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Chakraborty S, Velagic M, Connor S. Development of a simple, rapid, and sensitive molecular diagnostic assay for cholera. PLoS Negl Trop Dis 2023; 17:e0011113. [PMID: 36745674 PMCID: PMC9934353 DOI: 10.1371/journal.pntd.0011113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 02/16/2023] [Accepted: 01/19/2023] [Indexed: 02/07/2023] Open
Abstract
Cholera continues to inflict high rates of morbidity and mortality. Prompt identification of cholera cases facilitates rapid outbreak responses in the short term while providing reliable surveillance data to guide long-term policies and interventions. Microbiological stool culture, the current recognized gold standard for diagnosing cholera, has significant limitations. Rapid diagnostic tests (RDTs) represent promising alternatives for diagnosing cholera in areas with limited laboratory infrastructure. However, studies conducted with the current cholera RDTs demonstrated wide variations in sensitivity and specificity. To address this gap in the diagnosis of cholera, we developed a simple, rapid, and sensitive diagnostic assay, "Rapid LAMP based Diagnostic Test (RLDT)." With a novel, simple sample preparation method directly from the fecal samples along with lyophilized reaction strips and using established Loop-mediated Isothermal Amplification (LAMP) platform, cholera toxin gene (ctxA) and O1 (O1rfb) gene could be detected in less than an hour. Cholera RLDT assay is cold chain and electricity-free. To avoid any end-user bias, a battery-operated, handheld reader was used to read the RLDT results. The performance specifications of the cholera RLDT assay, including analytical sensitivity and specificity, were evaluated using direct fecal samples, dried fecal samples on filter paper, and environmental water samples spiked with cholera strain. The limit of detection (LOD) was ~104 CFU/gm of stool for both ctxA and O1 genes, corresponding to about 1 CFU of Vibrio cholerae per reaction within 40 minutes. The LOD was 10 bacteria per ml of environmental water when tested with RLDT directly, without enrichment. Being simple, RLDT has the potential to be applied in resource-poor endemic settings for rapid, sensitive, and reliable diagnosis of cholera.
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Affiliation(s)
- Subhra Chakraborty
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- * E-mail:
| | - Mirza Velagic
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Sean Connor
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
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Cao Q, Liang S, Lin F, Cao J, Wang L, Li H, Liu M, Wang Y, Zhao L, Cao X, Guo Y. Detection of Haemophilus influenzae by loop-mediated isothermal amplification coupled with nanoparticle-based lateral flow biosensor assay. BMC Microbiol 2022; 22:123. [PMID: 35513820 PMCID: PMC9069426 DOI: 10.1186/s12866-022-02547-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/27/2022] [Indexed: 11/20/2022] Open
Abstract
Background Haemophilus influenzae was the most aggressive pathogen and formed a major cause of bacterial meningitis and pneumonia in young children and infants, which need medical emergency requiring immediate diagnosis and treatment. However, From isolation to identification of H. influenzae, the traditional diagnose strategy was time-consuming and expensive. Therefore, the establishment of a convenient, highly sensitive, and stable detection system is urgent and critical. Results In this study, we used a combined method to detect H. influenzae. Six specific primers were designed on the basis of outer membrane protein P6 gene sequence of H. influenzae. The reaction condition such as the optimum temperature was 65℃, and the optimum reaction time was 30 min, respectively. Through the loop-mediated isothermal amplification (LAMP) in combination with nanoparticle-based lateral flow biosensor (LFB), the sensitivity of LAMP-LFB showed 100 fg was the lowest genomic DNA templates concentration in the pure cultures. Meanwhile, the specificity of H. influenzae-LAMP-LFB assay showed the exclusive positive results, which were detected in H. influenzae templates. In 55 clinical sputum samples, 22 samples were positive with LAMP-LFB method, which was in accordance with the traditional culture and Polymerase Chain Reaction (PCR) method. The accuracy in diagnosing H. influenzae with LAMP-LFB could reach 100%, compared to culture and PCR method, indicating the LAMP-LFB had more advantages in target pathogen detection. Conclusions Taken together, LAMP-LFB could be used as an effective diagnostic approach for H. influenzae in the conditions of basic and clinical labs, which would allow clinicians to make better informed decisions regarding patient treatment without delay. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02547-5.
