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Kuret S, Kalajzic N, Ruzdjak M, Grahovac B, Jezina Buselic MA, Sardelić S, Delic A, Susak L, Sutlovic D. Real-Time PCR Method as Diagnostic Tool for Detection of Periodontal Pathogens in Patients with Periodontitis. Int J Mol Sci 2024; 25:5097. [PMID: 38791137 PMCID: PMC11121222 DOI: 10.3390/ijms25105097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/02/2024] [Accepted: 05/05/2024] [Indexed: 05/26/2024] Open
Abstract
The most common type of periodontal disease is chronic periodontitis, an inflammatory condition caused by pathogenic bacteria in subgingival plaque. The aim of our study was the development of a real-time PCR test as a diagnostic tool for the detection and differentiation of five periodontopathogenic bacteria, Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Tannerella forsythia, Prevotella intermedia, and Treponema denticola, in patients with periodontitis. We compared the results of our in-house method with the micro-IDent® semiquantitative commercially available test based on the PCR hybridization method. DNA was isolated from subgingival plaque samples taken from 50 patients and then analyzed by both methods. Comparing the results of the two methods, they show a specificity of 100% for all bacteria. The sensitivity for A. actinomycetemcomitans was 97.5%, for P. gingivalis 96.88%, and for P. intermedia 95.24%. The sensitivity for Tannerella forsythia and T. denticola was 100%. The Spearman correlation factor of two different measurements was 0.976 for A. actinomycetemcomitans, 0.967 for P. gingivalis, 0.949 for P. intermedia, 0.966 for Tannerella forsythia, and 0.917 for T. denticola. In conclusion, the in-house real-time PCR method developed in our laboratory can provide information about relative amount of five bacterial species present in subgingival plaque in patients with periodontitis. It is likely that such a test could be used in dental diagnostics in assessing the efficacy of any treatment to reduce the bacterial burden.
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Affiliation(s)
- Sendi Kuret
- Department of Health Studies, University of Split, 21000 Split, Croatia;
| | - Nina Kalajzic
- Department of Health Studies, University of Split, 21000 Split, Croatia;
| | - Matija Ruzdjak
- Department of Biology, Faculty of Natural Science, University of Zagreb, 10000 Zagreb, Croatia;
| | | | | | - Sanda Sardelić
- Department of Microbiology, University Hospital Centre Split, 21000 Split, Croatia;
| | - Anja Delic
- Polyclinic Analysis, 21000 Split, Croatia; (A.D.); (L.S.)
| | - Lana Susak
- Polyclinic Analysis, 21000 Split, Croatia; (A.D.); (L.S.)
| | - Davorka Sutlovic
- Department of Health Studies, University of Split, 21000 Split, Croatia;
- Department of Toxicology and Pharmacogenetics, School of Medicine, University of Split, 21000 Split, Croatia
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Lu M, Sun X, Zhao Y, Zheng L, Lin J, Tang C, Chao K, Chen Y, Li K, Zhou Y, Xiao J. Low cycle number multiplex PCR: A novel strategy for the construction of amplicon libraries for next-generation sequencing. Electrophoresis 2024. [PMID: 38533931 DOI: 10.1002/elps.202300160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 02/11/2024] [Accepted: 02/15/2024] [Indexed: 03/28/2024]
Abstract
Multiplex PCR is a critical step when preparing amplicon library for next-generation sequencing. However, there are several challenges related to multiplex PCR including poor uniformity, nonspecific amplification, and primer-dimers. To address these issues, we propose a novel solution strategy that involves using a low cycle number (<10 cycles) in multiplex PCR and then employing carrier DNAs and magnetic beads for the selection of targeted products. This technique improves the amplicon uniformity while also reducing primer-dimers and PCR artifacts. To evaluate our technique, we initially utilized 120 DNA fragments from mouse genome containing single nucleotide polymorphism (SNP) sites. Sequencing results demonstrated that with only 7 cycles of multiplex PCR, 95.8% of the targeted SNP sites were mapped, with a coverage of at least 1×. The average sequencing depth of all amplicons was 1705.79 ± 1205.30×; 87% of them reached a coverage depth that exceeded 0.2-fold of the average sequencing depth. Our method had a greater uniformity (87%) when compared to Hi-Plex PCR (53.3%). Furthermore, we validated our strategy by randomly selecting 90 primer pairs twice from the initial set of 120 primer-pairs. Next, we used the same protocol to prepare amplicon libraries. The two groups had an average sequencing depth of 1013.30 ± 585.57× and 219.10 ± 158.27×, respectively; over 84% of the amplicons had a sequencing depth that exceeded 0.2-fold of average depth. These results suggest that the use of a low cycle number in multiplex PCR is a cost-effective and efficient approach for the preparation of amplicon libraries.
