Genetic identification and drug-resistance characterization of mycobacterium tuberculosis using a portable sequencing device. A pilot study

Autores
Cervantes, Jorge; Yokobori, Noemí; Hong, Bo Young
Año de publicación
2020
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Clinical management of tuberculosis (TB) in endemic areas is often challenged by a lack of resources including laboratories for Mycobacterium tuberculosis (Mtb) culture. Traditional phenotypic drug susceptibility testing for Mtb is costly and time consuming, while PCR-based methods are limited to selected target loci. We herein utilized a portable, USB-powered, long-read sequencing instrument (MinION), to investigate Mtb genomic DNA from clinical isolates to determine the presence of anti-TB drug-resistance conferring mutations. Data analysis platform EPI2ME and antibiotic-resistance analysis using the real time ARMA workflow, identified Mtb species as well as extensive resistance gene profiles. The approach was highly sensitive, being able to detect almost all described drug resistance conferring mutations based on previous whole genome sequencing analysis. Our findings are supportive of the practical use of this system as a suitable method for the detection of antimicrobial resistance genes, and effective in providing Mtb genomic information. Future improvements in the error rate through statistical analysis, drug resistance prediction algorithms and reference databases would make this a platform suited for the clinical setting. The small size, relatively inexpensive cost of the device, as well as its rapid and simple library preparation protocol and analysis, make it an attractive option for settings with limited laboratory infrastructure.
Fil: Cervantes, Jorge. Texas Tech University Health Sciences Center; Estados Unidos
Fil: Yokobori, Noemí. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Hong, Bo Young. The Jackson Laboratory for Genomic Medicine; Estados Unidos
Materia
DRUG RESISTANCE
MINION
NEXT-GENERATION SEQUENCING
TUBERCULOSIS
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/170039
Acceder
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network_name_str CONICET Digital (CONICET)
spelling Genetic identification and drug-resistance characterization of mycobacterium tuberculosis using a portable sequencing device. A pilot studyCervantes, JorgeYokobori, NoemíHong, Bo YoungDRUG RESISTANCEMINIONNEXT-GENERATION SEQUENCINGTUBERCULOSIShttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Clinical management of tuberculosis (TB) in endemic areas is often challenged by a lack of resources including laboratories for Mycobacterium tuberculosis (Mtb) culture. Traditional phenotypic drug susceptibility testing for Mtb is costly and time consuming, while PCR-based methods are limited to selected target loci. We herein utilized a portable, USB-powered, long-read sequencing instrument (MinION), to investigate Mtb genomic DNA from clinical isolates to determine the presence of anti-TB drug-resistance conferring mutations. Data analysis platform EPI2ME and antibiotic-resistance analysis using the real time ARMA workflow, identified Mtb species as well as extensive resistance gene profiles. The approach was highly sensitive, being able to detect almost all described drug resistance conferring mutations based on previous whole genome sequencing analysis. Our findings are supportive of the practical use of this system as a suitable method for the detection of antimicrobial resistance genes, and effective in providing Mtb genomic information. Future improvements in the error rate through statistical analysis, drug resistance prediction algorithms and reference databases would make this a platform suited for the clinical setting. The small size, relatively inexpensive cost of the device, as well as its rapid and simple library preparation protocol and analysis, make it an attractive option for settings with limited laboratory infrastructure.Fil: Cervantes, Jorge. Texas Tech University Health Sciences Center; Estados UnidosFil: Yokobori, Noemí. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Hong, Bo Young. The Jackson Laboratory for Genomic Medicine; Estados UnidosMDPI AG2020-09info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/170039Cervantes, Jorge; Yokobori, Noemí; Hong, Bo Young; Genetic identification and drug-resistance characterization of mycobacterium tuberculosis using a portable sequencing device. A pilot study; MDPI AG; Antibiotics; 9; 9; 9-2020; 1-152079-6382CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.mdpi.com/2079-6382/9/9/548info:eu-repo/semantics/altIdentifier/doi/10.3390/antibiotics9090548info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T10:06:45Zoai:ri.conicet.gov.ar:11336/170039instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-03 10:06:45.994CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Genetic identification and drug-resistance characterization of mycobacterium tuberculosis using a portable sequencing device. A pilot study
title Genetic identification and drug-resistance characterization of mycobacterium tuberculosis using a portable sequencing device. A pilot study
spellingShingle Genetic identification and drug-resistance characterization of mycobacterium tuberculosis using a portable sequencing device. A pilot study
Cervantes, Jorge
DRUG RESISTANCE
MINION
NEXT-GENERATION SEQUENCING
TUBERCULOSIS
