, Schulte-Hubbert B, Sitter H, Wielpütz MO, Hammermann J, Baumann I, Brunsmann F, Dieninghoff D, Eber E, Ellemunter H, Eschenhagen P, Evers C, Gruber S, Koitschev A, Ley-Zaporozhan J, Düesberg U, Mentzel HJ, Nüßlein T, Ringshausen FC, Sedlacek L, Smaczny C, Sommerburg O, Sutharsan S, Vonberg RP, Weber AK, Zerlik J. [CF Lung Disease - a German S3 Guideline: Pseudomonas aeruginosa]. Pneumologie 2024; 78:367-399. [PMID: 38350639 DOI: 10.1055/a-2182-1907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Cystic Fibrosis (CF) is the most common autosomal recessive genetic multisystemic disease. In Germany, it affects at least 8000 people. The disease is caused by mutations in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene leading to dysfunction of CFTR, a transmembrane chloride channel. This defect causes insufficient hydration of the airway epithelial lining fluid which leads to reduction of the mucociliary clearance.Even if highly effective, CFTR modulator therapy has been available for some years and people with CF are getting much older than before, recurrent and chronic infections of the airways as well as pulmonary exacerbations still occur. In adult CF life, Pseudomonas aeruginosa (PA) is the most relevant pathogen in colonisation and chronic infection of the lung, leading to further loss of lung function. There are many possibilities to treat PA-infection.This is a S3-clinical guideline which implements a definition for chronic PA-infection and demonstrates evidence-based diagnostic methods and medical treatment in order to give guidance for individual treatment options.
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Affiliation(s)
- Carsten Schwarz
- Klinikum Westbrandenburg GmbH, Standort Potsdam, Deutschland
| | - Jutta Bend
- Mukoviszidose Institut gGmbH, Bonn, Deutschland
| | | | - Michael Hogardt
- Klinikum der Johann Wolfgang Goethe-Universität Frankfurt am Main, Institut für Medizinische Mikrobiologie und Krankenhaushygiene, Frankfurt, Deutschland
| | - Christian Hügel
- Klinikum der Johann Wolfgang Goethe-Universität Frankfurt am Main, Deutschland
| | | | - Jochen G Mainz
- Klinikum Westbrandenburg, Standort Brandenburg an der Havel, Universitätsklinikum der Medizinischen Hochschule Brandenburg (MHB), Brandenburg an der Havel, Deutschland
| | - Ernst Rietschel
- Medizinische Fakultät der Universität zu Köln, Mukoviszidose-Zentrum, Klinik und Poliklinik für Kinder- und Jugendmedizin, Köln, Deutschland
| | - Sebastian Schmidt
- Ernst-Moritz-Arndt Universität Greifswald, Kinderpoliklinik, Allgemeine Pädiatrie, Greifswald, Deutschland
| | | | - Helmut Sitter
- Philipps-Universität Marburg, Institut für theoretische Medizin, Marburg, Deutschland
| | - Marc Oliver Wielpütz
- Universitätsklinikum Heidelberg, Klinik für Diagnostische und Interventionelle Radiologie, Heidelberg, Deutschland
| | - Jutta Hammermann
- Universitäts-Mukoviszidose-Zentrum "Christiane Herzog", Dresden, Deutschland
| | - Ingo Baumann
- Universität Heidelberg, Hals-Nasen-Ohrenklinik, Heidelberg, Deutschland
| | - Frank Brunsmann
- Allianz Chronischer Seltener Erkrankungen (ACHSE) e. V., Deutschland (Patient*innenvertreter)
| | | | - Ernst Eber
- Medizinische Universität Graz, Univ. Klinik für Kinder- und Jugendheilkunde, Klinische Abteilung für Pädiatrische Pulmonologie und Allergologie, Graz, Österreich
| | - Helmut Ellemunter
- Tirolkliniken GmbH, Department für Kinderheilkunde, Pädiatrie III, Innsbruck, Österreich
| | | | | | - Saskia Gruber
- Medizinische Universität Wien, Universitätsklinik für Kinder- und Jugendheilkunde, Wien, Österreich
| | - Assen Koitschev
- Klinikum Stuttgart - Standort Olgahospital, Klinik für Hals-Nasen-Ohrenkrankheiten, Stuttgart, Deutschland
| | - Julia Ley-Zaporozhan
- Klinik und Poliklinik für Radiologie, Kinderradiologie, LMU München, Deutschland
| | | | - Hans-Joachim Mentzel
- Universitätsklinikum Jena, Sektion Kinderradiologie, Institut für Diagnostische und Interventionelle Radiologie, Jena, Deutschland
| | - Thomas Nüßlein
- Gemeinschaftsklinikum Mittelrhein, Klinik für Kinder- und Jugendmedizin Koblenz und Mayen, Koblenz, Deutschland
| | - Felix C Ringshausen
- Medizinische Hochschule Hannover, Klinik für Pneumologie und Infektiologie und Deutsches Zentrum für Lungenforschung (DZL), Hannover, Deutschland
| | - Ludwig Sedlacek
- Medizinische Hochschule Hannover, Institut für Medizinische Mikrobiologie und Krankenhaushygiene, Hannover, Deutschland
| | - Christina Smaczny
- Klinikum der Johann Wolfgang Goethe-Universität Frankfurt am Main, Deutschland
| | - Olaf Sommerburg
- Universitätsklinikum Heidelberg, Sektion Pädiatrische Pneumologie, Allergologie und Mukoviszidose-Zentrum, Heidelberg, Deutschland
| | | | - Ralf-Peter Vonberg
- Medizinische Hochschule Hannover, Institut für Medizinische Mikrobiologie und Krankenhaushygiene, Hannover, Deutschland
| | | | - Jovita Zerlik
- Altonaer Kinderkrankenhaus gGmbH, Abteilung Physiotherapie, Hamburg, Deutschland
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Bowron LA, Acosta N, Thornton CS, Carpentero J, Waddell BJM, Bharadwaj L, Ebbert K, Castañeda-Mogollón D, Conly JM, Rabin HR, Surette MG, Parkins MD. The airway microbiome of persons with cystic fibrosis correlates with acquisition and microbiological outcomes of incident Stenotrophomonas maltophilia infection. Front Microbiol 2024; 15:1353145. [PMID: 38690371 PMCID: PMC11059027 DOI: 10.3389/fmicb.2024.1353145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 02/27/2024] [Indexed: 05/02/2024] Open
Abstract
Rationale Chronic infection with Stenotrophomonas maltophilia in persons with cystic fibrosis (pwCF) has been linked to an increased risk of pulmonary exacerbations and lung function decline. We sought to establish whether baseline sputum microbiome associates with risk of S. maltophilia incident infection and persistence in pwCF. Methods pwCF experiencing incident S. maltophilia infections attending the Calgary Adult CF Clinic from 2010-2018 were compared with S. maltophilia-negative sex, age (+/-2 years), and birth-cohort-matched controls. Infection outcomes were classified as persistent (when the pathogen was recovered in ≥50% of cultures in the subsequent year) or transient. We assessed microbial communities from prospectively biobanked sputum using V3-V4 16S ribosomal RNA (rRNA) gene sequencing, in the year preceding (Pre) (n = 57), at (At) (n = 22), and after (Post) (n = 31) incident infection. We verified relative abundance data using S. maltophilia-specific qPCR and 16S rRNA-targeted qPCR to assess bioburden. Strains were typed using pulse-field gel electrophoresis. Results Twenty-five pwCF with incident S. maltophilia (56% female, median 29 years, median FEV1 61%) with 33 total episodes were compared with 56 uninfected pwCF controls. Demographics and clinical characteristics were similar between cohorts. Among those with incident S. maltophilia infection, sputum communities did not cluster based on infection timeline (Pre, At, Post). Communities differed between the infection cohort and controls (n = 56) based on Shannon Diversity Index (SDI, p = 0.04) and clustered based on Aitchison distance (PERMANOVA, p = 0.01) prior to infection. At the time of incident S. maltophilia isolation, communities did not differ in SDI but clustered based on Aitchison distance (PERMANOVA, p = 0.03) in those that ultimately developed persistent infection versus those that were transient. S. maltophilia abundance within sputum was increased in samples from patients (Pre) relative to controls, measuring both relative (p = 0.004) and absolute (p = 0.001). Furthermore, S. maltophilia abundance was increased in sputum at incident infection in those who ultimately developed persistent infection relative to those with transient infection, measured relatively (p = 0.04) or absolute (p = 0.04), respectively. Conclusion Microbial community composition of CF sputum associates with S. maltophilia infection acquisition as well as infection outcome. Our study suggests sputum microbiome may serve as a surrogate for identifying infection risk and persistence risk.
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Affiliation(s)
- Lauren A. Bowron
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Nicole Acosta
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Christina S. Thornton
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
- Department of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jennifer Carpentero
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Barbara-Jean M. Waddell
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Lalit Bharadwaj
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Kirsten Ebbert
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
- Department of Pediatrics, University of Calgary, Calgary, AB, Canada
| | - Daniel Castañeda-Mogollón
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - John M. Conly
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
- Department of Medicine, University of Calgary, Calgary, AB, Canada
| | - Harvey R. Rabin
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
- Department of Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Michael D. Parkins
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
- Department of Medicine, University of Calgary, Calgary, AB, Canada
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3
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Abdelatti MAI, Abd El-Aziz NK, El-Naenaeey ESYM, Ammar AM, Alharbi NK, Alharthi A, Zakai SA, Abdelkhalek A. Antibacterial and Anti-Efflux Activities of Cinnamon Essential Oil against Pan and Extensive Drug-Resistant Pseudomonas aeruginosa Isolated from Human and Animal Sources. Antibiotics (Basel) 2023; 12:1514. [PMID: 37887215 PMCID: PMC10604284 DOI: 10.3390/antibiotics12101514] [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: 07/31/2023] [Revised: 09/29/2023] [Accepted: 09/29/2023] [Indexed: 10/28/2023] Open
Abstract
Pseudomonas aeruginosa is notorious for its ability to develop a high level of resistance to antimicrobial agents. Resistance-nodulation-division (RND) efflux pumps could mediate drug resistance in P. aeruginosa. The present study aimed to evaluate the antibacterial and anti-efflux activities of cinnamon essential oil either alone or combined with ciprofloxacin against drug resistant P. aeruginosa originated from human and animal sources. The results revealed that 73.91% of the examined samples were positive for P. aeruginosa; among them, 77.78% were of human source and 72.73% were recovered from animal samples. According to the antimicrobial resistance profile, 48.73% of the isolates were multidrug-resistant (MDR), 9.2% were extensive drug-resistant (XDR), and 0.84% were pan drug-resistant (PDR). The antimicrobial potential of cinnamon oil against eleven XDR and one PDR P. aeruginosa isolates was assessed by the agar well diffusion assay and broth microdilution technique. The results showed strong antibacterial activity of cinnamon oil against all tested P. aeruginosa isolates with inhibition zones' diameters ranging from 34 to 50 mm. Moreover, the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values of cinnamon oil against P. aeruginosa isolates ranged from 0.0562-0.225 µg/mL and 0.1125-0.225 µg/mL, respectively. The cinnamon oil was further used to evaluate its anti-efflux activity against drug-resistant P. aeruginosa by phenotypic and genotypic assays. The cartwheel test revealed diminished efflux pump activity post cinnamon oil exposure by two-fold indicating its reasonable impact. Moreover, the real-time quantitative polymerase chain reaction (RT-qPCR) results demonstrated a significant (p < 0.05) decrease in the expression levels of MexA and MexB genes of P. aeruginosa isolates treated with cinnamon oil when compared to the non-treated ones (fold changes values ranged from 0.4204-0.7474 for MexA and 0.2793-0.4118 for MexB). In conclusion, we suggested the therapeutic use of cinnamon oil as a promising antibacterial and anti-efflux agent against drug-resistant P. aeruginosa.