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Affiliation(s)
- Meng Lu
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Xiuxiu Sun
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Yuxin Zhao
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Linlin Zheng
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Junjie Lin
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Chen Tang
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Kaiyue Chao
- Shanghai Biowing Biotechnology Application Co., Ltd, Shanghai, P. R. China
| | - Ye Chen
- Shanghai Biowing Biotechnology Application Co., Ltd, Shanghai, P. R. China
| | - Kai Li
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Yuxun Zhou
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Junhua Xiao
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
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Lundberg DS, Pramoj Na Ayutthaya P, Strauß A, Shirsekar G, Lo WS, Lahaye T, Weigel D. Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community composition. eLife 2021; 10:e66186. [PMID: 34292157 PMCID: PMC8387020 DOI: 10.7554/elife.66186] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 07/19/2021] [Indexed: 12/26/2022] Open
Abstract
The ratio of microbial population size relative to the amount of host tissue, or 'microbial load', is a fundamental metric of colonization and infection, but it cannot be directly deduced from microbial amplicon data such as 16S rRNA gene counts. Because existing methods to determine load, such as serial dilution plating, quantitative PCR, and whole metagenome sequencing add substantial cost and/or experimental burden, they are only rarely paired with amplicon sequencing. We introduce host-associated microbe PCR (hamPCR), a robust strategy to both quantify microbial load and describe interkingdom microbial community composition in a single amplicon library. We demonstrate its accuracy across multiple study systems, including nematodes and major crops, and further present a cost-saving technique to reduce host overrepresentation in the library prior to sequencing. Because hamPCR provides an accessible experimental solution to the well-known limitations and statistical challenges of compositional data, it has far-reaching potential in culture-independent microbiology.
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Affiliation(s)
- Derek S Lundberg
- Department of Molecular Biology, Max Planck Institute for Developmental BiologyTübingenGermany
| | | | - Annett Strauß
- Department of Evolutionary Biology, Max Planck Institute for Developmental BiologyTübingenGermany
| | - Gautam Shirsekar
- Department of Molecular Biology, Max Planck Institute for Developmental BiologyTübingenGermany
| | - Wen-Sui Lo
- ZMBP-General Genetics, University of TübingenTübingenGermany
| | - Thomas Lahaye
- ZMBP-General Genetics, University of TübingenTübingenGermany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental BiologyTübingenGermany
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Bhanothu V, Venkatesan V. Conventional polymerase chain reaction and amplification refractory mutation system-multi-gene/ multi-primer PCR in the diagnosis of female genital tuberculosis. Arch Microbiol 2019; 201:267-281. [DOI: 10.1007/s00203-019-01631-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/12/2019] [Indexed: 01/18/2023]
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Soleimani M, Zolfaghari MR. Development and Comparison of In-house Line Probe Assay (LiPA) and SYBR Green Real-time PCR Regarding the Detection of Periodontal Pathogens. Avicenna J Med Biotechnol 2019; 11:80-87. [PMID: 30800247 PMCID: PMC6359689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Periodontal disease, which can become a chronic condition, is an inflammatory disease that upsets the soft and hard structures supporting the teeth. The aim of the present study was to design and develop an in-house Line Probe Assay (LiPA), to detect putative periodontitis-related bacterial pathogens, and compare it with SYBR Green Real-time PCR. METHODS The LiPA method was launched using biotinylated 16s rRNA universal primers and specific probes for each of the five bacteria including Aggregatibacter acti-nomycetemcomitans, Prevotella intermedia, Tannerella forsythia, Porphyromonas gingivalis and Treponema denticola. For this, optimized quantities of the primers and specific probes were dotted onto nylon membrane stripes in a defined pattern. Hybridization was performed between the probes and the single-stranded biotinylated PCR products. The stripes were developed via biotin-streptavidin reaction. Ultimately, the analytical and diagnostic sensitivity and specificity of the in-house LiPA was evaluated and compared with SYBR Green Real-time PCR. RESULTS The detection limit of the LiPA was 2760 copies of targeted genes. In testing analytical specificity, only signals corresponding to the specific biotinylated products were produced. The calculated diagnostic sensitivity of the LiPA for the five bacterial targets ranged from 96.4 to 100%, whereas the diagnostic specificity was between 90.9 and 100%. Comparing the results, no noticeable difference (p=0.4795) was observed between the two methods. CONCLUSION To screen periodontal pathogens, a simple, inexpensive and accurate method is desirable. The in-house LiPA, having advantages such as high specificity and sensitivity, and the ability to detect five major periodontal pathogens, offers the option of evaluating samples without the need for a post-PCR platform.
