Features of Mycobacterium bovis Complete Genomes Belonging to 5 Different Lineages

Charles, Ciriac; Condé, Cyril; Vorimore, Fabien; Cochard, Thierry; Michelet, Lorraine; Boschiroli, Maria‐Laura; Biet, Franck

doi:10.3390/microorganisms11010177

Cited by 3 publications

(2 citation statements)

References 71 publications

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“…Strain differences in host tropism, pathogenesis, or host excretion routes might result in different transmission dynamics [ 58 ]. The major Eu2 clonal complex clade under analysis showed a genomic diversity stabilization in recent times.…”

Section: Discussionmentioning

confidence: 99%

Genomic epidemiology sheds light on the emergence and spread of Mycobacterium bovis Eu2 Clonal Complex in Portugal

Pereira,

Reis,

Cunha

2023

Emerging Microbes & Infections

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Animal tuberculosis (TB) remains a serious concern for animal and human health. Mycobacterium bovis circulates in multi-host systems, dominated by the European 2 clonal complex (Eu2) in Iberia. In this work, we use genomic epidemiology to infer the emergence, spread, and spatiotemporal patterns of Eu2 in the official epidemiological risk area of animal TB in Portugal. Phylogenetic analysis of 144 M. bovis whole-genome sequences from cattle, wild boar, and red deer, representing the 2002–2021 period, distinguished three Eu2 clades that evolved independently. The major Eu2 clade underwent phylodynamic inferences to estimate the time and location of outbreaks, host transitions, and spatial diffusion as well. The origin of this Eu2 clade was attributed to the red deer population in the Castelo Branco district, near the border with Spain. Most host transitions were intraspecific (80%), while interspecific transmissions between wildlife species (wild boar-red deer), and between wild boar and cattle, were highly supported. Phylogeographic reconstruction evidenced that most transitions (82%) occur within municipalities, highlighting local transmission corridors. Our study indicates that M. bovis continues to spread at the cattle-wildlife interface within the animal TB hotspot area, possibly driven by the foraging behaviour of wild boar near agricultural lands. Red deer seems to be an important driver of TB within wildlife hosts, while the wild boar links the multi-host wildlife community and livestock. This work highlights the value of combining genomic epidemiology with phylodynamic inference to resolve host jumps and spatial patterns of M. bovis , providing real-time clues about points of intervention.

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Section: Discussionmentioning

confidence: 99%

Genomic epidemiology sheds light on the emergence and spread of Mycobacterium bovis Eu2 Clonal Complex in Portugal

Pereira,

Reis,

Cunha

2023

Emerging Microbes & Infections

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“…By analyzing the occurrence of insertion sequences (IS) IS6110 and IS1081, we were able to determine that all genomes contained a single copy of IS6110 and six copies of IS1081, respectively. Of the latter six copies, one copy was truncated (Charles et al, 2023) and not amplifiable using the GeneXpert MTB/RIF Ultra primers. The genomic positions of the IS were conserved across the sequences analyzed.…”

Section: Distribution Analysis Of Insertion Sequences Is6110 and Is1081mentioning

confidence: 99%

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

Ghielmetti,

Loubser,

Kerr

et al. 2023

Front. Microbiol.

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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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First Insight into the Whole Genome Sequencing Whole Variations in Mycobacterium bovis from Cattle in Morocco

Khoulane,

Fellahi,

Khayi

et al. 2024

Microorganisms

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Six cattle heads which tested positive against bovine tuberculosis (bTB) in Morocco were investigated to confirm the disease and to determine the source(s) of infection. Polymerase Chain Reaction (PCR) was directly performed on tissue samples collected from slaughtered animals. All investigated animals tested positive to PCR for the Mycobacterium bovis sub-type. Bacteriological isolation was conducted according to the technique recommended by WOAH for the cultivation of the Mycobacterium tuberculosis Complex (MBTC). Whole genome sequencing (WGS) was carried out on six mycobacterial isolates and the phylogenic tree was constructed. The six Moroccan isolates fit with clades II, III, IV, V and VII and were confirmed to belong to the clonal complexes Eu2, Unknown 2 and 7 as well as to sublineages La1.7.1, La1.2 and La1.8.2. The significant Single Nucleotide Polymorphism (SNPs) ranged from 84 to 117 between the isolates and the reference M. bovis strain and from 17 to 212 between the six isolates. Considering the high resolution of WGS, these results suggests that the source of infection of the bTB could be linked to imported animals as five of the investigated reactor animals were imported a few months prior. WGS can be a useful component to the Moroccan strategy to control bTB.

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Features of Mycobacterium bovis Complete Genomes Belonging to 5 Different Lineages

Cited by 3 publications

References 71 publications

Genomic epidemiology sheds light on the emergence and spread of Mycobacterium bovis Eu2 Clonal Complex in Portugal

Genomic epidemiology sheds light on the emergence and spread of Mycobacterium bovis Eu2 Clonal Complex in Portugal

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

First Insight into the Whole Genome Sequencing Whole Variations in Mycobacterium bovis from Cattle in Morocco

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