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Affiliation(s)
- Mohamed A. I. Abdelatti
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt; (E.-s.Y.M.E.-N.); (A.M.A.)
| | - Norhan K. Abd El-Aziz
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt; (E.-s.Y.M.E.-N.); (A.M.A.)
| | - El-sayed Y. M. El-Naenaeey
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt; (E.-s.Y.M.E.-N.); (A.M.A.)
| | - Ahmed M. Ammar
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt; (E.-s.Y.M.E.-N.); (A.M.A.)
| | - Nada K. Alharbi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia;
| | - Afaf Alharthi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia;
| | - Shadi A. Zakai
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Adel Abdelkhalek
- Food Safety, Hygiene and Technology Department, Faculty of Veterinary Medicine, Badr University in Cairo (BUC), Badr City 11829, Egypt;
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4
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CRISPR-Cas-mediated diagnostics. Trends Biotechnol 2022; 40:1326-1345. [PMID: 35595574 DOI: 10.1016/j.tibtech.2022.04.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/06/2022] [Accepted: 04/12/2022] [Indexed: 01/21/2023]
Abstract
An ideal molecular diagnostic method should be sensitive, specific, low cost, rapid, portable, and easy to operate. Traditional nucleic acid detection methods based mainly on PCR technology have not only high sensitivity and specificity, but also some limitations, such as the need for expensive equipment and skilled technicians, being both time and labor intensive, and difficult to implement in some regions. However, with the continuous development of CRISPR-Cas technology and its application in molecular diagnosis, new approaches have been used for the construction of molecular diagnostic systems. In this review, we discuss recent advances in CRISPR-based molecular diagnostic technologies and highlight the revolution they bring to the field of molecular diagnostics.
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Asker D, Awad TS, Raju D, Sanchez H, Lacdao I, Gilbert S, Sivarajah P, Andes DR, Sheppard DC, Howell PL, Hatton BD. Preventing Pseudomonas aeruginosa Biofilms on Indwelling Catheters by Surface-Bound Enzymes. ACS APPLIED BIO MATERIALS 2021; 4:8248-8258. [PMID: 35005941 DOI: 10.1021/acsabm.1c00794] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Implanted medical devices such as central venous catheters are highly susceptible to microbial colonization and biofilm formation and are a major risk factor for nosocomial infections. The opportunistic pathogen Pseudomonas aeruginosa uses exopolysaccharides, such as Psl, for both initial surface attachment and biofilm formation. We have previously shown that chemically immobilizing the Psl-specific glycoside hydrolase, PslGh, to a material surface can inhibit P. aeruginosa biofilm formation. Herein, we show that PslGh can be uniformly immobilized on the lumen surface of medical-grade, commercial polyethylene, polyurethane, and polydimethylsiloxane (silicone) catheter tubing. We confirmed that the surface-bound PslGh was uniformly distributed along the catheter length and remained active even after storage for 30 days at 4 °C. P. aeruginosa colonization and biofilm formation under dynamic flow culture conditions in vitro showed a 3-log reduction in the number of bacteria during the first 11 days, and a 2-log reduction by day 14 for PslGh-modified PE-100 catheters, compared to untreated catheter controls. In an in vivo rat infection model, PslGh-modified PE-100 catheters showed a ∼1.5-log reduction in the colonization of the clinical P. aeruginosa ATCC 27853 strain after 24 h. These results demonstrate the robust ability of surface-bound glycoside hydrolase enzymes to inhibit biofilm formation and their potential to reduce rates of device-associated infections.
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Affiliation(s)
- Dalal Asker
- Department of Materials Science & Engineering, University of Toronto, Toronto M5S 3E4, Canada.,Food Science & Technology Department, Alexandria University, Alexandria 21526, Egypt
| | - Tarek S Awad
- Department of Materials Science & Engineering, University of Toronto, Toronto M5S 3E4, Canada
| | - Deepa Raju
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto M5G 1X8, Canada
| | - Hiram Sanchez
- Department of Medicine, University of Wisconsin, 600 Highland Avenue, Madison 53706, Wisconsin, United States
| | - Ira Lacdao
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto M5G 1X8, Canada
| | - Stephanie Gilbert
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto M5G 1X8, Canada
| | - Piyanka Sivarajah
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto M5G 1X8, Canada
| | - David R Andes
- Department of Medicine, University of Wisconsin, 600 Highland Avenue, Madison 53706, Wisconsin, United States.,Medical Microbiology and Immunology, University of Wisconsin, Madison 53706, Wisconsin, United States
| | - Donald C Sheppard
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal H4A 3J1, Canada.,Department of Microbiology and Immunology, McGill University, Montreal H3A 0G4, Canada.,Department of Medicine, McGill University, Montreal H3A 0G4, Canada.,McGill Interdisciplinary Initiative in Infection and Immunity (MI4), Montreal H3A 0G4, Canada
| | - P Lynne Howell
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto M5G 1X8, Canada.,Department of Biochemistry, University of Toronto, Toronto M5S 3E4, Canada
| | - Benjamin D Hatton
- Department of Materials Science & Engineering, University of Toronto, Toronto M5S 3E4, Canada
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Dong K, Kang Z, Ji X, Zhang X, Cheng P, Sun B. A Loop-mediated Isothermal Amplification With a Nanoparticle-Based Lateral Flow Biosensor Assay to Detect Pseudomonas aeruginosa in Endophthalmitis. Transl Vis Sci Technol 2021; 10:26. [PMID: 34935909 PMCID: PMC8711014 DOI: 10.1167/tvst.10.14.26] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Pseudomonas aeruginosa is the most common bacteria causing endophthalmitis after cataract surgery. Vitreous fluid culture and molecular studies are commonly used in clinical diagnoses, but have disadvantages, such as a long culture cycle and low detection sensitivity. Here, we report a loop-mediated isothermal amplification (LAMP) method combined with the nanoparticles-lateral flow biosensor (LFB) method for rapid and specific detection of P. aeruginosa. Methods A set of six primers was designed to target the OprL gene of P. aeruginosa. Genomic DNA extracted from several gram-negative and gram-positive bacteria was used to determine the sensitivity and specificity of the analysis. LAMP reactions were conducted at 65 °C for 50 minutes, and results were reported using the LFB method. Results The DNA template of P. aeruginosa was specifically recognized by the P. aeruginosa-LAMP-LFB (PA-LAMP-LFB) method as no cross reactions were observed for non–P. aeruginosa templates. The analytical sensitivity of our assay was 100 fg per test for the pure cultured DNA template, and the result obtained using the LFB was consistent with that of colorimetric indicator detection. The whole test could be completed within 1h. This method was used to detect P. aeruginosa, Staphylococcus aureus, and Klebsiella pneumoniae; only P. aeruginosa was positive. The positive rates of P. aeruginosa detected by a traditional culture method, the LAMP-LFB method, and the fluorescence quantitative polymerase chain reaction method were 17.7%, 17.7%, and 13.3%, respectively. Conclusions The P. aeruginosa-LAMP-LFB method established here is a rapid, specific, and sensitive method for the detection of P. aeruginosa, which can be widely used.
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Affiliation(s)
- Kui Dong
- Shanxi Eye Hospital, Taiyuan, Shanxi, China
| | | | - Xuan Ji
- Shanxi Eye Hospital, Taiyuan, Shanxi, China
| | | | | | - Bin Sun
- Shanxi Eye Hospital, Taiyuan, Shanxi, China
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Contamination of Hospital Surfaces with Bacterial Pathogens under the Current COVID-19 Outbreak. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18179042. [PMID: 34501634 PMCID: PMC8431522 DOI: 10.3390/ijerph18179042] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 12/23/2022]
Abstract
The SARS-CoV-2 pandemic remains a global health issue for several reasons, such as the low vaccination rates and a lack of developed herd immunity to the evolution of SARS-CoV-2, as well as its potential inclination to elude neutralizing antibodies. It should be noted that the severity of the COVID-19 disease is significantly affected by the presence of co-infections. Comorbid conditions are caused not only by pathogenic and opportunistic microorganisms but also by some representatives of the environmental microbiome. The presence of patients with moderate and severe forms of the disease in hospitals indicates the need for epidemiological monitoring of (1) bacterial pathogens circulating in hospitals, especially the ESKAPE group pathogens, and (2) the microbiome of various surfaces in hospitals. In our study, we used combined methods based on PCR and NGS sequencing, which are widely used for epidemiological monitoring. Through this approach, we identified the DNA of pathogenic bacteria (Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, CoNS, and Achromobacter spp.) on various surfaces. We also estimated the microbiome diversity of surfaces and identified the potential reservoirs of infections using 16S rRNA profiling. Although we did not assess the viability of identified microorganisms, our results indicate the possible risks of insufficient regular disinfection of surfaces, regardless of department, at the Infectious Diseases Hospital. Controlling the transmission of nosocomial diseases is critical to the successful treatment of COVID-19 patients, the rational use of antimicrobial drugs, and timely decontamination measures.
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8
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Morilla R, Medrano FJ, Calzada A, Quintana E, Campano E, Friaza V, Calderón EJ, de la Horra C. Pneumocystis jirovecii among patients with cystic fibrosis and their household members. Med Mycol 2021; 59:849-854. [PMID: 33693837 PMCID: PMC8754488 DOI: 10.1093/mmy/myab010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/06/2021] [Accepted: 02/09/2021] [Indexed: 12/16/2022] Open
Abstract
We conducted a pilot study of patients with cystic fibrosis (CF) to assess intra-family transmission of P. jirovecii and compare it with data on other prevalent pathogens such as P. aeruginosa and S. pneumoniae, in which respiratory transmission has already been documented. Oral swab samples from 10 patients with CF and 15 household members were collected at baseline and 2 weeks later. P. aeruginosa and S. pneumoniae were assessed using standardized culture methods and PCR, and P. jirovecii was assessed using real and nested PCR, genotyping the positive samples by direct sequencing. P. aeruginosa cultures were positive for 7/10 (70%) of patients with CF at baseline and was identified by PCR in 8/10 (80%) of cases at baseline and 2 weeks later. S. pneumoniae cultures were negative for all patients, but the microorganism was identified by PCR in two cases. P. jirovecii was detected by real time and nested PCR in 5/10 (50%) of the patients at the two time points. In the household members, P. aeruginosa and P. jirovecii were identified in 7/15 (46.7%), and S. pneumoniae was identified in 8/15 (53,3%). The concordance of positive or negative pairs of patients with CF and their household members was 33.3% (5/15) for P. aeruginosa, 46.7% (7/15) for S. pneumonia and 93.3% (14/15) for P. jirovecii. The concordance for P. jirovecii genotypes among five pairs with available genotype was 100%. This study suggests for the first time the possible transmission of Pneumocystis in the home of patients with CF, indicating that patients and their household members are reservoirs and possible sources of infection.