title_short Genetic identification and drug-resistance characterization of mycobacterium tuberculosis using a portable sequencing device. A pilot study
title_full Genetic identification and drug-resistance characterization of mycobacterium tuberculosis using a portable sequencing device. A pilot study
title_fullStr Genetic identification and drug-resistance characterization of mycobacterium tuberculosis using a portable sequencing device. A pilot study
title_full_unstemmed Genetic identification and drug-resistance characterization of mycobacterium tuberculosis using a portable sequencing device. A pilot study
title_sort Genetic identification and drug-resistance characterization of mycobacterium tuberculosis using a portable sequencing device. A pilot study
dc.creator.none.fl_str_mv Cervantes, Jorge
Yokobori, Noemí
Hong, Bo Young
author Cervantes, Jorge
author_facet Cervantes, Jorge
Yokobori, Noemí
Hong, Bo Young
author_role author
author2 Yokobori, Noemí
Hong, Bo Young
author2_role author
author
dc.subject.none.fl_str_mv DRUG RESISTANCE
MINION
NEXT-GENERATION SEQUENCING
TUBERCULOSIS
topic DRUG RESISTANCE
MINION
NEXT-GENERATION SEQUENCING
TUBERCULOSIS
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Clinical management of tuberculosis (TB) in endemic areas is often challenged by a lack of resources including laboratories for Mycobacterium tuberculosis (Mtb) culture. Traditional phenotypic drug susceptibility testing for Mtb is costly and time consuming, while PCR-based methods are limited to selected target loci. We herein utilized a portable, USB-powered, long-read sequencing instrument (MinION), to investigate Mtb genomic DNA from clinical isolates to determine the presence of anti-TB drug-resistance conferring mutations. Data analysis platform EPI2ME and antibiotic-resistance analysis using the real time ARMA workflow, identified Mtb species as well as extensive resistance gene profiles. The approach was highly sensitive, being able to detect almost all described drug resistance conferring mutations based on previous whole genome sequencing analysis. Our findings are supportive of the practical use of this system as a suitable method for the detection of antimicrobial resistance genes, and effective in providing Mtb genomic information. Future improvements in the error rate through statistical analysis, drug resistance prediction algorithms and reference databases would make this a platform suited for the clinical setting. The small size, relatively inexpensive cost of the device, as well as its rapid and simple library preparation protocol and analysis, make it an attractive option for settings with limited laboratory infrastructure.
Fil: Cervantes, Jorge. Texas Tech University Health Sciences Center; Estados Unidos
Fil: Yokobori, Noemí. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Hong, Bo Young. The Jackson Laboratory for Genomic Medicine; Estados Unidos
description Clinical management of tuberculosis (TB) in endemic areas is often challenged by a lack of resources including laboratories for Mycobacterium tuberculosis (Mtb) culture. Traditional phenotypic drug susceptibility testing for Mtb is costly and time consuming, while PCR-based methods are limited to selected target loci. We herein utilized a portable, USB-powered, long-read sequencing instrument (MinION), to investigate Mtb genomic DNA from clinical isolates to determine the presence of anti-TB drug-resistance conferring mutations. Data analysis platform EPI2ME and antibiotic-resistance analysis using the real time ARMA workflow, identified Mtb species as well as extensive resistance gene profiles. The approach was highly sensitive, being able to detect almost all described drug resistance conferring mutations based on previous whole genome sequencing analysis. Our findings are supportive of the practical use of this system as a suitable method for the detection of antimicrobial resistance genes, and effective in providing Mtb genomic information. Future improvements in the error rate through statistical analysis, drug resistance prediction algorithms and reference databases would make this a platform suited for the clinical setting. The small size, relatively inexpensive cost of the device, as well as its rapid and simple library preparation protocol and analysis, make it an attractive option for settings with limited laboratory infrastructure.
publishDate 2020
dc.date.none.fl_str_mv 2020-09
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/170039
Cervantes, Jorge; Yokobori, Noemí; Hong, Bo Young; Genetic identification and drug-resistance characterization of mycobacterium tuberculosis using a portable sequencing device. A pilot study; MDPI AG; Antibiotics; 9; 9; 9-2020; 1-15
2079-6382
CONICET Digital
CONICET
url http://hdl.handle.net/11336/170039
identifier_str_mv Cervantes, Jorge; Yokobori, Noemí; Hong, Bo Young; Genetic identification and drug-resistance characterization of mycobacterium tuberculosis using a portable sequencing device. A pilot study; MDPI AG; Antibiotics; 9; 9; 9-2020; 1-15
2079-6382
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://www.mdpi.com/2079-6382/9/9/548
info:eu-repo/semantics/altIdentifier/doi/10.3390/antibiotics9090548
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv MDPI AG
publisher.none.fl_str_mv MDPI AG
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.13397

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