You can do one thing first precipitate the cells then you can use QIAamp  DNA mini kit but take care of eukaryotic contamination like host own cells DNA.

Thank you for your answer!

I found studies that used:

Wizard Genomic DNA  Purification Kit,

QIAmp DNA mini kit

QIAmp DNA blood mini kit,

Zymo Bacterial/Fungal DNA Kit

Trizol by Invitrogen

Most of the articles have different protocols and this makes choosing the right one quite difficult. Some even have "housemade" protocols or adapted commercial kits by adding proteinase K, lysozyme or other products.

Although, none seem to to anything about the fact that the bacterial cells in the ascites are mixed up with cells from the patient. Only one study selectively enriched by affinity chromatography the bactDNA. I’m guessing that since you have specific primes for your sequence of interest it shouldn’t bother you that much.

Try to do aggressive lysis with at least proteinase K, lysozyme or mechanical disruption.   

Thank you!

But what do you mean by aggressive lysis? The QIAamp protocol has a step with adding proteinase K and incubating at 56*C for 1-3h.

Do you think I should increase the quantity?

Dear Camelia

I have experience in fecal samples and incubating 1-2 h in the proteinase K treatments using the qiagen kit for stool samples with good results.

Increasing the proteinase K incubation time is recommended for bacterial lysis. In your scenario I would use 2 h and  also an insulin syringe as mechanical lysis (but try to avoid foam). 

Camelia,

This is a good question.  Sometimes I think that researchers simply use whatever method is most commonly reported in the papers that they (we) read.  I know I tend to do that.  After all, if it is working for others, why not use it?  But what method is best?  I think most kits from companies today that are commonly used by researchers will give comparable results.  I would look at papers from research groups that have been researching and publishing for a long time--what methods do they use?

You are right, if you are doing PCR with bacteria-specific primers, you do not need to worry about patient cells.  I have used Qiagen kits for extraction from swabs, blood spots, hair, and bacterial cultures, and I've been happy with them.  I've used Zymo PCR clean-up kits, and they worked well, so I would assume their extraction kits would work also.  If you are having trouble getting DNA, a bead-beating kit might be helpful, to break up tough cell walls.  But I think a longer Prot K incubation, and mechanical lysis (as Fausto suggested) should be sufficient.  Simply vortexing for a few minutes could be helpful as well.  If you do get foam, a longer centrifugation step before going to columns should take care of it.  You could add more Prot K, yes.  Some Qiagen manuals have instructions on adding more Prot K and longer incubations (for extraction from tough tissues, such as fingernails).  The Qiagen "Forensic DNA Mini Kit" if they still have such a product, might be helpful.