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Affiliation(s)
- Mohammad Soleimani
- Corresponding author: Mohammad Soleimani, Ph.D., Department of Microbiology, Qom Branch, Islamic Azad University, Qom, Iran, Tel: +98 251 7780001, Fax: +98 2517780001, E-mail:
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Mišić M, Čukić J, Vidanović D, Šekler M, Matić S, Vukašinović M, Baskić D. Prevalence of Genotypes That Determine Resistance of Staphylococci to Macrolides and Lincosamides in Serbia. Front Public Health 2017; 5:200. [PMID: 28894731 PMCID: PMC5581325 DOI: 10.3389/fpubh.2017.00200] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 07/24/2017] [Indexed: 11/30/2022] Open
Abstract
Macrolides, lincosamides, and streptogramins (MLS) resistance genes are responsible for resistance to these antibiotics in Staphylococcus infections. The purpose of the study was to analyze the distribution of the MLS resistance genes in community- and hospital-acquired Staphylococcus isolates. The MLS resistance phenotypes [constitutive resistance to macrolide–lincosamide–streptogramin B (cMLSb), inducible resistance to macrolide–lincosamide–streptogramin B (iMLSb), resistance to macrolide/macrolide–streptogramin B (M/MSb), and resistance to lincosamide–streptogramin A/streptogramin B (LSa/b)] were determined by double-disc diffusion method. The presence of the MLS resistance genes (ermA, ermB, ermC, msrA/B, lnuA, lnuB, and lsaA) were determined by end-point polymerase chain reaction in 179 isolates of staphylococci collected during 1-year period at the Center for Microbiology of Public Health Institute in Vranje. The most frequent MLS phenotype among staphylococcal isolates, both community-acquired and hospital-acquired, was iMLSb (33.4%). The second most frequent was M/MSb (17.6%) with statistically significantly higher number of hospital-acquired staphylococcal isolates (p < 0.05). MLS resistance was mostly determined by the presence of msrA/B (35.0%) and ermC (20.8%) genes. Examined phenotypes were mostly determined by the presence of one gene, especially by msrA/B (26.3%) and ermC (14.5%), but 15.6% was determined by a combination of two or more genes. M/MSb phenotype was the most frequently encoded by msrA/B (95.6%) gene, LSa/b phenotype by lnuA (56.3%) gene, and iMLSb phenotype by ermC (29.4%) and ermA (25.5%) genes. Although cMLSb phenotype was mostly determined by the presence of ermC (28.9%), combinations of two or more genes have been present too. This pattern was particularly recorded in methicillin-resistant Staphylococcus aureus (MRSA) (58.3%) and methicillin-resistant coagulase-negative staphylococci (MRCNS) (90.9%) isolates with cMLSB phenotype. The msrA/B gene and M/MSb phenotype were statistically significantly higher in hospital-acquired than community-acquired staphylococci strains (p < 0.05). There are no statistically significant differences between staphylococci harboring the rest of MLS resistance genes acquired in community and hospital settings (p > 0.05). The prevalence of iMLSb phenotypes may change over time, so it is necessary to perform periodic survey of MLS resistance phenotypes, particularly where the D-test is not performed routinely.
