Draft Genome Sequences of 142 Mycobacterium avium subsp.
            <i>paratuberculosis</i>
            Strains Isolated from Naturally Infected Dairy Cattle

Condé, Cyril; Branger, Maxime; Cochard, Thierry; Rossignol, Marie; Fourichon, Christine; Delafosse, Arnaud; Davergne, Aurore; Joly, Alain; Ngwa-Mbot, David; Journaux, L.; Guatteo, Raphaël R.; Schibler, Laurent; Biet, Franck

doi:10.1128/mra.00697-21

Cited by 3 publications

(5 citation statements)

References 12 publications

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“…paratuberculosis strains circulating in France ( Fig. 1 ; see Data Set 1 in Table S1 in the supplemental material) ( 20 ), 137 were selected for pangenome analysis. Genomes with less than 20× coverage or whose assembly yielded more than 400 contigs or <69.2% GC content were excluded from the analysis.…”

Section: Resultsmentioning

confidence: 99%

“…paratuberculosis ( 19 ). The culture and sequencing of the 182 isolates collected over a period of 4 years (2014 to 2018) are described elsewhere ( 20 ), except for PICSAR126, which was excluded in the present study because too many clade-specific SNPs were ambiguously assigned.…”

Section: Methodsmentioning

confidence: 99%

“…Illumina reads for Data Set 3 (Table S1) were downloaded from NCBI’s SRA database using fasterq-dump (v.2.10.1). Raw sequencing data were processed as previously described ( 20 ). Briefly, short reads were trimmed using fastp v.0.20.1 and a Phred scale base quality threshold of Q30.…”

Section: Methodsmentioning

confidence: 99%

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Genetic Features of Mycobacterium avium subsp. paratuberculosis Strains Circulating in the West of France Deciphered by Whole-Genome Sequencing

et al. 2022

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Mycobacterium avium subsp. paratuberculosis causes Johne's disease in ruminants, which is present worldwide and has significant negative impacts on the dairy cattle industry and animal welfare. Prevention and control of M. avium subsp. paratuberculosis infection are hampered by knowledge gaps in strain virulence, genotype distribution, and transmission dynamics.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Genetic Features of Mycobacterium avium subsp. paratuberculosis Strains Circulating in the West of France Deciphered by Whole-Genome Sequencing

et al. 2022

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“…Except for three isolates with suspected contaminants, all results were considered acceptable. Kraken2 was then used to perform taxonomic identification of the read using a custom-built database ( Wood et al, 2019 ) using NCBI RefSeq and 142 MAP sequences from the European Nucleotide Archive (ENA) ( Conde et al, 2021 ). KrakenTools was used to extract reads corresponding to the family Mycobactereaceae (NCBI TXID1762) ( Lu, 2020 ).…”

Section: Methodsmentioning

confidence: 99%

Genomic epidemiology of Mycobacterium avium subsp. paratuberculosis isolates from Canadian dairy herds provides evidence for multiple infection events

et al. 2023

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Mycobacterium avium subsp. paratuberculosis (MAP) is the pathogen responsible for paratuberculosis or Johne’s Disease (JD) in ruminants, which is responsible for substantial economic losses worldwide. MAP transmission primarily occurs through the fecal-oral route, and the introduction of an MAP infected animal into a herd is an important transmission route. In the current study, we characterized MAP isolates from 67 cows identified in 20 herds from the provinces of Quebec and Ontario, Canada. Whole genome sequencing (WGS) was performed and an average genome coverage (relative to K-10) of ∼14.9 fold was achieved. The total number of SNPs present in each isolate varied from 51 to 132 and differed significantly between herds. Isolates with the highest genetic variability were generally present in herds from Quebec. The isolates were broadly separated into two main clades and this distinction was not influenced by the province from which they originated. Analysis of 8 MIRU-VNTR loci and 11 SSR loci was performed on the 67 isolates from the 20 dairy herds and publicly available references, notably major genetic lineages and six isolates from the province of Newfoundland and Labrador. All 67 field isolates were phylogenetically classified as Type II (C-type) and according to MIRU-VNTR, the predominant type was INMV 2 (76.1%) among four distinct patterns. Multilocus SSR typing identified 49 distinct INMV SSR patterns. The discriminatory index of the multilocus SSR typing was 0.9846, which was much higher than MIRU-VNTR typing (0.3740). Although multilocus SSR analysis provides good discriminatory power, the resolution was not informative enough to determine inter-herd transmission. In select cases, SNP-based analysis was the only approach able to document disease transmission between herds, further validated by animal movement data. The presence of SNPs in several virulence genes, notably for PE, PPE, mce and mmpL, is expected to explain differential antigenic or pathogenetic host responses. SNP-based studies will provide insight into how MAP genetic variation may impact host-pathogen interactions. Our study highlights the informative power of WGS which is now recommended for epidemiological studies and to document mixed genotypes infections.

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“…Mycobacterium avium subspecies paratuberculosis (MAP) is the clinically and economically important agent of bovine paratuberculosis [ 1 ]. Commonly known as Johne’s disease, it is a debilitating chronic disease of the gastrointestinal tract that occurs worldwide in domestic and wild ruminants [ 2 , 3 ].…”

Section: Introductionmentioning

confidence: 99%

Mycobacterium avium subsp. paratuberculosis Infected Cows Reveal Divergent Immune Response in Bovine Peripheral Blood Derived Lymphocyte Proteome

et al. 2022

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Bovine paratuberculosis is a serious chronic disease of the gastrointestinal tract that causes economic losses and dramatically affects animal health in livestock. The underlying infectious agent, Mycobacterium avium subspecies paratuberculosis (MAP), cannot reliably be detected by standard diagnostic tests due to the long asymptomatic disease stage. The aim of this study was to detect proteomic changes in peripheral blood mononuclear cells (PBMC) from cows of the same herd with different MAP infection status after co-incubation with viable MAP in vitro using label-free LC-MS/MS. In our proteomic discovery experiment, we detected 2631 differentially regulated proteins between cows with negative MAP infection status (so-called MAP-resistant cows) and cows with positive MAP infection status (so-called persistently MAP-infected cows). In MAP-resistant cows, we detected enriched immune-related signaling pathways for TLR2 and MHC class II component proteins, among others, indicating a successful defensive immune response of the cows to MAP. In contrast, persistently MAP-infected cows were not directly enriched in immune-related signaling pathways associated with ITGA2B and KCNMA1, among others. The introduction of these distinct immune responses contributes to a better understanding of the bovine immune response and mechanisms of susceptibility to MAP.

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Draft Genome Sequences of 142 Mycobacterium avium subsp. paratuberculosis Strains Isolated from Naturally Infected Dairy Cattle

Cited by 3 publications

References 12 publications

Genetic Features of Mycobacterium avium subsp. paratuberculosis Strains Circulating in the West of France Deciphered by Whole-Genome Sequencing

Genetic Features of Mycobacterium avium subsp. paratuberculosis Strains Circulating in the West of France Deciphered by Whole-Genome Sequencing

Genomic epidemiology of Mycobacterium avium subsp. paratuberculosis isolates from Canadian dairy herds provides evidence for multiple infection events

Mycobacterium avium subsp. paratuberculosis Infected Cows Reveal Divergent Immune Response in Bovine Peripheral Blood Derived Lymphocyte Proteome

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