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Momo Kadia B, Ramsteijn AS, Dasi T, Fahmida U, Kulkarni B, Faye B, Htet MK, Sow D, Kalashikam RR, Sharma R, Sudibya ARP, Kusuma S, Angelin TC, Nurfadilah M, Jobarteh ML, Diop NS, Gabain I, Calvo-Urbano B, Ferguson E, Haggarty P, Heffernan C, Webster JP, Walker AW, Allen S. Assessment of the role of gut health in childhood stunting in a multisite, longitudinal study in India, Indonesia and Senegal: a UKRI GCRF Action Against Stunting Hub protocol. BMJ Paediatr Open 2024; 8:e001637. [PMID: 38417928 PMCID: PMC10900321 DOI: 10.1136/bmjpo-2022-001637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 01/15/2023] [Indexed: 03/01/2024] Open
Abstract
INTRODUCTION Childhood stunting has a complex aetiology, with poor gut health being an important contributor. This study will assess inter-relationships between maternal and infant gut health indices and infant linear growth. Inter-relationships between gut health indices, systemic inflammation and growth hormones in early childhood will also be assessed. METHODS AND ANALYSIS A longitudinal observational study of cohorts of 600 newborns and their mothers in India, Indonesia and Senegal will be conducted. Women will be recruited during pregnancy and their children followed up to age 24 months. Stool, urine and blood samples will be collected from the women and children for assessments of helminthic and protozoal parasites, bacterial pathogens, faecal microbiota taxa, biomarkers of environmental enteric dysfunction, systemic inflammation and growth hormones. Child anthropometric measurements will be collected at birth and at ages 3, 6, 9, 12, 18 and 24 months. The gut health indices will be integrated with cohort data from other Action Against Stunting Hub (AASH) workstreams for interdisciplinary analyses of childhood stunting and the development of a new typology of stunting. DISCUSSION This study will advance scientific understanding of the role of gut health in childhood stunting and will contribute to a broader knowledge of the complex aetiology of this condition as part of the interdisciplinary AASH research to reduce the global burden of childhood stunting. ETHICS AND DISSEMINATION This study has been approved by the relevant Ethics Committees in Senegal, India, and Indonesia and LSHTM. The results will be submitted for publication in peer-reviewed journals.
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Affiliation(s)
- Benjamin Momo Kadia
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | | | - Teena Dasi
- ICMR-National Institute of Nutrition, Hyderabad, India
| | - Umi Fahmida
- Southeast Asian Ministry of Education Organisation Regional Centre for Food and Nutrition (SEAMEO RECFON), East Jakarta, Indonesia
| | | | - Babacar Faye
- Service de Parasitologie-Mycologie, Faculté de Médecine, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
| | - Min Kyaw Htet
- Southeast Asian Ministry of Education Organisation Regional Centre for Food and Nutrition (SEAMEO RECFON), East Jakarta, Indonesia
| | - Doudou Sow
- Service de Parasitologie-Mycologie, UFR Sciences de la Santé, Université Gaston Berger, Saint Louis, Sénégal
| | | | - Ritu Sharma
- ICMR-National Institute of Nutrition, Hyderabad, India
| | - Arienta R P Sudibya
- Southeast Asian Ministry of Education Organisation Regional Centre for Food and Nutrition (SEAMEO RECFON), East Jakarta, Indonesia
| | - Sari Kusuma
- Southeast Asian Ministry of Education Organisation Regional Centre for Food and Nutrition (SEAMEO RECFON), East Jakarta, Indonesia
| | - Tiffany C Angelin
- Southeast Asian Ministry of Education Organisation Regional Centre for Food and Nutrition (SEAMEO RECFON), East Jakarta, Indonesia
| | - Mifa Nurfadilah
- Southeast Asian Ministry of Education Organisation Regional Centre for Food and Nutrition (SEAMEO RECFON), East Jakarta, Indonesia
| | - Modou Lamin Jobarteh
- Department of Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Ndeye Sokhna Diop
- Service de Parasitologie-Mycologie, Faculté de Médecine, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
| | - Isobel Gabain
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, London, UK
| | - Beatriz Calvo-Urbano
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, London, UK
| | - Elaine Ferguson
- Department of Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Paul Haggarty
- Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Claire Heffernan
- Department of Population Health, London School of Hygiene & Tropical Medicine, London, UK
- London International Development Centre, London, UK
| | - Joanne P Webster
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, London, UK
| | - Alan W Walker
- Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Stephen Allen
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
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Oyeyemi OT, Ogundahunsi O, Schunk M, Fatem RG, Shollenberger LM. Neglected tropical disease (NTD) diagnostics: current development and operations to advance control. Pathog Glob Health 2024; 118:1-24. [PMID: 37872790 PMCID: PMC10769148 DOI: 10.1080/20477724.2023.2272095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023] Open
Abstract
Neglected tropical diseases (NTDs) have become important public health threats that require multi-faceted control interventions. As late treatment and management of NTDs contribute significantly to the associated burdens, early diagnosis becomes an important component for surveillance and planning effective interventions. This review identifies common NTDs and highlights the progress in the development of diagnostics for these NTDs. Leveraging existing technologies to improve NTD diagnosis and improving current operational approaches for deployment of developed diagnostics are crucial to achieving the 2030 NTD elimination target. Point-of-care NTD (POC-NTD) diagnostic tools are recommended preferred diagnostic options in resource-constrained areas for mapping risk zones and monitoring treatment efficacy. However, few are currently available commercially. Technical training of remote health care workers on the use of POC-NTD diagnostics, and training of health workers on the psychosocial consequences of these diagnostics are critical in harnessing POC-NTD diagnostic potential. While the COVID-19 pandemic has challenged the possibility of achieving NTD elimination in 2030 due to the disruption of healthcare services and dwindling financial support for NTDs, the possible contribution of NTDs in exacerbating COVID-19 pandemic should motivate NTD health system strengthening.
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Affiliation(s)
- Oyetunde T. Oyeyemi
- Department of Biosciences and Biotechnology, University of Medical Sciences, Ondo, Nigeria
- Department of Biological Sciences, Old Dominion University, Virginia, USA
| | - Olumide Ogundahunsi
- The Central Office for Research and Development (CORD), University of Medical Sciences, Ondo, Nigeria
| | - Mirjam Schunk
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU) institution, Munich, Germany
| | - Ramzy G. Fatem
- Schistosome Biological Supply Center, Theodor Bilharz Research Institute, Giza, Egypt
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Chen W, Zhang JW, Qin BX, Xie HT, Zhang Z, Qiao XZ, Li SK, Asif M, Guo S, Cui LX, Wang PP, Dong LH, Guo QG, Jiang WJ, Ma P, Xia ZY, Lu CH, Zhang LQ. Quantitative detection of the Ralstonia solanacearum species complex in soil by qPCR combined with a recombinant internal control strain. Microbiol Spectr 2023; 11:e0021023. [PMID: 37966217 PMCID: PMC10715031 DOI: 10.1128/spectrum.00210-23] [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: 01/13/2023] [Accepted: 10/12/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE DNA-based detection and quantification of soil-borne pathogens, such as the Ralstonia solanacearum species complex (RSSC), plays a vital role in risk assessment, but meanwhile, precise quantification is difficult due to the poor purity and yield of the soil DNA retrieved. The internal sample process control (ISPC) strain RsPC we developed solved this problem and significantly improved the accuracy of quantification of RSSC in different soils. ISPC-based quantitative PCR detection is a method especially suitable for the quantitative detection of microbes in complex matrices (such as soil and sludge) containing various PCR inhibitors and for those not easy to lyse (like Gram-positive bacteria, fungi, and thick-wall cells like resting spores). In addition, the use of ISPC strains removes additional workload on the preparation of high-quality template DNA and facilitates the development of high-throughput quantitative detection techniques for soil microbes.
