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Čermáková E, Mukherjee S, Nováková D, Horká P, Zdeňková K, Demnerová K. Parvalbumin Gene: A Valuable Marker for Pike Authentication and Allergen Risk Assessment. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:12788-12797. [PMID: 38778779 PMCID: PMC11157528 DOI: 10.1021/acs.jafc.4c01410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 05/02/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
Fish from the pike (Esox) genus are valued in gastronomy for their superior meat quality. However, they can cause allergic reactions in sensitive consumers. This work aimed to fill the gap in the detection of pike allergens using molecular-biological techniques. New, fast, and accurate loop-mediated isothermal amplification (LAMP) and real-time PCR (qPCR) assays were designed to detect pike DNA using the parvalbumin gene as a marker. LAMP was assessed by electrophoresis, SYBR green optical detection, and real-time fluorescence detection. The latter was the most sensitive, detecting as little as 0.78 ng of pike DNA; the qPCR detection limit was 0.1 ng. The LAMP analysis took 20-70 min, which is significantly faster than qPCR. The study provides reliable detection and quantification of the parvalbumin gene in both fresh and processed samples and further highlights the versatility of the use of the parvalbumin gene for the authentication of food products and consumer protection via refined allergen risk assessment that is independent of the type of tissue or food processing method used.
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Affiliation(s)
- Eliška Čermáková
- Department
of Chemistry, Biochemistry and Food Microbiology, Food Research Institute Prague, Radiová 1285/7, Prague
10 102 00, Czech Republic
- Department
of Biochemistry and Microbiology, University
of Chemistry and Technology, Prague, Technická 5, Prague 6 166 28, Czech Republic
| | - Subham Mukherjee
- Department
of Chemistry, Biochemistry and Food Microbiology, Food Research Institute Prague, Radiová 1285/7, Prague
10 102 00, Czech Republic
- Lennard-Jones
School of Chemical and Physical Sciences, Keele University, Staffordshire ST5 5BG, United Kingdom
- Institute
for Environmental Studies, Faculty of Science, Charles University, Benatska 2, Prague 2 128
01, Czech Republic
| | - Denisa Nováková
- Department
of Biochemistry and Microbiology, University
of Chemistry and Technology, Prague, Technická 5, Prague 6 166 28, Czech Republic
| | - Petra Horká
- Institute
for Environmental Studies, Faculty of Science, Charles University, Benatska 2, Prague 2 128
01, Czech Republic
| | - Kamila Zdeňková
- Department
of Biochemistry and Microbiology, University
of Chemistry and Technology, Prague, Technická 5, Prague 6 166 28, Czech Republic
| | - Kateřina Demnerová
- Department
of Biochemistry and Microbiology, University
of Chemistry and Technology, Prague, Technická 5, Prague 6 166 28, Czech Republic
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2
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Yinur D, Moges B, Hassen A, Tessema TS. Loop mediated isothermal amplification as a molecular diagnostic assay: Application and evaluation for detection of Enterohaemorrhagic Escherichia coli (O157:H7). Pract Lab Med 2023; 37:e00333. [PMID: 37693632 PMCID: PMC10492192 DOI: 10.1016/j.plabm.2023.e00333] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 07/27/2023] [Accepted: 08/25/2023] [Indexed: 09/12/2023] Open
Abstract
Purpose This study aimed at evaluating the performance of the Loop Mediated Isothermal Amplification (LAMP) diagnostic test, which targets the putative Fimbria protein-encoding gene (Z3276) for rapid and specific detection of locally isolated enterohemorrhagic Escherichia coli (EHEC) O157:H7. Results A total number of 40 locally available bacteria isolates and standard strains, among them 6 entrohemorrhagic (O157:H7) and 10 entropathogenic E. coli, 7 non diarrheic E. coli strains and 13 non entrohemorrhagic shiga toxic (stx) E. coli isolates as well as 4 pathogenic non E. coli species were used to optimize and evaluate the LAMP assay. The LAMP amplified DNA samples were visualized as turbid DNA both by naked eye and gel electrophoresis followed by staining. The assay had a sensitivity of 100% (6/6), a specificity of 97.05% (33/34), and an efficiency of 97.5% (39/40). The assay was also exhibited with 100% negative predicted value and 85.7% positive predicted value. The LAMP assay was also 10-fold more sensitive than the conventional PCR assay; sensitivity was determined by serial dilution. The results of LAMP and the PCR tests showed very high agreement (k = 0.97) in the detection of the bacteria studied. Conclusion Compared with the performance of PCR and SMAC, LAMP assay was better in terms of efficiency, rapidity and cost-effectiveness, which can be used as a point-care diagnostic test in resource-limited laboratories.
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Affiliation(s)
- Degisew Yinur
- Department of Medical Biotechnology, Institute of Biotechnology, University of Gondar, Gondar, Ethiopia
| | - Biniam Moges
- Department of Biotechnology, Debre Berhan University, Debre Berhan, Ethiopia
| | - Aliyi Hassen
- Department of Biotechnology, Ambo University, Ambo, Ethiopia
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3
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Bennuru S, Kodua F, Drame PM, Dahlstrom E, Nutman TB. A Novel, Highly Sensitive Nucleic Acid Amplification Test Assay for the Diagnosis of Loiasis and its Use for Detection of Circulating Cell-Free DNA. J Infect Dis 2023; 228:936-943. [PMID: 37243712 PMCID: PMC11009493 DOI: 10.1093/infdis/jiad186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/25/2023] [Accepted: 05/24/2023] [Indexed: 05/29/2023] Open
Abstract
Mass drug administration programs targeting filarial infections depend on diagnostic tools that are sensitive and specific. The coendemicity of Loa loa with other filarial species often hampers the control programs. LL2634 was identified as the most promising target among several highly repeated targets, with sensitivity between 500 ag and 1 fg of genomic DNA. Using DNA from infected individuals, LL2643 quantitative polymerase chain reaction (qPCR) was positive in all individuals. LL2643 was detected in plasma-derived circulating cell-free DNA (ccfDNA) from 48 of 53 microfilariae-positive patients. Detection of ccfDNA in urine was possible, but it occurred rarely among those tested. Importantly, LL2643 ccfDNA became undetectable within 1 month following diethylcarbamazine (DEC) treatment and remained negative for at least a year. LL2643 offers a more sensitive and specific target for detection of L. loa infection and would be easily configurable to a point-of-contact assay. Clinical Trials Registration. NCT00001230 and NCT00090662.
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Affiliation(s)
- Sasisekhar Bennuru
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Frimpong Kodua
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Papa Makhtar Drame
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Eric Dahlstrom
- Genomics Unit, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Thomas B Nutman
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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4
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Kaur M, Ayarnah K, Duanis-Assaf D, Alkan N, Eltzov E. Paper-based colorimetric loop-mediated isothermal amplification (LAMP) assay for the identification of latent Colletotrichum in harvested fruit. Anal Chim Acta 2023; 1267:341394. [PMID: 37257967 DOI: 10.1016/j.aca.2023.341394] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 05/02/2023] [Accepted: 05/17/2023] [Indexed: 06/02/2023]
Abstract
Paper-based analytical devices (PADs) have gained enormous attention because of their low-cost, simple fabrication, and portability. Here, we propose a paper-based device for performing reverse transcription loop-mediated isothermal amplification (RT-LAMP) with real-time simultaneous detection of C. gloeosporioides latent infections in tomatoes. RT-LAMP-based PAD platform comprises a paper substrate on which the DNA amplification reaction occurs. Among different types of tested papers, cellulose membrane (grade 4) enabled effective visualization of the amplification result. The assay was found highly selective for the latent stage of C. gloeosporioides with lower limit of detection (LOD) of 0.5 pg of total extracted RNA. The developed assay generated the results within 40 min and hence can be efficiently employed for identifying C. gloeosporioides in resource-limited settings.
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Affiliation(s)
- Manpreet Kaur
- Department of Postharvest Science, Institute of Postharvest and Food Sciences, The Volcani Institute, Agricultural Research Organization, Bet Dagan, 50250, Israel; Institute of Biochemistry, Food Science and Nutrition, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Khadijah Ayarnah
- Department of Postharvest Science, Institute of Postharvest and Food Sciences, The Volcani Institute, Agricultural Research Organization, Bet Dagan, 50250, Israel; Institute of Biochemistry, Food Science and Nutrition, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Danielle Duanis-Assaf
- Department of Postharvest Science, Institute of Postharvest and Food Sciences, The Volcani Institute, Agricultural Research Organization, Bet Dagan, 50250, Israel; Institute of Biochemistry, Food Science and Nutrition, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Noam Alkan
- Department of Postharvest Science, Institute of Postharvest and Food Sciences, The Volcani Institute, Agricultural Research Organization, Bet Dagan, 50250, Israel
| | - Evgeni Eltzov
- Department of Postharvest Science, Institute of Postharvest and Food Sciences, The Volcani Institute, Agricultural Research Organization, Bet Dagan, 50250, Israel; Agro-Nanotechnology and Advanced Materials Research Center, Institute of Postharvest and Food Science, Department of Postharvest Science, Agricultural Research Organization, The Volcani Institute, Rishon LeZion, 7505101, Israel.