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Affiliation(s)
- Qilong Cao
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China.,Qingdao Haier Biotech Co. Ltd, Qingdao, 266109, China
| | | | - Feng Lin
- Qingdao Haier Biotech Co. Ltd, Qingdao, 266109, China.,School of Medicine, Huaqiao University, Quanzhou, 362021, Fujian, China
| | - Jun Cao
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Lin Wang
- Qingdao Haier Biotech Co. Ltd, Qingdao, 266109, China
| | - Hui Li
- Qingdao Haier Biotech Co. Ltd, Qingdao, 266109, China
| | - Mengyang Liu
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, 59 Haier Road, Qingdao, 266035, Shandong, China
| | - Yajuan Wang
- Dingzhou City People's Hospital, Heibei, 073099, China
| | - Lijun Zhao
- Dingzhou City People's Hospital, Heibei, 073099, China
| | - Xiaolong Cao
- Beijing Changping Institute for Tuberculosis Prevention and Treatment, Beijing, 102200, China.
| | - Yan Guo
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China.
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Xie M, Chen T, Xin X, Cai Z, Dong C, Lei B. Multiplex detection of foodborne pathogens by real-time loop-mediated isothermal amplification on a digital microfluidic chip. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.108824] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Chen D, Liang Z, Ren S, Alali W, Chen L. Rapid and Visualized Detection of Virulence-Related Genes of Vibrio cholerae in Water and Aquatic Products by Loop-Mediated Isothermal Amplification. J Food Prot 2022; 85:44-53. [PMID: 34436566 DOI: 10.4315/jfp-21-182] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/20/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT Vibrio cholerae can cause pandemic cholera in humans. The bacterium resides in aquatic environments worldwide. Continuous testing of V. cholerae contamination in water and aquatic products is imperative for food safety control and human health. In this study, a rapid and visualized method was developed for the first time based on loop-mediated isothermal amplification (LAMP) for detection of the important virulence-related genes ace, zot, cri, and nanH for toxins and the infectious process of V. cholerae. Three pairs of molecular probes targeting each of these genes were designed and synthesized. The one-step LAMP reaction was conducted at 65°C for 40 min. Positive results were inspected by the production of a light green color under visible light or green fluorescence under UV light (302 nm). Limit of detection of the LAMP method ranged from 1.85 to 2.06 pg per reaction of genomic DNA or 2.50 × 100 to 4.00 × 102 CFU per reaction for target genes of cell culture of V. cholerae, which was more sensitive than standard PCR. Inclusivity and exclusivity of the LAMP method were 100% for all target genes. The method showed similar high efficiency to a certain extent in rapid testing of spiked or collected specimens of water and aquatic products. Target genes were detected by absence from all water samples from various sources. However, high occurrences of the nanH gene were observed in intestinal samples derived from four species of fish and one species of shellfish, indicating a risk of potentially toxic V. cholerae in commonly consumed aquatic products. The results in this study provide a potential tool for rapid and visualized detection of V. cholerae in water and aquatic products. HIGHLIGHTS
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Affiliation(s)
- Dailing Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs of the People's Republic of China, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, People's Republic of China
| | - Zhili Liang
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs of the People's Republic of China, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, People's Republic of China
| | - Shunlin Ren
- Department of Internal Medicine, Virginia Commonwealth University/McGuire VA Medical Centre, Richmond, Virginia 23249, USA
| | - Walid Alali
- Department of Epidemiology and Biostatistics, Faculty of Public Health, Kuwait University, Kuwait City, Kuwait
| | - Lanming Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs of the People's Republic of China, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, People's Republic of China
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Han GR, Jang H, Ki H, Lee H, Kim MG. Reagent Filming for Universal Point-of-Care Diagnostics. SMALL METHODS 2021; 5:e2100645. [PMID: 34928024 DOI: 10.1002/smtd.202100645] [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: 06/15/2021] [Revised: 09/14/2021] [Indexed: 06/14/2023]
Abstract
Simplifying assays while maintaining the robustness of reagents is a challenge in diagnostics. This problem is exacerbated when translating quality diagnostic assays to developing countries that lack resources and infrastructure such as trained health workers, high-end equipment, and cold-chain systems. To solve this problem, in this study, a simple solution that films assay reagents to simplify the operation of diagnostic assays and preserve the stability of diagnostic reagents without using cold chains is presented. A polyvinyl-alcohol-based water-soluble film is used to encapsulate premeasured and premixed reagents. The reagent film, produced through a simple and scalable cast-drying process, provides a glassy inner matrix with abundant hydroxyl groups that can stabilize various reagents (ranging from chemicals to biological materials) by restricting molecular mobility and generating hydrogen bonds. The reagent film is applied to an enzymatic glucose assay, a high-sensitivity immunoassay for cardiac troponin, and a molecular assay for viral RNA detection, to test its practicability and universal applicability. The film-based assays result in excellent analytical/diagnostic performance and stable long-term reagent storage at elevated temperatures (at 25 or 37 °C, for six months), demonstrating clinical readiness. This technology advances the development and distribution of affordable high-quality diagnostics to resource-limited regions.