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Affiliation(s)
- Wei Chen
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian District, Beijing, China
| | - Jun-Wei Zhang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian District, Beijing, China
| | - Bi-Xia Qin
- Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Xixiangtang District, Nanning, China
| | - Hui-Ting Xie
- Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Xixiangtang District, Nanning, China
| | - Zhi Zhang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian District, Beijing, China
| | - Xiu-Ze Qiao
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian District, Beijing, China
| | - Shan-Kui Li
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian District, Beijing, China
| | - Muhammad Asif
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian District, Beijing, China
| | - Song Guo
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian District, Beijing, China
| | - Li-Xian Cui
- Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Xixiangtang District, Nanning, China
| | - Pei-Pei Wang
- Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs, IPM Innovation Centre of Hebei Province, Lianchi District, Baoding, China
| | - Li-Hong Dong
- Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs, IPM Innovation Centre of Hebei Province, Lianchi District, Baoding, China
| | - Qing-Gang Guo
- Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs, IPM Innovation Centre of Hebei Province, Lianchi District, Baoding, China
| | - Wen-Jun Jiang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian District, Beijing, China
| | - Ping Ma
- Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture and Rural Affairs, IPM Innovation Centre of Hebei Province, Lianchi District, Baoding, China
| | - Zhen-Yuan Xia
- Yunnan Academy of Tobacco Agricultural Sciences, Wuhua District, Kunming, China
| | - Can-Hua Lu
- Yunnan Academy of Tobacco Agricultural Sciences, Wuhua District, Kunming, China
| | - Li-Qun Zhang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Haidian District, Beijing, China
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Puchner KP, Bottazzi ME, Periago V, Grobusch M, Maizels R, McCarthy J, Lee B, Gaspari E, Diemert D, Hotez P. Vaccine value profile for Hookworm. Vaccine 2023:S0264-410X(23)00540-6. [PMID: 37863671 DOI: 10.1016/j.vaccine.2023.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 04/24/2023] [Accepted: 05/03/2023] [Indexed: 10/22/2023]
Abstract
Hookworm, a parasitic infection, retains a considerable burden of disease, affecting the most underprivileged segments of the general population in endemic countries and remains one of the leading causes of mild to severe anemia in Low and Middle Income Countries (LMICs), particularly in pregnancy and children under 5. Despite repeated large scale Preventive Chemotherapy (PC) interventions since more than 3 decades, there is broad consensus among scholars that elimination targets set in the newly launched NTD roadmap will require additional tools and interventions. Development of a vaccine could constitute a promising expansion of the existing arsenal against hookworm. Therefore, we have evaluated the biological and implementation feasibility of the vaccine development as well as the added value of such a novel tool. Based on pipeline landscaping and the current knowledge on key biological aspects of the pathogen and its interactions with the host, we found biological feasibility of development of a hookworm vaccine to be moderate. Also, our analysis on manufacturing and regulatory issues as well as potential uptake yielded moderate implementation feasibility. Modelling studies suggest a that introduction of a vaccine in parallel with ongoing integrated interventions (PC, WASH, shoe campaigns), could substantially reduce burden of disease in a cost - saving mode. Finally a set of actions are recommended that might impact positively the likelihood of timely development and introduction of a hookworm vaccine.
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Affiliation(s)
| | - Maria Elena Bottazzi
- National School of Tropical Medicine, Baylor College of Medicine, Baylor, TX, USA
| | | | - Martin Grobusch
- Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Amsterdam University Medical Centers, Location AMC, Amsterdam Infection & Immunity, Amsterdam Public Health, University of Amsterdam, Amsterdam, The Netherlands
| | - Rick Maizels
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - James McCarthy
- The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Bruce Lee
- Public Health Informatics, Computational, and Operations Research, Graduate School of Public Health and Health Policy, City University of New York, New York, NY, USA
| | - Erika Gaspari
- European & Developing Countries Clinical Trials Partnership (EDCTP), The Hague, The Netherlands
| | - David Diemert
- Department of Microbiology, Immunology & Tropical Medicine, George Washington University Medical Center, Washington, DC, USA
| | - Peter Hotez
- National School of Tropical Medicine, Baylor College of Medicine, Baylor, TX, USA
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Rotejanaprasert C, Chuaicharoen P, Prada JM, Thantithaveewat T, Adisakwattana P, Pan-ngum W. Evaluation of Kato-Katz and multiplex quantitative polymerase chain reaction performance for clinical helminth infections in Thailand using a latent class analysis. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220281. [PMID: 37598708 PMCID: PMC10440171 DOI: 10.1098/rstb.2022.0281] [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: 10/29/2022] [Accepted: 05/27/2023] [Indexed: 08/22/2023] Open
Abstract
Using an appropriate diagnostic tool is essential to soil-transmitted helminth control and elimination efforts. Kato-Katz (KK) is the most commonly used diagnostic, but recently other tools, such as real-time quantitative polymerase chain reaction (multiplex qPCR), are starting to be employed more. Here, we evaluated the performance of these two diagnostic tools for five helminth species in Thailand. In the absence of a gold standard, diagnostic performance can be evaluated using latent class analysis. Our results suggest that in moderate to high prevalence settings above 2% multiplex qPCR could be more sensitive than KK, this was particularly apparent for Opisthorchis viverrini in the northeastern provinces. However, for low prevalence, both diagnostics suffered from low sensitivity. Specificity of both diagnostics was estimated to be high (above 70%) across all settings. For some specific helminth infection such as O. viverrini, multiplex qPCR is still a preferable choice of diagnostic test. KK performed equally well in detecting Ascaris lumbricoides and Taenia solium when the prevalence is moderate to high (above 2%). Neither test performed well when the prevalence of infection is low (below 2%), and certainly in the case for hookworm and Trichuris trichiura. Combination of two or more diagnostic tests can improve the performance although the cost would be high. Development of new methods for helminth surveillance at the pre-elimination phase is therefore very important. This article is part of the theme issue 'Challenges and opportunities in the fight against neglected tropical diseases: a decade from the London Declaration on NTDs'.
