<!DOCTYPE article PUBLIC "-//NLM//DTD Journal Publishing DTD v2.3 20070202//EN" "journalpublishing.dtd">
<article article-type="research-article" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:mml="http://www.w3.org/1998/Math/MathML">
<front>
<journal-meta>
<journal-id journal-id-type="nlm-ta">Mac Vet Rev</journal-id>
<journal-title>Macedonian Veterinary Review</journal-title>
<issn pub-type="ppub">1409-7621</issn>
<issn pub-type="epub">1857-7415</issn>
<publisher>
<publisher-name>Faculty of Veterinary Medicine - Saints Cyril and Methodius University of Skopje, Macedonia</publisher-name>
<publisher-loc>Macedonia</publisher-loc>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="publisher-id">MVR-38-97</article-id>
<article-id pub-id-type="doi">10.14432/j.macvetrev.2015.01.038</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Original Scientific Article</subject>
</subj-group>
</article-categories>
<title-group>
<article-title>PCR ASSAY WITH HOST SPECIFIC INTERNAL CONTROL FOR <italic>STAPHYLOCOCCUS AUREUS</italic> FROM BOVINE MILK SAMPLES</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Cantekin</surname>
<given-names>Zafer</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
<xref ref-type="corresp" rid="cor1"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Ergun</surname>
<given-names>Yasar</given-names>
</name>
<xref ref-type="aff" rid="aff2">2</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Solmaz</surname>
<given-names>Hasan</given-names>
</name>
<xref ref-type="aff" rid="aff3">3</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>&#x00D6;zmen</surname>
<given-names>Gamze &#x00D6;zge</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Demir</surname>
<given-names>Melek</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Saidi</surname>
<given-names>Radhwane</given-names>
</name>
<xref ref-type="aff" rid="aff4">4</xref>
</contrib>
</contrib-group>
<aff id="aff1"><label>1</label><italic>Mustafa Kemal University, Faculty of Veterinary Medicine, Department of Microbiology, Tayfur Sokmen Campus 31000 Hatay, Turkey</italic></aff>
<aff id="aff2"><label>2</label><italic>Mustafa Kemal University, Faculty of Veterinary Medicine, Department of Obstetrics and Gynecology, Tayfur Sokmen Campus 31000 Hatay, Turkey</italic></aff>
<aff id="aff3"><label>3</label><italic>Y&#x00FC;z&#x00FC;nc&#x00FC; Y&#x0131;l University, Faculty of Pharmacy, Department of Pharmaceutical Microbiology, Campus, 65100 Van, Turkey</italic></aff>
<aff id="aff4"><label>4</label><italic>Department of Agronomy, Telidji Amar University, P. O. Box 37G, 03000 Laghouat, LBRA, Algeria</italic></aff>
<author-notes>
<corresp id="cor1">
<italic>Corresponding author</italic>: Dr. Zafer Cantekin, PhD <italic>E-mail address</italic>: <email xlink:href="zcantekin@hotmail.com">zcantekin@hotmail.com</email>
<italic>Present address:</italic> Mustafa Kemal University, Faculty of Veterinary Medicine, Department of Microbiology, Tayfur Sokmen Campus 31000 Hatay, Turkey <italic>Phone:</italic> +90 5304580107
</corresp>
</author-notes>
<pub-date pub-type="ppub">
<year>2015</year>
</pub-date>
<pub-date pub-type="epub">
<day>27</day>
<month>01</month>
<year>2015</year>
</pub-date>
<volume>38</volume>
<issue>1</issue>
<fpage>97</fpage>
<lpage>100</lpage>
<history>
<date date-type="received"><day>13</day><month>11</month><year>2014</year></date>
<date date-type="rev-recd"><day>13</day><month>01</month><year>2015</year></date>
<date date-type="accepted"><day>20</day><month>01</month><year>2015</year></date>
</history>
<permissions>
<copyright-statement>Copyright: &#x000a9; Cantekin Z.</copyright-statement>
<copyright-year>2015</copyright-year>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by-nc-sa/3.0">
<p>This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p>
</license>
</permissions>
<abstract>
