Demonstration of a fast and easy sample-to-answer protocol for tuberculosis screening in point-of-care settings: A proof of concept study

We sought to develop a smooth and low cost sample preparation and DNA extraction protocol, streamlined with a ready-to-use qPCR in a portable instrument to overcome some of the existing hurdles. Several solutions were evaluated as to their ability to liquefy a mucin-based matrix. Each liquefied matr...

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Veröffentlicht in:PloS one 2020-12, Vol.15 (12), p.e0242408-e0242408
Hauptverfasser: Ali, Nasir, Bello, Graziele Lima, Rossetti, Maria Lúcia Rosa, Krieger, Marco Aurelio, Costa, Alexandre Dias Tavares
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container_end_page e0242408
container_issue 12
container_start_page e0242408
container_title PloS one
container_volume 15
creator Ali, Nasir
Bello, Graziele Lima
Rossetti, Maria Lúcia Rosa
Krieger, Marco Aurelio
Costa, Alexandre Dias Tavares
description We sought to develop a smooth and low cost sample preparation and DNA extraction protocol, streamlined with a ready-to-use qPCR in a portable instrument to overcome some of the existing hurdles. Several solutions were evaluated as to their ability to liquefy a mucin-based matrix. Each liquefied matrix, supplemented with either Mycobacterium tuberculosis (MTB) H37Rv strain DNA or intact cells, was aliquoted onto a filter paper embedded with solubilizing agents, and was subsequently dried up. Most of the nucleic acids, including genomic DNA from the bacilli and the host, binds to the filter paper. Next, several protocols were evaluated to elute the DNA from the paper, using qPCR to detect the insertion sequence IS6110, a M. tuberculosis complex genomic marker. The limit of detection (LOD) of the best protocol was then evaluated using parallel seeding and colony counting. The protocol was also evaluated using seventeen sputum samples, previously characterized by the GeneXpert or culture. Two instruments (the ABI7500 Standard and the Q3-Plus system) and two reagents storage formats (frozen or ready-to-use) were evaluated. Solutions containing guanidine isothiocyanate exerted the best liquefying effect on the mucin-based matrix extracted from one 6-mm punches, followed by a brief incubation at 95°C. The resulting DNA contained impurities, but a simple 1:10 dilution elicited the detection of MTB and human genomic targets. The described protocol presented an apparent LOD of 02 CFU/mL of MTB. Challenging the protocol with previously characterized samples showed substantial agreement with GeneXpert MTB/RIF results (sensitivity of 90%, agreement of 88.9%, kappa coefficient of 0.77), and moderate agreement with culture results (sensitivity of 100%, agreement of 78.9%, kappa coefficient of 0.58). This work presents a sensitive proof-of-concept protocol for sputum liquefaction and decontamination followed by a simple DNA extraction procedure, in which the extraction steps are streamlined with a ready-to-use qPCR in a portable instrument that can be employed in low infrastructure settings.
doi_str_mv 10.1371/journal.pone.0242408
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Several solutions were evaluated as to their ability to liquefy a mucin-based matrix. Each liquefied matrix, supplemented with either Mycobacterium tuberculosis (MTB) H37Rv strain DNA or intact cells, was aliquoted onto a filter paper embedded with solubilizing agents, and was subsequently dried up. Most of the nucleic acids, including genomic DNA from the bacilli and the host, binds to the filter paper. Next, several protocols were evaluated to elute the DNA from the paper, using qPCR to detect the insertion sequence IS6110, a M. tuberculosis complex genomic marker. The limit of detection (LOD) of the best protocol was then evaluated using parallel seeding and colony counting. The protocol was also evaluated using seventeen sputum samples, previously characterized by the GeneXpert or culture. Two instruments (the ABI7500 Standard and the Q3-Plus system) and two reagents storage formats (frozen or ready-to-use) were evaluated. 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This work presents a sensitive proof-of-concept protocol for sputum liquefaction and decontamination followed by a simple DNA extraction procedure, in which the extraction steps are streamlined with a ready-to-use qPCR in a portable instrument that can be employed in low infrastructure settings.