Usually like in colony PCR we just mix the colony or in you case a swab in autoclaved distilled water (small volume 15-20ul) and try to mix colony or swab containing the sample into the water. And later use that water with dissolved sample as a template for PCR.

I won't add a swab tip directly to the PCR reaction, as it will absorb the liquid that may result in the changed buffer composition. I guess what Gopal suggested is the best way to go.   

In your work, can you switch out the swab tip for a sterile wooden applicator stick? I use mini wood dowels. These are good for colony PCR because the flat surface allows you to easily pick up bacteria, spot to a master plate, and then swish around in your PCR tube for PCR. If you could use a wooden applicator stick to get the sample, so no swab on the end or alternatively, you can use the sample on the swab and plate that out, and then select the colonies off of that for colony PCR. I buy the mini dowels from a craft store and autoclave to sterilize. Here's what they look like: http://www.michaels.com/creatology-mini-wood-dowels/10334887.html#q=mini+dowels&start=1 You might be able to get away with using an applicator with a cotton tip for PCR directly if you saturate the applicator tip in sterile water first before swabbing for your sample. This could potentially keep your tip from absorbing the PCR reaction (since it's saturated at the start) and allow you to swirl your sample in the reaction mix. I haven't tried doing this before, but you could try it with some control sample to see if this will work. I'm assuming you are trying to cut out the time it takes to wait for the streak plate to grow up before you can do PCR on the sample.  

Dear Simon,

maybe I did not get the real prupose or background of your question, but if you would like to improve the "pre-analytical" sensitivity of any detection assay (culture, antigen detection by ELISA or PCR/realtime PCR) you might thinking about trying a new generation of sampling swaps so called "eswaps" . (Invented and licensed by Copan, Italy). They are well suited in diagnostics in different  fields such  as bacteriology, virology or forensics.... -these swaps release almost 100% of the sampled material:

http://www.copanusa.com/products/collection-transport/eswab/

Kind regards

Wolf

Simon, I agree to you that  cotton swab would affect the thermodynamics of the PCR in efficiency, primer annealing, etc. Moreover, the effect can be target sequence-specific, because of large cotton wool surface and different distribution of charge and chemical groups due to cotton treatment during manufacturing. I see two possible benefits in such method: 1) one-step sample preparation and PCR in one tube; 2) elimination of contamination risk due to opening the sample tube. But, it looks difficult for common PCR tubes. Maybe, set of two tubes connected vertically will help?

Swab with sample microbe will release DNA into buffer after short heating at 94-99oC, and it is possible to use  the liquid   immediately for PCR. 

Hi,

I put the swab tip into the falcon tube, and add sterile distilled water (up to tip head) into tube. Use this sample for extraction and then PCR.

Everyone

Thank you for all your replies, they are very useful. I am interested in seeing if this is a viable method for retrieving biological information from a surface so I am going to try and see if the benefits outweigh the penalties. Before I started I just wanted to try and find out if anyone had looked into this beforehand. Your responses have helped me plan a way forward

Simon