<p><italic>Staphylococcus aureus</italic> is considered as one of the most important and common pathogens of bovine mastitis. Polymerase Chain Reaction is frequently proposed in the diagnosis of <italic>S. aureus</italic> directly from milk samples instead of classical culture. However, false-negative results may occur in the polymerase chain reaction analysis performed directly from clinical material. For the purpose of disclosing the false negative results, the use of internal amplification controls can be beneficial. Therefore, in this study a new polymerase chain reaction technique with host specific internal amplification control was developed by optimizing <italic>S. aureus</italic>-specific primers in combination with bovine specific primers. The effectiveness of the developed technique in this study was attempted in milk samples from bovine subclinical mastitis. This technique has the potential to detect <italic>S. aureus</italic> from bovine milk samples or dairy products.</p>
</abstract>
<kwd-group>
<kwd>bovine milk</kwd>
<kwd>internal control</kwd>
<kwd>polymerase chain reaction</kwd>
<kwd><italic>Staphylococcus aureus</italic></kwd>
</kwd-group>
</article-meta>
</front>
<body>
<sec id="sec1-1" sec-type="intro">
<title>INTRODUCTION</title>
<p><italic>Staphylococcus aureus</italic>, one of the most prevalent pathogens of clinical and subclinical bovine mastitis, can spread rapidly throughout the herd if management precautions are not taken (<xref ref-type="bibr" rid="ref1">1</xref>, <xref ref-type="bibr" rid="ref2">2</xref>). <italic>S. aureus</italic> is one of the most important and common pathogens of bovine mastitis. It causes significant economic losses in the dairy industry (<xref ref-type="bibr" rid="ref3">3</xref>). <italic>S. aureus</italic> damages milk-producing tissue and significantly decreases milk yield. In the early stages of infection, damage may be reversible, but when diagnosis is delayed, tissue damage is excessive and irreversible (<xref ref-type="bibr" rid="ref4">4</xref>). Therefore, a rapid and reliable method of identifying the bacteria responsible for mastitis is important for disease management in the herd (<xref ref-type="bibr" rid="ref5">5</xref>). Moreover, <italic>S. aureus</italic> infections are considered a serious problem that may affect public health because they can be transmitted by milk and milk products (<xref ref-type="bibr" rid="ref6">6</xref>).</p>
<p>While different methods have been used to detect these agents, bacterial culture is considered the gold standard method for identifying mastitis-causing microorganisms. However, conventional culture is slow, requiring 24&#x2013;48 h, and needs labour intensive study for definitive identification (<xref ref-type="bibr" rid="ref7">7</xref>, <xref ref-type="bibr" rid="ref8">8</xref>). Therefore, it is of commercial interest to accelerate this procedure by investigating alternative rapid DNA-based methods. PCR methods for detecting <italic>S. aureus</italic> in milk samples to identify cow mastitis have been proposed (<xref ref-type="bibr" rid="ref9">9</xref>, <xref ref-type="bibr" rid="ref10">10</xref>, <xref ref-type="bibr" rid="ref11">11</xref>). However, PCR analyses from direct clinical material can result in false negative results caused by inhibitors in the clinical specimens (<xref ref-type="bibr" rid="ref12">12</xref>, <xref ref-type="bibr" rid="ref13">13</xref>). Therefore the use of internal amplification controls with different strategies is recommended to determine false negative results of PCR analyses from direct clinical material or food samples (<xref ref-type="bibr" rid="ref14">14</xref>, <xref ref-type="bibr" rid="ref15">15</xref>).</p>
<p>The aim of the present study was to develop PCR analyses with internal amplification control to detect <italic>S. aureus</italic>. A specific primer set for <italic>S. aureus</italic> was used and combined with bovine-specific primers.</p>
</sec>
<sec id="sec1-2" sec-type="material|methods">
<title>MATERIAL AND METHODS</title>
<sec id="sec2-1">
<title>Samples and Primers</title>
<p>Total of 50 milk samples from subclinical bovine mastitis were obtained from cattle farms in the Hatay region (The clinical samples were taken with permission with MK&#x00DC; Local Ethics committee; Meeting Date 17.06.2010: Meeting No: 2010/02: Decision No: 30) and nucleic acids were extracted from milk samples using the phenol&#x2013;chloroform method. Extracted DNA was stored at &#x00AD;-20&#x00B0;C (<xref ref-type="bibr" rid="ref16">16</xref>).</p>
<p>Primers for <italic>S. aureus</italic> (Sau 327 and Sau 1645) and Bovine specific (12SM-FW and 12SBT-REV2) were used in this study. Simplex PCR protocols and procedures were carried out according to the recommendations in the literature for those primers. The properties of the primers used in this study are shown in <xref ref-type="table" rid="T1">Table 1</xref>.</p>