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Affiliation(s)
- Ruben Morilla
- Instituto de Biomedicina de Sevilla (Hospital Universitario Virgen del Rocío/ CSIC/ Universidad de Sevilla), 41013 Seville, Spain.,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,Department of Internal Medicine, Hospital Universitario Virgen del Rocío, 41013 Seville, Spain.,Department of Nursing, Universidad de Sevilla, Seville, Spain
| | - Francisco J Medrano
- Instituto de Biomedicina de Sevilla (Hospital Universitario Virgen del Rocío/ CSIC/ Universidad de Sevilla), 41013 Seville, Spain.,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,Department of Internal Medicine, Hospital Universitario Virgen del Rocío, 41013 Seville, Spain.,Department of Medicine, Universidad de Sevilla, 41013 Seville, Spain
| | - Ana Calzada
- Hospital Virgen de las Montañas de Villamartín, 11650 Cadiz, Spain
| | - Esther Quintana
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, 41013 Seville, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Elena Campano
- Instituto de Biomedicina de Sevilla (Hospital Universitario Virgen del Rocío/ CSIC/ Universidad de Sevilla), 41013 Seville, Spain
| | - Vicente Friaza
- Instituto de Biomedicina de Sevilla (Hospital Universitario Virgen del Rocío/ CSIC/ Universidad de Sevilla), 41013 Seville, Spain.,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Enrique J Calderón
- Instituto de Biomedicina de Sevilla (Hospital Universitario Virgen del Rocío/ CSIC/ Universidad de Sevilla), 41013 Seville, Spain.,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,Department of Internal Medicine, Hospital Universitario Virgen del Rocío, 41013 Seville, Spain.,Department of Medicine, Universidad de Sevilla, 41013 Seville, Spain
| | - Carmen de la Horra
- Instituto de Biomedicina de Sevilla (Hospital Universitario Virgen del Rocío/ CSIC/ Universidad de Sevilla), 41013 Seville, Spain.,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,Department of Microbiology and Parasitology, School of Pharmacy, University of Seville, 41013 Seville, Spain
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Chao L, Li J, Zhang Y, Pu H, Yan X. Application of next generation sequencing-based rapid detection platform for microbiological diagnosis and drug resistance prediction in acute lower respiratory infection. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1644. [PMID: 33490156 PMCID: PMC7812213 DOI: 10.21037/atm-20-7081] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background Acute lower respiratory infections (ALRIs) have a high mortality rate. We aimed to apply a platform that rapidly detects 36 microorganisms and 49 antibiotic resistance markers in the clinical diagnosis of ALRI and drug resistance prediction. Methods Multicenter collection of clinical samples from patients with ALRIs was carried out from 2017 to 2018. Sputum culture (SC) was performed, which provided two outcomes: the detected pathogens and the resistance to different antibiotics. Additionally, each sputum sample was used to extract deoxyribonucleic acids (DNAs) followed by high-throughput sequencing. Results Eleven commonly observed pathogens were surveyed, and for all samples with positive SC results (137 cases), the overall coverage was 95.62% according to the sequencing results. The receiver operating characteristic (ROC) curve was drawn, and cutoff reads of the most frequently detected pathogens were acquired. Overall, sequencing exhibited significantly higher sensitivity in the detection of pathogens compared with the traditional SC method, with a generally satisfactory specificity. Furthermore, we investigated the correlation between antibiotic resistance gene phenotypes and the actual outcomes of the drug sensitivity test, and some significant correlations were found, especially for the resistance to Amikacin in the presence of blaOXA7. Conclusions Sequencing-based sputum metagenomics can reveal a profile of the lung pathogen microbiome. The sequencing method offers both sufficient accuracy and significantly higher sensitivity in the detection of pathogens, and can be at least a complementary approach to traditional SC reporting. The sequencing technique also revealed some novel potential correlations between the presence of different pathogens, as well as new antimicrobial-resistant genes.
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Affiliation(s)
- Lingshan Chao
- Department of Respiratory and Critical Care Medicine, the Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Jihong Li
- Department of Laboratory Medicine, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Ya'nan Zhang
- Department of Science and Technology, Shanghai Pathogeno Medical Technology Co., Ltd., Shanghai, China
| | - Hao Pu
- Department of Science and Technology, Shanghai Pathogeno Medical Technology Co., Ltd., Shanghai, China
| | - Xixin Yan
- Department of Respiratory and Critical Care Medicine, the Second Hospital of Hebei Medical University, Shijiazhuang, China
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Prevalence of vancomycin-resistant enterococcus in Africa in one health approach: a systematic review and meta-analysis. Sci Rep 2020; 10:20542. [PMID: 33239734 PMCID: PMC7688635 DOI: 10.1038/s41598-020-77696-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 11/02/2020] [Indexed: 11/08/2022] Open
Abstract
Vancomycin-resistant enterococci are a global challenge currently as reported by the World Health Organization. It is also important to recognize that combating antimicrobial resistance needs to recognize the interconnections between people, animals, plants and their shared environment in creating public health, the so-called One Health approach. Although the presence of VRE has been described in many regions of the world, there is a lack of comprehensive data indicating their prevalence of in Africa. Therefore, this study aimed to aggregate the result of studies describing VRE reported across multiple regions in Africa. A literature search was conducted on PubMed, Google scholar, and Hinari with the term “Vancomycin resistance enterococcus in Africa” on August 1–3, 2019. All available articles were downloaded to “Endnote version 7.1” then to Microsoft Word 2013. Articles determined to meet our criteria for the review was extracted to Microsoft Excel 2013. Those articles that reported the prevalence of vancomycin resistance Enterococcus obtained from all sample types and published from 2010 to 2019 in the English language were included for the review. A meta-analysis was conducted with OpenMetaAnalyst version R.3.1.0 software. The effect size was determined using a binary random effect model and statically significant considered when p < 0.05. Heterogeneity determined with the inconsistency index. A leave one out analysis used to perform the sensitivity analysis. There were 151 articles identified from the database searches; of this, 36 articles included after extensive review with two independent authors. Out of 4073 samples collected, 1488 isolates identified with an overall pooled prevalence of VRE 26.8% (95% CI; 10.7–43.0%) in Africa with a one-health perspective. The analysis showed that considerable heterogeneity among the studies (I2 = 99.97%; p < 0.001). Subgroup analysis in-country, African region, laboratory method, year of publication, and sample source showed that a high prevalence was identified from South Africa (74.8%), South African regions (74.8%), PCR (959.2%), 2010–2015 years (30.3%) and environmental (52.2%), respectively. This meta-analysis indicates that there was a high-pooled prevalence of vancomycin-resistant enterococci in African. A lot should be done to prevent and control the transmission of vancomycin resistance enterococci to a human being from the environment in the continent.
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Tueffers L, Barbosa C, Bobis I, Schubert S, Höppner M, Rühlemann M, Franke A, Rosenstiel P, Friedrichs A, Krenz-Weinreich A, Fickenscher H, Bewig B, Schreiber S, Schulenburg H. Pseudomonas aeruginosa populations in the cystic fibrosis lung lose susceptibility to newly applied β-lactams within 3 days. J Antimicrob Chemother 2020; 74:2916-2925. [PMID: 31355848 DOI: 10.1093/jac/dkz297] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 06/06/2019] [Accepted: 06/14/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Chronic pulmonary infections by Pseudomonas aeruginosa require frequent intravenous antibiotic treatment in cystic fibrosis (CF) patients. Emergence of antimicrobial resistance is common in these patients, which to date has been investigated at long-term intervals only. OBJECTIVES To investigate under close to real-time conditions the dynamics of the response by P. aeruginosa to a single course of antibiotic therapy and the potentially associated rapid spread of antimicrobial resistance, as well as the impact on the airway microbiome. METHODS We investigated a cohort of adult CF patients that were treated with a single course of antimicrobial combination therapy. Using daily sampling during treatment, we quantified the expression of resistance by P. aeruginosa (median of six isolates per daily sample, 347 isolates in total), measured bacterial load by P. aeruginosa-specific quantitative PCR and characterized the airway microbiome with a 16S rRNA-based approach. WGS was performed to reconstruct intrapatient strain phylogenies. RESULTS In two patients, we found rapid and large increases in resistance to meropenem and ceftazidime. Phylogenetic reconstruction of strain relationships revealed that resistance shifts are probably due to de novo evolution and/or the selection of resistant subpopulations. We observed high interindividual variation in the reduction of bacterial load, microbiome composition and antibiotic resistance. CONCLUSIONS We show that CF-associated P. aeruginosa populations can quickly respond to antibiotic therapy and that responses are patient specific. Thus, resistance evolution can be a direct consequence of treatment, and drug efficacy can be lost much faster than usually assumed. The consideration of these patient-specific rapid resistance shifts can help to improve treatment of CF-associated infections, for example by deeper sampling of bacteria for diagnostics, repeated monitoring of pathogen susceptibility and switching between drugs.
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Affiliation(s)
- Leif Tueffers
- Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, Kiel, Germany
| | - Camilo Barbosa
- Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, Kiel, Germany
| | - Ingrid Bobis
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel Campus, Arnold-Heller-Straße 3, Kiel, Germany
| | - Sabine Schubert
- Institute of Infection Medicine, Christian-Albrechts-Universität zu Kiel and University Medical Center Schleswig-Holstein, Brunswiker Straße 4, Kiel, Germany
| | - Marc Höppner
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Rosalind-Franklin-Straße 12, Kiel, Germany
| | - Malte Rühlemann
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Rosalind-Franklin-Straße 12, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Rosalind-Franklin-Straße 12, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Rosalind-Franklin-Straße 12, Kiel, Germany
| | - Anette Friedrichs
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel Campus, Arnold-Heller-Straße 3, Kiel, Germany
| | | | - Helmut Fickenscher
- Institute of Infection Medicine, Christian-Albrechts-Universität zu Kiel and University Medical Center Schleswig-Holstein, Brunswiker Straße 4, Kiel, Germany
| | - Burkhard Bewig
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel Campus, Arnold-Heller-Straße 3, Kiel, Germany
| | - Stefan Schreiber
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel Campus, Arnold-Heller-Straße 3, Kiel, Germany.,Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Rosalind-Franklin-Straße 12, Kiel, Germany
| | - Hinrich Schulenburg
- Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, Kiel, Germany
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12
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Calvo-Lozano O, Aviñó A, Friaza V, Medina-Escuela A, S. Huertas C, Calderón EJ, Eritja R, Lechuga LM. Fast and Accurate Pneumocystis Pneumonia Diagnosis in Human Samples Using a Label-Free Plasmonic Biosensor. NANOMATERIALS 2020; 10:nano10061246. [PMID: 32604931 PMCID: PMC7353103 DOI: 10.3390/nano10061246] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 01/30/2023]
Abstract
Pneumocystis jirovecii is a fungus responsible for human Pneumocystis pneumonia, one of the most severe infections encountered in immunodepressed individuals. The diagnosis of Pneumocystis pneumonia continues to be challenging due to the absence of specific symptoms in infected patients. Moreover, the standard diagnostic method employed for its diagnosis involves mainly PCR-based techniques, which besides being highly specific and sensitive, require specialized personnel and equipment and are time-consuming. Our aim is to demonstrate an optical biosensor methodology based on surface plasmon resonance to perform such diagnostics in an efficient and decentralized scheme. The biosensor methodology employs poly-purine reverse-Hoogsteen hairpin probes for the detection of the mitochondrial large subunit ribosomal RNA (mtLSU rRNA) gene, related to P. jirovecii detection. The biosensor device performs a real-time and label-free identification of the mtLSU rRNA gene with excellent selectivity and reproducibility, achieving limits of detection of around 2.11 nM. A preliminary evaluation of clinical samples showed rapid, label-free and specific identification of P. jirovecii in human lung fluids such as bronchoalveolar lavages or nasopharyngeal aspirates. These results offer a door for the future deployment of a sensitive diagnostic tool for fast, direct and selective detection of Pneumocystis pneumonia disease.
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Affiliation(s)
- Olalla Calvo-Lozano
- Nanobiosensors and Bioanalytical Applications Group (NanoB2A), Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, CIBER in Bioengineering, Biomaterials and Nanomedicine and BIST, Campus UAB Bellaterra, 08193 Barcelona, Spain; (O.C.-L.); (C.S.H.); (L.M.L.)
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, CIBER in Bioengineering, Biomaterials and Nanomedicine c/Jordi Girona 18–26, 08034 Barcelona, Spain;
- Correspondence:
| | - Vicente Friaza
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville and CIBER in Epidemiology and Public Health, 41013 Seville, Spain; (V.F.); (E.J.C.)
| | - Alfonso Medina-Escuela
- Institute for Applied Microelectronics (IUMA), University of Las Palmas de Gran Canaria, 35017 Las Palmas, Spain;
| | - César S. Huertas
- Nanobiosensors and Bioanalytical Applications Group (NanoB2A), Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, CIBER in Bioengineering, Biomaterials and Nanomedicine and BIST, Campus UAB Bellaterra, 08193 Barcelona, Spain; (O.C.-L.); (C.S.H.); (L.M.L.)
