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

Condé, Cyril; Thézé, Julien; Cochard, Thierry; Rossignol, Marie‐Noëlle; Fourichon, Christine; Delafosse, Arnaud; Joly, Alain; Guatteo, Raphaël R.; Schibler, Laurent; Bannantine, John P.; Biet, Franck

doi:10.1128/spectrum.03392-22

Cited by 6 publications

(12 citation statements)

References 76 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…paratuberculosis (MAP) is a microorganism characterised by an extremely slow growth rate both in a controlled environment ( in vitro ) and within living organisms ( in vivo ). One of the consequences of this slow pace is a low mutation rate and the extremely well-conserved and closed core genome ( 14 , 15 , 17 , 20 ). In the field of MAP epidemiology, traditional population genetic and diversity analysis methods such as VNTR or SSR analysis have currently been largely supplanted by WGS approaches.…”

Section: Discussionmentioning

confidence: 99%

“…While the de novo method circumvents biases related to indels or genetic translocations, the less computationally intensive reference genome alignment is appropriated for reconstructing and comparing core genomes. Consequently, building epidemiological trees based on SNP analyses of the core genome remains the predominant approach in evaluating potential epidemiological links within the MAP field, due to its notably low mutation rate ( 14 , 17 , 19 , 20 ).…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

High clonality of Mycobacterium avium subsp. paratuberculosis field isolates from red deer revealed by two different methodological approaches of comparative genomic analysis

Turco,

Russo,

Pietrucci

et al. 2024

Front. Vet. Sci.

View full text Add to dashboard Cite

Mycobacterium avium subsp. paratuberculosis (MAP) is the aetiological agent of paratuberculosis (Johne’s disease) in both domestic and wild ruminants. In the present study, using a whole-genome sequence (WGS) approach, we investigated the genetic diversity of 15 Mycobacterium avium field strains isolated in the last 10 years from red deer inhabiting the Stelvio National Park and affected by paratuberculosis. Combining de novo assembly and a reference-based method, followed by a pangenome analysis, we highlight a very close relationship among 13 MAP field isolates, suggesting that a single infecting event occurred in this population. Moreover, two isolates have been classified as Mycobacterium avium subsp. hominissuis, distinct from the other MAPs under comparison but close to each other. This is the first time that this subspecies has been found in Italy in samples without evident epidemiological correlations, having been isolated in two different locations of the Stelvio National Park and in different years. Our study highlights the importance of a multidisciplinary approach incorporating molecular epidemiology and ecology into traditional infectious disease knowledge in order to investigate the nature of infectious disease in wildlife populations.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

High clonality of Mycobacterium avium subsp. paratuberculosis field isolates from red deer revealed by two different methodological approaches of comparative genomic analysis

Turco,

Russo,

Pietrucci

et al. 2024

Front. Vet. Sci.

View full text Add to dashboard Cite

show abstract

“…In our study, intra-herd variability was observed in four out of 11 herds, of which multiple samples per farm were analyzed. Another recent study analyzing MAP by WGS showed that MIRU-VNTR typing lacks resolution for fine tracing of MAP strain circulation between and within herds ( 15 ). Despite these limitations, MIRU-VNTR typing, in combination with the differentiation between C-type and S-type MAP including subtype identification, can disclose an interesting insight about the strain variability in view of a temporal or geographical distribution of INMV types and the proportions of C- and S-type MAP strains.…”

Section: Discussionmentioning

confidence: 99%

“…Various molecular techniques have been used for investigating genetic diversity among MAP, such as restriction fragment length polymorphism (10), short-sequence repeat and pulsed-field gel electrophoresis typing (11), mycobacterial interspersed repetitive unit and variable-number tandem repeat (MIRU-VNTR) (12) or single nucleotide polymorphism (SNP)-based assay (13). For an ultimate resolution of the phylogenetic relationships between strains, whole-genome sequencing (WGS) of isolates can be used (9,(14)(15)(16), however requiring cultured isolates, which are laborious and time-consuming to obtain. Bovine paratuberculosis is caused mostly by C-type MAP and only in a few cases by S-type strains of MAP (1).…”