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Affiliation(s)
- Gyeo-Re Han
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, Republic of Korea
| | - Hyungjun Jang
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, Republic of Korea
| | - Hangil Ki
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, Republic of Korea
| | - Hoyeon Lee
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, Republic of Korea
| | - Min-Gon Kim
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, Republic of Korea
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Saar M, Beissner M, Gültekin F, Maman I, Herbinger KH, Bretzel G. RLEP LAMP for the laboratory confirmation of leprosy: towards a point-of-care test. BMC Infect Dis 2021; 21:1186. [PMID: 34823479 PMCID: PMC8620619 DOI: 10.1186/s12879-021-06882-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 11/02/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Nucleic acid-based amplification tests (NAAT), above all (q)PCR, have been applied for the detection of Mycobacterium leprae in leprosy cases and household contacts with subclinical infection. However, their application in the field poses a range of technical challenges. Loop-mediated isothermal amplification (LAMP), as a promising point-of-care NAAT does not require sophisticated laboratory equipment, is easy to perform, and is applicable for decentralized diagnosis at the primary health care level. Among a range of gene targets, the M. leprae specific repetitive element RLEP is regarded as highly sensitive and specific for diagnostic applications. METHODS: Our group developed and validated a dry-reagent-based (DRB) RLEP LAMP, provided product specifications for customization of a ready-to-use kit (intended for commercial production) and compared it against the in-house prototype. The assays were optimized for application on a Genie® III portable fluorometer. For technical validation, 40 "must not detect RLEP" samples derived from RLEP qPCR negative exposed and non-exposed individuals, as well as from patients with other conditions and a set of closely related mycobacterial cultures, were tested together with 25 "must detect RLEP" samples derived from qPCR confirmed leprosy patients. For clinical validation, 150 RLEP qPCR tested samples were analyzed, consisting of the following categories: high-positive samples of multibacillary (MB) leprosy patients (> 10.000 bacilli/extract), medium-positive samples of MB leprosy patients (1.001-10.000 bacilli/extract), low-positive samples of MB leprosy patients (1-1.000 bacilli/extract), endemic controls and healthy non-exposed controls; each n = 30. RESULTS: Technical validation: both LAMP formats had a limit of detection of 1.000 RLEP copies, i.e. 43-27 bacilli, a sensitivity of 92% (in-house protocol)/100% (ready-to-use protocol) and a specificity of 100%. Reagents were stable for at least 1 year at 22 °C. Clinical validation: Both formats showed a negativity rate of 100% and a positivity rate of 100% for high-positive samples and 93-100% for medium positive samples, together with a positive predictive value of 100% and semi-quantitative results. The positivity rate for low-positive samples was 77% (in-house protocol)/43% (ready-to-use protocol) and differed significantly between both formats. CONCLUSIONS: The ready-to-use RLEP DRB LAMP assay constitutes an ASSURED test ready for field-based evaluation trials aiming for routine diagnosis of leprosy at the primary health care level.