- Integrated Photonics and Applications Centre, School of Engineering, RMIT University, Melbourne 3001, Australia
| | - Enrique J. Calderón
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville and CIBER in Epidemiology and Public Health, 41013 Seville, Spain; (V.F.); (E.J.C.)
- Department of Medicine, University of Seville, 41013 Seville, Spain
| | - Ramón Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, CIBER in Bioengineering, Biomaterials and Nanomedicine c/Jordi Girona 18–26, 08034 Barcelona, Spain;
| | - Laura M. Lechuga
- Nanobiosensors and Bioanalytical Applications Group (NanoB2A), Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, CIBER in Bioengineering, Biomaterials and Nanomedicine and BIST, Campus UAB Bellaterra, 08193 Barcelona, Spain; (O.C.-L.); (C.S.H.); (L.M.L.)
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Cao Y, Yu M, Dong G, Chen B, Zhang B. Digital PCR as an Emerging Tool for Monitoring of Microbial Biodegradation. Molecules 2020; 25:molecules25030706. [PMID: 32041334 PMCID: PMC7037809 DOI: 10.3390/molecules25030706] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/03/2020] [Accepted: 02/04/2020] [Indexed: 11/16/2022] Open
Abstract
Biodegradation of contaminants is extremely complicated due to unpredictable microbial behaviors. Monitoring of microbial biodegradation drives us to determine (1) the amounts of specific degrading microbes, (2) the abundance, and (3) expression level of relevant functional genes. To this endeavor, the cultivation independent polymerase chain reaction (PCR)-based monitoring technique develops from endpoint PCR, real-time quantitative PCR, and then into novel digital PCR. In this review, we introduce these three categories of PCR techniques and summarize the timely applications of digital PCR and its superiorities than qPCR for biodegradation monitoring. Digital PCR technique, emerging as the most accurately absolute quantification method, can serve as the most promising and robust tool for monitoring of microbial biodegradation.
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Affiliation(s)
| | | | | | - Bing Chen
- Correspondence: (B.C.); (B.Z.); Tel.: +1-709-864-8958 (B.C.); +1-709-864-3301 (B.Z.)
| | - Baiyu Zhang
- Correspondence: (B.C.); (B.Z.); Tel.: +1-709-864-8958 (B.C.); +1-709-864-3301 (B.Z.)
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14
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Barnell EK, Kang Y, Wurtzler EM, Griffith M, Chaudhuri AA, Griffith OL. Noninvasive Detection of High-Risk Adenomas Using Stool-Derived Eukaryotic RNA Sequences as Biomarkers. Gastroenterology 2019; 157:884-887.e3. [PMID: 31154021 PMCID: PMC6707888 DOI: 10.1053/j.gastro.2019.05.058] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 05/18/2019] [Accepted: 05/28/2019] [Indexed: 01/04/2023]
Affiliation(s)
- Erica K Barnell
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri; Division of Gastroenterology and Hepatology, Geneoscopy LLC, St Louis, Missouri
| | - Yiming Kang
- Division of Gastroenterology and Hepatology, Geneoscopy LLC, St Louis, Missouri; Department of Computer Science and Engineering, Washington University, St Louis, Missouri
| | | | - Malachi Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri; Department of Genetics, Washington University School of Medicine, St Louis, Missouri; Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, Missouri; Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri
| | - Aadel A Chaudhuri
- Department of Computer Science and Engineering, Washington University, St Louis, Missouri; Department of Genetics, Washington University School of Medicine, St Louis, Missouri; Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri; Department of Radiation Oncology, Washington University School of Medicine, St Louis, Missouri.
| | - Obi L Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri; Department of Genetics, Washington University School of Medicine, St Louis, Missouri; Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, Missouri; Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri.
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15
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Hassannejad N, Bahador A, Hayati Rudbari N, Modarressi MH, Parivar K. Comparison of OmpA Gene-Targeted Real-Time PCR with the Conventional Culture Method for Detection of Acinetobacter baumanii in Pneumonic BALB/c Mice. IRANIAN BIOMEDICAL JOURNAL 2019; 23. [PMID: 30665275 PMCID: PMC6707111 DOI: 10.29252/.23.2.159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
BACKGROUND Acinetobacter baumannii is an important pathogen in health care and is responsible for severe nosocomial and community-acquired pneumonia. To design novel therapeutic agents, a mouse model for A. baumannii pneumonia is essential. METHODS We described a mouse model of A. baumannii using clinical and 19606R standard strains for developing a quantitative real-time PCR (qRT-PCR) for rapid identification of A. baumannii infection from lung tissues of BALB/c mice. RESULTS To infect the mice, three doses of bacteria (0.5 × 108, 1 × 108, and 1.5 × 108 cfu/ml) were used. Lung tissues were cultured and compared with ompA gene. Clinical isolates had better positive results at day three with the highest dose than 19606 strain either in culture (4 versus 3) or in qRT-PCR (5 versus 4). However, qRT-PCR detection was 100%, the specificity was 70%, and the positive predictive value was 27%. CONCLUSION The qRT-PCR detection of A. baumannii in the BALB/c mice model has a higher sensitivity than the culture method.
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Affiliation(s)
- Niloofar Hassannejad
- Dept. of Cell Biology, Science and Research branch, Islamic Azad University, Tehran, Iran
| | - Abbas Bahador
- Dept. of Microbiology, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran; ,Co-correspondence: Abbas Bahador, Dept. of Microbiology, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Mobile: (+98-912) 2207431; E-mail:
| | - Nasim Hayati Rudbari
- Dept. of Cell Biology, Science and Research branch, Islamic Azad University, Tehran, Iran
| | | | - Kazem Parivar
- Dept. of Cell Biology, Science and Research branch, Islamic Azad University, Tehran, Iran; ,Corresponding Author: Kazem Parivar, Dept. of Cell Biology, Science and Research branch, Islamic Azad University, Tehran, Iran; Tel.: (+98-21) 44865179; E-mail:
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16
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Mangiaterra G, Amiri M, Di Cesare A, Pasquaroli S, Manso E, Cirilli N, Citterio B, Vignaroli C, Biavasco F. Detection of viable but non-culturable Pseudomonas aeruginosa in cystic fibrosis by qPCR: a validation study. BMC Infect Dis 2018; 18:701. [PMID: 30587160 PMCID: PMC6307279 DOI: 10.1186/s12879-018-3612-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 12/10/2018] [Indexed: 12/29/2022] Open
Abstract
Background Routine culture-based diagnosis of Pseudomonas aeruginosa lung infection in Cystic Fibrosis (CF) patients can be hampered by the phenotypic variability of the microorganism, including its transition to a Viable But Non-Culturable (VBNC) state. The aim of this study was to validate an ecfX-targeting qPCR protocol developed to detect all viable P. aeruginosa bacteria and to identify VBNC forms in CF sputum samples. Methods The study involved 115 P. aeruginosa strains of different origins and 10 non-P. aeruginosa strains and 88 CF sputum samples, 41 Culture-Positive (CP) and 47 Culture-Negative (CN). Spiking assays were performed using scalar dilutions of a mixture of live and dead P. aeruginosa ATCC 9027 and a pooled P. aeruginosa-free sputum batch. Total DNA from sputum samples was extracted by a commercial kit, whereas a crude extract was obtained from the broth cultures. Extracellular DNA (eDNA) interference was evaluated by comparing the qPCR counts obtained from DNase-treated and untreated aliquots of the same samples. The statistical significance of the results was assessed by the Wilcoxon test and Student’s t test. Results The newly-developed qPCR protocol identified 96.6% of the P. aeruginosa isolates; no amplification was obtained with strains belonging to different species. Spiking assays supported protocol reliability, since counts always matched the amount of live bacteria, thus excluding the interference of dead cells and eDNA. The protocol sensitivity threshold was 70 cells/ml of the original sample. Moreover, qPCR detected P. aeruginosa in 9/47 CN samples and showed higher bacterial counts compared with the culture method in 10/41 CP samples. Conclusions Our findings demonstrate the reliability of the newly-developed qPCR protocol and further highlight the need for harnessing a non-culture approach to achieve an accurate microbiological diagnosis of P. aeruginosa CF lung infection and a greater understanding of its evolution. Electronic supplementary material The online version of this article (10.1186/s12879-018-3612-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gianmarco Mangiaterra
- Department of Life and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, 60131, Ancona, Italy.
| | - Mehdi Amiri
- Department of Life and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Andrea Di Cesare
- Department of Earth, Environmental and Life Sciences, University of Genoa, Corso Europa, 26, 16132, Genoa, Italy
| | - Sonia Pasquaroli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Esther Manso
- Microbiology Laboratory, Azienda Ospedaliero-Universitaria, Ospedali Riuniti Umberto I°- G.M. Lancisi - G. Salesi, Ancona, Italy
| | - Natalia Cirilli
- Mother-Child Department, Cystic Fibrosis Referral Care Center, United Hospitals, Ancona, Italy
| | - Barbara Citterio
- Department of Biomolecular Sciences sect. Biotechnology, University of Urbino "Carlo Bo", Urbino, Italy
| | - Carla Vignaroli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Francesca Biavasco
- Department of Life and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, 60131, Ancona, Italy
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Wu Z, He D, Cui B, Jin Z. A bimodal (SERS and colorimetric) aptasensor for the detection of Pseudomonas aeruginosa. Mikrochim Acta 2018; 185:528. [PMID: 30382404 DOI: 10.1007/s00604-018-3073-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/26/2018] [Indexed: 01/15/2023]
Abstract
An aptamer based assay is described for the determination of Pseudomonas aeruginosa (P. aeruginosa). It is bimodal in that both surface enhanced Raman spectroscopy (SERS) and colorimetry are applied for quantitation. The aptamer against P. aeruginosa and its corresponding complementary DNA fragment (cDNA) were conjugated to two kinds of differently sized gold nanoparticles (AuNPs). The 30 nm AuNPs carrying the aptamer are used as color signal probes, while the cDNA-15 nm AuNP conjugates serve as SERS signalling probes. In the absence of P. aeruginosa, the two probes assemble to form the duplex structure. When the probes are exposed to P. aeruginosa, the aptamer dissociates from its cDNA and binds the target. After centrifugation, the SERS signal from the supernatant decreased, due to the decreased electromagnetic effect. On addition of 3,3',5,5'-tetramethylbenzidine (TMB) and hydrogen peroxide, a relatively rapid catalytic reaction between horseradish peroxidase (linked to the aptamer on the 30-nm AuNPs) and TMB occurred, resulting in the formation of a green color with an absorption peak at 640 nm. The reliability of the approach was validated by detecting different levels of P. aeruginosa in spiked tap water and chicken meat samples. The average recoveries ranged from 88% to 112%, confirming the practicality of this method. In our perception, this dual mode aptasensor paves the way for accurate and reliable determination of P. aeruginosa. Conceivably, the method has a wide scope in that it may be extended to the determination of various other species for which respective aptamers are available. Graphical abstract Schematic illustration of a bimodal aptasensor based on surface enhanced Raman scattering (SERS) and color change for the detection of Pseudomonas aeruginosa.
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Affiliation(s)
- Zhengzong Wu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, 250353, China.
| | - Deyun He
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Bo Cui
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, 250353, China.
| | - Zhengyu Jin
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
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Non-eluting, surface-bound enzymes disrupt surface attachment of bacteria by continuous biofilm polysaccharide degradation. Biomaterials 2018; 167:168-176. [DOI: 10.1016/j.biomaterials.2018.03.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 02/28/2018] [Accepted: 03/12/2018] [Indexed: 11/19/2022]
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Chen JW, Lau YY, Krishnan T, Chan KG, Chang CY. Recent Advances in Molecular Diagnosis of Pseudomonasaeruginosa Infection by State-of-the-Art Genotyping Techniques. Front Microbiol 2018; 9:1104. [PMID: 29892277 PMCID: PMC5985333 DOI: 10.3389/fmicb.2018.01104] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/08/2018] [Indexed: 12/02/2022] Open
Abstract
Pseudomonas aeruginosa is a rod-shaped Gram-negative bacterium which is notably known as a pathogen in humans, animals, and plants. Infections caused by P. aeruginosa especially in hospitalized patients are often life-threatening and rapidly increasing worldwide throughout the years. Recently, multidrug-resistant P. aeruginosa has taken a toll on humans' health due to the inefficiency of antimicrobial agents. Therefore, the rapid and advanced diagnostic techniques to accurately detect this bacterium particularly in clinical samples are indeed necessary to ensure timely and effective treatments and to prevent outbreaks. This review aims to discuss most recent of state-of-the-art molecular diagnostic techniques enabling fast and accurate detection and identification of P. aeruginosa based on well-developed genotyping techniques, e.g., polymerase chain reaction, pulse-field gel electrophoresis, and next generation sequencing. The advantages and limitations of each of the methods are also reviewed.
