Use of Pulse Field Gel Electrophoresis (PFGE) of DNA Restriction Fragments from Culture Isolates to Evaluate Epidemiologic Relatedness During an Infectious Disease Outbreak

 

Problem: During the outbreak of an infectious disease multiple patients may have the same culture isolate. It is important to separate those patients who are part of the outbreak from those who have acquired the organism by another mechanism. Patients who are part of the outbreak will have isolates that are similar; an isolate with different features is probably not part of the outbreak.

 

Protocol:

(1) DNA from pure culture isolates is extracted.

(2) The DNA from each isolate is treated with restriction enzymes.

(3) The treated DNA is then separated using pulse field gel electrophoresis.

(4) The pattern of fragments between the different isolates are then compared for similarities and differences.

 

Number of Fragment Differences from Reference Isolate	Category	Interpretation
0	indistinguishable (identical)	isolate part of outbreak
1 - 3	closely related	isolate probably part of the outbreak
4 - 6	possibly related	isolate is possible part of the outbreak
>= 7	different	isolate not part of outbreak

 

where:

• Table 2 has closely related with 2-3 fragment differences. 1 difference (as caused by a DNA addition) was not included, so I added it to the closely related category.

 

Limitations:

• The interpretation assumes that the mutation rate is relatively slow. If the mutation rate is very high then an isolate may be excluded.

• If there is limited genetic diversity in the isolates than organisms not part of the outbreak may be included.