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5
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Amambo GN, Innocentia N, Abong RA, Fombad FF, Njouendou AJ, Nietcho F, Ekanya R, Kien CA, Ebai R, Lenz B, Ritter M, Esum ME, Deribe K, Cho JF, Beng AA, Enyong PI, Li Z, Hübner MP, Pfarr K, Hoerauf A, Carlow C, Wanji S. Application of loop mediated isothermal amplification (LAMP) assays for the detection of Onchocerca volvulus, Loa loa and Mansonella perstans in humans and vectors. FRONTIERS IN TROPICAL DISEASES 2023; 3:1016176. [PMID: 36684508 PMCID: PMC7614089 DOI: 10.3389/fitd.2022.1016176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Conventional diagnosis of filarial infections is based on morphological identification of microfilariae using light microscopy and requires considerable expertise, is time-consuming, and can be subjective. Loop-mediated isothermal amplification (LAMP) has advantages over microscopy or PCR because of its operational simplicity, rapidity and versatility of readout options. LAMP assays represent a major step forward in improved filarial diagnostic tools suitable for low resource settings and field applicability. The study goal was to retrospectively evaluate the performance and suitability of the O-150, RF4, and Mp419 LAMP assays for diagnosing Onchocerca volvulus, Loa loa and Mansonella perstans infections, respectively, in humans and vectors under experimental and natural field conditions. Surveys were conducted in four health districts of Cameroon using skin snip and thick blood film methods to detect skin (O. volvulus) and blood (L. loa and M. perstans) dwelling microfilaria in humans. Engorged vectors (Simulium spp., Chrysops spp., and Culicoides spp.) were evaluated by LAMP. Dissected, wild-caught vectors were also analyzed. LAMP showed a prevalence of 40.4% (O. volvulus), 17.8% (L. loa) and 36.6% (M. perstans) versus 20.6% (O. volvulus), 17.4% (L. loa) and 33.8% (M. perstans) with microscopy. Simulium spp. were dissected for microscopy and pooled for LAMP. The O-150 LAMP assay infection rate was 4.3% versus 4.1% by microscopy. Chrysops spp. were dissected and analyzed individually in the LAMP assay. The RF4 LAMP assay infection rate was 23.5% versus 3.3% with microscopy. The RF4 LAMP assay also detected parasites in Chrysops spp. fed on low microfilaremic volunteers. The Mp419 LAMP assay infection rate was 0.2% for C. milnei and 0.04% for C. grahamii, while three other species were LAMP-negative. The sensitivity, species specificity, rapidity and ease of its use of these filarial LAMP assays, and validation of their performance in the field support use as alternatives to microscopy as diagnostic and surveillance tools in global health programs aimed to eliminate onchocerciasis.
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Affiliation(s)
- Glory Ngongeh Amambo
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
- Research Foundation in Tropical Diseases and Environment (REFOTDE), Buea, Cameroon
| | - Ngong Innocentia
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
- Research Foundation in Tropical Diseases and Environment (REFOTDE), Buea, Cameroon
| | - Raphael Awah Abong
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
- Research Foundation in Tropical Diseases and Environment (REFOTDE), Buea, Cameroon
| | - Fanny Fri Fombad
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
- Research Foundation in Tropical Diseases and Environment (REFOTDE), Buea, Cameroon
| | - Abdel Jelil Njouendou
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
- Department of Biomedical Science, Faculty of Health Sciences, University of Buea, Buea, Cameroon
| | - Franck Nietcho
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
| | - Relindis Ekanya
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
- Research Foundation in Tropical Diseases and Environment (REFOTDE), Buea, Cameroon
| | - Chi Anizette Kien
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
- Research Foundation in Tropical Diseases and Environment (REFOTDE), Buea, Cameroon
| | - Rene Ebai
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
- Research Foundation in Tropical Diseases and Environment (REFOTDE), Buea, Cameroon
| | - Benjamin Lenz
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany
| | - Manuel Ritter
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany
| | - Mathias Eyong Esum
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
- Research Foundation in Tropical Diseases and Environment (REFOTDE), Buea, Cameroon
| | - Kebede Deribe
- Global Health and Infection Department, Brighton and Sussex Medical School, Brighton, United Kingdom
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - Jerome Fru Cho
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
- Research Foundation in Tropical Diseases and Environment (REFOTDE), Buea, Cameroon
| | - Amuam Andrew Beng
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
- Research Foundation in Tropical Diseases and Environment (REFOTDE), Buea, Cameroon
| | - Peter Ivo Enyong
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
- Research Foundation in Tropical Diseases and Environment (REFOTDE), Buea, Cameroon
| | - Zhiru Li
- New England Biolabs, Ipswich, MA, United States
| | - Marc P. Hübner
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany
| | - Kenneth Pfarr
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany
| | - Achim Hoerauf
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany
- German-West African Centre for Global Health and Pandemic Prevention (G-WAC), Partner Site Bonn, Bonn, Germany
| | | | - Samuel Wanji
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
- Research Foundation in Tropical Diseases and Environment (REFOTDE), Buea, Cameroon
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Dual-mode visual detection strategies of viable pathogens for point-of-care testing. Biosens Bioelectron 2022; 221:114904. [DOI: 10.1016/j.bios.2022.114904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/31/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
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Dieki R, Nsi-Emvo E, Akue JP. The Human Filaria Loa loa: Update on Diagnostics and Immune Response. Res Rep Trop Med 2022; 13:41-54. [PMID: 35936385 PMCID: PMC9355020 DOI: 10.2147/rrtm.s355104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/03/2022] [Indexed: 11/24/2022] Open
Abstract
Loa loa loiasis was considered an anecdotal disease 30 years ago. Its spread in Equatorial Africa and the side effects associated with mass drug administration programs against filariasis in co-endemic areas have drawn the attention of the international research community. Progress in research conducted to date has provided insight into the immunobiology of this parasite. An interesting finding reported in several studies is that 70% of individuals with loiasis do not carry microfilariae in their blood, and 30% are microfilaremic, suggesting the involvement of several immunological mechanisms, as shown by elevated specific IgG4 and IgE levels signifying a potential cross-linking mechanism between the two isotypes via L. loa antigen to prevent allergy. A mechanism of anergy in the appearance of microfilariae in the peripheral blood results in immunological unresponsiveness in individuals with microfilariae. There is an interaction between other pathogens (parasites, bacteria, viruses) in individuals co-infected with L. loa. The strong antigen cross-reactivity between L. loa and lymphatic filarial worms warrants a re-evaluation of the distribution of the latter in co-endemic regions. The mechanism of concomitant immunity observed in the elimination of microfilariae or infective larvae (third-stage larvae, L3) may be used for the conception of an immunoprophylactic strategy.
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Affiliation(s)
- Roland Dieki
- Department of Parasitology, International Centre of Medical Research of Franceville, Franceville, Gabon
- Department of Chemistry, Université des Sciences et Techniques de Masuku (USTM), Franceville, Gabon
| | - Edouard Nsi-Emvo
- Department of Chemistry, Université des Sciences et Techniques de Masuku (USTM), Franceville, Gabon
| | - Jean Paul Akue
- Department of Parasitology, International Centre of Medical Research of Franceville, Franceville, Gabon
- Correspondence: Jean Paul Akue, Department of Parasitology, International Centre of Medical Research of Franceville, Franceville, BP 769, Gabon, Email
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Colorimetric and Real-Time Loop-Mediated Isothermal Amplification (LAMP) for Detection of Loa loa DNA in Human Blood Samples. Diagnostics (Basel) 2022; 12:diagnostics12051079. [PMID: 35626235 PMCID: PMC9139441 DOI: 10.3390/diagnostics12051079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/22/2022] [Accepted: 04/23/2022] [Indexed: 02/04/2023] Open
Abstract
Loiasis, caused by the filarial nematode Loa loa, is endemic in Central and West Africa. Loa loa has been associated with severe adverse reactions in high Loa-infected individuals receiving ivermectin during mass drug administration programs for the control of onchocerciasis and lymphatic filariasis. Diagnosis of loiasis still depends on microscopy in blood samples, but this is not effective for large-scale surveys. New diagnostics methods for loiasis are urgently needed. Previously, we developed a colorimetric high-sensitive and species-specific LAMP for Loa loa DNA detection. Here, we evaluate it in a set of 100 field-collected clinical samples stored as dried blood spots. In addition, Loa loa-LAMP was also evaluated in real-time testing and compared with microscopy and a specific PCR/nested PCR. A simple saponin/Chelex-based method was used to extract DNA. Colorimetric and real-time LAMP assays detected more samples with microscopy-confirmed Loa loa and Loa loa/Mansonella perstans mixed infections than PCR/nested-PCR. Samples with the highest Loa loa microfilariae counts were amplified faster in real-time LAMP assays. Our Loa loa-LAMP could be a promising molecular tool for the easy, rapid and accurate screening of patients for loiasis in endemic areas with low-resource settings. The real-time testing (feasible in a handheld device) could be very useful to rule out high-microfilariae loads in infected patients.
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Application of Loop-Mediated Isothermal Amplification (LAMP) in Sex Identification of Parrots Bred in Egypt. BIOLOGY 2022; 11:biology11040565. [PMID: 35453764 PMCID: PMC9029760 DOI: 10.3390/biology11040565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/16/2022] [Accepted: 04/05/2022] [Indexed: 11/17/2022]
Abstract
Over 400 of the 3800 tropical avian species are endangered or threatened. One of many solutions to conserve animal biodiversity is breeding animals in zoos or private animal farms. Animal breeding programs are difficult to implement in species with sexual monomorphism, such as parrots. Molecular biology methods offer a solution to determine the sex of these species. Therefore, in this study, we aimed to test the performance of PCR and LAMP techniques on sex identification for 21 parrot species belonging to three families, i.e., Psittacidae, Cacatuidae, and Psittaculidae. We established a protocol for DNA isolation from feathers in our laboratory and found optimal conditions for PCR and LAMP. We showed that the LAMP method with the use of the PSI-W primers set, developed by Centeno-Cuadros, functions in 17 previously untested species. Moreover, we found that further improvements are required in universal LAMP primers for the detection of parrot DNA, which are necessary for confirmation of the male sex. The LAMP method also proved to be more sensitive for female sex identification in contrast to the reference PCR test. Therefore, we conclude that LAMP is a suitable method for the routine diagnostic sex identification of parrots.