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Affiliation(s)
- Chawarat Rotejanaprasert
- Department of Tropical Hygiene, Mahidol University, Bangkok, Thailand
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Mahidol University, Bangkok, Thailand
| | | | - Joaquin M. Prada
- Faculty of Health and Medical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, UK
| | | | - Poom Adisakwattana
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Wirichada Pan-ngum
- Department of Tropical Hygiene, Mahidol University, Bangkok, Thailand
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Mahidol University, Bangkok, Thailand
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Ferreira SCM, Jarquín-Díaz VH, Heitlinger E. Amplicon sequencing allows differential quantification of closely related parasite species: an example from rodent Coccidia (Eimeria). Parasit Vectors 2023; 16:204. [PMID: 37330545 DOI: 10.1186/s13071-023-05800-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/03/2023] [Indexed: 06/19/2023] Open
Abstract
BACKGROUND Quantifying infection intensity is a common goal in parasitological studies. We have previously shown that the amount of parasite DNA in faecal samples can be a biologically meaningful measure of infection intensity, even if it does not agree well with complementary counts of transmission stages (oocysts in the case of Coccidia). Parasite DNA can be quantified at relatively high throughput using quantitative polymerase chain reaction (qPCR), but amplification needs a high specificity and does not simultaneously distinguish between parasite species. Counting of amplified sequence variants (ASVs) from high-throughput marker gene sequencing using a relatively universal primer pair has the potential to distinguish between closely related co-infecting taxa and to uncover the community diversity, thus being both more specific and more open-ended. METHODS We here compare qPCR to the sequencing-based amplification using standard PCR and a microfluidics-based PCR to quantify the unicellular parasite Eimeria in experimentally infected mice. We use multiple amplicons to differentially quantify Eimeria spp. in a natural house mouse population. RESULTS We show that sequencing-based quantification has high accuracy. Using a combination of phylogenetic analysis and the co-occurrence network, we distinguish three Eimeria species in naturally infected mice based on multiple marker regions and genes. We investigate geographical and host-related effects on Eimeria spp. community composition and find, as expected, prevalence to be largely explained by sampling locality (farm). Controlling for this effect, the novel approach allowed us to find body condition of mice to be negatively associated with Eimeria spp. abundance. CONCLUSIONS We conclude that amplicon sequencing provides the underused potential for species distinction and simultaneous quantification of parasites in faecal material. The method allowed us to detect a negative effect of Eimeria infection on the body condition of mice in the natural environment.
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Affiliation(s)
- Susana C M Ferreira
- Division of Computational Systems Biology, Center for Microbiology and Ecological Systems Science, University of Vienna, Djerassipl. 1, 1030, Vienna, Austria.
- Institute for Biology. Department of Molecular Parasitology, Humboldt-Universität zu Berlin (HU), Philippstr. 13, Haus 14, 10115, Berlin, Germany.