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Affiliation(s)
- Milena Mišić
- Department of Microbiology, Public Health Institute Vranje, Vranje, Serbia
| | - Jelena Čukić
- Department of Clinical Microbiology, Laboratory for Virology, Serology, Immunology and Molecular Diagnostics, Public Health Institute Kragujevac, Kragujevac, Serbia
| | - Dejan Vidanović
- Department of Laboratory Diagnostics, National Reference Laboratory for Avian Influenza and Newcastle Disease of Poultry Republic of Serbia, Veterinary Specialized Institute Kraljevo, Kraljevo, Serbia
| | - Milanko Šekler
- Department of Laboratory Diagnostics, National Reference Laboratory for Avian Influenza and Newcastle Disease of Poultry Republic of Serbia, Veterinary Specialized Institute Kraljevo, Kraljevo, Serbia
| | - Sanja Matić
- Faculty of Medical Sciences, Doctoral Studies, University of Kragujevac, Kragujevac, Serbia
| | - Mihailo Vukašinović
- Faculty of Medical Sciences, Doctoral Studies, University of Kragujevac, Kragujevac, Serbia
| | - Dejan Baskić
- Department of Clinical Microbiology, Laboratory for Virology, Serology, Immunology and Molecular Diagnostics, Public Health Institute Kragujevac, Kragujevac, Serbia.,Center for Molecular Medicine and Stem Cell Research, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
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Osmani Bojd M, Kamaladini H, Haddadi F, Vaseghi A. Thiolated AuNP probes and multiplex PCR for molecular detection of Staphylococcus epidermidis. Mol Cell Probes 2017; 34:30-36. [PMID: 28461258 DOI: 10.1016/j.mcp.2017.04.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/17/2017] [Accepted: 04/28/2017] [Indexed: 02/05/2023]
Abstract
The emergence of nanotechnology in biology helps to apply the gold nanoparticle probes for fast and accurate identification of pathogens compared to the time-consuming and non-precise phenotypic methods. In this study, two molecular methods have been established for the accurate identification of staphylococcus epidermidis from other coagulase-negative staphylococci. Multiplex PCR was performed using designed primers for Gmk2 and pta housekeeping genes, and SESB specific gene of S. epidermidis. Colorimetric detection by gold nanoparticle probes was carried out using two 20-base thiolated probes designed based on the sequence of pta housekeeping gene of S. epidermidis. The specificity of multiplex PCR and colorimetric assays were determined using genomic DNA of Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa and Acinetobacter baumannii as negative controls and no alteration was detected. To investigate the sensitivity of the primers and gold nanoparticle probes, different concentrations of the extracted DNA from S. epidermidis were used. Based on the results, the minimum required quantity of target DNA for multiplex PCR amplification was 1 ng/μL and for color and absorption alteration of solution in colorimetric assay was 20 ng/μL. Our results revealed that both methods were sufficiently specific and sensitive to detect S. epidermidis.
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Affiliation(s)
- Mahsa Osmani Bojd
- Department of Biology, Faculty of Basic Sciences, University of Zabol, Zabol, Iran
| | - Hossein Kamaladini
- Department of Biology, Faculty of Basic Sciences, University of Zabol, Zabol, Iran.
| | - Fatemeh Haddadi
- Department of Biology, Faculty of Basic Sciences, University of Zabol, Zabol, Iran
| | - Akbar Vaseghi
- Young Researchers and Elite Club, Ardabil Branch, Islamic Azad University, Ardabil, Iran
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Ma X, Xu W, Chen C, Lu Z, Li J. A microfabrication-free nanoliter droplet array for nucleic acid detection combined with isothermal amplification. Analyst 2016; 140:4370-3. [PMID: 25988200 DOI: 10.1039/c5an00573f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A nanoliter droplet array based on a hydrophilic-hydrophobic patterned chip is developed without using microfabrication technology. Combined with the isothermal amplification technology, it has been applied to perform nucleic acid detection, showing excellent specificity and sensitivity. As a versatile platform, it is used to detect three gene targets successfully.