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Affiliation(s)
- Jian-Woon Chen
- International Genome Centre, Jiangsu University, Zhenjiang, China
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Yin Yin Lau
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Thiba Krishnan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- International Genome Centre, Jiangsu University, Zhenjiang, China
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Chien-Yi Chang
- School of Chemistry and Biosciences, University of Bradford, Bradford, United Kingdom
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Early detection using qPCR of Pseudomonas aeruginosa infection in children with cystic fibrosis undergoing eradication treatment. J Cyst Fibros 2018. [PMID: 29525410 DOI: 10.1016/j.jcf.2018.02.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Infection with Pseudomonas aeruginosa (Pa) with a chronic phenotype is associated with antibiotic eradication therapy (AET) failure. Our objective was to determine whether higher levels of Pa (detected using qPCR) prior to culture positivity were associated with AET failure in pediatric CF patients. METHODS Pa-specific qPCR was performed on stored sputa prior to culture positivity in pediatric CF patients with new-onset culture-positive Pa infections undergoing AET with a 28-day course of tobramycin-inhaled solution (TIS). DNA concentrations were compared in patients in whom AET was successful (Eradicated) to those with persistently positive sputum cultures (Persistent). RESULTS Forty-seven patients were included. AET was successful in 32 cases (68%), but failed in 15 cases (32%). Median sputum Pa-specific DNA concentration preceding the positive sputum culture was 2.2 × 10-6 μg/mL in Eradicated cases compared to 3 × 10-5 μg/mL in Persistent cases (p = 0.14). There was no significant difference in DNA concentration in the last sputum sample prior to culture positivity, nor in maximal DNA values. There was also no difference in sputum Pa DNA concentrations in patients who had a mucoid (compared to non-mucoid) Pa infection. CONCLUSIONS Pediatric CF patients with new-onset Pa infections have detectable Pa-specific DNA in the year preceding a positive culture, however, there is no significant difference in Pa DNA concentrations between patients in whom AET is successful compared to those in whom it fails. Therefore, early molecular detection of Pa may not lead to improved eradication success rates.
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Tynan A, Mawhinney L, Armstrong ME, O'Reilly C, Kennedy S, Caraher E, Jülicher K, O'Dwyer D, Maher L, Schaffer K, Fabre A, McKone EF, Leng L, Bucala R, Bernhagen J, Cooke G, Donnelly SC. Macrophage migration inhibitory factor enhances Pseudomonas aeruginosa biofilm formation, potentially contributing to cystic fibrosis pathogenesis. FASEB J 2017; 31:5102-5110. [PMID: 28768722 DOI: 10.1096/fj.201700463r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 07/17/2017] [Indexed: 12/13/2022]
Abstract
Macrophage migration inhibitory factor (MIF) is a key proinflammatory mediator that we have previously shown to be associated with an aggressive clinical phenotype in cystic fibrosis. It possesses unique tautomerase enzymatic activity. However, to date, no human-derived substrate has been identified that has the capacity to interact with this cytokine's unique tautomerase activity. This led us to hypothesize that MIF may have the capacity to interact with external substrates. We describe for the first time how Pseudomonas aeruginosa can utilize human recombinant MIF (rMIF) to significantly (P < 0.01) enhance its endogenous biofilm formation. Our in vivo studies demonstrate that utilizing a small-molecular-weight inhibitor targeting MIF's tautomerase activity (SCD-19) significantly reduces the inflammatory response in a murine pulmonary chronic P. aeruginosa model. In addition, we show that in in vitro experiments, pretreatment of P. aeruginosa with rMIF is associated with reduced bacterial killing by tobramycin. Our novel findings support the concept of an anti-MIF strategy that targets this enzymatic activity as a potential future antibacterial therapeutic approach.-Tynan, A., Mawhinney, L., Armstrong, M. E., O'Reilly, C., Kennedy, S., Caraher, E., Jülicher, K., O'Dwyer, D., Maher, L., Schaffer, K., Fabre, A., McKone, E. F., Leng, L., Bucala, R., Bernhagen, J., Cooke, G., Donnelly, S. C. Macrophage migration inhibitory factor enhances Pseudomonas aeruginosa biofilm formation, potentially contributing to cystic fibrosis pathogenesis.
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Affiliation(s)
- Aisling Tynan
- Department of Medicine, Tallaght Hospital, Trinity College, Dublin, Ireland
| | - Leona Mawhinney
- Department of Medicine, Tallaght Hospital, Trinity College, Dublin, Ireland
| | | | - Ciaran O'Reilly
- Department of Medicine, Tallaght Hospital, Trinity College, Dublin, Ireland
| | - Sarah Kennedy
- Department of Science, Centre for Microbial Host Interactions, Institute of Technology Tallaght, Dublin, Ireland
| | - Emma Caraher
- Department of Science, Centre for Microbial Host Interactions, Institute of Technology Tallaght, Dublin, Ireland
| | - Karen Jülicher
- Department of Medicine, Tallaght Hospital, Trinity College, Dublin, Ireland
| | - David O'Dwyer
- St. Vincent's University Hospital, University College Dublin, Dublin, Ireland.,School of Medicine, University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Lewena Maher
- St. Vincent's University Hospital, University College Dublin, Dublin, Ireland.,School of Medicine, University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Kirsten Schaffer
- St. Vincent's University Hospital, University College Dublin, Dublin, Ireland.,School of Medicine, University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Aurélie Fabre
- St. Vincent's University Hospital, University College Dublin, Dublin, Ireland.,School of Medicine, University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Edward F McKone
- St. Vincent's University Hospital, University College Dublin, Dublin, Ireland.,School of Medicine, University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Lin Leng
- Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Richard Bucala
- Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Jürgen Bernhagen
- Institute of Biochemistry and Molecular Cell Biology, RWTH Aachen University, Aachen, Germany.,Vascular Biology, Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians-University, Munich, Germany
| | - Gordon Cooke
- Department of Science, Centre for Microbial Host Interactions, Institute of Technology Tallaght, Dublin, Ireland
| | - Seamas C Donnelly
- Department of Medicine, Tallaght Hospital, Trinity College, Dublin, Ireland;
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A magnetic relaxation switch aptasensor for the rapid detection of Pseudomonas aeruginosa using superparamagnetic nanoparticles. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2142-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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23
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Molecular Identification of Staphylococcus aureus in Airway Samples from Children with Cystic Fibrosis. PLoS One 2016; 11:e0147643. [PMID: 26808658 PMCID: PMC4726467 DOI: 10.1371/journal.pone.0147643] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 01/06/2016] [Indexed: 02/05/2023] Open
Abstract
Background Staphylococcus aureus is a common and significant pathogen in cystic fibrosis. We sought to determine if quantitative PCR (qPCR) and 16S rRNA gene sequencing could provide a rapid, culture-independent approach to the identification of S. aureus airway infections. Methods We examined the sensitivity and specificity of two qPCR assays, targeting the femA and 16S rRNA gene, using culture as the gold standard. In addition, 16S rRNA gene sequencing to identify S. aureus directly from airway samples was evaluated. DNA extraction was performed with and without prior enzymatic digestion. Results 87 samples [42 oropharyngeal (OP) and 45 expectorated sputum (ES)] were analyzed. 59 samples (68%) cultured positive for S. aureus. Using standard extraction techniques, sequencing had the highest sensitivity for S. aureus detection (85%), followed by FemA qPCR (52%) and 16SrRNA qPCR (34%). For all assays, sensitivity was higher from ES samples compared to OP swabs. Specificity of the qPCR assays was 100%, but 21.4% for sequencing due to detection of S. aureus in low relative abundance from culture negative samples. Enzymatic digestion increased the sensitivity of qPCR assays, particularly for OP swabs. Conclusion Sequencing had a high sensitivity for S. aureus, but low specificity. While femA qPCR had higher sensitivity than 16S qPCR for detection of S. aureus, neither assay was as sensitive as sequencing. The significance of S. aureus detection with low relative abundance by sequencing in culture-negative specimens is not clear.
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Fazeli H, Sadighian H, Esfahani BN, Pourmand MR. Genetic characterization of Pseudomonas aeruginosa-resistant isolates at the university teaching hospital in Iran. Adv Biomed Res 2015; 4:156. [PMID: 26380241 PMCID: PMC4550956 DOI: 10.4103/2277-9175.161583] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 08/19/2014] [Indexed: 11/05/2022] Open
Abstract
Background: Pseudomonas aeruginosa is an opportunistic pathogen that is commonly responsible for nosocomial infections. The aim of this study was to perform a genotyping analysis of the Pseudomonas aeruginosa-resistant isolates by the multilocus sequence typing (MLST) method at the university teaching hospital in Iran. Materials and Methods: Antimicrobial susceptibility was analyzed for P. aeruginosa isolates. Ceftazidime-resistant (CAZres) isolates with a positive double-disc synergy test were screened for the presence of extended-spectrum β-lactamase-encoding genes. Phenotypic tests to detect the metallo-β-lactamase strains of P. aeruginosa were performed on imipenem-resistant (IMPres) isolates. Selected strains were characterized by MLST. Results: Of 35 P. aeruginosa isolates, 71%, 45% and 45% of isolates were CAZres, IMPres and multidrug resistant (MDR), respectively. Fifty-seven percent of the isolates carried the blaOXAgroup-1. All the five typed isolates were ST235. Isolates of ST235 that were MDR showed a unique resistance pattern. Conclusion: This study shows a high rate of MDR P. aeruginosa isolates at the university teaching hospital in Iran. It seems MDR isolates of P. aeruginosa ST235 with unique resistance pattern disseminated in this hospital.
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Affiliation(s)
- Hossein Fazeli
- Department of Microbiology, Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical sciences, Isfahan, Iran
| | - Hooman Sadighian
- Department of Microbiology, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran ; Department of Microbiology, Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical sciences, Isfahan, Iran
| | - Bahram Nasr Esfahani
- Department of Microbiology, Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical sciences, Isfahan, Iran
| | - Mohammad Reza Pourmand
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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Lagares A, Agaras B, Bettiol MP, Gatti BM, Valverde C. A cultivation-independent PCR-RFLP assay targeting oprF gene for detection and identification of Pseudomonas spp. in samples from fibrocystic pediatric patients. J Microbiol Methods 2015; 114:66-74. [DOI: 10.1016/j.mimet.2015.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Revised: 05/06/2015] [Accepted: 05/06/2015] [Indexed: 01/10/2023]
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Detection of Pseudomonas aeruginosa by a triplex polymerase chain reaction assay based on lasI/R and gyrB genes. J Infect Public Health 2015; 8:314-22. [PMID: 25863575 DOI: 10.1016/j.jiph.2015.03.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 02/24/2015] [Accepted: 03/08/2015] [Indexed: 01/21/2023] Open
Abstract
Pseudomonas aeruginosa is a nosocomial pathogen, which, due to its inherent and acquired resistance to a wide range of antibiotics, causes high mortality rates. Therefore, rapid detection of the bacterium with high specificity and sensitivity plays a critical role in the control of the pathogenic bacterium. The aim of this study was to evaluate the accuracy and specificity of a prompt detection of the bacterium based on a triplex polymerase chain reaction that amplifies the lasI, lasR and gyrB genes. For this purpose, 30 clinical isolates of P. aeruginosa and 30 wound biopsy samples were retrieved from clinical diagnostic laboratories. After the extraction of the chromosomal DNA, the desired genes were amplified using uniplex and triplex PCR with appropriate primers. The specificity of the primers was evaluated by a comparison of the PCR results for P. aeruginosa clinical samples and non-Pseudomonas species control samples. The sensitivity of the primers was determined using a serial dilution of the genomic DNA template (100 ng to 100 fg) and by a comparison of the PCR and bacterial culture results. The results showed that the triplex PCR assay was positive for all of the samples (100%), while the PCR identifications were negative for non-Pseudomonas species. Additionally, at 10(-4) and 10(-5) diluted genomic DNA from P. aeruginosa (10 pg and 1 pg), the triplex PCR test was positive for the Las and gyrB genes in all of the samples, respectively. Based on these results, the designed primers can be used for the rapid, specific and sensitive diagnosis of P. aeruginosa in a triplex PCR assay.
