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Dumont-Leblond N, Veillette M, Racine C, Joubert P, Duchaine C. Development of a robust protocol for the characterization of the pulmonary microbiota. Commun Biol 2021; 4:164. [PMID: 33547364 PMCID: PMC7864980 DOI: 10.1038/s42003-021-01690-5] [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] [Received: 06/04/2020] [Accepted: 01/11/2021] [Indexed: 12/13/2022] Open
Abstract
The lack of methodological standardization diminishes the validity of results obtained and the conclusions drawn when studying the lung microbiota. We report the validation of a complete 16S rRNA gene amplicon sequencing workflow, from patient recruitment to bioinformatics, tailored to the constrains of the pulmonary environment. We minimize the impact of contaminants and establish negative controls to track and account for them at every step. Enzymatic and mechanical homogenization combined to commercially available extraction kits allow for a fast and reliable extraction of bacterial DNA. The DNA extraction kits have a significant impact on the bacterial composition of the controls. The bacterial signatures of extracted cancerous and healthy human tissues from 5 patients are highly distinguishable from methodological controls. Our work expands our understanding of low microbial burdened environments analysis. This article is to be a starting point towards methodological standardization and the implementation of proper sampling procedures in the study of lung microbiota. Nathan Dumont-Leblond et al. present a protocol for lung microbiota analysis, including all steps from patient recruitment to bioinformatics. The data show how methodological variation, such as use of different DNA extraction kits, can impact the results and represent an important step toward methods standardization in the pulmonary microbiome field.
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Affiliation(s)
- Nathan Dumont-Leblond
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC, Canada.,Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC, Canada
| | - Marc Veillette
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC, Canada
| | - Christine Racine
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC, Canada
| | - Philippe Joubert
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC, Canada.,Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Université Laval, Quebec City, QC, Canada
| | - Caroline Duchaine
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC, Canada. .,Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC, Canada.
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Farraj SA, El-Kafrawy SA, Kumosani TA, Yousef JM, Azhar EI. Evaluation of Extraction Methods for Clinical Metagenomic Assay. Microorganisms 2020; 8:microorganisms8081128. [PMID: 32727010 PMCID: PMC7465710 DOI: 10.3390/microorganisms8081128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/23/2020] [Accepted: 07/25/2020] [Indexed: 02/02/2023] Open
Abstract
(1) Background: Clinical metagenomics is a promising approach that helps to identify etiological agents in cases of unknown infections. For the efficient detection of an unknown pathogen, the extraction method must be carefully selected for the maximum recovery of nucleic acid from different microorganisms. The aim of this study was to evaluate different extraction methods that have the ability to isolate nucleic acids from different types of pathogens with good quality and quantity for efficient use in clinical metagenomic identification. (2) Methods: A mock sample spiked with five different pathogens was used for the comparative evaluation of different commercial extraction kits. Extracted samples were subjected to library preparation and run on MiSeq. The selected extraction method based on the outcome of the comparative evaluation was used subsequently for the nucleic acid isolation of all infectious agents in clinical respiratory samples with multiple infections. (3) Results: The protocol using the PowerViral® Environmental RNA-DNA Isolation Kit with a 5-min bead beating step achieved the best results with a low starting volume. The analysis of the tested clinical specimens showed the ability to successfully identify different types of pathogens. (4) Conclusions: The optimized extraction protocol in this study is recommended for clinical metagenomics application in specimens with multiple infections from different taxa.
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Affiliation(s)
- Suha A. Farraj
- Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (S.A.F.); (T.A.K.); (J.M.Y.)
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Shreif A. El-Kafrawy
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Clinical Pathology Department, National Liver Institute, Menoufia University, Shebin El-Kom 32511, Egypt
- Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Taha A. Kumosani
- Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (S.A.F.); (T.A.K.); (J.M.Y.)
- Central Laboratory for Food and Nutrition, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Jehad M. Yousef
- Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (S.A.F.); (T.A.K.); (J.M.Y.)
- Department of Biochemistry, College of Sciences, University of Jeddah, Jeddah 23890, Saudi Arabia
| | - Esam I. Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Correspondence:
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Alotaibi NM, Chen V, Hollander Z, Leipsic JA, Hague CJ, Murphy DT, DeMarco ML, FitzGerald JM, McManus BM, Ng RT, Sin DD. Phenotyping and outcomes of hospitalized COPD patients using rapid molecular diagnostics on sputum samples. Int J Chron Obstruct Pulmon Dis 2019; 14:311-319. [PMID: 30774328 PMCID: PMC6350828 DOI: 10.2147/copd.s188186] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Background Etiologies of acute exacerbations of chronic obstructive pulmonary disease (AECOPD) are heterogeneous. We phenotyped severe AECOPD based on molecular pathogen detection of sputum samples collected at hospitalization of COPD patients and determined their outcomes. Methods We phenotyped 72 sputum samples of COPD patients who were hospitalized with a primary diagnosis of AECOPD using a molecular array that detected common bacterial and viral respiratory pathogens. Based on these results, the patients were classified into positive or negative pathogen groups. The pathogen-positive group was further divided into virus or bacteria subgroups. Admission day 1 blood samples were assayed for N-terminal prohormone brain natriuretic peptide, CRP, and complete blood counts. Results A total of 52 patients had a positive result on the array, while 20 patients had no pathogens detected. The most common bacterial pathogen detected was Haemophilus influenzae and the most common virus was rhinovirus. The pathogen-negative group had the worse outcomes with longer hospital stays (median 6.5 vs 5 days for bacteria-positive group, P=0.02) and a trend toward increased 1-year mortality (P=0.052). The bacteria-positive group had the best prognosis, whereas the virus-positive group had outcomes somewhere in between the bacteria-positive and pathogen-negative groups. Conclusion Molecular diagnostics on sputum can rapidly phenotype serious AECOPD into bacteria-, virus-, or pathogen-negative groups. The bacteria-positive group appears to have the best prognosis, while pathogen-negative group has the worst. These data suggest that AECOPD is a heterogeneous event and that accurate phenotyping of AECOPD may lead to novel management strategies that are personalized and more precise.