<table-wrap id="T1" position="float">
<label>Table 1</label>
<caption><p>Properties of primers used in the study</p></caption>
<table frame="hsides" rules="groups" width="100%">
<thead>
<tr>
<th align="left">Primer names</th>
<th align="left">Target Gene</th>
<th align="left">GC Contents (&#x0025;)</th>
<th align="left">Melting Temperature</th>
<th align="left">Sequences of primers</th>
<th align="left">Length of amplicons</th>
<th align="center">References</th>
</tr>
</thead>
<tbody>
<tr>
<td align="left">Sau 327</td>
<td align="left" rowspan="2">23S rRNA</td>
<td align="left">45</td>
<td align="left">63 &#x00B0;C</td>
<td align="left">5&#x2019;-GGACGACATTAGACGAATCA-3&#x2019;</td>
<td align="left" rowspan="2">1318 bp</td>
<td align="center" rowspan="2">10</td>
</tr>
<tr>
<td align="left">Sau 1645</td>
<td align="left">45</td>
<td align="left">63 &#x00B0;C</td>
<td align="left">5&#x2019;-CGGGCACCTATTTTCTATCT-3&#x2019;</td>
</tr>
<tr>
<td align="left">12SM-FW</td>
<td align="left" rowspan="2">12S rRNA gene sequences</td>
<td align="left">39</td>
<td align="left">65 &#x00B0;C</td>
<td align="left">5&#x2019;-CTAGAGGAGCCTGTTCTATAATCGATAA-3&#x2019;</td>
<td align="left" rowspan="2">346 bp</td>
<td align="center" rowspan="2">17</td>
</tr>
<tr>
<td align="left">12SBT-REV2</td>
<td align="left">37</td>
<td align="left">65 &#x00B0;C</td>
<td align="left">5&#x2019;-AAATAGGGTTAGATGCACTGAATCCAT-3&#x2019;</td>
</tr>
</tbody>
</table>
</table-wrap>
</sec>
<sec id="sec2-2">
<title>Optimisation of internally controlled PCR mix</title>
<p>All procedures and protocols for multiplex PCR assays were optimized according to Henegariu et al., (<xref ref-type="bibr" rid="ref18">18</xref>). The amplification mixture for multiplex PCR was carried out in a final volume of 25 &#x00B5;L. The mixture consisted of 200 ng of extracted DNA template, different amounts of 1.5U of <italic>Taq</italic>DNA polymerase (Vivantis Technologies), 2 &#x00B5;L of 10x PCR buffer (10X ViBuffer A without MgCl<sub>2</sub>), 3 mM MgCl<sub>2</sub>, 200 &#x00B5;M each of dNTPs (Vivantis Technologies), 20 pmol of primer pair (Sau 327 and Sau 1645) specific for <italic>S. aureus</italic>, and 5 pmol primers (12SM-FW and 12SBT-REV2) specific for bovine gene.</p>
<p>Amplification was carried out after an initial denaturation at 95&#x00B0;C for 3 min. The PCR protocol was: 60 s of template denaturation at 94&#x00B0;C, 60 s of different primer annealing temperatures at 54&#x00B0;C, and 90 s of primer extension at 72&#x00B0;C (total of 35 cycles), with a final extension at 72&#x00B0;C for 5 min. The amplified PCR products were electrophoresed in 1.5&#x0025; agarose gel and stained with ethidium bromide (0.5 mg/mL), and the DNA bands were visualised under UV light.</p>
</sec>
</sec>
<sec id="sec1-3" sec-type="results">
<title>RESULTS</title>
<sec id="sec2-3">
<title>Simplex PCR reaction results</title>
<p>In the PCR analyses of milk samples, 3 of 50 samples were found to be <italic>S. aureus</italic> bysimplex PCR and the specific amplification products (1318 bp). They are shown in <xref ref-type="fig" rid="F1">Figure 1</xref>. <italic>S. aureus&#x2013;</italic> specific bands were amplified very effectively with simplex PCR.</p>
<fig id="F1">
<label>Figure 1</label>
<caption>
<p>Results of simplex PCR from milk samples with <italic>S. aureus</italic> specific primers. M: 100bp plus marker. Lanes 1, 2, and 4: <italic>S. aureus</italic>-specific bands with Sau 327 and Sau 1645 primers (1318 bp). Lane 5: Distilled Water (Negative Control)</p>
</caption>
<graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="MVR-38-97-g001.tif"/>
</fig>
</sec>
<sec id="sec2-4">
<title>Multiplex PCR reaction results</title>
<p>In the PCR analysis results, specific bands for bovine gene as an internal control and specific bands for <italic>S. aureus</italic> were amplified effectively in the same PCR mixture; the amplification products are shown in <xref ref-type="fig" rid="F2">Figure 2</xref>.</p>
<fig id="F2">
<label>Figure 2</label>
<caption>
