Bead beating tube and method for extracting deoxyribonucleic acid and/or ribonucleic acid from microorganisms
The present disclosure provides improved methods for bead beating and a bead beating system useful therefor. The present disclosure further provides methods of using the bead beating system to extract nucleic acids from cells containing the nucleic acids.
1. A method for producing a lysate from cells contained in blood containing an anticoagulant, comprising:
agitating the blood within a bead beating system in the absence of any additive other than the anticoagulant, under conditions sufficient to lyse both a fungal pathogen and a bacterial pathogen and provide a lysate suitable for PCR amplification of DNA from the fungal pathogen, when present, and the bacterial pathogen, when present, said bead beating system comprising (i) a sample tube or blood collection tube and (ii) beads.
2. The method of claim 1 , wherein the beads are adapted to lyse yeast or filamentous fungi.
3. The method of claim 1 , which comprises agitating the blood under conditions sufficient to (i) lyse Candida albicans and (ii) provide a lysate suitable for PCR amplification of DNA from Candida albicans , when the Candida albicans is present.
4. The method of claim 3 , which comprises agitating the blood under conditions sufficient to (i) lyse Staphylococcus aureus and (ii) provide a lysate suitable for PCR amplification of DNA from Staphylococcus aureus , when the Staphylococcus aureus is present.
5. The method of claim 4 , which comprises agitating the blood under conditions sufficient to (i) lyse Escherichia coli and (ii) provide a lysate suitable for PCR amplification of DNA from Escherichia coli , when the Escherichia coli is present.
6. The method of claim 3 , which comprises agitating the blood under conditions sufficient to (i) lyse Escherichia coli and (ii) provide a lysate suitable for PCR amplification of DNA from Escherichia coli , when the Escherichia coli is present.
7. The method of claim 1 , which comprises agitating the blood under conditions sufficient to (i) lyse Staphylococcus aureus and (ii) provide a lysate suitable for PCR amplification of DNA from Staphylococcus aureus , when the Staphylococcus aureus is present.
8. The method of claim 7 , which comprises agitating the blood under conditions sufficient to (i) lyse Escherichia coli and (ii) provide a lysate suitable for PCR amplification of DNA from Escherichia coli , when the Escherichia coli is present.
9. The method of claim 1 , which comprises agitating the blood under conditions sufficient to (i) lyse Escherichia coli and (ii) provide a lysate suitable for PCR amplification of DNA from Escherichia coli , when the Escherichia coli is present.
10. The method of claim 1 , wherein the agitating comprises subjecting the bead beating system to an oscillating motion.
11. The method of claim 1 , wherein the agitating is performed with a vortexer or a homogenizer.
12. The method of claim 1 , wherein the agitating comprises subjecting the bead beating system to 2000 or more oscillations per minute.
13. The method of claim 1 , wherein the agitating is performed for 25-60 seconds.
14. The method of claim 1 , wherein the agitating is performed for 1-2 minutes.
15. The method of claim 1 , wherein the anticoagulant is EDTA, citrate, oxalate or heparin.
16. The method of claim 1 , wherein the cells comprise one or more pathogens.
17. The method of claim 16 , wherein the cells comprise one or more bacterial pathogens, viral pathogens, fungal pathogens, or a combination thereof.
18. The method of claim 17 , wherein the cells comprise one or more fungal pathogens.
19. The method of claim 18 , wherein the one or more fungal pathogens comprise Candida albicans.
20. The method of claim 17 , wherein the cells comprise one or more bacterial pathogens.
21. The method of claim 20 , wherein the one or more bacterial pathogens comprise Staphylococcus aureus.
22. The method of claim 20 , wherein the one or more bacterial pathogens comprise Escherichia coli.
23. The method of claim 1 , wherein the blood comprises cells from multiple species.
24. The method of claim 1 , further comprising purifying one or more nucleic acids from the lysate.
25. The method of claim 1 , further comprising analyzing one or more nucleic acids from the lysate.