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Affiliation(s)
- Xiaodong Ma
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, P. R. China.
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Ravan H, Amandadi M, Sanadgol N. A highly specific and sensitive loop-mediated isothermal amplification method for the detection of Escherichia coli O157:H7. Microb Pathog 2015; 91:161-5. [PMID: 26724736 DOI: 10.1016/j.micpath.2015.12.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 12/19/2015] [Accepted: 12/22/2015] [Indexed: 01/25/2023]
Abstract
E. coli O157:H7 is one of the most important foodborne pathogen that causes some human illnesses such as bloody diarrhea, hemolytic-uremic syndrome, and kidney failure. We developed a loop-mediated isothermal amplification (LAMP) assay with six special primers that target a highly specific 299-bp region of the Z3276 gene for the detection of E. coli O157:H7. Among 117 bacterial strains tested in this study, positive results were only obtained from E. coli O157:H7 strains. The sensitivity level of the Z3276-LAMP assay was determined to be 5 CFU/reaction tube in pure bacterial culture. Moreover, the LAMP assay was successfully applied to artificially contaminated ground beef with a sensitivity level of 10(3) CFU/mL without pre-enrichment and 10 CFU/mL after a 4-h pre-enrichment. In conclusion, the present LAMP assay would be a useful and powerful tool for the rapid, sensitive, and specific diagnosis of E. coli O157:H7 strains in resource limited laboratories.
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Affiliation(s)
- Hadi Ravan
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Mojdeh Amandadi
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Nima Sanadgol
- Department of Biology, Faculty of Science, Zabol University, Zabol, Iran; Pharmaceutical Science Research Center (PSRC), Tehran University of Medical Sciences (TUMS), Tehran, Iran
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Hanapi UK, Desa MNM, Ismail A, Mustafa S. A higher sensitivity and efficiency of common primer multiplex PCR assay in identification of meat origin using NADH dehydrogenase subunit 4 gene. Journal of Food Science and Technology 2014; 52:4166-75. [PMID: 26139881 DOI: 10.1007/s13197-014-1459-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 06/14/2014] [Accepted: 06/27/2014] [Indexed: 11/26/2022]
Abstract
A Common Primer Multiplex PCR (CP-M-PCR) was developed to detect meat origin of four groups of animal (pig, ruminant, avian and rabbit). This method demonstrated higher sensitivity and efficiency than the conventional multiplex PCR. In this approach, a common forward primer was designed in the 5' end of a homologous region of mitochondrial NADH dehyrogenase subunit 4 (Nad 4) gene sequences of all the animal groups. Specific adapter reverse primers were designed by adding an adapter sequence at the 5' end. The same adapter sequence was used as the common adapter reverse primer. The primers generated specific fragments of 267, 370, 504, and 548 bp lengths for pig, ruminant, avian and rabbit meats, respectively. The use of adapter sequence at the 5' end of the common adapter reverse primers increased the efficiency of the amplification and the application of a common forward primer solved the complexity in multiplex PCR system. Bands of specific amplification can be detected in the PCR assays containing as low as 10(-6) μM of adapter reverse primer. This result indicated that the sensitivity was tremendously increased as compared to the conventional multiplex PCR (10(-3) μM). CP-M-PCR detection limit of the DNA samples was 0.1 ng for the four groups of meats. CP-M-PCR has greatly improved the sensitivity and efficiency of the PCR system for a more reliable and accurate outcome than conventional multiplex PCR system.
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Affiliation(s)
- Ummi Kalthum Hanapi
- Halal Products Research Institute, Putra Infoport, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Mohd Nasir Mohd Desa
- Halal Products Research Institute, Putra Infoport, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia ; Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Amin Ismail
- Halal Products Research Institute, Putra Infoport, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia ; Department of Nutrition and Dietetic, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Shuhaimi Mustafa
- Halal Products Research Institute, Putra Infoport, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia ; Department of Microbiology, Faculty of Biotechnology and Molecular Biology, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
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