Genetic diversity of bovineMycobacterium aviumsubsp.paratuberculosisdiscriminated by IS1311PCR-REA, MIRU-VNTR, and MLSSR genotyping

Park, Hong-Tae; Park, Hyun-Eui; Park, Woo Bin; Kim, Suji; Hur, Tai Young; Jung, Young-Hoon; Yoo, Han Sang

doi:10.4142/jvs.2018.19.5.627

Cited by 6 publications

(6 citation statements)

References 31 publications

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“…Genome sequencing was conducted with five M. avium subsp. paratuberculosis (MAP) strains that were isolated from Korea as previously described [ 18 ]. Three strains, MAPK_CN9, MAPK_CN7, and MAPK_CN4, were isolated from a farm in the Chungcheongnamdo region, and two other strains, MAPK_JB16 and MAPK_JJ1, were isolated from two farms in Jeollabukdo and Jejudo (Figure 1 A).…”

Section: Resultsmentioning

confidence: 99%

“…Two of these sequences were identical to MIRU292 and VNTR25 [ 9 ], and the other five were considered novel TRs. In a previous study, MIRU-VNTR typing discriminated MAPK strains into two types, INMV2 and INMV68, corresponding to the C-type and B-type, respectively [ 18 ]. However, in silico typing with the novel TR candidates discriminated the Korean strains into four different types (Table 2 ).…”

Section: Resultsmentioning

confidence: 99%

“…In our previous study, 19 MAP isolates were obtained from 10 cattle herds in 5 provinces in Korea, and their genetic diversity was analyzed [ 18 ]. Genetic classification using IS 1311 PCR-REA, MIRU-VNTR, and MLSSR typing was employed to differentiate the isolates into 5 different groups.…”

Section: Methodsmentioning

confidence: 99%

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Genomic diversity of Mycobacterium avium subsp. paratuberculosis: pangenomic approach for highlighting unique genomic features with newly constructed complete genomes

Lim

Park

et al. 2021

Vet Res

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Mycobacterium avium subsp. paratuberculosis (MAP) is a causative agent of Johne’s disease, which is a chronic granulomatous enteropathy in ruminants. Determining the genetic diversity of MAP is necessary to understand the epidemiology and biology of MAP, as well as establishing disease control strategies. In the present study, whole genome-based alignment and comparative analysis were performed using 40 publicly available MAP genomes, including newly sequenced Korean isolates. First, whole genome-based alignment was employed to identify new genomic structures in MAP genomes. Second, the genomic diversity of the MAP population was described by pangenome analysis. A phylogenetic tree based on the core genome and pangenome showed that the MAP was differentiated into two major types (C- and S-type), which was in keeping with the findings of previous studies. However, B-type strains were discriminated from C-type strains. Finally, functional analysis of the pangenome was performed using three virulence factor databases (i.e., PATRIC, VFDB, and Victors) to predict the phenotypic diversity of MAP in terms of pathogenicity. Based on the results of the pangenome analysis, we developed a real-time PCR technique to distinguish among S-, B- and C-type strains. In conclusion, the results of our study suggest that the phenotypic differences between MAP strains can be explained by their genetic polymorphisms. These results may help to elucidate the diversity of MAP, extending from genomic features to phenotypic traits.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Genomic diversity of Mycobacterium avium subsp. paratuberculosis: pangenomic approach for highlighting unique genomic features with newly constructed complete genomes

Lim

Park

et al. 2021

Vet Res

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“…Park et al (2018) classified bison-type MAP strains isolated from Korea, which were identified only by INMV 68 in the MIRU-VNTR typing, into three subtypes by MIRU-VNTR and eight subtypes by multilocus short sequence repeat (MLSSR) typing [90]. The HGDI values in the MIRU-VNTR and MLSSR were calculated to be 0.567 and 0.866, respectively, suggesting the combination of MLSSR typing in MAP genotyping [90]. Additionally, and as described in this manuscript, MAP suggested that each locus had a generally low h value, so that MIRU-VNTR typing could not provide a sufficient epidemiological implication for MAP.…”

Section: Comparison Of Vntr Using Other Genetic Typing Methodsmentioning

confidence: 99%

Differential Genotyping of Mycobacterium avium Complex and Its Implications in Clinical and Environmental Epidemiology

