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Lee SM, Balakrishnan HK, Doeven EH, Yuan D, Guijt RM. Chemical Trends in Sample Preparation for Nucleic Acid Amplification Testing (NAAT): A Review. BIOSENSORS 2023; 13:980. [PMID: 37998155 PMCID: PMC10669371 DOI: 10.3390/bios13110980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023]
Abstract
Nucleic acid amplification testing facilitates the detection of disease through specific genomic sequences and is attractive for point-of-need testing (PONT); in particular, the early detection of microorganisms can alert early response systems to protect the public and ecosystems from widespread outbreaks of biological threats, including infectious diseases. Prior to nucleic acid amplification and detection, extensive sample preparation techniques are required to free nucleic acids and extract them from the sample matrix. Sample preparation is critical to maximize the sensitivity and reliability of testing. As the enzymatic amplification reactions can be sensitive to inhibitors from the sample, as well as from chemicals used for lysis and extraction, avoiding inhibition is a significant challenge, particularly when minimising liquid handling steps is also desirable for the translation of the assay to a portable format for PONT. The reagents used in sample preparation for nucleic acid testing, covering lysis and NA extraction (binding, washing, and elution), are reviewed with a focus on their suitability for use in PONT.
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Affiliation(s)
- Soo Min Lee
- Centre for Regional and Rural Futures (CeRRF), Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia
| | - Hari Kalathil Balakrishnan
- Department of Chemical Engineering, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates;
| | - Egan H. Doeven
- School of Life and Environmental Sciences, Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia;
| | - Dan Yuan
- School of Mechanical and Mining Engineering, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Rosanne M. Guijt
- Centre for Regional and Rural Futures (CeRRF), Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia
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Raksakmanut R, Thanyasrisung P, Sritangsirikul S, Kitsahawong K, Seminario AL, Pitiphat W, Matangkasombut O. Prediction of Future Caries in 1-Year-Old Children via the Salivary Microbiome. J Dent Res 2023; 102:626-635. [PMID: 36919874 PMCID: PMC10399075 DOI: 10.1177/00220345231152802] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Dental caries is the most common chronic disease in children that causes negative effects on their health, development, and well-being. Early preventive interventions are key to reduce early childhood caries prevalence. An efficient strategy is to provide risk-based targeted prevention; however, this requires an accurate caries risk predictor, which is still lacking for infants before caries onset. We aimed to develop a caries prediction model based on the salivary microbiome of caries-free 1-y-old children. Using a nested case-control design within a prospective cohort study, we selected 30 children based on their caries status at 1-y follow-up (at 2 y old): 10 children who remained caries-free, 10 who developed noncavitated caries, and 10 who developed cavitated caries. Saliva samples collected at baseline before caries onset were analyzed through 16S rRNA gene sequencing. The results of β diversity analysis showed a significant difference in salivary microbiome composition between children who remained caries-free and those who developed cavitated caries at 2 y old (analysis of similarities, Benjamini-Hochberg corrected, P = 0.042). The relative abundance of Prevotella nanceiensis, Leptotrichia sp. HMT 215, Prevotella melaninogenica, and Campylobacter concisus in children who remained caries-free was significantly higher than in children who developed cavitated caries (Wilcoxon rank sum test, P = 0.024, 0.040, 0.049, and 0.049, respectively). These taxa were also identified as biomarkers for children who remained caries-free (linear discriminant analysis effect size, linear discriminant analysis score = 3.69, 3.74, 3.53, and 3.46). A machine learning model based on these 4 species distinguished between 1-y-old children who did and did not develop cavitated caries at 2 y old, with an accuracy of 80%, sensitivity of 80%, and specificity of 80% (area under the curve, 0.8; 95% CI, 44.4 to 97.5). Our findings suggest that these salivary microbial biomarkers could assist in predicting future caries in caries-free 1-y-old children and, upon validation, are promising for development into an adjunctive tool for caries risk prediction for prevention and monitoring.
