Limits...
Limitations of variable number of tandem repeat typing identified through whole genome sequencing of Mycobacterium avium subsp. paratuberculosis on a national and herd level.

Ahlstrom C, Barkema HW, Stevenson K, Zadoks RN, Biek R, Kao R, Trewby H, Haupstein D, Kelton DF, Fecteau G, Labrecque O, Keefe GP, McKenna SL, De Buck J - BMC Genomics (2015)

Bottom Line: Whole genome sequencing (WGS) offers a detailed assessment of the SNP-level diversity and genetic relationship of isolates, whereas several molecular typing techniques used to investigate the molecular epidemiology of MAP, such as variable number of tandem repeat (VNTR) typing, target relatively unstable repetitive elements in the genome that may be too unpredictable to draw accurate conclusions.A herd-level analysis of MAP isolates demonstrated that VNTR typing may both over-estimate and under-estimate the relatedness of MAP isolates found within a single herd.VNTR typing often failed to identify closely and distantly related isolates, limiting the applicability of using this typing scheme to study the molecular epidemiology of MAP at a national and herd-level.

View Article: PubMed Central - PubMed

Affiliation: University of Calgary, Calgary, Alberta, Canada. cahlstro@ucalgary.ca.

ABSTRACT

Background: Mycobacterium avium subsp. paratuberculosis (MAP), the causative bacterium of Johne's disease in dairy cattle, is widespread in the Canadian dairy industry and has significant economic and animal welfare implications. An understanding of the population dynamics of MAP can be used to identify introduction events, improve control efforts and target transmission pathways, although this requires an adequate understanding of MAP diversity and distribution between herds and across the country. Whole genome sequencing (WGS) offers a detailed assessment of the SNP-level diversity and genetic relationship of isolates, whereas several molecular typing techniques used to investigate the molecular epidemiology of MAP, such as variable number of tandem repeat (VNTR) typing, target relatively unstable repetitive elements in the genome that may be too unpredictable to draw accurate conclusions. The objective of this study was to evaluate the diversity of bovine MAP isolates in Canadian dairy herds using WGS and then determine if VNTR typing can distinguish truly related and unrelated isolates.

Results: Phylogenetic analysis based on 3,039 SNPs identified through WGS of 124 MAP isolates identified eight genetically distinct subtypes in dairy herds from seven Canadian provinces, with the dominant type including over 80% of MAP isolates. VNTR typing of 527 MAP isolates identified 12 types, including "bison type" isolates, from seven different herds. At a national level, MAP isolates differed from each other by 1-2 to 239-240 SNPs, regardless of whether they belonged to the same or different VNTR types. A herd-level analysis of MAP isolates demonstrated that VNTR typing may both over-estimate and under-estimate the relatedness of MAP isolates found within a single herd.

Conclusions: The presence of multiple MAP subtypes in Canada suggests multiple introductions into the country including what has now become one dominant type, an important finding for Johne's disease control. VNTR typing often failed to identify closely and distantly related isolates, limiting the applicability of using this typing scheme to study the molecular epidemiology of MAP at a national and herd-level.

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Related in: MedlinePlus

Circularized maximum likelihood phylogenetic tree with each polymorphic VNTR locus concentrically displayed (inner to outer: 292, X3, 25, 47, 7, and 10). Branch lengths are not shown to scale. Blue represents the most common repeat number within each locus, red indicates a larger repeat number, and green represents a smaller repeat number. A dotted line indicates the VNTR type that represents each locus combination and the subtype (I-VIII) of each isolate/clade is indicated by a black dot located at the ancestral node of the isolate(s) within that subtype.
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Fig4: Circularized maximum likelihood phylogenetic tree with each polymorphic VNTR locus concentrically displayed (inner to outer: 292, X3, 25, 47, 7, and 10). Branch lengths are not shown to scale. Blue represents the most common repeat number within each locus, red indicates a larger repeat number, and green represents a smaller repeat number. A dotted line indicates the VNTR type that represents each locus combination and the subtype (I-VIII) of each isolate/clade is indicated by a black dot located at the ancestral node of the isolate(s) within that subtype.

Mentions: Additionally, there was evidence of convergent evolution in four of six VNTR types in which more than one isolate per type was sequenced (INMV 2, 3, 6, and 77) (Figure 1). Locus-specific changes in repeat length are presented in Figure 4. Locus 10 had the most instances of convergent evolution (five times), whereas loci 47 and X3 appeared to be relatively stable.Figure 4


Limitations of variable number of tandem repeat typing identified through whole genome sequencing of Mycobacterium avium subsp. paratuberculosis on a national and herd level.

