Evaluation of Moleculare Typing Techniques

Evaluation of

Molecular Typing Techniques

Thomas WenigerDepartment of Periodontology

University of Münster, Germany

tweniger@uni-muenster.de

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

tweniger@uni-muenster.de