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

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....

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Main Authors: 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
Format: Article
Language:English
Published: Frontiers Media S.A. 2023-11-01
Series:Frontiers in Microbiology
Subjects:
Online Access:https://www.frontiersin.org/articles/10.3389/fmicb.2023.1307440/full
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author Giovanni Ghielmetti
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
author_facet Giovanni Ghielmetti
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
author_sort Giovanni Ghielmetti
collection DOAJ
description 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.
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spelling doaj.art-035cd5620d664fca87da5559c4c3e9712023-11-22T13:51:37ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2023-11-011410.3389/fmicb.2023.13074401307440Advancing animal tuberculosis surveillance using culture-independent long-read whole-genome sequencingGiovanni Ghielmetti0Giovanni Ghielmetti1Johannes Loubser2Tanya J. Kerr3Tod Stuber4Tyler Thacker5Lauren C. Martin6Michaela A. O'Hare7Sinegugu K. Mhlophe8Abisola Okunola9Andre G. Loxton10Robin M. Warren11Mark H. Moseley12Michele A. Miller13Wynand J. Goosen14Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South AfricaSection of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, SwitzerlandDivision of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South AfricaDivision of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South AfricaNational Veterinary Services Laboratories, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA, United StatesNational Veterinary Services Laboratories, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA, United StatesDivision of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South AfricaDivision of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South AfricaDivision of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South AfricaDivision of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South AfricaDivision of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South AfricaDivision of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South AfricaSchool of Biological Sciences, University of Aberdeen, Aberdeen, United KingdomDivision of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South AfricaDivision of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South AfricaAnimal 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.https://www.frontiersin.org/articles/10.3389/fmicb.2023.1307440/fulladaptive samplingAfrican buffaloesculture-independentMycobacterium bovisnext-generation sequencingwhole-genome sequencing
spellingShingle Giovanni Ghielmetti
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
Advancing animal tuberculosis surveillance using culture-independent long-read whole-genome sequencing
Frontiers in Microbiology
adaptive sampling
African buffaloes
culture-independent
Mycobacterium bovis
next-generation sequencing
whole-genome sequencing
title Advancing animal tuberculosis surveillance using culture-independent long-read whole-genome sequencing
title_full Advancing animal tuberculosis surveillance using culture-independent long-read whole-genome sequencing
title_fullStr Advancing animal tuberculosis surveillance using culture-independent long-read whole-genome sequencing
title_full_unstemmed Advancing animal tuberculosis surveillance using culture-independent long-read whole-genome sequencing
title_short Advancing animal tuberculosis surveillance using culture-independent long-read whole-genome sequencing
title_sort advancing animal tuberculosis surveillance using culture independent long read whole genome sequencing
topic adaptive sampling
African buffaloes
culture-independent
Mycobacterium bovis
next-generation sequencing
whole-genome sequencing
url https://www.frontiersin.org/articles/10.3389/fmicb.2023.1307440/full
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