Shin

2020

Microorganisms

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In recent decades, the incidence and prevalence of nontuberculous mycobacteria (NTM) have greatly increased, becoming a major worldwide public health problem. Among numerous NTM species, the Mycobacterium avium complex (MAC) is the most predominant species, causing disease in humans. MAC is recognized as a ubiquitous microorganism, with contaminated water and soil being established sources of infection. However, the reason for the recent increase in MAC-associated disease has not yet been fully elucidated. Furthermore, human MAC infections are associated with a variety of infection sources. To improve the determination of infection sources and epidemiology of MAC, feasible and reliable genotyping methods are required to allow for the characterization of the epidemiology and biology of MAC. In this review, we discuss genotyping methods, such as pulsed-field gel electrophoresis, a variable number of tandem repeats, mycobacterial interspersed repetitive-unit-variable number of tandem repeats, and repetitive element sequence-based PCR that have been applied to elucidate the association between the MAC genotypes and epidemiological dominance, clinical phenotypes, evolutionary process, and control measures of infection. Characterizing the association between infection sources and the epidemiology of MAC will allow for the development of novel preventive strategies for the effective control of MAC infection.

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“…In one study, MIRU-VNTR typing was unable to distinguish between Type I and Type III sheep strains ( 13 ). However, tests such as MIRU-VNTR, SSR and PCR-based assays are able to distinguish MAP strains with higher efficiency when combined with each other or other techniques such as IS 900 RFLP ( 34 – 37 ). Despite these techniques being more advanced they still provide limited insight into the functional consequences of genetic diversity and have been shown at times to both underestimate and overestimate the diversity of MAP in some scenarios.…”

Section: Introductionmentioning

confidence: 99%

Comparative Genomics of Mycobacterium avium Subspecies Paratuberculosis Sheep Strains

et al. 2021

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Mycobacterium avium subspecies paratuberculosis (MAP) is the aetiological agent of Johne's disease (JD), a chronic enteritis that causes major losses to the global livestock industry. Further, it has been associated with human Crohn's disease. Several strains of MAP have been identified, the two major groups being sheep strain MAP, which includes the Type I and Type III sub-lineages, and the cattle strain or Type II MAP lineage, of which bison strains are a sub-grouping. Major genotypic, phenotypic and pathogenic variations have been identified in prior comparisons, but the research has predominately focused on cattle strains of MAP. In countries where the sheep industries are more prevalent, however, such as Australia and New Zealand, ovine JD is a substantial burden. An information gap exists regarding the genomic differences between sheep strain sub-lineages and the relevance of Type I and Type III MAP in terms of epidemiology and/or pathogenicity. We therefore investigated sheep MAP isolates from Australia and New Zealand using whole genome sequencing. For additional context, sheep MAP genome datasets were downloaded from the Sequence Read Archive and GenBank. The final dataset contained 18 Type III and 16 Type I isolates and the K10 cattle strain MAP reference genome. Using a pan-genome approach, an updated global phylogeny for sheep MAP from de novo assemblies was produced. When rooted with the K10 cattle reference strain, two distinct clades representing the lineages were apparent. The Australian and New Zealand isolates formed a distinct sub-clade within the type I lineage, while the European type I isolates formed another less closely related group. Within the type III lineage, isolates appeared more genetically diverse and were from a greater number of continents. Querying of the pan-genome and verification using BLAST analysis revealed lineage-specific variations (n = 13) including genes responsible for metabolism and stress responses. The genetic differences identified may represent important epidemiological and virulence traits specific to sheep MAP. This knowledge will potentially contribute to improved vaccine development and control measures for these strains.

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Genetic diversity of bovineMycobacterium aviumsubsp.paratuberculosisdiscriminated by IS1311PCR-REA, MIRU-VNTR, and MLSSR genotyping

Cited by 6 publications

References 31 publications

Genomic diversity of Mycobacterium avium subsp. paratuberculosis: pangenomic approach for highlighting unique genomic features with newly constructed complete genomes

Genomic diversity of Mycobacterium avium subsp. paratuberculosis: pangenomic approach for highlighting unique genomic features with newly constructed complete genomes

Differential Genotyping of Mycobacterium avium Complex and Its Implications in Clinical and Environmental Epidemiology

Comparative Genomics of Mycobacterium avium Subspecies Paratuberculosis Sheep Strains

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