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Affiliation(s)
- Malkin Saar
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-University (LMU) Munich, Leopoldstrasse 5, 80802, Munich, Germany.
| | - Marcus Beissner
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-University (LMU) Munich, Leopoldstrasse 5, 80802, Munich, Germany
| | - Fatih Gültekin
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-University (LMU) Munich, Leopoldstrasse 5, 80802, Munich, Germany
| | - Issaka Maman
- Ministère de la Santé, Institut National d'Hygiène (INH), Lomé, Togo
| | - Karl-Heinz Herbinger
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-University (LMU) Munich, Leopoldstrasse 5, 80802, Munich, Germany
| | - Gisela Bretzel
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-University (LMU) Munich, Leopoldstrasse 5, 80802, Munich, Germany
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Chamanrokh P, Colwell RR, Huq A. Loop-Mediated Isothermal Amplification (LAMP) Assay for Rapid Detection of viable but non-culturable Vibrio cholerae O1. Can J Microbiol 2021; 68:103-110. [PMID: 34793252 DOI: 10.1139/cjm-2021-0142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Vibrio cholerae, an important waterborne pathogen, is a rod-shaped bacterium that naturally exists in aquatic environments. When conditions are unfavorable for growth, the bacterium can undergo morphological and physiological changes to assume a coccoid morphology. This stage in its life cycle is referred to as viable but non-culturable (VBNC) since VBNC cells do not grow on conventional bacteriological culture media. The current study compared polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP) to detect and identify VBNC V. cholerae. Because it is difficult to detect and identify VBNC V. cholerae, the results of the current study are useful in showing LAMP to be more sensitive and rapid than PCR in detecting and identifying non-culturable, coccoid forms of V. cholerae. Furthermore, the LAMP method is effective in detecting and identifying very low numbers of coccoid VBNC V. cholerae in environmental water samples, with the added benefit of being inexpensive to perform.
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Affiliation(s)
- Parastoo Chamanrokh
- University of Maryland College Park, Maryland Pathogen Research Institute, College Park, Maryland, United States;
| | - Rita R Colwell
- University of Maryland at College Park, 1068, Maryland Pathogen Research Institute, College Park, Maryland, United States.,University of Maryland at College Park, 1068, Maryland Institute of Applied Environmental Health, College Park, Maryland, United States.,University of Maryland at College Park, 1068, CBCB. UMIACS, College Park, Maryland, United States.,Johns Hopkins University Bloomberg School of Public Health, 25802, Baltimore, Maryland, United States;
| | - Anwar Huq
- University of Maryland at College Park, 1068, Maryland Pathogen Research Institute, College Park, Maryland, United States;
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8
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Lee PY, Wong YP, Othman S, Chee HY. Room-temperature stable loop-mediated isothermal amplification (LAMP) reagents to detect leptospiral DNA. ASIAN BIOMED 2021; 15:183-189. [PMID: 37551329 PMCID: PMC10388737 DOI: 10.2478/abm-2021-0023] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Background Loop-mediated isothermal amplification (LAMP) is one of the most promising tools for rapidly detecting Leptospira spp. However, LAMP is hampered by cold storage to maintain the enzymatic activity of Bst DNA polymerase. Objective To overcome the drawback of cold storage requirement for LAMP reagents we modified the reagents by adding sucrose as stabilizer. We then sought to determine the stability at room temperature of the premixed LAMP reagents containing sucrose. Method Premixed LAMP reagents with sucrose and without sucrose were prepared. The prepared mixtures were stored at room temperature for up to 60 days, and were subjected to LAMP reactions at various intervals using rat kidney samples to detect leptospiral DNA. Results The premixed LAMP reagents with sucrose remained stable for 45 days while sucrose-free premixed LAMP reagents showed no amplification from day 1 of storage at room temperature up to day 14. Conclusion The LAMP reagent system can be refined by using sucrose as stabilizer, thus allowing their storage at room temperature without the need for cold storage. The modified method enables greater feasibility of LAMP for field surveillance and epidemiology in resource-limited settings.
