Advancing animal tuberculosis surveillance using culture-independent long-read whole-genome sequencing

Giovanni Ghielmetti; Johannes Loubser; Tanya J. Kerr; Tod Stuber; Tyler Thacker; Lauren C. Martin; Michaela A. O'Hare; Sinegugu K. Mhlophe; Abisola Okunola; Andre G. Loxton; Robin M. Warren; Mark H. Moseley; Michele A. Miller; Wynand J. Goosen

doi:10.3389/fmicb.2023.1307440

Advancing animal tuberculosis surveillance using culture-independent long-read whole-genome sequencing

Giovanni Ghielmetti, Johannes Loubser, Tanya J. Kerr, Tod Stuber, Tyler Thacker, Lauren C. Martin, Michaela A. O'Hare, Sinegugu K. Mhlophe, Abisola Okunola, Andre G. Loxton, Robin M. Warren, Mark H. Moseley, Michele A. Miller, Wynand J. Goosen^* (Corresponding Author)

^*Corresponding author for this work

Aberdeen Centre For Environmental Sustainability

Stellenbosch University

Research output: Contribution to journal › Article › peer-review

1 Citation (Scopus)

2 Downloads (Pure)

Abstract

Animal tuberculosis is a significant infectious disease affecting both livestock and wildlife populations worldwide. Effective disease surveillance and characterization of Mycobacterium bovis (M. bovis) strains are essential for understanding transmission dynamics and implementing control measures. Currently, sequencing of genomic information has relied on culture-based methods, which are time-consuming, resource-demanding, and concerning in terms of biosafety. This study explores the use of culture-independent long-read whole-genome sequencing (WGS) for a better understanding of M. bovis epidemiology in African buffaloes (Syncerus caffer). By comparing two sequencing approaches, we evaluated the efficacy of Illumina WGS performed on culture extracts and culture-independent Oxford Nanopore adaptive sampling (NAS). Our objective was to assess the potential of NAS to detect genomic variants without sample culture. In addition, culture-independent amplicon sequencing, targeting mycobacterial-specific housekeeping and full-length 16S rRNA genes, was applied to investigate the presence of microorganisms, including nontuberculous mycobacteria. The sequencing quality obtained from DNA extracted directly from tissues using NAS is comparable to the sequencing quality of reads generated from culture-derived DNA using both NAS and Illumina technologies. We present a new approach that provides complete and accurate genome sequence reconstruction, culture independently, and using an economically affordable technique.

Original language	English
Article number	1307440
Number of pages	13
Journal	Frontiers in Microbiology
Volume	14
Early online date	21 Nov 2023
DOIs	https://doi.org/10.3389/fmicb.2023.1307440
Publication status	Published - 21 Nov 2023

Bibliographical note

Acknowledgments
Some of the figures (Figures 4–6 and Supplementary Material S1) were generated using BioRender and draw.io, respectively.
Funding
The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This research was funded by the Wellcome Foundation (grant #222941/Z/21/Z), the South African Medical Research Council, American Association of Zoo Veterinarians Wild Animal Health Fund [S005651 and S007355], the National Research Foundation South African Research Chair Initiative [grant #86949], and MHM was supported by Wellcome
Trust (grant #216634/Z/19/Z). AGL is supported by the EDCTP TESA III network (CSA2020NoE-3104).

Data Availability Statement

Data availability statement
The datasets presented in this study can be found in online repositories available at: ncbi.nlm.nih.gov/bioproject/PRJEB63553 under project reference number PRJEB63553

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.3389/fmicb.2023.1307440Licence: CC BY

Ghielmetti_etal_FM_Advancing_Animal_Tuberculosis_VoR
© 2023 Ghielmetti, Loubser, Kerr, Stuber, Thacker, Martin, O’Hare, Mhlophe, Okunola, Loxton, Warren, Moseley, Miller and Goosen. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. https://creativecommons.org/licenses/by/4.0/
Final published version, 2.55 MBLicence: CC BY

Cite this

Ghielmetti, G., Loubser, J., Kerr, T. J., Stuber, T., Thacker, T., Martin, L. C., O'Hare, M. A., Mhlophe, S. K., Okunola, A., Loxton, A. G., Warren, R. M., Moseley, M. H., Miller, M. A., & Goosen, W. J. (2023). Advancing animal tuberculosis surveillance using culture-independent long-read whole-genome sequencing. Frontiers in Microbiology, 14, Article 1307440. https://doi.org/10.3389/fmicb.2023.1307440

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title = "Advancing animal tuberculosis surveillance using culture-independent long-read whole-genome sequencing",

abstract = "Animal tuberculosis is a significant infectious disease affecting both livestock and wildlife populations worldwide. Effective disease surveillance and characterization of Mycobacterium bovis (M. bovis) strains are essential for understanding transmission dynamics and implementing control measures. Currently, sequencing of genomic information has relied on culture-based methods, which are time-consuming, resource-demanding, and concerning in terms of biosafety. This study explores the use of culture-independent long-read whole-genome sequencing (WGS) for a better understanding of M. bovis epidemiology in African buffaloes (Syncerus caffer). By comparing two sequencing approaches, we evaluated the efficacy of Illumina WGS performed on culture extracts and culture-independent Oxford Nanopore adaptive sampling (NAS). Our objective was to assess the potential of NAS to detect genomic variants without sample culture. In addition, culture-independent amplicon sequencing, targeting mycobacterial-specific housekeeping and full-length 16S rRNA genes, was applied to investigate the presence of microorganisms, including nontuberculous mycobacteria. The sequencing quality obtained from DNA extracted directly from tissues using NAS is comparable to the sequencing quality of reads generated from culture-derived DNA using both NAS and Illumina technologies. We present a new approach that provides complete and accurate genome sequence reconstruction, culture independently, and using an economically affordable technique.",