| | - Víctor Hugo Jarquín-Díaz
- Institute for Biology. Department of Molecular Parasitology, Humboldt-Universität zu Berlin (HU), Philippstr. 13, Haus 14, 10115, Berlin, Germany
- Leibniz-Institut Für Zoo- Und Wildtierforschung (IZW) im Forschungsverbund Berlin E.V., Alfred-Kowalke-Straße 17, 10315, Berlin, Germany
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin Berlin, Berlin, Germany
- Experimental and Clinical Research Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Lindenberger Weg 80, 13125, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Emanuel Heitlinger
- Institute for Biology. Department of Molecular Parasitology, Humboldt-Universität zu Berlin (HU), Philippstr. 13, Haus 14, 10115, Berlin, Germany
- Leibniz-Institut Für Zoo- Und Wildtierforschung (IZW) im Forschungsverbund Berlin E.V., Alfred-Kowalke-Straße 17, 10315, Berlin, Germany
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Papaiakovou M, Fraija-Fernández N, James K, Briscoe AG, Hall A, Jenkins TP, Dunn J, Levecke B, Mekonnen Z, Cools P, Doyle SR, Cantacessi C, Littlewood DTJ. Evaluation of genome skimming to detect and characterise human and livestock helminths. Int J Parasitol 2023; 53:69-79. [PMID: 36641060 DOI: 10.1016/j.ijpara.2022.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/08/2022] [Accepted: 12/08/2022] [Indexed: 01/13/2023]
Abstract
The identification of gastrointestinal helminth infections of humans and livestock almost exclusively relies on the detection of eggs or larvae in faeces, followed by manual counting and morphological characterisation to differentiate species using microscopy-based techniques. However, molecular approaches based on the detection and quantification of parasite DNA are becoming more prevalent, increasing the sensitivity, specificity and throughput of diagnostic assays. High-throughput sequencing, from single PCR targets through to the analysis of whole genomes, offers significant promise towards providing information-rich data that may add value beyond traditional and conventional molecular approaches; however, thus far, its utility has not been fully explored to detect helminths in faecal samples. In this study, low-depth whole genome sequencing, i.e. genome skimming, has been applied to detect and characterise helminth diversity in a set of helminth-infected human and livestock faecal material. The strengths and limitations of this approach are evaluated using three methods to characterise and differentiate metagenomic sequencing data based on (i) mapping to whole mitochondrial genomes, (ii) whole genome assemblies, and (iii) a comprehensive internal transcribed spacer 2 (ITS2) database, together with validation using quantitative PCR (qPCR). Our analyses suggest that genome skimming can successfully identify most single and multi-species infections reported by qPCR and can provide sufficient coverage within some samples to resolve consensus mitochondrial genomes, thus facilitating phylogenetic analyses of selected genera, e.g. Ascaris spp. Key to this approach is both the availability and integrity of helminth reference genomes, some of which are currently contaminated with bacterial and host sequences. The success of genome skimming of faecal DNA is dependent on the availability of vouchered sequences of helminths spanning both taxonomic and geographic diversity, together with methods to detect or amplify minute quantities of parasite nucleic acids in mixed samples.
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Affiliation(s)
- Marina Papaiakovou
- Natural History Museum, Cromwell Road, London, UK; Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Natalia Fraija-Fernández
- Natural History Museum, Cromwell Road, London, UK; Marine Zoology Unit, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Spain
| | - Katherine James
- Natural History Museum, Cromwell Road, London, UK; Interdisciplinary Computing and Complex BioSystems, School of Computing, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew G Briscoe
- Natural History Museum, Cromwell Road, London, UK; NatureMetrics, Surrey Research Park, Guildford, UK
| | - Andie Hall
- Natural History Museum, Cromwell Road, London, UK
| | - Timothy P Jenkins
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK; Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Julia Dunn
- Department of Infectious Disease Epidemiology, Imperial College, London W2 1PG, UK
| | - Bruno Levecke
- Department of Translational Physiology, Infectiology and Public Health, Ghent University, Merelbeke, Belgium
| | - Zeleke Mekonnen
- Jimma University Institute of Health (JUIH), Jimma, Ethiopia
| | - Piet Cools
- Department of Translational Physiology, Infectiology and Public Health, Ghent University, Merelbeke, Belgium
| | | | - Cinzia Cantacessi
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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Effect of incorporation of bead-beating during DNA extraction for quantitative polymerase chain reaction-based detection of Trichuris trichiura in stool samples in community settings: a systematic review. J Helminthol 2023; 97:e15. [PMID: 36722449 DOI: 10.1017/s0022149x2200092x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
This meta-analysis was designed to assess the effect of the addition of a bead-beating (BB) step during DNA extraction to effectively isolate Trichuris trichiura DNA from stool samples for quantitative polymerase chain reaction (qPCR)-based diagnosis. qPCR-based molecular studies comparing the inclusion of a bead-beating step during the DNA extraction from stool samples with extraction without the step were included in the analysis. Studies using real patient samples in community settings were included. The PubMed database and Google search engine were searched in December 2019. Risk of bias and applicability were assessed using the Quality Assessment of Diagnostic Accuracy Studies-2 checklist. Odds ratios (ORs) for individual studies were combined to estimate the random effects model OR. A total of six independent sub-studies were gathered from two published original articles. The division of the two major studies into six sub-studies was indispensable due to the nature of the study carried out. 128 of the total 192 samples (in all studies) were positive for T. trichiura when BB was used during DNA extraction compared to 108/192 when BB was excluded. The combined OR was 1.66 (95% confidence interval: 1.059 to 2.602). Though only two articles were included in the study, six exclusive individual sub-studies were analyzed. Inherent differences in the background prevalence of helminths in the study population could impact the sensitivity of qPCR. It was found that the inclusion of the BB step during DNA extraction significantly increased the sensitivity of the test. This study was not registered in any database.