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Affiliation(s)
- Pui-Yuei Lee
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400Serdang, Selangor, Malaysia
| | - Yien-Ping Wong
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400Serdang, Selangor, Malaysia
| | - Shuhaidah Othman
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400Serdang, Selangor, Malaysia
| | - Hui-Yee Chee
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400Serdang, Selangor, Malaysia
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Wong Tzeling JM, Engku Nur Syafirah EAR, Irekeola AA, Yusof W, Aminuddin Baki NN, Zueter A, Harun A, Chan YY. One-step, multiplex, dual-function oligonucleotide of loop-mediated isothermal amplification assay for the detection of pathogenic Burkholderia pseudomallei. Anal Chim Acta 2021; 1171:338682. [PMID: 34112436 DOI: 10.1016/j.aca.2021.338682] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 11/18/2022]
Abstract
This study highlights the development of a multiplex real-time loop-mediated isothermal amplification assay. The developed assay employed a dual-function oligonucleotide (DFO) which simultaneously monitors the emitted amplification signals and accelerates the amplification process. The DFO was a modification of loop primer (LP); the 5'-end and 3'-end of the LP was tagged with fluorophore and quencher, respectively. The DFO was quenched in its unbound state and fluoresces only when it anneals to the specific target during the amplification process. With the same working mechanism as LP, DFO allowed the detection of target genes in less than 1 h in a real time monitoring system. We demonstrated this detection platform with Burkholderia pseudomallei, the causative agent of melioidosis. An internal amplification control (IAC) was incorporated in the assay to rule out false negative result and to demonstrate that the assay was successfully developed in a multiplex system. The assay was 100% specific when it was evaluated against 96 B. pseudomallei clinical isolates and 48 other bacteria species. The detection limit (sensitivity) of the developed assay was 1 fg/μl of B. pseudomallei genomic DNA and 18.2 CFU/ml at the bacterial cell level. In spiked blood samples, the assay's detection limit was 14 CFU/ml. The assay's diagnostic evaluation showed 100% diagnostic sensitivity, diagnostic specificity, positive predictive value, and negative predictive value. An integrated multiplex LAMP and real-time monitoring system was successfully developed, simplifying the workflow for the rapid and specific nucleic acid diagnostic test.
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Affiliation(s)
- Jilien Michelle Wong Tzeling
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - E A R Engku Nur Syafirah
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - Ahmad Adebayo Irekeola
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia; Microbiology Unit, Department of Biological Sciences, College of Natural and Applied Sciences, Summit University Offa, PMB 4412, Offa Kwara State, Nigeria.
| | - Wardah Yusof
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - Nurul Najian Aminuddin Baki
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - AbdelRahman Zueter
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia; Department of Medical Laboratory Sciences, Faculty of Applied Health Sciences, The Hashemite University, 13133, Zarqa, Jordan.
| | - Azian Harun
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia; Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - Yean Yean Chan
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia; Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia.
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Fang W, Cai Y, Zhu L, Wang H, Lu Y. Rapid and Highly Sensitive Detection of Toxigenic Vibrio cholerae Based on Recombinase-Aided Amplification Combining with Lateral Flow Assay. FOOD ANAL METHOD 2020. [DOI: 10.1007/s12161-020-01909-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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11
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Nieuwkerk DM, Korajkic A, Valdespino EL, Herrmann MP, Harwood VJ. Critical review of methods for isothermal amplification of nucleic acids for environmental analysis. J Microbiol Methods 2020; 179:106099. [PMID: 33159993 DOI: 10.1016/j.mimet.2020.106099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/27/2020] [Accepted: 10/31/2020] [Indexed: 10/23/2022]
Abstract
The past 30 years have seen the emergence and proliferation of isothermal amplification methods (IAMs) for rapid, sensitive detection and quantification of nucleic acids in a variety of sample types. These methods share dependence on primers and probes with quantitative PCR, but they differ in the specific enzymes and instruments employed, and are frequently conducted in a binary, rather than quantitative format. IAMs typically rely on simpler instruments than PCR analyses due to the maintenance of a single temperature throughout the amplification reaction, which could facilitate deployment of IAMs in a variety of environmental and field settings. This review summarizes the mechanisms of the most common IAM methods and their use in studies of pathogens, harmful algae and fecal indicators in environmental waters, feces, wastewater, reclaimed water, and tissues of aquatic animals. Performance metrics of sensitivity, specificity and limit of detection are highlighted, and the potential for use in monitoring and regulatory contexts is discussed.
