General principles

in typing of bacteria

Valeria Bortolaia
vabo@food.dtu.dk
 Questions to address…

• What does ”typing of bacteria” mean?

• How do we perform genotyping of bacteria?

• Which method should we choose to type bacteria?

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 Typing of bacteria

• Typing (and subtyping) allow differentiation of bacteria beyond

the species and subspecies level

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 Typing of bacteria

• Typing methods can be phenotypic and genotypic

• Phenotyping: characterization of bacteria based on expressed

traits (e.g. sugar fermentation, antimicrobial resistance, etc.)

• Genotyping: characterization of bacteria based on genetic

content
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 How do we perform genotyping?

Chromosomal
DNA
Plasmid
DNA

AR genes; virulence genes; etc.

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Description/analysis of genetic content… E- learning
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 Description of genetic content
Information on whole
genomic content…
from isolate to strain

Information on
chromosomal
background

Information on the
vector of specific
Information on gene(s) (e.g. plasmid
6 specific gene(s) DNA) E- learning
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 Genotyping methods: two main categories
Band-based Sequence-based

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 Genotyping methods: examples

DNA banding-pattern DNA sequencing

• PFGE • MLST
• RFLP • Gene sequencing
• AFLP • Whole Genome
Sequencing
• RAPD
• SNP analysis
• MLVA • cgMLST
• …
• PCR-RFLP
• …
•…
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 How to choose a genotyping method

Characteristics of typing methods

• Typeability
• Discriminatory power
• Reproducibility
• Rapidity
• Cost We should consider the purpose…
• Lab capacity • Tracing outbreaks
•… • Long-term surveillance
• …. E- learning
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 Key messages

• There are many methods to type/characterize bacteria

• All methods have advantages and disadvantages

The choice of a typing method

depends on the question to answer!

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Thank you for your attention!

General principles
in typing and subtyping of bacteria

Valeria Bortolaia
vabo@food.dtu.dk