Ahlstrom C, Barkema HW, Stevenson K, Zadoks RN, Biek R, Kao R, Trewby H, Haupstein D, Kelton DF, Fecteau G, Labrecque O, Keefe GP, McKenna SL, De Buck J - BMC Genomics (2015)

Circularized maximum likelihood phylogenetic tree with each polymorphic VNTR locus concentrically displayed (inner to outer: 292, X3, 25, 47, 7, and 10). Branch lengths are not shown to scale. Blue represents the most common repeat number within each locus, red indicates a larger repeat number, and green represents a smaller repeat number. A dotted line indicates the VNTR type that represents each locus combination and the subtype (I-VIII) of each isolate/clade is indicated by a black dot located at the ancestral node of the isolate(s) within that subtype.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4356054&req=5

Fig4: Circularized maximum likelihood phylogenetic tree with each polymorphic VNTR locus concentrically displayed (inner to outer: 292, X3, 25, 47, 7, and 10). Branch lengths are not shown to scale. Blue represents the most common repeat number within each locus, red indicates a larger repeat number, and green represents a smaller repeat number. A dotted line indicates the VNTR type that represents each locus combination and the subtype (I-VIII) of each isolate/clade is indicated by a black dot located at the ancestral node of the isolate(s) within that subtype.
Mentions: Additionally, there was evidence of convergent evolution in four of six VNTR types in which more than one isolate per type was sequenced (INMV 2, 3, 6, and 77) (Figure 1). Locus-specific changes in repeat length are presented in Figure 4. Locus 10 had the most instances of convergent evolution (five times), whereas loci 47 and X3 appeared to be relatively stable.Figure 4

Bottom Line: Whole genome sequencing (WGS) offers a detailed assessment of the SNP-level diversity and genetic relationship of isolates, whereas several molecular typing techniques used to investigate the molecular epidemiology of MAP, such as variable number of tandem repeat (VNTR) typing, target relatively unstable repetitive elements in the genome that may be too unpredictable to draw accurate conclusions.A herd-level analysis of MAP isolates demonstrated that VNTR typing may both over-estimate and under-estimate the relatedness of MAP isolates found within a single herd.VNTR typing often failed to identify closely and distantly related isolates, limiting the applicability of using this typing scheme to study the molecular epidemiology of MAP at a national and herd-level.

View Article: PubMed Central - PubMed

Affiliation: University of Calgary, Calgary, Alberta, Canada. cahlstro@ucalgary.ca.

ABSTRACT

Background: Mycobacterium avium subsp. paratuberculosis (MAP), the causative bacterium of Johne's disease in dairy cattle, is widespread in the Canadian dairy industry and has significant economic and animal welfare implications. An understanding of the population dynamics of MAP can be used to identify introduction events, improve control efforts and target transmission pathways, although this requires an adequate understanding of MAP diversity and distribution between herds and across the country. Whole genome sequencing (WGS) offers a detailed assessment of the SNP-level diversity and genetic relationship of isolates, whereas several molecular typing techniques used to investigate the molecular epidemiology of MAP, such as variable number of tandem repeat (VNTR) typing, target relatively unstable repetitive elements in the genome that may be too unpredictable to draw accurate conclusions. The objective of this study was to evaluate the diversity of bovine MAP isolates in Canadian dairy herds using WGS and then determine if VNTR typing can distinguish truly related and unrelated isolates.

Results: Phylogenetic analysis based on 3,039 SNPs identified through WGS of 124 MAP isolates identified eight genetically distinct subtypes in dairy herds from seven Canadian provinces, with the dominant type including over 80% of MAP isolates. VNTR typing of 527 MAP isolates identified 12 types, including "bison type" isolates, from seven different herds. At a national level, MAP isolates differed from each other by 1-2 to 239-240 SNPs, regardless of whether they belonged to the same or different VNTR types. A herd-level analysis of MAP isolates demonstrated that VNTR typing may both over-estimate and under-estimate the relatedness of MAP isolates found within a single herd.

Conclusions: The presence of multiple MAP subtypes in Canada suggests multiple introductions into the country including what has now become one dominant type, an important finding for Johne's disease control. VNTR typing often failed to identify closely and distantly related isolates, limiting the applicability of using this typing scheme to study the molecular epidemiology of MAP at a national and herd-level.

Show MeSH
Related in: MedlinePlus