author = "Giovanni Ghielmetti and Johannes Loubser and Kerr, {Tanya J.} and Tod Stuber and Tyler Thacker and Martin, {Lauren C.} and O'Hare, {Michaela A.} and Mhlophe, {Sinegugu K.} and Abisola Okunola and Loxton, {Andre G.} and Warren, {Robin M.} and Moseley, {Mark H.} and Miller, {Michele A.} and Goosen, {Wynand J.}",

note = "Acknowledgments Some of the figures (Figures 4–6 and Supplementary Material S1) were generated using BioRender and draw.io, respectively. Funding The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This research was funded by the Wellcome Foundation (grant #222941/Z/21/Z), the South African Medical Research Council, American Association of Zoo Veterinarians Wild Animal Health Fund [S005651 and S007355], the National Research Foundation South African Research Chair Initiative [grant #86949], and MHM was supported by Wellcome Trust (grant #216634/Z/19/Z). AGL is supported by the EDCTP TESA III network (CSA2020NoE-3104).",

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AU - Stuber, Tod

AU - Thacker, Tyler

AU - Martin, Lauren C.

AU - O'Hare, Michaela A.

AU - Mhlophe, Sinegugu K.

AU - Okunola, Abisola

AU - Loxton, Andre G.

AU - Warren, Robin M.

AU - Moseley, Mark H.

AU - Miller, Michele A.

AU - Goosen, Wynand J.

N1 - Acknowledgments Some of the figures (Figures 4–6 and Supplementary Material S1) were generated using BioRender and draw.io, respectively. Funding The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This research was funded by the Wellcome Foundation (grant #222941/Z/21/Z), the South African Medical Research Council, American Association of Zoo Veterinarians Wild Animal Health Fund [S005651 and S007355], the National Research Foundation South African Research Chair Initiative [grant #86949], and MHM was supported by Wellcome Trust (grant #216634/Z/19/Z). AGL is supported by the EDCTP TESA III network (CSA2020NoE-3104).

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N2 - Animal tuberculosis is a significant infectious disease affecting both livestock and wildlife populations worldwide. Effective disease surveillance and characterization of Mycobacterium bovis (M. bovis) strains are essential for understanding transmission dynamics and implementing control measures. Currently, sequencing of genomic information has relied on culture-based methods, which are time-consuming, resource-demanding, and concerning in terms of biosafety. This study explores the use of culture-independent long-read whole-genome sequencing (WGS) for a better understanding of M. bovis epidemiology in African buffaloes (Syncerus caffer). By comparing two sequencing approaches, we evaluated the efficacy of Illumina WGS performed on culture extracts and culture-independent Oxford Nanopore adaptive sampling (NAS). Our objective was to assess the potential of NAS to detect genomic variants without sample culture. In addition, culture-independent amplicon sequencing, targeting mycobacterial-specific housekeeping and full-length 16S rRNA genes, was applied to investigate the presence of microorganisms, including nontuberculous mycobacteria. The sequencing quality obtained from DNA extracted directly from tissues using NAS is comparable to the sequencing quality of reads generated from culture-derived DNA using both NAS and Illumina technologies. We present a new approach that provides complete and accurate genome sequence reconstruction, culture independently, and using an economically affordable technique.

AB - Animal tuberculosis is a significant infectious disease affecting both livestock and wildlife populations worldwide. Effective disease surveillance and characterization of Mycobacterium bovis (M. bovis) strains are essential for understanding transmission dynamics and implementing control measures. Currently, sequencing of genomic information has relied on culture-based methods, which are time-consuming, resource-demanding, and concerning in terms of biosafety. This study explores the use of culture-independent long-read whole-genome sequencing (WGS) for a better understanding of M. bovis epidemiology in African buffaloes (Syncerus caffer). By comparing two sequencing approaches, we evaluated the efficacy of Illumina WGS performed on culture extracts and culture-independent Oxford Nanopore adaptive sampling (NAS). Our objective was to assess the potential of NAS to detect genomic variants without sample culture. In addition, culture-independent amplicon sequencing, targeting mycobacterial-specific housekeeping and full-length 16S rRNA genes, was applied to investigate the presence of microorganisms, including nontuberculous mycobacteria. The sequencing quality obtained from DNA extracted directly from tissues using NAS is comparable to the sequencing quality of reads generated from culture-derived DNA using both NAS and Illumina technologies. We present a new approach that provides complete and accurate genome sequence reconstruction, culture independently, and using an economically affordable technique.

U2 - 10.3389/fmicb.2023.1307440

DO - 10.3389/fmicb.2023.1307440

M3 - Article

SN - 1664-302X

VL - 14

JO - Frontiers in Microbiology

JF - Frontiers in Microbiology

M1 - 1307440

ER -

Advancing animal tuberculosis surveillance using culture-independent long-read whole-genome sequencing

Abstract

Bibliographical note

Data Availability Statement

UN SDGs

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