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Davey ML, Kamenova S, Fossøy F, Solberg EJ, Davidson R, Mysterud A, Rolandsen CM. Faecal metabarcoding provides improved detection and taxonomic resolution for non-invasive monitoring of gastrointestinal nematode parasites in wild moose populations. Parasit Vectors 2023; 16:19. [PMID: 36653864 PMCID: PMC9847159 DOI: 10.1186/s13071-022-05644-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 12/28/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Although wild ungulate populations are heavily monitored throughout Europe, we understand little of how parasites affect population dynamics, and there is no systematic, long-term monitoring of parasite diversity and parasite loads. Such monitoring is in part hampered by a lack of time- and cost-effective assay methodologies with high sensitivity and good taxonomic resolution. DNA metabarcoding has been successfully used to characterize the parasitic nemabiome with high taxonomic resolution in a variety of wild and domestic hosts. However, in order to implement this technique in large-scale, potentially non-invasive monitoring of gastrointestinal parasitic nematodes (GIN), protocol optimization is required to maximize biodiversity detection, whilst maintaining time- and cost-effectiveness. METHODS Faecal samples were collected from a wild moose population and GIN communities were characterized and quantified using both parasitological techniques (egg and larva counting) and DNA metabarcoding of the ITS2 region of rDNA. Three different isolation methods were compared that differed in the volume of starting material and cell lysis method. RESULTS Similar nematode faunas were recovered from all samples using both parasitological and metabarcoding methods, and the approaches were largely congruent. However, metabarcoding assays showed better taxonomic resolution and slightly higher sensitivity than egg and larvae counts. The metabarcoding was not strictly quantitative, but the proportion of target nematode sequences recovered was correlated with the parasitologically determined parasite load. Species detection rates in the metabarcoding assays were maximized using a DNA isolation method that included mechanical cell disruption and maximized the starting material volume. CONCLUSIONS DNA metabarcoding is a promising technique for the non-invasive, large-scale monitoring of parasitic GINs in wild ungulate populations, owing to its high taxonomic resolution, increased assay sensitivity, and time- and cost-effectiveness. Although metabarcoding is not a strictly quantitative method, it may nonetheless be possible to create a management- and conservation-relevant index for the host parasite load from this data. To optimize the detection rates and time- and cost-effectiveness of metabarcoding assays, we recommend choosing a DNA isolation method that involves mechanical cell disruption and maximizes the starting material volume.
