Implementation of whole genome sequencing for tuberculosis diagnostics in a low-middle income, high MDR-TB burden country

Abstract Whole genome sequencing (WGS) is revolutionary for diagnostics of TB and its mutations associated with drug-resistances, but its uptake in low- and middle-income countries is hindered by concerns of implementation feasibility. Here, we provide a proof of concept for its successful implement...

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Autores principales:	Monica Vogel, Christian Utpatel, Caroline Corbett, Thomas A. Kohl, Altyn Iskakova, Sevim Ahmedov, Uladzimir Antonenka, Viola Dreyer, Ainura Ibrahimova, Chynara Kamarli, Dilorom Kosimova, Vanessa Mohr, Evgeni Sahalchyk, Meerim Sydykova, Nagira Umetalieva, Abdylat Kadyrov, Gulmira Kalmambetova, Stefan Niemann, Harald Hoffmann
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/3e5fcabad3dd49d4ae4aea89d3f6fd40
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spelling	oai:doaj.org-article:3e5fcabad3dd49d4ae4aea89d3f6fd402021-12-02T16:31:02ZImplementation of whole genome sequencing for tuberculosis diagnostics in a low-middle income, high MDR-TB burden country10.1038/s41598-021-94297-z2045-2322https://doaj.org/article/3e5fcabad3dd49d4ae4aea89d3f6fd402021-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-94297-zhttps://doaj.org/toc/2045-2322Abstract Whole genome sequencing (WGS) is revolutionary for diagnostics of TB and its mutations associated with drug-resistances, but its uptake in low- and middle-income countries is hindered by concerns of implementation feasibility. Here, we provide a proof of concept for its successful implementation in such a setting. WGS was implemented in the Kyrgyz Republic. We estimated needs of up to 55 TB-WGS per week and chose the MiSeq platform (Illumina, USA) because of its capacity of up to 60 TB-WGS per week. The project’s timeline was completed in 93-weeks. Costs of large equipment and accompanying costs were 222,065 USD and 8462 USD, respectively. The first 174 WGS costed 277 USD per sequence, but this was skewed by training inefficiencies. Based on real prices and presuming optimal utilization of WGS capacities, WGS costs could drop to 167 and 141 USD per WGS using MiSeq Reagent Kits v2 (500-cycles) and v3 (600-cycles), respectively. Five trainings were required to prepare the staff for autonomous WGS which cost 48,250 USD. External assessment confirmed excellent performance of WGS by the Kyrgyz laboratory in an interlaboratory comparison of 30 M. tuberculosis genomes showing complete agreeance of results.Monica VogelChristian UtpatelCaroline CorbettThomas A. KohlAltyn IskakovaSevim AhmedovUladzimir AntonenkaViola DreyerAinura IbrahimovaChynara KamarliDilorom KosimovaVanessa MohrEvgeni SahalchykMeerim SydykovaNagira UmetalievaAbdylat KadyrovGulmira KalmambetovaStefan NiemannHarald HoffmannNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-9 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Monica Vogel Christian Utpatel Caroline Corbett Thomas A. Kohl Altyn Iskakova Sevim Ahmedov Uladzimir Antonenka Viola Dreyer Ainura Ibrahimova Chynara Kamarli Dilorom Kosimova Vanessa Mohr Evgeni Sahalchyk Meerim Sydykova Nagira Umetalieva Abdylat Kadyrov Gulmira Kalmambetova Stefan Niemann Harald Hoffmann Implementation of whole genome sequencing for tuberculosis diagnostics in a low-middle income, high MDR-TB burden country
description	Abstract Whole genome sequencing (WGS) is revolutionary for diagnostics of TB and its mutations associated with drug-resistances, but its uptake in low- and middle-income countries is hindered by concerns of implementation feasibility. Here, we provide a proof of concept for its successful implementation in such a setting. WGS was implemented in the Kyrgyz Republic. We estimated needs of up to 55 TB-WGS per week and chose the MiSeq platform (Illumina, USA) because of its capacity of up to 60 TB-WGS per week. The project’s timeline was completed in 93-weeks. Costs of large equipment and accompanying costs were 222,065 USD and 8462 USD, respectively. The first 174 WGS costed 277 USD per sequence, but this was skewed by training inefficiencies. Based on real prices and presuming optimal utilization of WGS capacities, WGS costs could drop to 167 and 141 USD per WGS using MiSeq Reagent Kits v2 (500-cycles) and v3 (600-cycles), respectively. Five trainings were required to prepare the staff for autonomous WGS which cost 48,250 USD. External assessment confirmed excellent performance of WGS by the Kyrgyz laboratory in an interlaboratory comparison of 30 M. tuberculosis genomes showing complete agreeance of results.
format	article
author	Monica Vogel Christian Utpatel Caroline Corbett Thomas A. Kohl Altyn Iskakova Sevim Ahmedov Uladzimir Antonenka Viola Dreyer Ainura Ibrahimova Chynara Kamarli Dilorom Kosimova Vanessa Mohr Evgeni Sahalchyk Meerim Sydykova Nagira Umetalieva Abdylat Kadyrov Gulmira Kalmambetova Stefan Niemann Harald Hoffmann
author_facet	Monica Vogel Christian Utpatel Caroline Corbett Thomas A. Kohl Altyn Iskakova Sevim Ahmedov Uladzimir Antonenka Viola Dreyer Ainura Ibrahimova Chynara Kamarli Dilorom Kosimova Vanessa Mohr Evgeni Sahalchyk Meerim Sydykova Nagira Umetalieva Abdylat Kadyrov Gulmira Kalmambetova Stefan Niemann Harald Hoffmann
author_sort	Monica Vogel
title	Implementation of whole genome sequencing for tuberculosis diagnostics in a low-middle income, high MDR-TB burden country
title_short	Implementation of whole genome sequencing for tuberculosis diagnostics in a low-middle income, high MDR-TB burden country
title_full	Implementation of whole genome sequencing for tuberculosis diagnostics in a low-middle income, high MDR-TB burden country
title_fullStr	Implementation of whole genome sequencing for tuberculosis diagnostics in a low-middle income, high MDR-TB burden country
title_full_unstemmed	Implementation of whole genome sequencing for tuberculosis diagnostics in a low-middle income, high MDR-TB burden country
title_sort	implementation of whole genome sequencing for tuberculosis diagnostics in a low-middle income, high mdr-tb burden country
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/3e5fcabad3dd49d4ae4aea89d3f6fd40
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Implementation of whole genome sequencing for tuberculosis diagnostics in a low-middle income, high MDR-TB burden country

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