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Dieki R, Eyang-Assengone ER, Makouloutou-Nzassi P, Bangueboussa F, Nsi Emvo E, Akue JP. Comparison of six methods for Loa loa genomic DNA extraction. PLoS One 2022; 17:e0265582. [PMID: 35312712 PMCID: PMC8936488 DOI: 10.1371/journal.pone.0265582] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 03/05/2022] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES Good-quality and sufficient DNA is essential for diagnostics and vaccine development. We aimed to compare six DNA extraction techniques applied to Loa loa microfilariae in order to evaluate the purity and integrity of extracts in terms of quality and quantity. METHODS The microfilariae were purified via a Percoll gradient procedure with blood from hyper-microfilaremic individuals (> 30,000 microfilaria [mf]/ml). DNA extraction was carried out in duplicate at a rate of 350,000 mf/tube for each technique: phenol/chloroform, commercial Qiagen kit, salting out, Tris-EDTA, methanol, and cetyltrimethylammonium bromide (CTAB). The integrity, purity, concentration, and quality of the DNA extracts were successively verified by agarose gel electrophoresis, spectrophotometry (A260/A280 and A260/A230 wavelength ratio), Qubit fluorometry, and endonuclease and polymerase activity. The six techniques were compared on the basis of the following parameters: concentration, purity, efficiency, effectiveness, integrity, safety of the technique, as well as cost and duration of the protocol. RESULTS The ratios of the optical densities of the extracts A260/A280 and A260/A230 were, respectively: phenol/chloroform (1.82; 1.11), Qiagen (1.93; 1.36), salting-out (1.9; 2.04), Tris-EDTA (1.99; 1.183), methanol (2.126; 1.343), and CTAB (2.01; 2.426). The DNA yield was: phenol/chloroform (3.920 μg), Qiagen (10.280 μg), salting-out (10.390 μg), Tris-EDTA (0.5528 μg), methanol (0.1036 μg), and CTAB (1.115 μg). Endonuclease and polymerase activity was demonstrated by digestion of DNA and through amplicons obtained via polymerase chain reaction assays with phenol/chloroform, Qiagen, and salting-out extracts. CONCLUSION The phenol/chloroform, Qiagen, and salting-out DNA extracts were all of good quality. Salting out had the best yield followed by Qiagen and then phenol/chloroform. Endonuclease and polymerase activity was effective in all three extracts despite the presence of some contaminants. These methods are therefore suitable for the extraction of DNA from Loa loa microfilariae. Tris-EDTA and methanol did not show adequate sensitivity, while CTAB was found to be unsuitable.
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Affiliation(s)
- Roland Dieki
- Département de Parasitologie, Centre International de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
- Laboratoire de Recherche en Biochimie (LAREBIO), Faculté des Sciences, Université des Sciences et Techniques de Masuku (USTM), Franceville, Gabon
| | | | | | - Félicien Bangueboussa
- Unité de Recherches en Ecologie de la Santé (URES/CIRMF), BP. 769 Franceville, Gabon
| | - Edouard Nsi Emvo
- Laboratoire de Recherche en Biochimie (LAREBIO), Faculté des Sciences, Université des Sciences et Techniques de Masuku (USTM), Franceville, Gabon
| | - Jean Paul Akue
- Département de Parasitologie, Centre International de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
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11
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Moon YJ, Lee SY, Oh SW. A Review of Isothermal Amplification Methods and Food-Origin Inhibitors against Detecting Food-Borne Pathogens. Foods 2022; 11:foods11030322. [PMID: 35159473 PMCID: PMC8833899 DOI: 10.3390/foods11030322] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 02/06/2023] Open
Abstract
The isothermal amplification method, a molecular-based diagnostic technology, such as loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA), is widely used as an alternative to the time-consuming and labor-intensive culture-based detection method. However, food matrices or other compounds can inhibit molecular-based diagnostic technologies, causing reduced detection efficiencies, and false-negative results. These inhibitors originating from food are polysaccharides and polyphenolic compounds in berries, seafood, and vegetables. Additionally, magnesium ions needed for amplification reactions can also inhibit molecular-based diagnostics. The successful removal of inhibitors originating from food and molecular amplification reaction is therefore proposed to enhance the efficiency of molecular-based diagnostics and allow accurate detection of food-borne pathogens. Among molecular-based diagnostics, PCR inhibitors have been reported. Nevertheless, reports on the mechanism and removal of isothermal amplification method inhibitors are insufficient. Therefore, this review describes inhibitors originating from food and some compounds inhibiting the detection of food-borne pathogens during isothermal amplification.
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Risch F, Ritter M, Hoerauf A, Hübner MP. Human filariasis-contributions of the Litomosoides sigmodontis and Acanthocheilonema viteae animal model. Parasitol Res 2021; 120:4125-4143. [PMID: 33547508 PMCID: PMC8599372 DOI: 10.1007/s00436-020-07026-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/20/2020] [Indexed: 12/16/2022]
Abstract
Filariae are vector-borne parasitic nematodes that are endemic worldwide, in tropical and subtropical regions. Important human filariae spp. include Onchocerca volvulus, Wuchereria bancrofti and Brugia spp., and Loa loa and Mansonella spp. causing onchocerciasis (river blindness), lymphatic filariasis (lymphedema and hydrocele), loiasis (eye worm), and mansonelliasis, respectively. It is estimated that over 1 billion individuals live in endemic regions where filarial diseases are a public health concern contributing to significant disability adjusted life years (DALYs). Thus, efforts to control and eliminate filarial diseases were already launched by the WHO in the 1970s, especially against lymphatic filariasis and onchocerciasis, and are mainly based on mass drug administration (MDA) of microfilaricidal drugs (ivermectin, diethylcarbamazine, albendazole) to filarial endemic areas accompanied with vector control strategies with the goal to reduce the transmission. With the United Nations Sustainable Development Goals (SDGs), it was decided to eliminate transmission of onchocerciasis and stop lymphatic filariasis as a public health problem by 2030. It was also requested that novel drugs and treatment strategies be developed. Mouse models provide an important platform for anti-filarial drug research in a preclinical setting. This review presents an overview about the Litomosoides sigmodontis and Acanthocheilonema viteae filarial mouse models and their role in immunological research as well as preclinical studies about novel anti-filarial drugs and treatment strategies.
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Affiliation(s)
- Frederic Risch
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Manuel Ritter
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Achim Hoerauf
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Bonn, Germany
| | - Marc P Hübner
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany.
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Bonn, Germany.
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Jawla J, Kumar RR, Mendiratta S, Agarwal R, Singh P, Saxena V, Kumari S, Boby N, Kumar D, Rana P. On-site paper-based Loop-Mediated Isothermal Amplification coupled Lateral Flow Assay for pig tissue identification targeting mitochondrial CO I gene. J Food Compost Anal 2021. [DOI: 10.1016/j.jfca.2021.104036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Panich W, Tejangkura T, Chontananarth T. Novel high-performance detection of Raillietina echinobothrida, Raillietina tetragona, and Raillietina cesticillus using loop-mediated isothermal amplification coupled with a lateral flow dipstick (LAMP-LFD). Vet Parasitol 2021; 292:109396. [PMID: 33711620 DOI: 10.1016/j.vetpar.2021.109396] [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] [Received: 12/06/2020] [Revised: 02/15/2021] [Accepted: 02/24/2021] [Indexed: 11/16/2022]
Abstract
Cestodes belonging to the genus Raillietina are a major veterinary health problem in the poultry industry, especially in chickens (Gallus gallus domesticus) and ducks (Anas playtrhynchos domesticus). In this study, loop-mediated isothermal amplification coupled with a lateral flow dipstick (LAMP-LFD) assay was established and validated for the detection of R. echinobothrida, R. tetragona, and R. cesticillus in one reaction. The LAMP-LFD assay can be completed in 75 min under isothermal conditions at 66 °C and the results can be obtained by observation with the naked eye. This assay was very specific and had no cross-amplification with other closely related parasites (Cotugnia sp., Diorchis formosensis, Fimbriaria sp., Echinostoma sp., E. miyagawai, Hypoderaeum conoideum, Prosthogonimus cuneatus, and Ascaridia galli) or their definitive hosts (G. g. domesticus, A. p. domesticus). The sensitivity of the LAMP-LFD assay was detected with three Raillietina species at 0.5 ng, which was enough for gravid proglottid DNA detection. The accuracy test showed that the LAMP-LFD assay demonstrated accurate verification results when compared to morphological results. This is a novel LAMP-LFD assay that is highly specific and sensitive for the detection of Raillietina species. It can be applied to detection for epidemiological investigations, monitoring programs, surveillance, control, and to solve veterinary health problems for the poultry industry in Raillietina endemic areas.
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Affiliation(s)
- Wasin Panich
- Applied Parasitology Research Laboratory, Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand
| | - Thanawan Tejangkura
- Applied Parasitology Research Laboratory, Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand; Center of Excellence in Animal, Plant and Parasitic Biotechnology, Srinakharinwirot University, Bangkok, 10110, Thailand
| | - Thapana Chontananarth
- Applied Parasitology Research Laboratory, Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand; Center of Excellence in Animal, Plant and Parasitic Biotechnology, Srinakharinwirot University, Bangkok, 10110, Thailand.