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Affiliation(s)
- Marie L. Davey
- grid.420127.20000 0001 2107 519XNorwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Stefaniya Kamenova
- grid.5510.10000 0004 1936 8921University of Oslo, Oslo, Norway ,grid.19477.3c0000 0004 0607 975XNorwegian University of Life Sciences, Ås, Norway
| | - Frode Fossøy
- grid.420127.20000 0001 2107 519XNorwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Erling J. Solberg
- grid.420127.20000 0001 2107 519XNorwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Rebecca Davidson
- grid.410549.d0000 0000 9542 2193Norwegian Veterinary Institute, Tromsø, Norway
| | - Atle Mysterud
- grid.420127.20000 0001 2107 519XNorwegian Institute for Nature Research (NINA), Trondheim, Norway ,grid.5510.10000 0004 1936 8921University of Oslo, Oslo, Norway
| | - Christer M. Rolandsen
- grid.420127.20000 0001 2107 519XNorwegian Institute for Nature Research (NINA), Trondheim, Norway
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Jayakody NK, Kumbukgahadeniya PL, Silva A, Wickramasinghe ND, Wickramasinghe S, McManus DP, Weerakoon KG. The accuracy of nucleic acid amplification tests (NAATs) in detecting human intestinal nematode infections: A protocol for a systematic review and meta-analysis. PLoS One 2022; 17:e0278920. [PMID: 36508427 PMCID: PMC9744273 DOI: 10.1371/journal.pone.0278920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022] Open
Abstract
Human intestinal nematode infections are a global public health issue as they can result in considerable morbidity in infected individuals, mainly in developing countries. These infections continue to go undiagnosed, as they tend to be mainly endemic in resource-poor communities where there is a shortage of experienced laboratory staff and relevant diagnostic technologies. This is further exacerbated by the nature of intermittent shedding of eggs and larvae by these parasites. Diagnostic methods range from simple morphological identification to more specialised high-throughput sequencing technologies. Microscopy-based methods, although simple, are labour-intensive and considerably less sensitive than molecular methods which are rapid and have high levels of accuracy. Molecular methods use nucleic acid amplification (NAA) to amplify the deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) fragments of the parasite to detect and determine its presence using different technologies (NAAT). They have increased the sensitivity of detection and quantitation of intestinal nematode infections, especially in low infection intensity settings. The absence of a gold standard test limits current diagnosis and, in turn, restricts intervention measures and effective control efforts. The objective of this review is to determine the accuracy of NAATs in detecting human intestinal nematode infections using Kato-Katz as the reference test for the most common soil-transmitted helminth (STH) infections and the scotch tape test for enterobiasis and Baermann method for strongyloidiasis. Relevant studies will be identified by searches in electronic databases. Two reviewers will independently screen the literature against eligibility criteria. The methodological quality of studies will then be appraised by two reviewers using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. Discrepancies will be addressed by a third reviewer. The true positives, false positives, true negatives and false negatives of all the studies will be extracted into contingency tables. In paired forest plots, study-specific sensitivity and specificity with a 95 per cent confidence interval will be displayed. The systematic review of this protocol will report the diagnostic accuracy of currently available NAATs for the detection of human intestinal nematode infections. This will help healthcare providers and administrators determine the diagnostic method to be used in different clinical and preventive settings. Trial registration: PROSPERO registration number for this protocol is CRD42022315730.
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Affiliation(s)
- Nalini Kaushalya Jayakody
- Faulty of Medicine, Department of Parasitology, Wayamba University of Sri Lanka, Kuliyapitiya, Sri Lanka
- Faculty of Medicine and Allied Sciences, Department of Parasitology, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka
- * E-mail: (KGW); (NKJ)
| | | | - Anjana Silva
- Faculty of Medicine and Allied Sciences, Department of Parasitology, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka
| | - Nuwan Darshana Wickramasinghe
- Faculty of Medicine and Allied Sciences, Department of Community Medicine, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka
| | - Susiji Wickramasinghe
- Faculty of Medicine, Department of Parasitology, University of Peradeniya, Kandy, Sri Lanka
| | | | - Kosala Gayan Weerakoon
- Faculty of Medicine and Allied Sciences, Department of Parasitology, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
- * E-mail: (KGW); (NKJ)
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11
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Advantages and Limitations of Microscopy and Molecular Detections for Diagnosis of Soil-transmitted Helminths: An Overview. Helminthologia 2022; 59:321-340. [PMID: 36875683 PMCID: PMC9979072 DOI: 10.2478/helm-2022-0034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 10/31/2022] [Indexed: 02/05/2023] Open
Abstract
World Health Organization (WHO) reported that over 1.5 billion people are infected by soil-transmitted helminths (STH) worldwide in sub-Saharan Africa, the United States of America, China, and East Asia. Heavy infections and polyparasitism are associated with higher morbidity rates, and the patients are exposed to increased vulnerability to other diseases. Therefore, accurate diagnosis followed by mass treatment for morbidity control is necessary.STH diagnosis commonly involves the microscopic observation of the presence of the STH eggs and larvae in the faecal samples. Furthermore, molecular approaches are increasingly utilised in monitoring and surveillance as they show higher sensitivity. Their capability to differentiate hookworm species is an advantage over the Kato-Katz technique. This review discusses the advantages and limitations of microscopy and various molecular tools used for STH detection.