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Affiliation(s)
- Dana M Nieuwkerk
- University of South Florida, Department of Integrative Biology, 4202 E. Fowler Ave, Tampa, FL 33620, USA
| | - Asja Korajkic
- US Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Erika L Valdespino
- University of South Florida, Department of Integrative Biology, 4202 E. Fowler Ave, Tampa, FL 33620, USA
| | - Michael P Herrmann
- US Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Valerie J Harwood
- University of South Florida, Department of Integrative Biology, 4202 E. Fowler Ave, Tampa, FL 33620, USA.
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Foo PC, Nurul Najian AB, Muhamad NA, Ahamad M, Mohamed M, Yean Yean C, Lim BH. Loop-mediated isothermal amplification (LAMP) reaction as viable PCR substitute for diagnostic applications: a comparative analysis study of LAMP, conventional PCR, nested PCR (nPCR) and real-time PCR (qPCR) based on Entamoeba histolytica DNA derived from faecal sample. BMC Biotechnol 2020; 20:34. [PMID: 32571286 PMCID: PMC7310076 DOI: 10.1186/s12896-020-00629-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 06/16/2020] [Indexed: 12/18/2022] Open
Abstract
Background This study reports the analytical sensitivity and specificity of a Loop-mediated isothermal amplification (LAMP) and compares its amplification performance with conventional PCR, nested PCR (nPCR) and real-time PCR (qPCR). All the assays demonstrated in this study were developed based on Serine-rich Entamoeba histolytica protein (SREHP) gene as study model. Results A set of SREHP gene specific LAMP primers were designed for the specific detection of Entamoeba histolytica. This set of primers recorded 100% specificity when it was evaluated against 3 medically important Entamoeba species and 75 other pathogenic microorganisms. These primers were later modified for conventional PCR, nPCR and qPCR applications. Besides, 3 different post-LAMP analyses including agarose gel electrophoresis, nucleic acid lateral flow immunoassay and calcein-manganese dye techniques were used to compare their limit of detection (LoD). One E. histolytica trophozoite was recorded as the LoD for all the 3 post-LAMP analysis methods when tested with E. histolytica DNA extracted from spiked stool samples. In contrast, none of the PCR method outperformed LAMP as both qPCR and nPCR recorded LoD of 100 trophozoites while the LoD of conventional PCR was 1000 trophozoites. Conclusions The analytical sensitivity comparison among the conventional PCR, nPCR, qPCR and LAMP reveals that the LAMP outperformed the others in terms of LoD and amplification time. Hence, LAMP is a relevant alternative DNA-based amplification platform for sensitive and specific detection of pathogens.
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Affiliation(s)
- Phiaw Chong Foo
- Acarology Unit, Infectious Disease Research Centre, Institute for Medical Research, Ministry of Health Malaysia, National Institutes of Health Complex, Bandar Setia Alam, 40170, Shah Alam, Selangor, Malaysia. .,Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - A B Nurul Najian
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.,Bacteriology Unit, Infectious Disease Research Centre, Institute for Medical Research, Ministry of Health Malaysia, National Institutes of Health Complex, Bandar Setia Alam, 40170, Shah Alam, Selangor, Malaysia
| | - Nuramin A Muhamad
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Mariana Ahamad
- Acarology Unit, Infectious Disease Research Centre, Institute for Medical Research, Ministry of Health Malaysia, National Institutes of Health Complex, Bandar Setia Alam, 40170, Shah Alam, Selangor, Malaysia
| | - Maizan Mohamed
- Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, City Campus, Pengkalan Chepa, Locked bag 36, 16100, Kota Bharu, Kelantan, Malaysia
| | - Chan Yean Yean
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.,Hospital USM, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Boon Huat Lim
- School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia
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13
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Wan J, Guo J, Lu Z, Bie X, Lv F, Zhao H. Development of a test kit for visual loop-mediated isothermal amplification of Salmonella in spiked ready-to-eat fruits and vegetables. J Microbiol Methods 2019; 169:105830. [PMID: 31891738 DOI: 10.1016/j.mimet.2019.105830] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 12/25/2019] [Accepted: 12/27/2019] [Indexed: 02/02/2023]