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Li J, Cui Z, Li X, Zhang L. Review of zoonotic amebiasis: Epidemiology, clinical signs, diagnosis, treatment, prevention and control. Res Vet Sci 2021; 136:174-181. [PMID: 33676155 DOI: 10.1016/j.rvsc.2021.02.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/11/2021] [Accepted: 02/26/2021] [Indexed: 02/07/2023]
Abstract
Amebiasis is a disease caused by the protozoan parasite Entamoeba histolytica, which mainly shows symptoms of acute diarrhea, dysentery, amebic colitis, and amebic liver abscesses. As the fourth leading parasitic cause of human mortality, E. histolytica mainly infect children in developing countries, transmitted by food and water contamination. In the majority of infected individuals, Entamoeba sp. asymptomatically colonizes the large intestine and self-limiting, while in others, the parasite breaches the mucosal epithelial barrier to cause amebic colitis and can disseminate to soft organs to cause abscesses. Metronidazole (MTZ) is the recommended and most widely used drug for treating the invasive amebiasis. No amebiasis vaccine has been approved for human clinical trials to date, but many recent vaccine development studies hold promise. For the prevention and control of amebiasis, improvement of water purification systems and hygiene practices could decrease disease incidence. In this review, we focus on the epidemiology, transmission, clinical signs, pathogenesis, diagnosis, treatment, prevention and control of the zoonotic amebiasis.
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Affiliation(s)
- Junqiang Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhaohui Cui
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiaoying Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Longxian Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China.
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Amambo GN, Abong RA, Fombad FF, Njouendou AJ, Nietcho F, Beng AA, Manuel R, Esum ME, Deribe K, Cho JF, Enyong PI, Poole C, Hoerauf A, Carlow C, Wanji S. Validation of loop-mediated isothermal amplification for the detection of Loa loa infection in Chrysops spp in experimental and natural field conditions. Parasit Vectors 2021; 14:19. [PMID: 33407819 PMCID: PMC7788981 DOI: 10.1186/s13071-020-04506-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/30/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The mass drug administration of ivermectin for onchocerciasis control has contributed to a significant drop in Loa loa microfilaria loads in humans that has, in turn, led to reduction of infection levels in Chrysops vectors. Accurate parasite detection is essential for assessing loiasis transmission as it provides a potential alternative or indirect strategy for addressing the problem of co-endemic loiasis and lymphatic filariasis through the Onchocerciasis Elimination Programme and it further reflects the true magnitude of the loiasis problem as excess human mortality has been reported to be associated with the disease. Although microscopy is the gold standard for detecting the infection, the sensitivity of this method is compromised when the intensity of infection is low. The loop-mediated isothermal amplification (LAMP) assay of parasite DNA is an alternative method for detecting infection which offers operational simplicity, rapidity and versatility of visual readout options. The aim of this study was to validate the Loa loa LAMP assay for the detection of infected Chrysops spp. under experimental and natural field conditions. METHODS Two sets of 18 flies were fed on volunteers with either a low (< 10 mf/ml) or high (> 30,000mf/ml) microfilarial load. The fed flies were maintained under laboratory conditions for 14 days and then analysed using LAMP for the detection of L. loa infection. In addition, a total of 9270 flies were collected from the north-west, east, and south-west regions (SW 1 and 2) of Cameroon using sweep nets and subjected to microscopy (7841 flies) and LAMP (1291 flies plus 138 nulliparous flies) analyses. RESULTS The LAMP assay successfully detected parasites in Chrysops fed on volunteers with both low and high microfilariaemic loads. Field validation and surveillance studies revealed LAMP-based infection rates ranging from 0.5 to 31.6%, with the lowest levels in SW 2 and the highest infection rates in SW 1. The LAMP assay detected significantly higher infection rates than microscopy in four of the five study sites. CONCLUSION This study demonstrated the potential of LAMP as a simple surveillance tool. It was found to be more sensitive than microscopy for the detection of experimental and natural L. loa infections in Chrysops vectors.
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Affiliation(s)
- Glory Ngongeh Amambo
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, P.O. Box 63, Buea, Cameroon
- Research Foundation in Tropical Diseases and Environment (REFOTDE), P.O. Box 474, Buea, Cameroon
| | - Raphael Awah Abong
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, P.O. Box 63, Buea, Cameroon
- Research Foundation in Tropical Diseases and Environment (REFOTDE), P.O. Box 474, Buea, Cameroon
| | - Fanny Fri Fombad
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, P.O. Box 63, Buea, Cameroon
- Research Foundation in Tropical Diseases and Environment (REFOTDE), P.O. Box 474, Buea, Cameroon
| | - Abdel Jelil Njouendou
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, P.O. Box 63, Buea, Cameroon
- Department of Biomedical science, Faculty of Health Sciences, University of Buea, P.O. Box 63, Buea, Cameroon
| | - Franck Nietcho
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, P.O. Box 63, Buea, Cameroon
| | - Amuam Andrew Beng
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, P.O. Box 63, Buea, Cameroon
- Research Foundation in Tropical Diseases and Environment (REFOTDE), P.O. Box 474, Buea, Cameroon
| | - Ritter Manuel
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany
| | - Mathias Eyong Esum
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, P.O. Box 63, Buea, Cameroon
- Research Foundation in Tropical Diseases and Environment (REFOTDE), P.O. Box 474, Buea, Cameroon
| | - Kebede Deribe
- Global Health and Infection Department, Brighton and Sussex Medical School, Brighton, BN1 9PX, UK
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - Jerome Fru Cho
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, P.O. Box 63, Buea, Cameroon
- Research Foundation in Tropical Diseases and Environment (REFOTDE), P.O. Box 474, Buea, Cameroon
| | - Peter Ivo Enyong
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, P.O. Box 63, Buea, Cameroon
- Research Foundation in Tropical Diseases and Environment (REFOTDE), P.O. Box 474, Buea, Cameroon
| | | | - Achim Hoerauf
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany
| | | | - Samuel Wanji
- Parasites and Vector Research Unit (PAVRU), Department of Microbiology and Parasitology, University of Buea, P.O. Box 63, Buea, Cameroon.
- Research Foundation in Tropical Diseases and Environment (REFOTDE), P.O. Box 474, Buea, Cameroon.
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Tembo M, Adediji AO, Bouvaine S, Chikoti PC, Seal SE, Silva G. A quick and sensitive diagnostic tool for detection of Maize streak virus. Sci Rep 2020; 10:19633. [PMID: 33184360 PMCID: PMC7661706 DOI: 10.1038/s41598-020-76612-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/29/2020] [Indexed: 11/09/2022] Open
Abstract
Maize streak virus disease (MSVD), caused by Maize streak virus (MSV; genus Mastrevirus), is one of the most severe and widespread viral diseases that adversely reduces maize yield and threatens food security in Africa. An effective control and management of MSVD requires robust and sensitive diagnostic tests capable of rapid detection of MSV. In this study, a loop-mediated isothermal amplification (LAMP) assay was designed for the specific detection of MSV. This test has shown to be highly specific and reproducible and able to detect MSV in as little as 10 fg/µl of purified genomic DNA obtained from a MSV-infected maize plant, a sensitivity 105 times higher to that obtained with polymerase chain reaction (PCR) in current general use. The high degree of sequence identity between Zambian and other African MSV isolates indicate that this LAMP assay can be used for detecting MSV in maize samples from any region in Africa. Furthermore, this assay can be adopted in minimally equipped laboratories and with potential use in plant clinic laboratories across Africa strengthening diagnostic capacity in countries dealing with MSD.
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Affiliation(s)
- Mathias Tembo
- Zambia Agriculture Research Institute, Mount Makulu Research Station, P/Bag 7, Lusaka, Zambia.
| | - Adedapo O Adediji
- Department of Crop Protection and Environmental Biology, Faculty of Agriculture, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Sophie Bouvaine
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, ME4 4TB, Kent, UK
| | - Patrick C Chikoti
- Zambia Agriculture Research Institute, Mount Makulu Research Station, P/Bag 7, Lusaka, Zambia
| | - Susan E Seal
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, ME4 4TB, Kent, UK
| | - Gonҫalo Silva
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, ME4 4TB, Kent, UK
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Varsha V, Aishwarya S, Murchana S, Naveen G, Ramya M, Rathinasabapathi P. Correction pen based paper fluidic device for the detection of multiple gene targets of Leptospira using Loop Mediated Isothermal Amplification. J Microbiol Methods 2020; 174:105962. [PMID: 32473300 DOI: 10.1016/j.mimet.2020.105962] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 04/02/2020] [Accepted: 05/19/2020] [Indexed: 10/24/2022]
Abstract
Paper-based nucleic acid testing techniques are increasingly in demand. Hence, we have developed a simple and cheap paper fluidic device to detect multiple gene targets in Leptospira. Fluidic channels of the penta-clover device are drawn using a correction pen on Whatman filter paper 1. The fluid blocks the pores of the paper, avoiding leakage and ensuring the equal flow of sample to the reaction pads. The target genes are amplified by performing Loop-Mediated Isothermal Amplification (LAMP) with dry reaction components. Thecolor change of leuco crystal violetallows real-time monitoring of a positive amplification. The difference in color intensity is captured with a smartphone and analyzed using image processing software. The device amplifies the target within 15 min, detects the pathogen at a concentration as low as 50 attogram μL-1, detects Leptospira in blood samples without prior treatment and differentiates the Leptospira species even after 21 days of storage at room temperature.