Section: Introductionmentioning

confidence: 99%

Strain diversity in Mycobacterium avium subsp. paratuberculosis-positive bovine fecal samples collected in Switzerland

et al. 2023

View full text Add to dashboard Cite

Paratuberculosis or Johne’s disease is a chronic intestinal disease in domestic and wild ruminants. It affects global dairy economy and is caused by Mycobacterium avium subsp. paratuberculosis (MAP). The objective of this study was to analyze strain diversity in MAP-positive fecal samples by using a particular single nucleotide polymorphism (SNP) distinguishing between cattle (C-) and sheep (S-) type MAP and analysis of SNPs within gyrA and gyrB genes differentiating between Types I, II, and III. Moreover, mycobacterial interspersed repetitive unit and variable-number tandem repeat (MIRU-VNTR) analysis using eight established loci was performed. A total of 90 fecal samples from diseased animals presenting diarrhea and/or weight loss, originating from 59 bovine herds across 16 cantons of Switzerland were screened by PCR for the MAP-specific F57 and IS900 genes and were further subtyped. 96.7% and 3.3% of the samples contained C- and S-type MAP, respectively. Ten INRA Nouzilly MIRU-VNTR (INMV) profiles, with a discriminatory index of 0.802, calculated based on 65 epidemiological independent genotypes, were detected: INMV 1 (33.8%), INMV 2 (23.1%), INMV 6 (16.9%), INMV 9 (9.2%), INMV 116 (4.6%), INMV 3 (3.1%), INMV 5 (3.1%) and INMV 72 (1.5%), including two novel INMV profiles, namely INMV 253 (3.1%; S-type III) and INMV 252 (1.5%; C-type). INMV 1, INMV 2, and INMV 6 comprised almost 75% of the F57- and IS900-positive samples. Typing data from 11 herds suggest that there are some herds with intra-herd diversity of genotypes. The results of this study indicate a heterogeneity of MAP in Switzerland.

show abstract

“…These include the 8 locus Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeat (MIRU-VNTR) and the 11 locus SSR typing methods, both of which are commonly used in epidemiology and source tracking studies ( 24 , 25 ). More recently, whole-genome sequencing (WGS) followed by single-nucleotide polymorphism (SNP) analysis has allowed for strain typing at a much higher resolution than previously possible, leading to the deciphering of new information ( 23 , 26 – 28 ).…”

Section: Introductionmentioning

confidence: 99%

Investigating in vivo Mycobacterium avium subsp. paratuberculosis microevolution and mixed strain infections

et al. 2023

View full text Add to dashboard Cite

Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne’s Disease (JD) in ruminants, which is responsible for significant economic loss to the global dairy industry. Mixed strain infection (MSI) refers to the concurrent infection of a susceptible host with genetically distinct strains of a pathogen, whereas within-host changes in an infecting strain leading to genetically distinguishable progeny is called microevolution. The two processes can influence host-pathogen dynamics, disease progression and outcomes, but not much is known about their prevalence and impact on JD. Therefore, we obtained up to 10 MAP isolates each from 14 high-shedding animals and subjected them to whole-genome sequencing. Twelve of the 14 animals examined showed evidence for the presence of MSIs and microevolution, while the genotypes of MAP isolates from the remaining two animals could be attributed solely to microevolution. All MAP isolates that were otherwise isogenic had differences in short sequence repeats (SSRs), of which SSR1 and SSR2 were the most diverse and homoplastic. Variations in SSR1 and SSR2, which are located in ORF1 and ORF2 , respectively, affect the genetic reading frame, leading to protein products with altered sequences and computed structures. The ORF1 gene product is predicted to be a MAP surface protein with possible roles in host immune modulation, but nothing could be inferred regarding the function of ORF2. Both genes are conserved in Mycobacterium avium complex members, but SSR1-based modulation of ORF1 reading frames seems to only occur in MAP, which could have potential implications on the infectivity of this pathogen. IMPORTANCE Johne’s disease (JD) is a major problem in dairy animals, and concerns have been raised regarding the association of Mycobacterium avium subsp. paratuberculosis (MAP) with Crohn’s disease in humans. MAP is an extremely slow-growing bacterium with low genome evolutionary rates. Certain short sequence repeats (SSR1 and SSR2) in the MAP chromosome are highly variable and evolve at a faster rate than the rest of the chromosome. In the current study, multiple MAP isolates with genetic variations such as single-nucleotide polymorphisms, and more noticeably, diverse SSRs, could simultaneously infect animals. Variations in SSR1 and SSR2 affect the products of the respective genes containing them. Since multiple MAP isolates can infect the same animal and the possibility that the pathogen undergoes further changes within the host due to unstable SSRs, this could provide a compensative mechanism for an otherwise slow-evolving pathogen to increase phenotypic diversity for overcoming host responses.

show abstract

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

Cited by 6 publications

References 76 publications

High clonality of Mycobacterium avium subsp. paratuberculosis field isolates from red deer revealed by two different methodological approaches of comparative genomic analysis

High clonality of Mycobacterium avium subsp. paratuberculosis field isolates from red deer revealed by two different methodological approaches of comparative genomic analysis

Strain diversity in Mycobacterium avium subsp. paratuberculosis-positive bovine fecal samples collected in Switzerland

Investigating in vivo Mycobacterium avium subsp. paratuberculosis microevolution and mixed strain infections

Contact Info

Product

Resources

About