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Rashno Taee S, Khansarinejad B, Abtahi H, Najafimosleh M, Ghaznavi-Rad E. Detection of algD, oprL and exoA Genes by New Specific Primers as an Efficient, Rapid and Accurate Procedure for Direct Diagnosis of Pseudomonas aeruginosa Strains in Clinical Samples. Jundishapur J Microbiol 2014; 7:e13583. [PMID: 25632330 PMCID: PMC4295320 DOI: 10.5812/jjm.13583] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Revised: 09/22/2013] [Accepted: 01/22/2014] [Indexed: 11/25/2022] Open
Abstract
Background: Pseudomonas aeruginosa is an opportunistic pathogen that infects patients with cystic fibrosis, burning wounds, ophthalmic traumas and immunodeficiency. Objectives: The aim of the present study was to compare the efficiency of newly designed primer sets with some previously published primers for PCR detection of exoA, oprL and algD genes from P. aeruginosa. Materials and Methods: A total of 150 clinical specimens were inoculated into the routine and selective culture media for P. aeruginosa isolation. Specific primers were designed by bioinformatics analysis for detection of the virulence genes determinants, exoA, oprL and algD. The sequences of these three genes were obtained from NCBI and multiple alignments were performed to find the conserved sequences of each gene to design the primers. Multiple alignment and primer design steps were carried out by the AlleleID software, version 7.0. Results: Microbiological culture methods resulted 70 P. aeruginosa strains isolated from 70 of the 150 clinical specimens. The results of the PCR assay using the newly designed exoA, oprL and algD primer sets were positive in 68, 70 and 69 clinical samples which represent 97.2%, 100% and 98% sensitivity for each primer set, respectively. The PCR results using previously published exoA, oprL and algD primer sets were positive only in 57, 49 and 28 specimens that correspond to 81.5%, 70% and 40% sensitivity, respectively. Conclusions: The results of the present study showed that in comparison with previously published primer sets, P. aeruginosa infection can be diagnosed with higher sensitivity and specificity by the conventional PCR assay using the newly designed primers. It was also shown that the results of the PCR assay on clinical samples of severe infections became positive much earlier than the results of conventional culture method.
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Affiliation(s)
- Sedighe Rashno Taee
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Arak University of Medical Sciences, Arak, IR Iran
| | - Behzad Khansarinejad
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Arak University of Medical Sciences, Arak, IR Iran
| | - Hamid Abtahi
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Arak University of Medical Sciences, Arak, IR Iran
| | - Mohammad Najafimosleh
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, IR Iran
| | - Ehsanollah Ghaznavi-Rad
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Arak University of Medical Sciences, Arak, IR Iran
- Molecular Research Center, Faculty of Medicine, Arak University of Medical Sciences, Arak, IR Iran
- Corresponding author: Ehsanollah Ghaznavi-Rad, Department of Medical Microbiology, Faculty of Medicine, Arak University of Medical Sciences, Arak, IR Iran. Tel: +98-8634173526, Fax: +98-8634173526, E-mail:
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28
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Fazeli H, Sadighian H, Esfahani BN, Pourmand MR. Molecular epidemiology and mechanisms of antimicrobial resistance in Pseudomonas aeruginosa isolates causing burn wound infection in Iran. J Chemother 2013; 26:222-8. [PMID: 24070432 DOI: 10.1179/1973947813y.0000000132] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
In this study, the contributions of different resistance mechanisms in Pseudomonas aeruginosa isolates were investigated among burned patients. The real-time reverse transcription polymerase chain reaction was performed to determine the expression level of mexY, ampC, and oprD for isolates. Also the isolates were typed by multilocus sequence typing (MLST). Seventy-five per cent of clinical isolates were multidrug resistant. The bla(OXA group-I) and blaPER alleles were identified in 28 and 10 P. aeruginosa isolates, respectively. The majority of bla(PER) positive isolates belonged to the same MLST clone and was identified as ST235. The types of remaining isolates were ST360 and ST861. Among 10 bla(PER) positive isolates, eight isolates demonstrated reduced oprD expression and mexY overexpression. Our data further highlight the epidemic potential of the international clone ST235. According to the results, different resistant mechanisms identified among ST235 isolates that were resistant to ceftazidime, imipenem, ciprofloxacin, and amikacin.
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Deschaght P, Schelstraete P, Van Simaey L, Vanderkercken M, Raman A, Mahieu L, Van daele S, De Baets F, Vaneechoutte M. Is the improvement of CF patients, hospitalized for pulmonary exacerbation, correlated to a decrease in bacterial load? PLoS One 2013; 8:e79010. [PMID: 24312174 PMCID: PMC3843661 DOI: 10.1371/journal.pone.0079010] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 09/19/2013] [Indexed: 02/06/2023] Open
Abstract
Background Cystic Fibrosis (CF) patients are vulnerable to airway colonization with Pseudomonas aeruginosa. In case eradication fails after antibiotic treatment, patients become chronically colonized with P. aeruginosa, with recurrent pulmonary exacerbation, for which patients typically are hospitalized for 2 weeks and receive intravenous antibiotic treatment. Normally, improvement of the patients' health is established. Aim Determination of the correspondence between patient improvement and changes of the P. aeruginosa and total bacterial load in the sputum. Methods Eighteen CF patients with exacerbation were included for a total of 27 hospitalization episodes. At day 1, 8 and 15, inflammation and lung function parameters were determined, together with the P. aeruginosa load in the sputum using culture, quantitative PCR (qPCR) and propidium monoazide qPCR. Results Patients improved during hospitalization (decrease in levels of C-reactive protein, white blood cell counts and erythrocyte sedimentation rate, increase of FEV1), reaching normal values already after one week. Also the P. aeruginosa load and the total bacterial load decreased during the first week of antibiotic treatment (p<0.05), except for patients with a low lung function (FEV1≤39.4%), for whom no significant decrease of P. aeruginosa was established. Comparison of culture-based and propidium monoazide qPCR-based quantification of P. aeruginosa showed that at the end of the treatment on average 62% of the P. aeruginosa cells are not cultivable, indicating that many cells are alive but dormant, or dead but still structurally intact. Conclusion Improvement of the clinical status is accompanied with a decrease of the P. aeruginosa load, whereby both occur mainly during the first week of antibiotic treatment. However, for patients with a low lung function, no decrease of the P. aeruginosa load is observed. Comparison of detection techniques shows that a large amount of noncultivable or dead bacteria are present in the samples.
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Affiliation(s)
- Pieter Deschaght
- Laboratory Bacteriology Research (LBR), Faculty of Medicine & Health Sciences, Universiteit Gent, Ghent, Belgium
| | | | - Leen Van Simaey
- Laboratory Bacteriology Research (LBR), Faculty of Medicine & Health Sciences, Universiteit Gent, Ghent, Belgium
| | | | - Ann Raman
- MucoCenter Ghent, Ghent University Hospital (UZ Gent), Ghent, Belgium
| | - Linda Mahieu
- MucoCenter Ghent, Ghent University Hospital (UZ Gent), Ghent, Belgium
| | - Sabine Van daele
- MucoCenter Ghent, Ghent University Hospital (UZ Gent), Ghent, Belgium
| | - Frans De Baets
- MucoCenter Ghent, Ghent University Hospital (UZ Gent), Ghent, Belgium
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research (LBR), Faculty of Medicine & Health Sciences, Universiteit Gent, Ghent, Belgium
- * E-mail:
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Le Gall F, Le Berre R, Rosec S, Hardy J, Gouriou S, Boisramé-Gastrin S, Vallet S, Rault G, Payan C, Héry-Arnaud G. Proposal of a quantitative PCR-based protocol for an optimal Pseudomonas aeruginosa detection in patients with cystic fibrosis. BMC Microbiol 2013; 13:143. [PMID: 24088260 PMCID: PMC3691768 DOI: 10.1186/1471-2180-13-143] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 06/13/2013] [Indexed: 12/04/2022] Open
Abstract
Background The lung of patients with cystic fibrosis (CF) is particularly sensitive to Pseudomonas aeruginosa. This bacterium plays an important role in the poor outcome of CF patients. During the disease progress, first acquisition of P. aeruginosa is the key-step in the management of CF patients. Quantitative PCR (qPCR) offers an opportunity to detect earlier the first acquisition of P. aeruginosa by CF patients. Given the lack of a validated protocol, our goal was to find an optimal molecular protocol for detection of P. aeruginosa in CF patients. Methods We compared two formerly described qPCR formats in early detection of P. aeruginosa in CF sputum samples: a qPCR targeting oprL gene, and a multiplex PCR targeting gyrB and ecfX genes. Results Tested in vitro on a large panel of P. aeruginosa isolates and others gram-negative bacilli, oprL qPCR exhibited a better sensitivity (threshold of 10 CFU/mL versus 730 CFU/mL), whereas the gyrB/ecfX qPCR exhibited a better specificity (90% versus 73%). These results were validated ex vivo on 46 CF sputum samples positive for P. aeruginosa in culture. Ex vivo assays revealed that qPCR detected 100 times more bacterial cells than culture-based method did. Conclusion Based on these results, we proposed a reference molecular protocol combining the two qPCRs, which offers a sensitivity of 100% with a threshold of 10 CFU/mL and a specificity of 100%. This combined qPCR-based protocol can be adapted and used for other future prospective studies.
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Affiliation(s)
- Florence Le Gall
- EA 3882-Laboratoire de Biodiversité et d'Ecologie Microbienne (LUBEM), SFR 148 ScInBioS, Faculté de Médecine, Université de Brest, Brest F-29200, France.
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Fothergill JL, Ledson MJ, Walshaw MJ, McNamara PS, Southern KW, Winstanley C. Comparison of real time diagnostic chemistries to detect Pseudomonas aeruginosa in respiratory samples from cystic fibrosis patients. J Cyst Fibros 2013; 12:675-81. [PMID: 23726365 DOI: 10.1016/j.jcf.2013.04.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 03/28/2013] [Accepted: 04/19/2013] [Indexed: 11/16/2022]
Abstract
BACKGROUND Early eradication therapy is key to keeping the airways Pseudomonas aeruginosa infection-free and rapid identification is essential. METHODS We used rapid DNA extraction and qPCR assays to detect bacterial, P. aeruginosa and strain-specific targets in samples using two qPCR chemistries. Using 459 respiratory samples from adult and children CF patients, we compared two qPCR methods to culture-based methods in terms of sensitivity and time to result. RESULTS For adult samples, there was 100% concordance between methods. There was no clear pattern in fluctuations in P. aeruginosa number during exacerbation. In child samples, qPCR methods identified additional P. aeruginosa positive samples. The time-to-result was reduced by over 24h and copy number and colony forming unit could differ dramatically in some samples. CONCLUSION If adopted, these methods could significantly improve early P. aeruginosa detection in diagnostic laboratories and therefore play a pivotal role in prolonging infection-free airways in CF patients.