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Affiliation(s)
- Venkatesh Varsha
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Kancheepuram (District), Tamil Nadu, India
| | - Sitaraman Aishwarya
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Kancheepuram (District), Tamil Nadu, India
| | - Sarma Murchana
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Kancheepuram (District), Tamil Nadu, India
| | - Gattuboyena Naveen
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Kancheepuram (District), Tamil Nadu, India
| | - Mohandass Ramya
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Kancheepuram (District), Tamil Nadu, India
| | - Pasupathi Rathinasabapathi
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Kancheepuram (District), Tamil Nadu, India.
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Rapid and Sensitive Detection of Citrus tristeza virus Using Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) Assay. Methods Mol Biol 2020. [PMID: 31222701 DOI: 10.1007/978-1-4939-9558-5_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Loop-mediated isothermal amplification (LAMP) is one recently developed gene amplification technique that emerges as a simple and quick diagnostic tool for early detection of nucleic acid targets. The LAMP technique works on the principle of strand displacement activity of Bst polymerase. It contains a set of four specially designed primers, which recognizes six different regions on the target nucleotide sequence. In the LAMP reaction, amplification is carried out in an isothermal conditions (60-65°C) using simple and inexpensive device like water bath or dry bath. Additional benefits of LAMP technique are that final results can be seen directly with naked eyes by adding intercalating dye SYBR Green I in the reaction tube. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is one of the novel techniques used for detection of RNA targets. The technology has been successfully applied for rapid and sensitive detection of Citrus tristeza virus (CTV) by using four oligo-primers, targeting a conserved coat protein gene (CPG) of an Indian CTV isolate. The result of assay is visible in naked eyes easily in the presence of SYBR Green I (100×) or on 1.5% agarose gel electrophoresis. CTV-RT-LAMP could be used away from plant pathology laboratories even in remote location.
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In Silico Identification of Novel Biomarkers and Development of New Rapid Diagnostic Tests for the Filarial Parasites Mansonella perstans and Mansonella ozzardi. Sci Rep 2019; 9:10275. [PMID: 31311985 PMCID: PMC6635353 DOI: 10.1038/s41598-019-46550-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 06/29/2019] [Indexed: 02/02/2023] Open
Abstract
Mansonelliasis is a widespread yet neglected tropical infection of humans in Africa and South America caused by the filarial nematodes, Mansonella perstans, M. ozzardi, M. rodhaini and M. streptocerca. Clinical symptoms are non-distinct and diagnosis mainly relies on the detection of microfilariae in skin or blood. Species-specific DNA repeat sequences have been used as highly sensitive biomarkers for filarial nematodes. We have developed a bioinformatic pipeline to mine Illumina reads obtained from sequencing M. perstans and M. ozzardi genomic DNA for new repeat biomarker candidates which were used to develop loop-mediated isothermal amplification (LAMP) diagnostic tests. The M. perstans assay based on the Mp419 repeat has a limit of detection of 0.1 pg, equivalent of 1/1000th of a microfilaria, while the M. ozzardi assay based on the Mo2 repeat can detect as little as 0.01 pg. Both LAMP tests possess remarkable species-specificity as they did not amplify non-target DNAs from closely related filarial species, human or vectors. We show that both assays perform successfully on infected human samples. Additionally, we demonstrate the suitability of Mp419 to detect M. perstans infection in Culicoides midges. These new tools are field deployable and suitable for the surveillance of these understudied filarial infections.
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Deng MH, Zhong LY, Kamolnetr O, Limpanont Y, Lv ZY. Detection of helminths by loop-mediated isothermal amplification assay: a review of updated technology and future outlook. Infect Dis Poverty 2019; 8:20. [PMID: 30905322 PMCID: PMC6432754 DOI: 10.1186/s40249-019-0530-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 03/07/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Helminths are endemic in more than half of the world's countries, raising serious public health concerns. Accurate diagnosis of helminth infection is crucial to control strategies. Traditional parasitological methods, serological tests and PCR-based assays are the major means of the diagnosis of helminth infection, but they are time-consuming and/or expensive, and sometimes provide inaccurate results. Loop mediated isothermal amplification (LAMP) assay, a sensitive, simple and rapid method was therefore developed for detection of helminths. This study aims to discuss the current status of application of LAMP on helminths detection and to make a comprehensive evaluation about this updated technology and its future outlook by comparing with several other diagnostic methods. MAIN BODY This review summarizes LAMP assay applied for helminth detection and helminthiasis surveillance. The basic principle of LAMP is introduced to help better understand its characteristics and each reported assay is assessed mainly based on its detection sensitivity, specificity and limitations, in comparison with other common diagnostic tests. Moreover, we discuss the limitations of the assays so as to clarify some potential ways of improvement. CONCLUSIONS Here, we summarize and discuss the advantages, disadvantages and promising future of LAMP in heliminth detection, which is expected to help update current knowledge and future perspectives of LAMP in highly sensitive and specific diagnosis and surveillance of helminthiasis and other parasitic diseases, and can contribute to the elimination of the diseases from endemic areas.
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Affiliation(s)
- Miao-Han Deng
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080 China
| | - Lan-Yi Zhong
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080 China
| | - Okanurak Kamolnetr
- Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400 Thailand
| | - Yanin Limpanont
- Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400 Thailand
| | - Zhi-Yue Lv
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080 China
- Provincial Engineering Technology Research Center for Biological Vector Control, Guangzhou, 510080 China
- Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 519000 China
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Kumari S, Kumar RR, Mendiratta SK, Kumar D, Rana P, Kumar D, Jawla J. Species-specific loop-mediated isothermal amplification (LAMP) assay for identification of tissue of cattle origin by targeting mitochondrial gene sequences. 3 Biotech 2019; 9:69. [PMID: 30729093 PMCID: PMC6363609 DOI: 10.1007/s13205-019-1595-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 01/24/2019] [Indexed: 01/15/2023] Open
Abstract
The present study was carried out with the objective of development of species-specific loop-mediated isothermal amplification (LAMP) assay for identification of tissue of cattle origin. The cattle-specific LAMP primer set was designed by targeting mitochondrial D-loop gene. The conditions for LAMP reaction for amplification of template DNA from cattle using designed cattle-specific primer set were optimized for the components of mixture and temperature of reaction. Amplified products were analysed using SYBR Green I dye and by agarose gel electrophoresis. The developed species-specific LAMP assay was evaluated for its specificity, sensitivity and validated in laboratory on samples from known, coded, binary meat admixture with other than cattle at relative percentage of 20%, 10%, 5% and 1%, Phire tissue direct PCR master mix treated tissues of cattle and on species-specific polymerase chain reaction assay positive samples. The developed LAMP assay using self-designed primer set was highly specific, amplifying the DNA template exclusively from cattle tissue under the optimized LAMP reaction conditions. The sensitivity assay using serially diluted DNA templates revealed lowest level of detection as 0.01 ng of absolute DNA from target species. Laboratory validation substantiated the accuracy of assay in known/unknown (coded) samples and up to the 1% level of admixture in binary meat sample. DNA present in supernatant of Phire Animal tissue kit treated samples were also amplified successfully eliminating the extra step of extraction of genomic DNA. The developed assays exhibited comparable results with previously established species-specific PCR assay taken as gold standards. Thus, it was concluded that developed species-specific loop-mediated isothermal amplification assay was effective in identification of tissue of cattle origin.
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Affiliation(s)
- Sarita Kumari
- Department of Livestock Products Technology, PGIVER, RAJUVAS, Jaipur, India
| | - Rajiv Ranjan Kumar
- Division of Livestock Products Technology, Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122 India
| | - Sanjod Kumar Mendiratta
- Division of Livestock Products Technology, Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122 India
| | - Deepak Kumar
- Division of Veterinary Biotechnology, IVRI, Izatnagar, India
| | - Preeti Rana
- Department of Livestock Products Technology, CVASc, DUVASU, Mathura, India
| | - Dhananjay Kumar
- Division of Livestock Products Technology, Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122 India
| | - Jyoti Jawla
- Division of Livestock Products Technology, Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122 India
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Rodríguez-García Á, Mares RE, Muñoz PLA, Meléndez-López SG, Licea-Navarro AF, Ramos MA. DNA Extraction with DNAzol and LAMP, Performed in a Heating Block as a Simple Procedure for Detection of Mycobacterium tuberculosis in Sputum Specimens. Methods Protoc 2018; 1:E37. [PMID: 31164577 PMCID: PMC6481065 DOI: 10.3390/mps1040037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 10/16/2018] [Accepted: 10/19/2018] [Indexed: 12/03/2022] Open
Abstract
Tuberculosis (TB) remains as a major public health issue in developing countries. Accurate detection is essential for the proper management of patients with active disease. Here, we present a simple DNAzol-LAMP (loop-mediated isothermal amplification) procedure for the detection of Mycobacterium tuberculosis in sputum specimens. Twenty smear-positive sputum samples were analyzed as follows: (i) Genetic material was extracted by a standard DNAzol protocol, and (ii) mycobacterial DNA was detected by a typical TB-specific loop-mediated isothermal amplification method. Results and diagnostic test performance attests to the suitability of the proposed procedure.
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Affiliation(s)
- Álvaro Rodríguez-García
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Tijuana, BCN 22390, Mexico.
