Identification of Streptococcus parasanguinis DNA contamination in human buccal DNA samples
© Mahfuz et al.; licensee BioMed Central Ltd. 2013
Received: 7 May 2013
Accepted: 14 November 2013
Published: 22 November 2013
The use of buccal swabs in clinical and scientific studies is a very popular method of collecting DNA, due to its non-invasive nature of collection. However, contamination of the DNA sample may interfere with analysis.
Here we report the finding of Streptococcus parasanguinis bacterial DNA contamination in human buccal DNA samples, which led to preferential amplification of bacterial sequence with PCR primers designed against human sequence.
Contamination of buccal-derived DNA with bacterial DNA can be significant, and may influence downstream genetic analysis. One needs to be aware of possible bacterial contamination when interpreting abnormal findings following PCR amplification of buccal swab DNA samples.
Buccal swabs are a popular, inexpensive and non-invasive method of collecting DNA samples. It is a convenient procedure for collecting DNA from geographically isolated populations for larger cohort studies , and has the advantage of avoiding the stressful process of venepuncture. When using buccal swab DNA, sampling or processing considerations may be important for obtaining optimal results . If buccal swabs are not collected and/or handled properly, potential complications may occur during subsequent analysis . Problems that can affect the interpretation include contamination, degradation, and insufficient yield [4–6]. Here we report a significant Streptococcus parasanguinis DNA contamination in human buccal-derived DNA. This bacteria is the most abundant microorganism in the mouth, and a primary colonizer of human tooth surfaces [7, 8] that plays an important role in dental plaque formation [9, 10].
To our knowledge, there have been no previous reports of Streptococcus parasanguinis contamination affecting genetic analysis of buccal swab DNA. It is not unexpected to have Streptococcal DNA contamination in DNA from a human buccal swab, due to the high abundance in oral microflora [12, 13]. In addition, when a buccal sample is collected, researchers generally do not enquire whether there is any oral disease. This might influence the quality of DNA isolated from buccal swabs. Under such circumstances, a blood sample may be a preferable method for obtaining DNA. A comparison of blood- and buccal-derived DNA from a Danish nurse cohort has previously been reported. 100% of the blood-derived DNA samples could be genotyped or PCR amplified, whereas only 23% of the DNA samples from mouth swabs could be PCR amplified and none of the swab-derived DNA samples could be genotyped .
Our finding demonstrates that bacterial contamination may be a significant contributor to the total amount of DNA isolated from a buccal swab, and may explain why an apparently sufficient quantity of high quality DNA does not perform as expected in human-specific PCR amplifications.
Wei Cheng and Stefan J White: Joint senior authors.
We are grateful to Royal Children Hospital, Melbourne, Sick Kids, Toronto and Hostal Universitario La Paz, Madrid for providing the DNA samples. Research in the authors’ laboratories is supported by the Jack Brockhoff Foundation, the Helen Macpherson Smith Trust, the Marian and E. H. Flack Trust, and Monash University. MIMR receives funding from the Victorian Government’s Operational Infrastructure Support Program. IM is supported by a Monash Graduate Scholarship (MGS) and Faculty of Medicine, Nursing and Health Science International Postgraduate Scholarship (MIPS).
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