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Evaluation of Moleculare Typing Techniques

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Evaluation of Moleculare Typing Techniques: Typability, Stability, Reproducibility, Discriminatory Power, Concordance

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Evaluation of Moleculare Typing Techniques

  1. 1. Evaluation of Molecular Typing Techniques Thomas Weniger Department of Periodontology University of Münster, Germany tweniger@uni-muenster.de
  2. 2. Typing: Phenotypic and/or genetic analysis of bacterial isolates, below the species/subspecies level, performed in order to generate strain/clone-specific fingerprints […] van Belkum et al., (2007). CMI, 13:1
  3. 3. PFGE MLST flaAothers C. jejuni: Different typing methods
  4. 4. Questions Suitable methods Discriminatory power Time span Outbreak investigations Short-term/local surveillance Control of hygiene measures PFGE, RFLP, AFLP, RA-PCR, VNTR, SLST, micro-array high weeks - month Long-term/global epidemiological studies Population genetics Analysis of population-based interventions, e.g. vaccination (MLEE), MLST, micro-array, in part SLST low years 6-AM 4 Typing questions & suitable methods
  5. 5. Typing system performance Convenience
  6. 6. A A B Stability
  7. 7. A A Reproducibility B A
  8. 8. A B C D E E Typing method 1 Discriminatory power
  9. 9. A B C D E E Typing method 1 a b c c b b Typing method 2 DI: 0.933 [0.805 – 1.0] DI: 0.733 [0.53 – 0.936] Discriminatory power
  10. 10. AAA B C Epidemiological Concordance
  11. 11. Typing system performance Convenience
  12. 12.  Costs  Rapidity  Ease of use Convenience
  13. 13. Typing system concordance - Rand‘s index - adjusted Rand‘s index - Wallace coefficients Carrico et al. (2006) JCM 44: 2524 PFGE versus MLST MLST same different PFGE same a b different c d
  14. 14. Rand (1971) J. Am. Stat. Assoc. 66 Hubert & Arabie (1985) J. Classification 2
  15. 15. Wallace (1983) J. Am. Stat. Assoc. 78
  16. 16. A B C D E E a b c c b b Typing method 1 Typing method 2 Isolate 1 Isolate 2 Isolate 3 Isolate 4 Isolate 5 Isolate 6 Typing system concordance
  17. 17. Example • 42 Campylobacter isolates • 2 outbreaks • 12 sporadic cases • Typing by PFGE, MLST, flaA, and flaB sequencing. Mellmann et al. (2004). JCM 42: 4840
  18. 18. Example Mellmann et al. (2004). JCM 42: 4840
  19. 19. Example DI Method No. of types No. of most frequent type Index of diversity (95% CI) PFGE 19 8 0.944 (0.909-0.979) MLST ST 14 12 0.886 (0.825-0.948) flaA 13 6 0.920 (0.895-0.944) flaB 12 8 0.902 (0.871-0.934)
  20. 20. Concordances Gold-standard: PFGE Rand‘s coefficent Adjusted Rand‘s coefficient: Wallace‘s coefficient W1 MLST ST 0.94 0.615 0.979 flaA 0.948 0.588 0.75 flaB 0.958 0.706 1.0 Result: “In conclusion, PFGE remains the most discriminatory typing method for Campylobacter. However, flaB typing is a rapid, reproducible, discriminatory, and stable screening tool. ”
  21. 21. Calculation helper http://www.ridom.de/epicompare/ Ridom EpiCompare (free software)
  22. 22. Calculation helper http://darwin.phyloviz.net/ComparingPartitions/index.php?link=Home Comparing partitions (free webpage)
  23. 23. Summary
  24. 24. Evaluation of Molecular Typing Techniques Image Credits Biohazard by Szczur http://www.flickr.com/photos/szczur/54101979/ Tips by PlaxcoLab: http://www.flickr.com/photos/34857812@N04/3235836272/ Blackboard by ©Miss cicicola.Z: http://www.flickr.com/photos/cicicola-zy/1430894423/ aboutpixel.de / postkasten...damals © mpdrei master aboutpixel.de / laptop © Peter Ehmann aboutpixel.de / Reagiernder Bürgermeister von Berlin. © Andi Streidl aboutpixel.de / notizen 04 © Bernd Boscolo aboutpixel.de / Kleingeld © daylight aboutpixel.de / Busstation © Konstantin Gastmann aboutpixel.de / Pinwand © Alexander Kreher Bildquelle: aboutpixel.de / Blutplatte © Ute Pelz we*ge / photocase.com Some images from www.morguefile.com Thomas Weniger University of Münster, Germany tweniger@uni-muenster.de

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