- Laboratorio de Diagnóstico Clínico, Hospital General de Tijuana, Vía de la Juventud Oriente 4910, Tijuana, BCN 22010, Mexico.
| | - Rosa E Mares
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Tijuana, BCN 22390, Mexico.
| | - Patricia L A Muñoz
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Tijuana, BCN 22390, Mexico.
| | - Samuel G Meléndez-López
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Tijuana, BCN 22390, Mexico.
| | - Alexei F Licea-Navarro
- Departamento de Innovación Biomédica, Centro de Investigación Científica y Educación Superior de Ensenada, Carretera Ensenada-Tijuana 3918, Ensenada, BCN 22860, Mexico.
| | - Marco A Ramos
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Tijuana, BCN 22390, Mexico.
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Akue JP, Eyang-Assengone ER, Dieki R. Loa loa infection detection using biomarkers: current perspectives. Res Rep Trop Med 2018; 9:43-48. [PMID: 30050354 PMCID: PMC6047611 DOI: 10.2147/rrtm.s132380] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Loa loa is originally a restricted filarial worm from central Africa and some west African countries. However, numerous imported cases are being reported throughout the world due to human movement. Traditionally, its diagnosis is based on identification of microfilariae in the peripheral blood or the passage of the adult worm under the conjunctiva. However, few patients have microfilariae in their peripheral blood, while the majority of infected people are amicrofilaremic (without microfilariae in their blood), despite clinical symptoms suggesting L. loa infection. This situation suggests that diagnoses based on the presence of microfilariae in the blood or the ocular passage of an adult worm, are not sensitive. Therefore, it seems necessary to search for biomarkers to remedy this situation. Furthermore, L. loa is a major obstacle in the control of other filarial worms in areas where these filariae are co-endemic. To develop a diagnostic tool based on a biomarker, several approaches have been considered using antibodies, antigens or nucleic acid detection. However, none of the diagnostic techniques in loiasis based on biomarkers has reached the point of care as have microscopic detection of microfilariae or observation of ocular passage of a worm.
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Affiliation(s)
- Jean Paul Akue
- Department of Parasitology, Centre International of Medical Research of Franceville, Franceville, Gabon,
| | - Elsa-Rush Eyang-Assengone
- Department of Parasitology, Centre International of Medical Research of Franceville, Franceville, Gabon, .,Department of Infectiologie Tropicale, Ecole Doctorale Régionale d'Afrique Centrale, Franceville, Gabon
| | - Roland Dieki
- Department of Parasitology, Centre International of Medical Research of Franceville, Franceville, Gabon,
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25
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Gandasegui J, Fernández-Soto P, Muro A, Simões Barbosa C, Lopes de Melo F, Loyo R, de Souza Gomes EC. A field survey using LAMP assay for detection of Schistosoma mansoni in a low-transmission area of schistosomiasis in Umbuzeiro, Brazil: Assessment in human and snail samples. PLoS Negl Trop Dis 2018. [PMID: 29534072 PMCID: PMC5849311 DOI: 10.1371/journal.pntd.0006314] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Background In Brazil, schistosomiasis is a parasitic disease of public health relevance, mainly in poor areas where Schistosoma mansoni is the only human species encountered and Biomphalaria straminea is one of the intermediate host snails. A nested-PCR based on a specific mitochondrial S. mansoni minisatellite DNA region has been successfully developed and applied as a reference method in Brazil for S. mansoni detection, mainly in host snails for epidemiological studies. The amplification efficiency of LAMP is known to be higher than PCR. The present work aimed to assess the utility of our previously described SmMIT-LAMP assay for S. mansoni detection in human stool and snail samples in a low-transmission area of schistosomiasis in the municipality of Umbuzeiro, Paraíba State, Northeast Region of Brazil. Methodology/Principal findings A total of 427 human stool samples were collected during June-July 2016 in the municipality of Umbuzeiro and an overall prevalence of 3.04% (13/427) resulted positive by duplicate Kato-Katz thick smear. A total of 1,175 snails identified as Biomphalaria straminea were collected from 14 breeding sites along the Paraíba riverbank and distributed in 46 pools. DNA from human stool samples and pooled snails was extracted using the phenol/chloroform method. When performing the SmMIT-LAMP assay a total of 49/162 (30.24%) stool samples resulted positive, including 12/13 (92.31%) that were Kato-Katz positive and 37/149 (24.83%) previously Kato-Katz negative. By nested-PCR, only 1/46 pooled DNA snail samples was positive. By SmMIT-LAMP assay, the same sample also resulted positive and an additional one was positive from a different breeding site. Data of human and snail surveys were used to build risk maps of schistosomiasis incidence using kernel density analysis. Conclusions/Significance This is the first study in which a LAMP assay was evaluated in both human stool and snail samples from a low-transmission schistosomiasis-endemic area. Our SmMIT-LAMP proved to be much more efficient in detection of S. mansoni in comparison to the 'gold standard' Kato-Katz method in human stool samples and the reference molecular nested-PCR in snails. The SmMIT-LAMP has demonstrated to be a useful molecular tool to identify potential foci of transmission in order to build risk maps of schistosomiasis. In Brazil, around 1.8 million people, mostly in the northeastern region of the country, are thought to be infected with Schistosoma mansoni. Snails of the genus Biomphalaria serve as intermediate hosts of the S. mansoni. A special program for schistosomiasis control was implemented more than 40 years ago in Brazil, decreasing prevalence, morbidity, and mortality over the past years. PCR-based diagnostic methods have been successfully applied in a few endemic areas of schistosomiasis in Brazil, although they are not still widely used due to the highly technical requirements making them unviable for routine application in field conditions. Loop-mediated isothermal amplification (LAMP) technology could be a powerful tool to apply for point-of-care testing in resource-poor settings. In previous work, a LAMP-based method to detect S. mansoni DNA, called SmMIT-LAMP, was developed by our research group to detect S. mansoni DNA testing stool samples from experimentally infected mice. Here, with the aim to apply SmMIT-LAMP as a cost-effective molecular tool for the detection of S. mansoni in field applicable conditions, we assess SmMIT-LAMP in human and snail samples collected in an endemic area of Brazil. The results obtained by Kato-Katz analysis of human stool samples and nested-PCR performed in snails were compared with the SmMIT-LAMP assay. It is the first time that a LAMP-based method has been used to identify potential transmission foci and to evaluate the epidemiological risk of acquiring schistosomiasis.
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Affiliation(s)
- Javier Gandasegui
- 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
| | - Pedro 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
- * E-mail: (PFS); (AM)
| | - Antonio 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
- * E-mail: (PFS); (AM)
| | - Constança Simões Barbosa
- Schistosomiasis Laboratory and Reference Service, Department of Parasitology, Aggeu Magalhães Institute, Fiocruz - Ministry of Health (MoH), Recife, Pernambuco, Brazil
| | - Fabio Lopes de Melo
- Schistosomiasis Laboratory and Reference Service, Department of Parasitology, Aggeu Magalhães Institute, Fiocruz - Ministry of Health (MoH), Recife, Pernambuco, Brazil
| | - Rodrigo Loyo
- Schistosomiasis Laboratory and Reference Service, Department of Parasitology, Aggeu Magalhães Institute, Fiocruz - Ministry of Health (MoH), Recife, Pernambuco, Brazil
| | - Elainne Christine de Souza Gomes
- Schistosomiasis Laboratory and Reference Service, Department of Parasitology, Aggeu Magalhães Institute, Fiocruz - Ministry of Health (MoH), Recife, Pernambuco, Brazil
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Abbasian F, Ghafar-Zadeh E, Magierowski S. Microbiological Sensing Technologies: A Review. Bioengineering (Basel) 2018; 5:E20. [PMID: 29498670 PMCID: PMC5874886 DOI: 10.3390/bioengineering5010020] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 02/23/2018] [Accepted: 02/23/2018] [Indexed: 12/13/2022] Open
Abstract
Microorganisms have a significant influence on human activities and health, and consequently, there is high demand to develop automated, sensitive, and rapid methods for their detection. These methods might be applicable for clinical, industrial, and environmental applications. Although different techniques have been suggested and employed for the detection of microorganisms, and the majority of these methods are not cost effective and suffer from low sensitivity and low specificity, especially in mixed samples. This paper presents a comprehensive review of microbiological techniques and associated challenges for bioengineering researchers with an engineering background. Also, this paper reports on recent technological advances and their future prospects for a variety of microbiological applications.
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Affiliation(s)
- Firouz Abbasian
- Biologically Inspired Sensors and Actuators Laboratory, Department of EECS, Lassonde School of Engineering, York University, Toronto, ON M3J 1P3, Canada.
| | - Ebrahim Ghafar-Zadeh
- Biologically Inspired Sensors and Actuators Laboratory, Department of EECS, Lassonde School of Engineering, York University, Toronto, ON M3J 1P3, Canada.
| | - Sebastian Magierowski
- Biologically Inspired Sensors and Actuators Laboratory, Department of EECS, Lassonde School of Engineering, York University, Toronto, ON M3J 1P3, Canada.