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Affiliation(s)
- R Raksakmanut
- Graduate Program in Oral Biology and Center of Excellence on Oral Microbiology and Immunology, Faculty of Dentistry, Chulalongkorn University, Wang-Mai, Pathumwan, Bangkok, Thailand
| | - P Thanyasrisung
- Department of Microbiology and Center of Excellence on Oral Microbiology and Immunology, Faculty of Dentistry, Chulalongkorn University, Wang-Mai, Pathumwan, Bangkok, Thailand
| | - S Sritangsirikul
- Department of Pediatric Dentistry, Faculty of Dentistry, Chulalongkorn University, Wang-Mai, Pathumwan, Bangkok, Thailand.,PhD Program in Oral Sciences, Faculty of Dentistry, Khon Kaen University, Muang District, Khon Kaen, Thailand
| | - K Kitsahawong
- Division of Pediatric Dentistry, Department of Preventive Dentistry, Faculty of Dentistry, Khon Kaen University, Muang District, Khon Kaen, Thailand
| | - A L Seminario
- Department of Pediatric Dentistry, School of Dentistry, University of Washington, WA, USA
| | - W Pitiphat
- Division of Dental Public Health, Department of Preventive Dentistry, Faculty of Dentistry, Khon Kaen University, Muang District, Khon Kaen, Thailand
| | - O Matangkasombut
- Department of Microbiology and Center of Excellence on Oral Microbiology and Immunology, Faculty of Dentistry, Chulalongkorn University, Wang-Mai, Pathumwan, Bangkok, Thailand.,Research Laboratory of Biotechnology, Chulabhorn Research Institute, Laksi, Bangkok, Thailand
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Lee Y, Cho HS, Choi M, Prathap S, Soundrarajan N, Choi Y, Song H, Hong K, Park C. Comparison of DNA/RNA yield and integrity between PMAP36-mediated and other bacterial lysis methods. J Microbiol Methods 2021; 193:106396. [PMID: 34921868 DOI: 10.1016/j.mimet.2021.106396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/13/2021] [Accepted: 12/13/2021] [Indexed: 11/25/2022]
Abstract
Currently, several methods are available for the isolation of bacterial DNA and RNA. However, the diversity and complexity of cell envelope structures limit their efficiency depending on the target bacterial species. In this study, we compared the differences in yield and integrity of RNA prepared from four gram-negative and six gram-positive bacterial species using bead-beating, bacteriolytic protein, and PMAP36-vortexing methods. Similarly, we also compared the efficiency of DNA extraction from Staphylococcus aureus. Physical disruption of bacterial cells showed versatility in breaking cells against all tested species; however, a decrease in the integrity of isolated DNA and RNA was observed. Among membranolytic proteins, PMAP36 showed the most promising results, in terms of both the yield and integrity of the prepared nucleic acids. Our results show that each method has inherent advantages and disadvantages depending on its application. Therefore, the characteristics of each method and target species should be considered before the extraction of bacterial DNA and RNA.
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Affiliation(s)
- Yunjung Lee
- Department of stem cell and regenerative biotechnology, Konkuk University, Gwangjin-gu, Seoul, South Korea
| | - Hye-Sun Cho
- Department of stem cell and regenerative biotechnology, Konkuk University, Gwangjin-gu, Seoul, South Korea
| | - Munjeong Choi
- Department of stem cell and regenerative biotechnology, Konkuk University, Gwangjin-gu, Seoul, South Korea
| | - Somasundaram Prathap
- Department of stem cell and regenerative biotechnology, Konkuk University, Gwangjin-gu, Seoul, South Korea
| | | | - Youngsok Choi
- Department of stem cell and regenerative biotechnology, Konkuk University, Gwangjin-gu, Seoul, South Korea
| | - Hyuk Song
- Department of stem cell and regenerative biotechnology, Konkuk University, Gwangjin-gu, Seoul, South Korea
| | - Kwonho Hong
- Department of stem cell and regenerative biotechnology, Konkuk University, Gwangjin-gu, Seoul, South Korea
| | - Chankyu Park
- Department of stem cell and regenerative biotechnology, Konkuk University, Gwangjin-gu, Seoul, South Korea.
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