Abstract
The purpose of this study was to assemble two types of loop-mediated isothermal amplification (LAMP) kit that have the ability to visually detect Salmonella in ready-to-eat fruits and vegetables. The reaction results were obtained within 20-40 min after addition of DNA and can be discerned by the naked eye or an amplification plot. The stability of the LAMP wet kit was evident after multiple freezing and thawing cycles, and the one-step LAMP lyophilized kit was further evolved to allow ambient temperature transport for deployment in resource-limited settings. The cost-effective wet kit had the ability to detect minimum amounts of 1.8 CFU/ml Salmonella DNA without enrichment, while the sensitivity of the one-step LAMP lyophilized kit was only 9.8 × 103 CFU/ml. They both have good anti-interference, as they were both able to detect 2.1 × 102 CFU/ml Salmonella mixed with 106 CFU/ml four non-Salmonella strain mixture. Moreover, cucumber and lettuce that were contaminated with an initial inoculation of 1.7 CFU of Salmonella/10 g showed detection within a reaction time of 30 min after 10 h enrichment. The present research setup is a convenient and practical kit for Salmonella rapid detection that has good application prospects in food safety monitoring.
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Affiliation(s)
- Jiajia Wan
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Jianping Guo
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Xiaomei Bie
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China.
| | - Fengxia Lv
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Haizhen Zhao
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
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14
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Xu M, Fu H, Chen D, Shao Z, Zhu J, Alali WQ, Chen L. Simple Visualized Detection Method of Virulence-Associated Genes of Vibrio cholerae by Loop-Mediated Isothermal Amplification. Front Microbiol 2019; 10:2899. [PMID: 31921074 PMCID: PMC6932958 DOI: 10.3389/fmicb.2019.02899] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 12/02/2019] [Indexed: 12/18/2022] Open
Abstract
Vibrio cholerae is a leading waterborne pathogenic bacterium worldwide. It can cause human cholera that is still pandemic in developing nations. Detection of V. cholerae contamination in drinking water and aquatic products is imperative for assuring food safety. In this study, a simple, sensitive, specific, and visualized method was developed based on loop-mediated isothermal amplification (LAMP) (designated sssvLAMP) to detect virulence-associated (ctxA, tcpA, hapA, mshA, pilA, and tlh) and species-specific (lolB) genes of V. cholerae. Three pairs of oligonucleotide primers (inner, outer, and loop primers) were designed and or synthesized to target each of these genes. The optimal conditions of the sssvLAMP method was determined, and one-step sssvLAMP reaction was performed at 65°C for 40 min. Positive results were simply read by the naked eye via color change (from orange to light green) under the visible light, or by the production of green fluorescence under the UV light (260 nm). The sssvLAMP method was more efficient in detecting 6.50 × 101-6.45 × 104-fold low number of V. cholerae cells, and more sensitive in V. cholerae genomic DNA (1.36 × 10-2-4.42 × 10-6 ng/reaction) than polymerase chain reaction (PCR) method. Among 52 strains of V. cholerae and 50 strains of non-target species (e.g., other Vibrios and common pathogens) examined, the sensitivity and specificity of the sssvLAMP method were 100% for all the target genes. Similar high efficiency of the method was observed when tested with spiked samples of water and aquatic products, as well as human stool specimens. Water from various sources and commonly consumed fish samples were promptly screened by this simple and efficient visualized method and diversified variation in the occurrence of the target genes was observed. V. cholerae strains could be mostly detected by the presence of hapA and tlh alone or in combination with other genes, indicating a variable risk of potentially pathogenic non-O1/O139 strains in edible food products. This novel LAMP method can be a promising tool to address the increasing need of food safety control of aquatic products.