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Affiliation(s)
- Nawaf M Alotaibi
- Centre for Heart Lung Innovation, James Hogg Research Centre, St Paul's Hospital, Vancouver, BC, Canada, .,Department of Medicine, Division of Pulmonary Medicine, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Virginia Chen
- Centre for Heart Lung Innovation, James Hogg Research Centre, St Paul's Hospital, Vancouver, BC, Canada, .,Institute for Heart and Lung Health, Vancouver, BC, Canada, .,PROOF Centre of Excellence, Vancouver, BC, Canada
| | - Zsuzsanna Hollander
- Centre for Heart Lung Innovation, James Hogg Research Centre, St Paul's Hospital, Vancouver, BC, Canada, .,Institute for Heart and Lung Health, Vancouver, BC, Canada, .,PROOF Centre of Excellence, Vancouver, BC, Canada
| | | | - Cameron J Hague
- Department of Radiology, St Paul's Hospital, Vancouver, BC, Canada
| | - Darra T Murphy
- Department of Radiology, St Paul's Hospital, Vancouver, BC, Canada
| | - Mari L DeMarco
- Centre for Heart Lung Innovation, James Hogg Research Centre, St Paul's Hospital, Vancouver, BC, Canada, .,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - J M FitzGerald
- Institute for Heart and Lung Health, Vancouver, BC, Canada, .,Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada, .,The Lung Centre, Vancouver General Hospital, Vancouver, BC, Canada
| | - Bruce M McManus
- Centre for Heart Lung Innovation, James Hogg Research Centre, St Paul's Hospital, Vancouver, BC, Canada, .,Institute for Heart and Lung Health, Vancouver, BC, Canada, .,PROOF Centre of Excellence, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Raymond T Ng
- PROOF Centre of Excellence, Vancouver, BC, Canada.,Department of Computer Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Don D Sin
- Centre for Heart Lung Innovation, James Hogg Research Centre, St Paul's Hospital, Vancouver, BC, Canada, .,Institute for Heart and Lung Health, Vancouver, BC, Canada, .,Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, BC, Canada,
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Webb JR, Price EP, Somprasong N, Schweizer HP, Baird RW, Currie BJ, Sarovich DS. Development and validation of a triplex quantitative real-time PCR assay to detect efflux pump-mediated antibiotic resistance in Burkholderia pseudomallei. Future Microbiol 2018; 13:1403-1418. [PMID: 30256166 PMCID: PMC6190177 DOI: 10.2217/fmb-2018-0155] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/23/2018] [Indexed: 01/12/2023] Open
Abstract
AIM To develop a probe-based triplex quantitative real-time PCR assay to simultaneously detect the upregulation of the efflux pumps AmrAB-OprA, BpeAB-OprB and BpeEF-OprC in Burkholderia pseudomallei strains exhibiting increased minimum inhibitory concentrations toward meropenem, doxycycline or trimethoprim-sulfamethoxazole. METHODS The triplex assay was developed and subsequently tested on RNA isolated from eight clinical and eight laboratory-generated B. pseudomallei mutants harboring efflux pump regulator mutations. RESULTS The triplex assay accurately detected efflux pump upregulation in all clinical and laboratory mutants, which corresponded with decreased antibiotic susceptibility or antibiotic resistance. CONCLUSION Rapid detection of antibiotic resistance provides clinicians with a tool to identify potential treatment failure in near real time, enabling informed alteration of treatment during an infection and improved patient outcomes.
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Affiliation(s)
- Jessica R Webb
- Global & Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Erin P Price
- Global & Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Nawarat Somprasong
- Department of Molecular Genetics & Microbiology, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Herbert P Schweizer
- Department of Molecular Genetics & Microbiology, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Robert W Baird
- Departments of Infectious Diseases & Pathology & Northern Territory Medical Program, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Bart J Currie
- Global & Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- Departments of Infectious Diseases & Pathology & Northern Territory Medical Program, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Derek S Sarovich
- Global & Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
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Liu W, Das J, Mepham AH, Nemr CR, Sargent EH, Kelley SO. A fully-integrated and automated testing device for PCR-free viral nucleic acid detection in whole blood. LAB ON A CHIP 2018; 18:1928-1935. [PMID: 29881833 DOI: 10.1039/c8lc00371h] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Integrated devices for automated nucleic acid testing (NAT) are critical for infectious disease diagnosis to be performed outside of centralized laboratories. The gold standard methods for NAT are enzymatic amplification methods like the polymerase chain reaction that typically require expensive equipment and highly-trained personnel, limiting use in low-resource settings. A low-cost, integrated, rapid, portable and user-friendly point-of-care (POC) nucleic acid diagnostic device will improve the accessibility of NAT. Here, we present a fully integrated and simple-to-use POC device operated by a passive fluidic method that is able to perform a sequential multi-step assay to detect viral nucleic acids in blood. This simple device enabled the rapid detection of hepatitis C virus in blood in approximately 30 minutes with minimal sample handling by the user.
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Affiliation(s)
- Wenhan Liu
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, M5S 3G9 Canada.
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