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27
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Sabalza M, Yasmin R, Barber CA, Castro T, Malamud D, Kim BJ, Zhu H, Montagna RA, Abrams WR. Detection of Zika virus using reverse-transcription LAMP coupled with reverse dot blot analysis in saliva. PLoS One 2018; 13:e0192398. [PMID: 29401479 PMCID: PMC5798782 DOI: 10.1371/journal.pone.0192398] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 01/23/2018] [Indexed: 12/20/2022] Open
Abstract
In recent years, there have been increasing numbers of infectious disease outbreaks that spread rapidly to population centers resulting from global travel, population vulnerabilities, environmental factors, and ecological disasters such as floods and earthquakes. Some examples of the recent outbreaks are the Ebola epidemic in West Africa, Middle East respiratory syndrome coronavirus (MERS-Co) in the Middle East, and the Zika outbreak through the Americas. We have created a generic protocol for detection of pathogen RNA and/or DNA using loop-mediated isothermal amplification (LAMP) and reverse dot-blot for detection (RDB) and processed automatically in a microfluidic device. In particular, we describe how a microfluidic assay to detect HIV viral RNA was converted to detect Zika virus (ZIKV) RNA. We first optimized the RT-LAMP assay to detect ZIKV RNA using a benchtop isothermal amplification device. Then we implemented the assay in a microfluidic device that will allow analyzing 24 samples simultaneously and automatically from sample introduction to detection by RDB technique. Preliminary data using saliva samples spiked with ZIKV showed that our diagnostic system detects ZIKV RNA in saliva. These results will be validated in further experiments with well-characterized ZIKV human specimens of saliva. The described strategy and methodology to convert the HIV diagnostic assay and platform to a ZIKV RNA detection assay provides a model that can be readily utilized for detection of the next emerging or re-emerging infectious disease.
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Affiliation(s)
- Maite Sabalza
- Department of Basic Sciences, New York University College of Dentistry, New York, New York, United States of America
- * E-mail:
| | - Rubina Yasmin
- Rheonix, Inc., Ithaca, New York, United States of America
| | - Cheryl A. Barber
- Department of Basic Sciences, New York University College of Dentistry, New York, New York, United States of America
| | - Talita Castro
- Department of Basic Sciences, New York University College of Dentistry, New York, New York, United States of America
- Stomatology Department, School of Dentistry, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Daniel Malamud
- Department of Basic Sciences, New York University College of Dentistry, New York, New York, United States of America
- Department of Medicine, New York University School of Medicine, New York, New York, United States of America
| | - Beum Jun Kim
- Rheonix, Inc., Ithaca, New York, United States of America
| | - Hui Zhu
- Rheonix, Inc., Ithaca, New York, United States of America
| | | | - William R. Abrams
- Department of Basic Sciences, New York University College of Dentistry, New York, New York, United States of America
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28
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Development of a simple and rapid reverse transcription-loop mediated isothermal amplification (RT-LAMP) assay for sensitive detection of Citrus tristeza virus. J Virol Methods 2017; 250:6-10. [DOI: 10.1016/j.jviromet.2017.09.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/21/2017] [Accepted: 09/05/2017] [Indexed: 11/18/2022]
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29
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Bennuru S, O'Connell EM, Drame PM, Nutman TB. Mining Filarial Genomes for Diagnostic and Therapeutic Targets. Trends Parasitol 2017; 34:80-90. [PMID: 29031509 DOI: 10.1016/j.pt.2017.09.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/12/2017] [Accepted: 09/20/2017] [Indexed: 02/04/2023]
Abstract
Filarial infections of humans cause some of the most important neglected tropical diseases. The global efforts for eliminating filarial infections by mass drug administration programs may require additional tools (safe macrofilaricidal drugs, vaccines, and diagnostic biomarkers). The accurate and sensitive detection of viable parasites is essential for diagnosis and for surveillance programs. Current community-wide treatment modalities do not kill the adult filarial worms effectively; hence, there is a need to identify and develop safe macrofilaricidal drugs. High-throughput sequencing, mass spectroscopy methods and advances in computational biology have greatly accelerated the discovery process. Here, we describe post-genomic developments toward the identification of diagnostic biomarkers and drug targets for the filarial infection of humans.
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Affiliation(s)
- Sasisekhar Bennuru
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Elise M O'Connell
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Papa M Drame
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Thomas B Nutman
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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30
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Poole CB, Li Z, Alhassan A, Guelig D, Diesburg S, Tanner NA, Zhang Y, Evans TC, LaBarre P, Wanji S, Burton RA, Carlow CKS. Colorimetric tests for diagnosis of filarial infection and vector surveillance using non-instrumented nucleic acid loop-mediated isothermal amplification (NINA-LAMP). PLoS One 2017; 12:e0169011. [PMID: 28199317 PMCID: PMC5310896 DOI: 10.1371/journal.pone.0169011] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 11/19/2016] [Indexed: 11/26/2022] Open
Abstract
Accurate detection of filarial parasites in humans is essential for the implementation and evaluation of mass drug administration programs to control onchocerciasis and lymphatic filariasis. Determining the infection levels in vector populations is also important for assessing transmission, deciding when drug treatments may be terminated and for monitoring recrudescence. Immunological methods to detect infection in humans are available, however, cross-reactivity issues have been reported. Nucleic acid-based molecular assays offer high levels of specificity and sensitivity, and can be used to detect infection in both humans and vectors. In this study we developed loop-mediated isothermal amplification (LAMP) tests to detect three different filarial DNAs in human and insect samples using pH sensitive dyes for enhanced visual detection of amplification. Furthermore, reactions were performed in a portable, non-instrumented nucleic acid amplification (NINA) device that provides a stable heat source for LAMP. The efficacy of several strand displacing DNA polymerases were evaluated in combination with neutral red or phenol red dyes. Colorimetric NINA-LAMP assays targeting Brugia Hha I repeat, Onchocerca volvulus GST1a and Wuchereria bancrofti LDR each exhibit species-specificity and are also highly sensitive, detecting DNA equivalent to 1/10-1/5000th of one microfilaria. Reaction times varied depending on whether a single copy gene (70 minutes, O. volvulus) or repetitive DNA (40 min, B. malayi and W. bancrofti) was employed as a biomarker. The NINA heater can be used to detect multiple infections simultaneously. The accuracy, simplicity and versatility of the technology suggests that colorimetric NINA-LAMP assays are ideally suited for monitoring the success of filariasis control programs.
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Affiliation(s)
| | - Zhiru Li
- New England Biolabs, Ipswich, MA United States of America
| | - Andy Alhassan
- New England Biolabs, Ipswich, MA United States of America
| | - Dylan Guelig
- PATH, Seattle, Washington, United States of America
| | | | | | - Yinhua Zhang
- New England Biolabs, Ipswich, MA United States of America
| | | | - Paul LaBarre
- PATH, Seattle, Washington, United States of America
| | - Samuel Wanji
- Research Foundation in Tropical Diseases and Environment, Buea, Cameroon
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31
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Lagatie O, Merino M, Batsa Debrah L, Debrah AY, Stuyver LJ. An isothermal DNA amplification method for detection of Onchocerca volvulus infection in skin biopsies. Parasit Vectors 2016; 9:624. [PMID: 27906100 PMCID: PMC5134125 DOI: 10.1186/s13071-016-1913-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/24/2016] [Indexed: 12/20/2022] Open
Abstract
Background Diagnostic procedures for the diagnosis of infection with the nematode parasite Onchocerca volvulus are currently based on the microscopic detection of microfilariae in skin biopsies. Alternative approaches based on amplification of parasitic DNA in these skin biopsies are currently being explored. Mostly this is based on the detection of the O-150 repeat sequence using PCR based techniques. Methods An isothermal, loop-mediated amplification method has been designed using the mitochondrial O. volvulus cox1 gene as a target. Results Analysis of dilution series of synthetic DNA containing the targeted sequence show a non-linear dose-response curve, as is usually the case for isothermal amplification methods. Evaluation of cross-reactivity with the heterologous sequence from the closely related parasites Wuchereria bancrofti, Loa loa and Brugia malayi demonstrated strong specificity, as none of these sequences was amplified. The assay however amplified both O. volvulus and O. ochengi DNA, but with a different melting point that can be used to discriminate between the species. Evaluation of this assay in a set of skin snip biopsies collected in an endemic area in Ghana showed a high correlation with O-150 qPCR and also demonstrated a similar sensitivity. Compared to qPCR, LAMP had a sensitivity of 88.2% and a specificity of 99.2%. Conclusions We have developed a sensitive and specific loop-mediated amplification method for detection of O. volvulus DNA in skin biopsies that is capable of providing results within 30 min. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1913-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ole Lagatie
- Janssen Diagnostics, Janssen R&D, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Michelle Merino
- Janssen Diagnostics, Janssen R&D, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Linda Batsa Debrah
- Kumasi Centre for Collaborative Research into Tropical medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Alexander Y Debrah
- Faculty of Allied Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Lieven J Stuyver
- Janssen Diagnostics, Janssen R&D, Turnhoutseweg 30, 2340, Beerse, Belgium
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Can Lymphatic Filariasis Be Eliminated by 2020? Trends Parasitol 2016; 33:83-92. [PMID: 27765440 DOI: 10.1016/j.pt.2016.09.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 09/10/2016] [Accepted: 09/20/2016] [Indexed: 12/25/2022]
Abstract
Interventions against neglected tropical diseases (NTD), including lymphatic filariasis (LF), scaled up dramatically after the signing of the London Declaration (LD) in 2012. LF is targeted for elimination by 2020, but some countries are considered not on track to meet the 2020 target using the recommended preventive chemotherapy and morbidity management strategies. In this Opinion article we review the prospects for achieving LF elimination by 2020 in the light of the renewed global action against NTDs and the global efforts to achieve the sustainable development goals (SDGs) by 2030. We conclude that LF can be eliminated by 2020 using cross-sectoral and integrated approaches because of the compound effect of the other SDG activities related to poverty reduction and water and sanitation.
