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Mycobacteria PFGE Database

Introduction

Pulsed-field gel electrophoresis (PFGE) can detect genetic differences between various strains of Mycobacterium avium subsp. paratuberculosis and therefore is a useful tool for epidemiological studies of paratuberculosis. In order to compare the epidemiological data from different laboratories and obtain a global prospective, it is imperative that a standardised procedure and appropriate nomenclature are used. We have optimised a standard operating procedure for the PFGE analysis of M.a.paratuberculosis and suggested a system of nomenclature that could be adopted by laboratories using this technique for genotyping. To facilitate the comparison of data from isolates examined in different laboratories, we have established a PFGE database for M.a.paratuberculosis using the software BioNumerics or GelCompar II (Applied Maths NV). We also maintain a reference panel of strains representative of the different PFGE profiles in the database. We encourage other laboratories to use these resources and contribute their own data.

 

PFGE Database

The database has been set up using BioNumerics or GelCompar II software (Applied Maths NV).

Access

If you would like access to the PFGE database, please contact Dr Karen Stevenson by email karen.stevenson@moredun.ac.uk. You are respectfully requested to acknowledge the use of the database in any ensuing publications.

Data submission

For data to be added to the database it is imperative that:

  • The new PFGE profile is generated using the standard operating procedure described on this website
  • The ATTC BAA-968 M.a.paratuberculosis K10 strain (or any strain with a confirmed [1-1] profile) and the recommended molecular weight markers (midrange II PFG Markers New England Biolabs N35525) are included on the gel

Once you have generated images of your PFGE profiles, compare them with the profiles in the current database using GelCompar or BioNumerics software. For access to the database see above. If you have identified a new PFGE profile, Moredun will assign a profile number and add the data to the database. Profile numbers must be assigned only by Moredun to avoid any duplication. We will only add the data with your permission and will respect any wish to withhold the data until publication. For this reason, the list of profile numbers on the website and in the database may not be completely up to date. To submit data to the database, email the Tiff files of the profiles or the relevant BioNumerics/GelCompar II data bundle to karen.stevenson@moredun.ac.uk.

Your images must have a minimum resolution of 480 x 640 pixels and 8 bit, 12 bit or 16 bit. Please send a subculture of the M.a.paratuberculosis strain that has the new PFGE profile to the address below for inclusion in the reference panel of strains:

 

PFGE Reference Strain Collection

Moredun will maintain a collection of M.a.paratuberculosis isolates representative of all the profiles in the PFGE database. These isolates will be made available to researchers on request. As we do not receive specific funding for this, we request that you cover the cost of culture and courier services. Please note that we cannot supply strains that are available commercially and have been deposited in national culture collections. This includes the M.a.paratuberculosis K10 strain available from ATCC. For some strains you may need to sign a Materials Transfer Agreement supplied by the laboratory that submitted the strain.

 

PFGE Nomenclature

The different PFGE profiles for each enzyme have been assigned numbers with the ATCC BAA-968 K10 strain designated profile 1 in each case. This system is used to distinguish the nomenclature for PFGE from the alphabetical and numerical system described for IS900-RFLP (Pavlik et al. 1995) and http://www.vri.cz/labs/tbc/DNA_fingerprinting_of_mycobacter.html). The different SnaBI-SpeI multiplex PFGE profiles have been expressed as the number of the SnaBI profile separated by a hyphen from the number of the SpeI profile enclosed in square brackets. For example, the multiplex PFGE profile of an isolate that has a SnaBI profile of 2 and a SpeI profile of 3 is expressed as [2-3]. This system was chosen as it is easy to add additional profiles and gives some indication as to the genetic relationship between isolates.

Attachments

AttachmentSize
File Relevant Johne's Publications.pdf306.12 KB

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Printed from http://www.moredun.org.uk/research/research-%40-moredun/diseases-of-the-gut/paratb-%28johnes-disease%29/mycobacteria-pfge-database on 23/05/17 02:07:38 AM

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