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Affiliation(s)
- J L Fothergill
- NIHR Biomedical Research Centre in Microbial Disease, Royal Liverpool Hospital, Prescott Rd, Liverpool L7 8XP, UK; Institute of Infection and Global Health, University of Liverpool, Ronald Ross Building, West Derby St, Liverpool L69 7BE, UK.
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Robinson KM, Alcorn JF. T-Cell Immunotherapy in Cystic Fibrosis. Am J Respir Crit Care Med 2013; 187:564-6. [DOI: 10.1164/rccm.201212-2201ed] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Passariello C, Lucchese A, Pera F, Gigola P. Clinical, Microbiological and Inflammatory Evidence of the Efficacy of Combination Therapy Including Serratiopeptidase in the Treatment of Periimplantitis. EUR J INFLAMM 2012. [DOI: 10.1177/1721727x1201000322] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The present study was aimed to evaluate the effect of introducing administration of the proteolytic enzyme serratiopeptidase in the combined mechanical-antibiotic treatment of periimplantitis (PI). Two randomized groups of 64 adults with a diagnosis of PI were studied over a 6-month period. All patients were treated with a combined mechanical and antibiotic protocol for 15 days. The experimental group (EG) was administered antibiotic and serratiopeptidase, while the control group was administered antibiotic alone. To evaluate the effects of the two treatment protocols, clinical and radiographic indices, the concentration of IL-lβ, IL-6 and TNF-α in the gingival crevicular fluid, the amount of total bacteria] DNA and the presence of specific bacteria were assessed at baseline and at 6 months from treatment. Success rates of combined treatments at 6 months were 96.9% and 78.1% for the EG and CG respectively ( P≤0.01). Implants of the EG showed greater enhancement of clinical, microbiological and inflammatory parameters as compared to those of the CG. Microbiological analyses showed that resistance to combined therapy was constantly associated with the isolation of bacterial species that are not common periodontal pathogens (mainly S.aureus and P.aeruginosa). The data demonstrate that the addition of serratiopeptidase to combined mechanical-antibiotic treatment protocols of periimplantitis significantly improves outcomes and suggest that serratiopeptidase acts at different levels during the healing process.
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Affiliation(s)
- C. Passariello
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, Rome, Italy
| | - A. Lucchese
- Department of Medical-Surgical Sciences of Communication and Behaviour, School of Dentistry, University of Ferrara, Ferrara, Italy
| | - F. Pera
- Department of Implantology and Prosthetic Dentistry, University of Turin, Turin, Italy
| | - P. Gigola
- Department of Surgical Specialties, Radiologic and Medico-Forensic Sciences University of Brescia, Brescia, Italy
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Rudkjøbing VB, Thomsen TR, Alhede M, Kragh KN, Nielsen PH, Johansen UR, Givskov M, Høiby N, Bjarnsholt T. The microorganisms in chronically infected end-stage and non-end-stage cystic fibrosis patients. ACTA ACUST UNITED AC 2012; 65:236-44. [DOI: 10.1111/j.1574-695x.2011.00925.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 12/12/2011] [Accepted: 12/13/2011] [Indexed: 12/31/2022]
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35
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Adamali H, Armstrong ME, McLaughlin AM, Cooke G, McKone E, Costello CM, Gallagher CG, Leng L, Baugh JA, Fingerle-Rowson G, Bucala RJ, McLoughlin P, Donnelly SC. Macrophage migration inhibitory factor enzymatic activity, lung inflammation, and cystic fibrosis. Am J Respir Crit Care Med 2012; 186:162-9. [PMID: 22592805 DOI: 10.1164/rccm.201110-1864oc] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Macrophage migration inhibitory factor (MIF) is a proinflammatory mediator with unique tautomerase enzymatic activity; the precise function has not been clearly defined. We previously demonstrated that individual patients with cystic fibrosis (CF) who are genetically predisposed to be high MIF producers develop accelerated end-organ injury. OBJECTIVES To characterize the effects of the MIF-CATT polymorphism in patients with CF ex vivo. To investigate the role of MIF's tautomerase activity in a murine model of Pseudomonas aeruginosa infection. METHODS MIF and tumor necrosis factor (TNF)-α protein levels were assessed in plasma or peripheral blood mononuclear cell (PBMC) supernatants by ELISA. A murine pulmonary model of chronic Pseudomonas infection was used in MIF wild-type mice (mif(+/+)) and in tautomerase-null, MIF gene knockin mice (mif (P1G/P1G)). MEASUREMENTS AND MAIN RESULTS MIF protein was measured in plasma and PBMCs from 5- and 6-CATT patients with CF; LPS-induced TNF-α production from PBMCs was also assessed. The effect of a specific inhibitor of MIF-tautomerase activity, ISO-1, was investigated in PBMCs. In the murine infection model, total weight loss, differential cell counts, bacterial load, and intraacinar airspace/tissue volume were measured. MIF and TNF-α levels were increased in 6-CATT compared with 5-CATT patients with CF. LPS-induced TNF-α production from PBMCs was attenuated in the presence of ISO-1. In a murine model of Pseudomonas infection, significantly less pulmonary inflammation and bacterial load was observed in mif(P1G/P1G) compared with mif(+/+) mice. CONCLUSIONS MIF-tautomerase activity may provide a novel therapeutic target in patients with chronic inflammatory diseases such as CF, particularly those patients who are genetically predisposed to produce increased levels of this cytokine.
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Affiliation(s)
- Huzaifa Adamali
- School of Medicine and Medical Science, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
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Frosth S, Slettemeås JS, Jørgensen HJ, Angen Ø, Aspán A. Development and comparison of a real-time PCR assay for detection of Dichelobacter nodosus with culturing and conventional PCR: harmonisation between three laboratories. Acta Vet Scand 2012; 54:6. [PMID: 22293440 PMCID: PMC3292931 DOI: 10.1186/1751-0147-54-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 01/31/2012] [Indexed: 11/15/2022] Open
Abstract
Background Ovine footrot is a contagious disease with worldwide occurrence in sheep. The main causative agent is the fastidious bacterium Dichelobacter nodosus. In Scandinavia, footrot was first diagnosed in Sweden in 2004 and later also in Norway and Denmark. Clinical examination of sheep feet is fundamental to diagnosis of footrot, but D. nodosus should also be detected to confirm the diagnosis. PCR-based detection using conventional PCR has been used at our institutes, but the method was laborious and there was a need for a faster, easier-to-interpret method. The aim of this study was to develop a TaqMan-based real-time PCR assay for detection of D. nodosus and to compare its performance with culturing and conventional PCR. Methods A D. nodosus-specific TaqMan based real-time PCR assay targeting the 16S rRNA gene was designed. The inclusivity and exclusivity (specificity) of the assay was tested using 55 bacterial and two fungal strains. To evaluate the sensitivity and harmonisation of results between different laboratories, aliquots of a single DNA preparation were analysed at three Scandinavian laboratories. The developed real-time PCR assay was compared to culturing by analysing 126 samples, and to a conventional PCR method by analysing 224 samples. A selection of PCR-products was cloned and sequenced in order to verify that they had been identified correctly. Results The developed assay had a detection limit of 3.9 fg of D. nodosus genomic DNA. This result was obtained at all three laboratories and corresponds to approximately three copies of the D. nodosus genome per reaction. The assay showed 100% inclusivity and 100% exclusivity for the strains tested. The real-time PCR assay found 54.8% more positive samples than by culturing and 8% more than conventional PCR. Conclusions The developed real-time PCR assay has good specificity and sensitivity for detection of D. nodosus, and the results are easy to interpret. The method is less time-consuming than either culturing or conventional PCR.
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Szeliga J, Jackowski M, Kłodzińska E, Buszewski B, Kupczyk W. Clinical application of a rapid microbiological test based on capillary zone electrophoresis to assess local skin infection. BMC Res Notes 2011; 4:467. [PMID: 22035265 PMCID: PMC3219748 DOI: 10.1186/1756-0500-4-467] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 10/30/2011] [Indexed: 11/26/2022] Open
Abstract
Background The basic clinical problem associated with infection treatment is the fact that classic, commonly and routinely used isolation and identification methods are based on long-term processes of a phenotypic analysis of microorganisms. Consequently sometimes, especially in small centres, rapid implementation of antibacterial treatment becomes delayed. The work presents the initial results of rapid microbiological identification based on an original method of capillary zone electrophoresis (CZE). The study involved the analysis of 78 biological samples from post-operative wounds and trophic ulcers. Results The attempt was made to identify individual bacterial species based on characteristic features of electropherograms achieved. Finally, G(+) cocci type bacteria and different G(-) rods were identified with sensitivity of 88.1% and specificity of 100%. Conclusions Based on the clinical trials using an electrophoretic technique in the field of microbiological diagnostics of infected exudate from a post-operative wound it can be concluded that it is a rapid and relatively sensitive method for initial identification of infectious pathogens.
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Affiliation(s)
- Jacek Szeliga
- Department of General, Gastroenterological and Oncological Surgery, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, ul, Sw, Jozefa 53/59 PL-87-100 Toruń, Poland.
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Lee CS, Wetzel K, Buckley T, Wozniak D, Lee J. Rapid and sensitive detection of Pseudomonas aeruginosa in chlorinated water and aerosols targeting gyrB gene using real-time PCR. J Appl Microbiol 2011; 111:893-903. [PMID: 21794031 PMCID: PMC3173516 DOI: 10.1111/j.1365-2672.2011.05107.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
AIMS For the rapid detection of Pseudomonas aeruginosa from chlorinated water and aerosols, gyrB gene-based real-time PCR assay was developed and investigated. METHODS AND RESULTS Two novel primer sets (pa722F/746MGB/899R and pa722F/746MGB/788R) were designed using the most updated 611 Pseudomonas and 748 other bacterial gyrB genes for achieving high specificity. Their specificity showed 100% accuracy when tested with various strains including clinical isolates from cystic fibrosis patients. The assay was tested with Ps. aeruginosa-containing chlorinated water and aerosols to simulate the waterborne and airborne transmission routes (detection limit 3·3 × 10² CFU per PCR-2·3 × 10³ CFU per PCR). No chlorine interference in real-time PCR was observed at drinking water level (c. 1 mg l⁻¹), but high level of chorine (12 mg l⁻¹) interfered the assay, and thus neutralization was needed. Pseudomonas aeruginosa in aerosol was successfully detected after capturing with gelatin filters with minimum 2 min of sampling time when the initial concentration of 10⁴ CFU ml⁻¹ bacteria existed in the nebulizer. CONCLUSIONS A highly specific and rapid assay (2-3 h) was developed by targeting gyrB gene for the detection of Ps. aeruginosa in chlorinated water and aerosols, combined with optimized sample collection methods and sample processing, so the direct DNA extraction from either water or aerosol was possible while achieving the desired sensitivity of the method. SIGNIFICANCE AND IMPACT OF THE STUDY The new assay can provide timely and accurate risk assessment to prevent Ps. aeruginosa exposure from water and aerosol, resulting in reduced disease burden, especially among immune-compromised and susceptible individuals. This approach can be easily utilized as a platform technology for the detection of other types of micro-organisms, especially for those that are transmitted via water and aerosol routes, such as Legionella pneumophila.
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Affiliation(s)
- C S Lee
- College of Public Health, Division of Environmental Health Sciences, The Ohio State University, Columbus, OH 43210, USA.