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Affiliation(s)
- Mengjie Xu
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Huiyu Fu
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Dailing Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Zehuai Shao
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Jun Zhu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Walid Q. Alali
- Department of Epidemiology and Biostatistics, Faculty of Public Health, Kuwait University, Safat, Kuwait
| | - Lanming Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
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15
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García-Bernalt Diego J, Fernández-Soto P, Crego-Vicente B, Alonso-Castrillejo S, Febrer-Sendra B, Gómez-Sánchez A, Vicente B, López-Abán J, Muro A. Progress in loop-mediated isothermal amplification assay for detection of Schistosoma mansoni DNA: towards a ready-to-use test. Sci Rep 2019; 9:14744. [PMID: 31611563 PMCID: PMC6791938 DOI: 10.1038/s41598-019-51342-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/27/2019] [Indexed: 12/30/2022] Open
Abstract
Schistosomiasis is one of the most prevalent Neglected Tropical Disease, affecting approximately 250 million people worldwide. Schistosoma mansoni is the most important species causing human intestinal schistosomiasis. Despite significant efforts in recent decades, the global disease burden of schistosomiasis remains extremely high. This could partly be attributed to the absence of accurate diagnostic tools, primarily in endemic areas. Loop-mediated isothermal amplification (LAMP) is increasingly used in molecular diagnostics as a field-friendly alternative to many other complex molecular methods and it has been proposed as an ideal candidate for revolutionizing point-of-care molecular diagnostics. In a previous work, a LAMP-based method to detect S. mansoni DNA (SmMIT-LAMP) was developed by our research group for early diagnosis of active schistosomiasis in an experimental infection murine model. The SmMIT-LAMP has been further successfully evaluated in both human stool and snail samples and, recently, in human urine samples. In this study, we developed an important improvement for SmMIT-LAMP molecular assay, transforming it into a cold maintenance dry format suitable for potentially manufacturing as kit for ready-to-use for schistosomiasis diagnosis. This procedure could be applied to create dry LAMP kits for a laboratory setting and for diagnostic applications for other neglected tropical diseases.
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Affiliation(s)
- J García-Bernalt Diego
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - P Fernández-Soto
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain.
| | - B Crego-Vicente
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - S Alonso-Castrillejo
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - B Febrer-Sendra
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - A Gómez-Sánchez
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - B Vicente
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - J López-Abán
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - A Muro
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain.
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16
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Leung V, Brooks M, Emerson S, Ali M, Filipe CDM. Ready-to-use thermally stable mastermix pills for molecular biology applications. Biotechnol Prog 2018; 35:e2764. [PMID: 30536873 DOI: 10.1002/btpr.2764] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/14/2018] [Accepted: 12/06/2018] [Indexed: 11/12/2022]
Abstract
Rolling circle amplification (RCA), polymerase chain reaction (PCR), and loop-mediated isothermal amplification (LAMP), are powerful tools that can be used for gene manipulation, pathogen detection, and infectious disease diagnostics. However, these techniques require trained personnel, as the pipetting steps involved can lead to contamination and, consequently, erroneous results. Furthermore, many of the reagents used in molecular biology are thermally labile and must be kept within a cold-chain. In this article, we present a simple and cost-effective method that allows molecular biology reagents to be thermally stabilized into ready-to-use mastermixes via drying in pullulan and trehalose films. Our experimental results demonstrate that this method is capable of preserving the activity of RCA, PCR, LAMP, ligase, polynucleotide kinase, and Klenow fragment mastermixes for at least 3 months at ambient conditions. Thus, stabilizing reagents via drying in pullulan and trehalose film may allow for a drastic reduction in the number of pipetting steps and the elimination of the need for a cold chain. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2764, 2019.
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Affiliation(s)
- Vincent Leung
- Dept. of Chemical Engineering, 1280 Main Street West, McMaster University, Hamilton, L8S 4L7, Ontario, Canada
| | - Meredith Brooks
- Dept. of Chemical Engineering, 1280 Main Street West, McMaster University, Hamilton, L8S 4L7, Ontario, Canada
| | - Sophia Emerson
- Dept. of Chemical Engineering, 1280 Main Street West, McMaster University, Hamilton, L8S 4L7, Ontario, Canada
| | - Monsur Ali
- Biointerfaces Inst., McMaster University, Hamilton, L8S 4L7, Ontario, Canada
| | - Carlos D M Filipe
- Dept. of Chemical Engineering, 1280 Main Street West, McMaster University, Hamilton, L8S 4L7, Ontario, Canada
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