<p>Results of multiplex PCR from milk samples. M: 100bp plus marker. 1&#x2013;4: bovine-specific bands with 12SM-FW and 12SBT-REV2 primers (346 bp); 1, 2, and 4: <italic>S. aureus</italic>&#x2013;specific bands with Sau 327 and Sau 1645 primers (1318 bp); 5: Distilled Water (Negative Control)</p>
</caption>
<graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="MVR-38-97-g002.tif"/>
</fig>
</sec>
</sec>
<sec id="sec1-4" sec-type="discussion">
<title>DISCUSSION</title>
<p><italic>Staphylococcus aureus</italic> is considered an important and common pathogen causing bovine mastitis that can also be dangerous to human health. There are some studies including PCR detection of <italic>S. aureus</italic> from bovine milk samples (<xref ref-type="bibr" rid="ref9">9</xref>, <xref ref-type="bibr" rid="ref10">10</xref>, <xref ref-type="bibr" rid="ref11">11</xref>). However, in the PCR analyses from clinical material false negative results can be encountered due to inhibitory substances. In order to avoid these false negative results, using internal control was recommended (<xref ref-type="bibr" rid="ref12">12</xref>, <xref ref-type="bibr" rid="ref13">13</xref>). Particularly, using of host specific internal control can be useful to determine false negative results due to mistakes in sampling, DNA extraction or preparing PCR mixtures and thermal cycler failures (<xref ref-type="bibr" rid="ref14">14</xref>, <xref ref-type="bibr" rid="ref15">15</xref>, <xref ref-type="bibr" rid="ref19">19</xref>). Therefore, a PCR technique with host specific internal control was developed in this study by combining <italic>S. aureus</italic> specific primers and cow specific primers.</p>
<p>In this study a preliminary type, a specific primer set for <italic>S. aureus</italic>, was combined with specific bovine gene primers to develop an easy and rapid multiplex PCR system with high specificity. Using this optimised combination, a PCR analysis with an internal control specific for bovine genes was developed to detect <italic>S. aureus</italic>. The primer sets successfully amplified the target genes in the multiplex PCR without nonspecific or additional bands. There was no difficulty in discriminating between each band for the target strain (1318 bp) and the internal control (346 bp). Despite the low numbers of positive samples used in this study, the authors are confident that the developed technique will be reproducible in larger experiments.</p>
<p>At the end of the optimisation experiments, the best amplification results were obtained by decreasing 10x PCR buffer (2 &#x00B5;L) and host-specific primers 12SM-FW and 12SBT-REV2 (internal control, 5 pmol) and increasing to 20 pmol primers (Sau 327 and Sau 1645) specific for <italic>S. aureus</italic>. While low and high concentrations of MgCl<sub>2</sub> negatively affected the multiplex PCR, the best results were obtained with 3 mM of MgCl<sub>2</sub> concentration. The other important parameter was the annealing temperature: the best results were obtained at 54&#x00B0;C. The effects of these parameters were found to be in agreement with the recommendations of Henegariu et al. (<xref ref-type="bibr" rid="ref18">18</xref>) and Phuektes et al. (<xref ref-type="bibr" rid="ref20">20</xref>).</p>
<p>Despite the small number of samples analysed, the results of this preliminary study showed that this method can be used as a reliable and effective method for the diagnosis of <italic>S. aureus</italic> in the individual bovine milk or bulk milk samples. This technique should be tried for <italic>S. aureus</italic> detection from bovine milk products</p>
<p>In conclusion, conventional PCR has already become widespread and is less expensive than other molecular techniques. The developed technique in this study might have the potential to detect <italic>S. aureus</italic> from bovine clinical samples. This method can be used for detecting <italic>S. aureus</italic> in the bovine milk or milk products. The technique can also be extended to detect other contagious mastitis pathogens, such as <italic>Streptococcus agalactiae</italic> and <italic>Trueperella pyogenes</italic>.</p>
</sec>
</body>
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<p><bold>Competing Interests:</bold> The authors have declared that no competing interests exist.</p>
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