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

BMC Genomics
Christina AhlstromJeroen De Buck

Abstract

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. Phylogenetic analysis based on 3,039 SNPs identified through WGS of 124 MAP isolates identified eight genetically distinct subtypes in dairy herds from...Continue Reading

References

Jun 18, 2003·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Christophe SolaNalin Rastogi
Oct 8, 2003·Systematic Biology·Stéphane Guindon, Olivier Gascuel
Sep 29, 2004·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Paul KeimDavid M Wagner
Feb 28, 2006·FEMS Microbiology Letters·Cath ArnoldSaheer Gharbia
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
May 30, 2009·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Talima PearsonPaul Keim
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Nov 20, 2009·Inflammatory Bowel Diseases·Marcel A Behr
Jan 25, 2011·The Veterinary Record·R A SkuceS W J McDowell
Apr 8, 2011·Nucleic Acids Research·Ivica Letunic, Peer Bork
Jun 21, 2011·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Josephine F ReyesMark M Tanaka
Nov 1, 2011·PloS One·Linnéa Smeds, Axel Künstner
Mar 27, 2012·Briefings in Bioinformatics·Iain MilneDavid Marshall
Jul 5, 2012·PLoS Computational Biology·R Zachariah AandahlMark M Tanaka
Aug 1, 2012·Nature Methods·Diego DarribaDavid Posada
Mar 1, 2013·BMC Infectious Diseases·Josephine M BryantDick van Soolingen
Aug 21, 2014·Journal of Veterinary Diagnostic Investigation : Official Publication of the American Association of Veterinary Laboratory Diagnosticians, Inc·Jane OakeyDavid Waltisbuhl

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Citations

Nov 4, 2015·Annual Review of Animal Biosciences·Lingling LiVivek Kapur
Mar 2, 2016·International Journal of Mycobacteriology·Ganesh G SonawaneBhupendra N Tripathi
Mar 12, 2016·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Zsuzsanna RónaiMiklós Gyuranecz
Nov 12, 2016·Preventive Veterinary Medicine·N MarquetouxM Stevenson
Mar 8, 2017·PloS One·Wayne PfeifferBruce A Rideout
Dec 13, 2017·Frontiers in Veterinary Science·Christina AhlstromJane Heller
Dec 18, 2015·Journal of Clinical Microbiology·Célia LeãoKaren Stevenson
Dec 20, 2018·International Journal of Veterinary Science and Medicine·Ahmad FawzyTobias Eisenberg
Feb 9, 2017·Epidemiology and Infection·B R ImperialeM I Romano
Mar 5, 2021·Frontiers in Veterinary Science·Rachel MizziKarren M Plain
May 5, 2021·Microbial Genomics·Gizat AlmawAndries J van Tonder

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Methods Mentioned

BETA
ELISA

Software Mentioned

SAMtools
ConDeTri
SAM
BWA
jModelTest
PhyML

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