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0242408</identifier><identifier>PMID: 33315885</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Bacilli ; Biology and Life Sciences ; Brazil ; Cell culture ; Costs ; Culture ; Decontamination ; Deoxyribonucleic acid ; Diagnosis ; Dilution ; DNA ; DNA, Bacterial - isolation &amp; purification ; Filter paper ; Genomics ; Guanidine ; Humans ; Impurities ; Isothiocyanate ; Leprosy ; Limit of Detection ; Liquefaction ; Mass Screening - economics ; Mass Screening - instrumentation ; Mass Screening - methods ; Medical diagnosis ; Medical screening ; Medical tests ; Medicine and Health Sciences ; Methods ; Microscopy ; Mucin ; Mycobacterium tuberculosis - genetics ; Mycobacterium tuberculosis - isolation &amp; purification ; Nucleic acids ; Nucleotide sequence ; Physical Sciences ; Point-of-Care Systems ; Proof of Concept Study ; Punches ; Reagents ; Real-Time Polymerase Chain Reaction - economics ; Real-Time Polymerase Chain Reaction - instrumentation ; Real-Time Polymerase Chain Reaction - methods ; Research and analysis methods ; Sample preparation ; Sensitivity ; Specimen Handling - economics ; Specimen Handling - methods ; Sputum ; Sputum - microbiology ; Tuberculosis ; Tuberculosis, Pulmonary - diagnosis ; Tuberculosis, Pulmonary - microbiology ; Viscosity</subject><ispartof>PloS one, 2020-12, Vol.15 (12), p.e0242408-e0242408</ispartof><rights>COPYRIGHT 2020 Public Library of Science</rights><rights>2020 Ali et al. 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Several solutions were evaluated as to their ability to liquefy a mucin-based matrix. Each liquefied matrix, supplemented with either Mycobacterium tuberculosis (MTB) H37Rv strain DNA or intact cells, was aliquoted onto a filter paper embedded with solubilizing agents, and was subsequently dried up. Most of the nucleic acids, including genomic DNA from the bacilli and the host, binds to the filter paper. Next, several protocols were evaluated to elute the DNA from the paper, using qPCR to detect the insertion sequence IS6110, a M. tuberculosis complex genomic marker. The limit of detection (LOD) of the best protocol was then evaluated using parallel seeding and colony counting. The protocol was also evaluated using seventeen sputum samples, previously characterized by the GeneXpert or culture. Two instruments (the ABI7500 Standard and the Q3-Plus system) and two reagents storage formats (frozen or ready-to-use) were evaluated. Solutions containing guanidine isothiocyanate exerted the best liquefying effect on the mucin-based matrix extracted from one 6-mm punches, followed by a brief incubation at 95°C. The resulting DNA contained impurities, but a simple 1:10 dilution elicited the detection of MTB and human genomic targets. The described protocol presented an apparent LOD of 02 CFU/mL of MTB. Challenging the protocol with previously characterized samples showed substantial agreement with GeneXpert MTB/RIF results (sensitivity of 90%, agreement of 88.9%, kappa coefficient of 0.77), and moderate agreement with culture results (sensitivity of 100%, agreement of 78.9%, kappa coefficient of 0.58). This work presents a sensitive proof-of-concept protocol for sputum liquefaction and decontamination followed by a simple DNA extraction procedure, in which the extraction steps are streamlined with a ready-to-use qPCR in a portable instrument that can be employed in low infrastructure settings.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>33315885</pmid><doi>10.1371/journal.pone.0242408</doi><tpages>e0242408</tpages><orcidid>https://orcid.org/0000-0001-8434-2152</orcidid><oa>free_for_read</oa></addata></record>
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identifier ISSN: 1932-6203
ispartof PloS one, 2020-12, Vol.15 (12), p.e0242408-e0242408
issn 1932-6203
1932-6203
language eng
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source MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Public Library of Science (PLoS); PubMed Central; Free Full-Text Journals in Chemistry
subjects Bacilli
Biology and Life Sciences
Brazil
Cell culture
Costs
Culture
Decontamination
Deoxyribonucleic acid
Diagnosis
Dilution
DNA
DNA, Bacterial - isolation & purification
Filter paper
Genomics
Guanidine
Humans
Impurities
Isothiocyanate
Leprosy
Limit of Detection
Liquefaction
Mass Screening - economics
Mass Screening - instrumentation
Mass Screening - methods
Medical diagnosis
Medical screening
Medical tests
Medicine and Health Sciences
Methods
Microscopy
Mucin
Mycobacterium tuberculosis - genetics
Mycobacterium tuberculosis - isolation & purification
Nucleic acids
Nucleotide sequence
Physical Sciences
Point-of-Care Systems
Proof of Concept Study
Punches
Reagents
Real-Time Polymerase Chain Reaction - economics
Real-Time Polymerase Chain Reaction - instrumentation
Real-Time Polymerase Chain Reaction - methods
Research and analysis methods
Sample preparation
Sensitivity
Specimen Handling - economics
Specimen Handling - methods
Sputum
Sputum - microbiology
Tuberculosis
Tuberculosis, Pulmonary - diagnosis
Tuberculosis, Pulmonary - microbiology
Viscosity
title Demonstration of a fast and easy sample-to-answer protocol for tuberculosis screening in point-of-care settings: A proof of concept study
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