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Evaluation of Moleculare Typing Techniques: Typability, Stability, Reproducibility, Discriminatory Power, Concordance
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Evaluation of
Molecular Typing Techniques
Thomas WenigerDepartment of Periodontology
University of Münster, Germany
Typing:
Phenotypic and/or genetic analysis of bacterial isolates,
below the species/subspecieslevel, performed in order to
generate strain/clone-specificfingerprints […]
van Belkum et al., (2007). CMI, 13:1
PFGE MLST
flaAothers
C. jejuni: Different typing methods
Questions Suitable methodsDiscriminatory
power
Time
span
Outbreak investigations
Short-term/local surveillance
Control of hygiene measures
PFGE, RFLP,
AFLP, RA-PCR,
VNTR, SLST,
micro-array
highweeks -
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
Typing systemperformance
Convenience
A
A
B
Stability
A
A
Reproducibility
B
A
A
B
C
D
E
E
Typing method 1Discriminatorypower
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]
Discriminatorypower
AAA
B
C
Epidemiological Concordance
Typing systemperformance
Convenience
Costs
Rapidity
Ease of use
Convenience
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
Rand (1971) J. Am. Stat. Assoc. 66Hubert & Arabie (1985) J. Classification 2
Wallace (1983) J. Am. Stat. Assoc. 78
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
Example
• 42 Campylobacter
isolates
• 2 outbreaks
• 12 sporadic cases
• Typing by PFGE,
MLST, flaA, and flaB
sequencing.
Mellmann et al. (2004). JCM 42: 4840
Example
Mellmann et al. (2004). JCM 42: 4840
Example DI
Method No. of typesNo. of most
frequent typeIndex 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)
Concordances
Gold-standard: PFGE
Rand‘scoefficent
AdjustedRand‘scoefficient:
Wallace‘scoefficient 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. ”
Calculation helper
http://www.ridom.de/epicompare/
Ridom EpiCompare (free software)
Calculation helper
http://darwin.phyloviz.net/ComparingPartitions/index.php?link=Home
Comparing partitions (free webpage)
Summary
Evaluation of
Molecular Typing Techniques
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Thomas WenigerUniversity of Münster, Germany