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Deschaght P, Van daele S, De Baets F, Vaneechoutte M. PCR and the detection of Pseudomonas aeruginosa in respiratory samples of CF patients. A literature review. J Cyst Fibros 2011; 10:293-7. [DOI: 10.1016/j.jcf.2011.05.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 05/23/2011] [Accepted: 05/25/2011] [Indexed: 10/18/2022]
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Stressmann FA, Rogers GB, Marsh P, Lilley AK, Daniels TWV, Carroll MP, Hoffman LR, Jones G, Allen CE, Patel N, Forbes B, Tuck A, Bruce KD. Does bacterial density in cystic fibrosis sputum increase prior to pulmonary exacerbation? J Cyst Fibros 2011; 10:357-65. [PMID: 21664196 DOI: 10.1016/j.jcf.2011.05.002] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2011] [Revised: 05/13/2011] [Accepted: 05/15/2011] [Indexed: 01/17/2023]
Abstract
BACKGROUND Cystic Fibrosis (CF) lung disease is characterised by an inexorable decline in lung function, punctuated by periods of symptomatic worsening known as pulmonary exacerbations (referred to here as CFPE). Despite their clinical significance, the cause of CFPE remains undetermined. It has been suggested that an increase in bacterial density may be a trigger, although this has not been shown empirically. METHODS Here, a previously validated quantitative PCR-based approach was used to assess numbers of Pseudomonas aeruginosa and of total bacteria in respiratory secretions from patients during the period leading up to CFPE. Sputum samples collected from 12 adult CF patients were selected retrospectively to fall approximately 21, 14, 7 and 0 days prior to CFPE diagnosis. In addition, the relationships between clinical parameters (FEV(1), temperature and patient reported outcome measures) and microbiological data were investigated. RESULTS No significant changes either in total bacterial or P. aeruginosa numbers were identified prior to CFPE. Of all the correlations tested, only temperature showed a significant correlation with total bacterial numbers in the period leading to CFPE. CONCLUSIONS These findings strongly suggest that CFPE do not generally result from increased bacterial density within the airways. Instead, data presented here are consistent with alternative models of pulmonary exacerbation.
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Affiliation(s)
- Franziska A Stressmann
- Molecular Microbiology Research Laboratory, Institute of Pharmaceutical Sciences, 150 Stamford Street, Franklin-Wilkins Building, King's College London, London, SE1 9NH, UK
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Rogers GB, Marsh P, Stressmann AF, Allen CE, Daniels TVW, Carroll MP, Bruce KD. The exclusion of dead bacterial cells is essential for accurate molecular analysis of clinical samples. Clin Microbiol Infect 2011; 16:1656-8. [PMID: 20148918 DOI: 10.1111/j.1469-0691.2010.03189.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The DNA-based techniques used to detect bacteria in clinical samples are unable to discriminate between live bacteria, dead bacteria, and extracellular DNA. This failure to limit analysis to viable bacterial cells represents a significant problem, leading to false-positive results, as well as a failure to resolve the impact of antimicrobial therapy. The use of propidium monoazide treatment significantly reduces the contribution of dead cells and extracellular DNA to such culture-independent analyses. Here, the increased ability to resolve the impact of antibiotic therapy on Pseudomonas aeruginosa load in cystic fibrosis respiratory samples reveals statistically significant changes that would otherwise go undetected.
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Jangpatarapongsa K, Polpanich D, Yamkamon V, Dittharot Y, Peng-On J, Thiramanas R, Hongeng S, Jootar S, Charoenmak L, Tangboriboonrat P. DNAdetection of chronic myelogenous leukemia by magnetic nanoparticles. Analyst 2011; 136:354-8. [DOI: 10.1039/c0an00374c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Feizabadi MM, Majnooni A, Nomanpour B, Fatolahzadeh B, Raji N, Delfani S, Habibi M, Asadi S, Parvin M. Direct detection of Pseudomonas aeruginosa from patients with healthcare associated pneumonia by real time PCR. INFECTION GENETICS AND EVOLUTION 2010; 10:1247-51. [DOI: 10.1016/j.meegid.2010.08.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 08/09/2010] [Accepted: 08/13/2010] [Indexed: 11/30/2022]
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Jarvis LM, Mulligan K, Dunsford TH, McGowan K, Petrik J. Suitability of an automated nucleic acid extractor (easyMAG) for use with hepatitis C virus and human immunodeficiency virus type 1 nucleic acid amplification testing. J Virol Methods 2010; 171:364-8. [PMID: 21126541 DOI: 10.1016/j.jviromet.2010.11.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 11/16/2010] [Accepted: 11/22/2010] [Indexed: 10/18/2022]
Abstract
Serological screening assays have greatly reduced, but not eliminated, the risk of transmission of viral infections by transfusion of blood and blood products. In addition, the 1999 regulation of the European Agency for the Evaluation of Medicinal Products requiring all plasma for fractionation to have tested negative for hepatitis C virus (HCV) RNA (CPMP/BWP/390/97, 1998) led many blood transfusion services to introduce nucleic acid amplification technology (NAT) to screen blood donations for HCV, and in some services for human immunodeficiency virus (HIV) and hepatitis B virus (HBV). BioMérieux's second-generation system, the NucliSENS easyMAG, was evaluated as a suitable platform for the automated extraction of nucleic acids for use with the existing SNBTS NAT assays. Two nucleic acid extraction protocols were examined, either lysis on the easyMAG (on board) or a 30-min pre-incubation of the sample with lysis buffer at 37 °C (off board). Off board lysis was found to extract nucleic acid more efficiently for both HCV and HIV NAT assays although the improvement was more marked with HIV. The 95% limit of detections (LODs) were 10.11 IU/ml (on board) and 7.21 IU/ml (off board) for HCV and 55.11 IU/ml (on board) and 34.13 (off board) for HIV. Using the more sensitive off board lysis, nucleic acid extraction specificity, robustness and reliability of the easyMAG were examined and over 10,000 Scottish blood donations (in 107 pools of 95 donations) were tested for HCV and HIV in parallel with the existing assay. The results indicate that the easyMAG is a suitable and flexible nucleic acid extraction system, providing high quality nucleic acids and a rapid response alternative to commercial, fully automated, approved blood screening platforms.
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Affiliation(s)
- L M Jarvis
- Scottish National Blood Transfusion Service Transfusion Transmissible Infections Group, Scottish National Blood Transfusion Service, 21 Ellen's Glen Road, Edinburgh EH177QT, United Kingdom.
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Billard-Pomares T, Herwegh S, Wizla-Derambure N, Turck D, Courcol R, Husson MO. Application of quantitative PCR to the diagnosis and monitoring of Pseudomonas aeruginosa colonization in 5-18-year-old cystic fibrosis patients. J Med Microbiol 2010; 60:157-161. [PMID: 20947668 DOI: 10.1099/jmm.0.023838-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Early detection of Pseudomonas aeruginosa and early aggressive treatment are recommended to delay chronic infection in cystic fibrosis (CF) patients. The aim of this study was to assess a quantitative PCR (q-PCR) assay for the diagnosis of early P. aeruginosa colonization in 23 young CF patients (group A, age range 7-18 years) and to survey the eradication of P. aeruginosa in 10 young CF patients (group B, age range 5-18 years) after an initial antibiotic treatment. q-PCR results for consecutive sputum samples from each patient during a period of 18 months were compared with bacterial cultures during the same period plus an additional period of 12 months, and with concomitant clinical signs of pulmonary exacerbation. The q-PCR and bacterial cultures were negative for 17 of the 23 patients in group A and six of the 10 patients in group B during the study period. However, consecutive positive q-PCR results were observed for one patient in group A and three patients in group B, while the bacterial cultures for the same sputum sample remained negative. They preceded positive P. aeruginosa bacterial cultures at 7 and 8 months for two patients in group B. These positive results were associated with a worsening of the clinical status of patients, but pulmonary exacerbation appeared non-specific for the diagnosis of early P. aeruginosa colonization since pulmonary exacerbations were observed in patients in whom q-PCR or bacterial culture remained negative. In conclusion, q-PCR may be a useful additional tool to provide information on the P. aeruginosa status of CF patients.
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Affiliation(s)
| | - Stéphanie Herwegh
- Department of Microbiology, Lille University Hospital, Lille, France
| | - Nathalie Wizla-Derambure
- Cystic Fibrosis Center, Department of Pediatrics, Jeanne de Flandre Lille University Children's Hospital, Lille, France
| | - Dominique Turck
- Inserm 995 Unit, IFR 114, Lille Nord de France University, Lille, France.,Cystic Fibrosis Center, Department of Pediatrics, Jeanne de Flandre Lille University Children's Hospital, Lille, France
| | - René Courcol
- Department of Microbiology, Lille University Hospital, Lille, France
| | - Marie-Odile Husson
- Inserm 995 Unit, IFR 114, Lille Nord de France University, Lille, France.,Cystic Fibrosis Center, Department of Pediatrics, Jeanne de Flandre Lille University Children's Hospital, Lille, France.,Department of Microbiology, Lille University Hospital, Lille, France
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Logan C, Habington A, Lennon G, Cronin F, O'Sullivan N. Evaluation of the efficacy of real-time polymerase chain reaction for the routine early detection of Pseudomonas aeruginosa in cystic fibrosis sputum and throat swab specimens. Diagn Microbiol Infect Dis 2010; 68:358-65. [PMID: 20884156 DOI: 10.1016/j.diagmicrobio.2010.07.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Revised: 07/08/2010] [Accepted: 07/21/2010] [Indexed: 12/19/2022]
Abstract
A longitudinal study of 2099 sputa and throat swabs received from 183 pediatric cystic fibrosis patients over a 29-month period was used to evaluate the efficacy of real-time polymerase chain reaction (PCR) for the early detection of Pseudomonas aeruginosa as compared to microbiologic culture. Real-time PCR resulted in an increased number of specimens identified as P. aeruginosa positive. The sensitivity of culture was 82% (373/453) and of PCR was 93% (420/453) when considering both positive culture and PCR results as true positives. Of the 80 specimens identified as PCR positive/culture negative for P. aeruginosa, the subsequent patient sample in 32.5% (26/80) of specimens concerned was identified as P. aeruginosa culture positive, suggesting that PCR has the potential to detect P. aeruginosa earlier than the microbiologic culture. Real-time PCR analysis found no evidence of the Liverpool and Manchester epidemic P. aeruginosa strains in the cohort examined. The findings of this study highlight the importance of specimen collection protocols to ensure that adequate samples are received at the laboratory for testing, thereby minimizing the potential for reporting of false-negative P. aeruginosa culture results.
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Affiliation(s)
- Catriona Logan
- Department of Microbiology, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland.
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Deschaght P, Schelstraete P, Lopes dos Santos Santiago G, Van Simaey L, Haerynck F, Van Daele S, De Wachter E, Malfroot A, Lebecque P, Knoop C, Casimir G, Boboli H, Pierart F, Desager K, Vaneechoutte M, De Baets F. Comparison of culture and qPCR for the detection of Pseudomonas aeruginosa in not chronically infected cystic fibrosis patients. BMC Microbiol 2010; 10:245. [PMID: 20868481 PMCID: PMC2949703 DOI: 10.1186/1471-2180-10-245] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Accepted: 09/24/2010] [Indexed: 11/15/2022] Open
Abstract
Background Pseudomonas aeruginosa is the major respiratory pathogen causing severe lung infections among CF patients, leading to high morbidity and mortality. Once infection is established, early antibiotic treatment is able to postpone the transition to chronic lung infection. In order to optimize the early detection, we compared the sensitivity of microbiological culture and quantitative PCR (qPCR) for the detection of P. aeruginosa in respiratory samples of not chronically infected CF patients. Results In this national study, we followed CF patients during periods between 1 to 15 months. For a total of 852 samples, 729 (86%) remained P. aeruginosa negative by both culture and qPCR, whereas 89 samples (10%) were positive by both culture and qPCR. Twenty-six samples were negative by culture but positive by qPCR, and 10 samples were positive by culture but remained negative by qPCR. Five of the 26 patients with a culture negative, qPCR positive sample became later P. aeruginosa positive both by culture and qPCR. Conclusion Based on the results of this study, it can be concluded that qPCR may have a predictive value for impending P. aeruginosa infection for only a limited number of patients.
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Affiliation(s)
- Pieter Deschaght
- Laboratory for Bacteriology Research, Ghent University Hospital, Ghent University, Ghent, Belgium.
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Development and application of a loop-mediated isothermal amplification method on rapid detection of Pseudomonas aeruginosa strains. World J Microbiol Biotechnol 2010. [DOI: 10.1007/s11274-010-0429-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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