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33
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Poole CB, Ettwiller L, Tanner NA, Evans TC, Wanji S, Carlow CKS. Genome Filtering for New DNA Biomarkers of Loa loa Infection Suitable for Loop-Mediated Isothermal Amplification. PLoS One 2015; 10:e0139286. [PMID: 26414073 PMCID: PMC4586141 DOI: 10.1371/journal.pone.0139286] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 09/09/2015] [Indexed: 11/18/2022] Open
Abstract
Loa loa infections have emerged as a serious public health problem in patients co-infected with Onchocerca volvulus or Wuchereria bancrofti because of severe adverse neurological reactions after treatment with ivermectin. Accurate diagnostic tests are needed for careful mapping in regions where mass drug administration is underway. Loop-mediated isothermal amplification (LAMP) has become a widely adopted screening method because of its operational simplicity, rapidity and versatility of visual detection readout options. Here, we present a multi-step bioinformatic pipeline to generate diagnostic candidates suitable for LAMP and experimentally validate this approach using one of the identified candidates to develop a species-specific LAMP assay for L. loa. The pipeline identified ~140 new L. loa specific DNA repeat families as putative biomarkers of infection. The consensus sequence of one family, repeat family 4 (RF4), was compiled from ~ 350 sequences dispersed throughout the L. loa genome and maps to a L. loa-specific region of the long terminal repeats found at the boundaries of Bel/Pao retrotransposons. PCR and LAMP primer sets targeting RF4 specifically amplified L. loa but not W. bancrofti, O. volvulus, Brugia malayi, human or mosquito DNA. RF4 LAMP detects the DNA equivalent of one microfilaria (100 pg) in 25-30 minutes and as little as 0.060 pg of L. loa DNA (~1/1600th of a microfilaria) purified from spiked blood samples in approximately 50 minutes. In summary, we have successfully employed a bioinformatic approach to mine the L. loa genome for species-specific repeat families that can serve as new DNA biomarkers for LAMP. The RF4 LAMP assay shows promise as a field tool for the implementation and management of mass drug administration programs and warrants further testing on clinical samples as the next stage in development towards this goal.
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Affiliation(s)
| | | | - Nathan A. Tanner
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Thomas C. Evans
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Samuel Wanji
- Research Foundation in Tropical Diseases and Environment, Buea, Cameroon
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The relationship between microfilaraemic and amicrofilaraemic loiasis involving co-infection with Mansonella perstans and clinical symptoms in an exposed population from Gabon. J Helminthol 2015; 90:469-75. [DOI: 10.1017/s0022149x15000607] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
AbstractThe relationship between the frequency of loiasis objective symptoms and microfilaraemic or amicrofilaraemic infection was assessed in 1148 exposed patients also infected, or not, with Mansonella perstans. Filarial infections were detected by direct microscopy, leucoconcentration and serology, with prevalence values of 39.5% Loa loa, 5.6% M. perstans and 3.4% co-infection with both filarial species. Amicrofilaraemic or occult loiasis (OL) predominated among L. loa-infected individuals, with a prevalence of 58.2%. Hypermicrofilaraemia (>8000 microfilariae (mf)/ml) was found in 18.4% of L. loa microfilaraemic patients, with 25.7% of them harbouring more than 30,000 mf/ml. Up to 34% of patients with OL showed evidence of Calabar swelling, compared with 26.3% of microfilaraemic patients (P= 0.03). Overall 5.3% of patients presented with adult worm migration across the eye, representing 16.3% of microfilaraemic individuals and 11.4% of amicrofilaraemic patients (P= 0.13). This symptom was similarly found in patients with more than 30,000 mf/ml (22%), those with microfilaraemia between 8 and 30,000 mf/ml (15.4%) and also in individuals with low or without microfilaraemia (16.1%) (P= 0.7). Five (14.3%) hypermicrofilaraemic patients did not present any L. loa-specific objective symptoms, as well as all the patients with single M. perstans infection. The presence of adult eye worm migration as a strong predictor of high microfilaraemia density would obscure the real burden of L. loa hypermicrofilaraemia in exposed individuals. For epidemiological purposes and control strategies, the mapping of L. loa in endemic areas should also take into account the group of patients with occult loiasis.
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Expanding the MDx toolbox for filarial diagnosis and surveillance. Trends Parasitol 2015; 31:391-400. [DOI: 10.1016/j.pt.2015.04.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 04/10/2015] [Accepted: 04/13/2015] [Indexed: 11/17/2022]
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Buonfrate D, Formenti F, Perandin F, Bisoffi Z. Novel approaches to the diagnosis of Strongyloides stercoralis infection. Clin Microbiol Infect 2015; 21:543-52. [PMID: 25887711 DOI: 10.1016/j.cmi.2015.04.001] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 03/31/2015] [Accepted: 04/01/2015] [Indexed: 12/23/2022]
Abstract
Strongyloides stercoralis differs from the other soil-transmitted helminths because it puts infected subjects at risk of a fatal syndrome (in cases of immunosuppression for medical conditions, immunosuppressant therapies, or both). Chronic strongyloidiasis is often a non-severe condition, or is sometimes even asymptomatic, but diagnosis and effective therapy are essential in order to eradicate the infection and the life-long risk involved. Therefore, diagnostic methods need to be highly sensitive. Stool microscopy and the Kato-Katz technique are commonly used in prevalence studies, but they are inadequate for S. stercoralis detection. This is probably the main reason why the global prevalence has long been underestimated. Concentration methods, the Baermann technique and Koga agar plate culture have better, but still unsatisfactory, sensitivity. Serological tests have demonstrated higher sensitivity; although some authors have concerns about their specificity, it is possible to define cut-off values over which infection is almost certain. In particular, the luciferase immunoprecipitation system technique combined with a recombinant antigen (NIE) demonstrated a specificity of almost 100%. ELISA coproantigen detection has also shown promising results, but still needs full evaluation. Molecular diagnostic methods are currently available in a few referral centres as in-house techniques. In this review, on the basis of the performance of the different diagnostic methods, we outline diagnostic strategies that could be proposed for different purposes, such as: prevalence studies in endemic areas; individual diagnosis and screening; and monitoring of cure in clinical care and clinical trials.
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Affiliation(s)
- D Buonfrate
- Centre for Tropical Diseases, Sacro Cuore Hospital, Negrar, Verona, Italy
| | - F Formenti
- Centre for Tropical Diseases, Sacro Cuore Hospital, Negrar, Verona, Italy
| | - F Perandin
- Centre for Tropical Diseases, Sacro Cuore Hospital, Negrar, Verona, Italy
| | - Z Bisoffi
- Centre for Tropical Diseases, Sacro Cuore Hospital, Negrar, Verona, Italy.
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Alhassan A, Makepeace BL, LaCourse EJ, Osei-Atweneboana MY, Carlow CKS. A simple isothermal DNA amplification method to screen black flies for Onchocerca volvulus infection. PLoS One 2014; 9:e108927. [PMID: 25299656 PMCID: PMC4191976 DOI: 10.1371/journal.pone.0108927] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 10/09/2014] [Indexed: 11/30/2022] Open
Abstract
Onchocerciasis is a debilitating neglected tropical disease caused by infection with the filarial parasite Onchocerca volvulus. Adult worms live in subcutaneous tissues and produce large numbers of microfilariae that migrate to the skin and eyes. The disease is spread by black flies of the genus Simulium following ingestion of microfilariae that develop into infective stage larvae in the insect. Currently, transmission is monitored by capture and dissection of black flies and microscopic examination of parasites, or using the polymerase chain reaction to determine the presence of parasite DNA in pools of black flies. In this study we identified a new DNA biomarker, encoding O. volvulus glutathione S-transferase 1a (OvGST1a), to detect O. volvulus infection in vector black flies. We developed an OvGST1a-based loop-mediated isothermal amplification (LAMP) assay where amplification of specific target DNA is detectable using turbidity or by a hydroxy naphthol blue color change. The results indicated that the assay is sensitive and rapid, capable of detecting DNA equivalent to less than one microfilaria within 60 minutes. The test is highly specific for the human parasite, as no cross-reaction was detected using DNA from the closely related and sympatric cattle parasite Onchocerca ochengi. The test has the potential to be developed further as a field tool for use in the surveillance of transmission before and after implementation of mass drug administration programs for onchocerciasis.
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Affiliation(s)
- Andy Alhassan
- Division of Genome Biology, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Benjamin L. Makepeace
- Institute of Infection & Global Health, University of Liverpool, Liverpool, United Kingdom
| | | | | | - Clotilde K. S. Carlow
- Division of Genome Biology, New England Biolabs, Ipswich, Massachusetts, United States of America
- * E-mail:
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Shrinking the lymphatic filariasis map: update on diagnostic tools for mapping and transmission monitoring. Parasitology 2014; 141:1912-7. [PMID: 25225828 DOI: 10.1017/s0031182014001231] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Lymphatic filariasis (LF), which is highly endemic in 73 countries worldwide, is targeted for elimination by 2020. The strategy for achieving this goal is based on 4 sequential programmatic steps: mapping, Mass drug administration (MDA) implementation, post-MDA surveillance and verification of LF elimination. All 4 stages of the implementation process are dependent on the availability of user friendly and highly sensitive rapid diagnostic tools. By the end of 2012, 59 countries had completed mapping for LF and Eritrea was the only country yet to start the process. Rolling out new diagnostic tools to facilitate the mapping process will enable an accelerated shrinking of the LF map to zero endemic countries by 2020. When the Global Programme to Eliminate Lymphatic Filariasis was launched in 2000, diagnostic tools for LF were limited to clinical examination, detection of microfilaria (MF) by microscopy in night blood samples and detection of antibodies to native-antigen preparations. There has been a significant improvement in the traditional LF diagnostic methods in recent years and some new tools are now available. This paper provides an update on the human diagnostic tests available for LF and their current applications as tools in mapping and transmission monitoring. The values of entomological indicators and parasite detection and speciation methods applied to vector populations are also discussed.
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