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Gomes ECDS, Barbosa Júnior WL, Melo FLD. Evaluation of SmITS1-LAMP performance to diagnosis schistosomiasis in human stool samples from an endemic area in Brazil. Exp Parasitol 2022; 242:108389. [DOI: 10.1016/j.exppara.2022.108389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 09/09/2022] [Accepted: 09/21/2022] [Indexed: 11/04/2022]
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13
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Buonfrate D, Tamarozzi F, Paradies P, Watts MR, Bradbury RS, Bisoffi Z. The diagnosis of human and companion animal Strongyloides stercoralis infection: Challenges and solutions. A scoping review. ADVANCES IN PARASITOLOGY 2022; 118:1-84. [PMID: 36088083 DOI: 10.1016/bs.apar.2022.07.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Strongyloidiasis is the infection caused by soil-transmitted nematodes of Strongyloides species, infecting humans and some animals. Strongyloides stercoralis is the species with most clinical and epidemiological relevance in humans and dogs, due to its high prevalence and its capacity of inducing a life-threatening hyperinfection. Diagnosis of strongyloidiasis is challenging, due to the absence of a single reference standard test with high sensitivity and specificity, which also hampers the estimation of the accuracy of other diagnostic tests. In this chapter, we review the deployment and performance of the parasitological, immunological, molecular tests for the diagnosis of strongyloidiasis in humans and in dogs. Further, we comment the available evidence from genotyping studies that have addressed the zoonotic potential of S. stercoralis. Finally, we discuss the use of different diagnostic methods in relation to the purpose (i.e., screening, individual diagnosis, inclusion in a clinical trial) and the setting (endemic/non-endemic areas) and report the accuracy figures reported by systematic reviews on either parasitological, serological or molecular techniques published in literature.
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Affiliation(s)
- Dora Buonfrate
- Department of Infectious Tropical diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy.
| | - Francesca Tamarozzi
- Department of Infectious Tropical diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Paola Paradies
- Department of Emergency and Organs Transplantation, Veterinary Section, Campus of Veterinary Medicine, University of Bari, Bari, Italy
| | - Matthew R Watts
- Centre for Infectious Diseases and Microbiology, Institute of Clinical Pathology and Medical Research - New South Wales Health Pathology and Sydney Institute for Infectious Diseases, Westmead Hospital, University of Sydney, Sydney, New South Wales, Australia
| | - Richard S Bradbury
- School of Health and Life Sciences, Federation University Australia, Berwick, VC, Australia
| | - Zeno Bisoffi
- Department of Infectious Tropical diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy; Department of Diagnostics and Public Health, University of Verona, Verona, Italy
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14
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Grau-Pujol B, Gandasegui J, Escola V, Marti-Soler H, Cambra-Pellejà M, Demontis M, Brienen EAT, Jamine JC, Muchisse O, Cossa A, Sacoor C, Cano J, Van Lieshout L, Martinez-Valladares M, Muñoz J. Single-Nucleotide Polymorphisms in the Beta-Tubulin Gene and Its Relationship with Treatment Response to Albendazole in Human Soil-Transmitted Helminths in Southern Mozambique. Am J Trop Med Hyg 2022; 107:tpmd210948. [PMID: 35895348 PMCID: PMC9490645 DOI: 10.4269/ajtmh.21-0948] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 05/02/2022] [Indexed: 11/17/2022] Open
Abstract
Soil-transmitted helminth (STH) cornerstone control strategy is mass drug administration (MDA) with benzimidazoles. However, MDA might contribute to selection pressure for anthelmintic resistance, as occurred in livestock. The aim of this study is to evaluate the treatment response to albendazole and the relationship with the presence of putative benzimidazole resistance single-nucleotide polymorphisms (SNPs) in the β-tubulin gene of STH in Southern Mozambique. After screening 819 participants, we conducted a cohort study with 184 participants infected with STH in Manhiça district, Southern Mozambique. A pretreatment and a posttreatment stool samples were collected and the STH infection was identified by duplicate Kato-Katz and quantitative polymerase chain reaction (qPCR). Cure rate and egg reduction rates were calculated. Putative benzimidazole resistance SNPs (F167Y, F200T, and E198A) in Trichuris trichiura and Necator americanus were assessed by pyrosequencing. Cure rates by duplicate Kato-Katz and by qPCR were 95.8% and 93.6% for Ascaris lumbricoides, 28% and 7.8% for T. trichiura, and 88.9% and 56.7% for N. americanus. Egg reduction rate by duplicate Kato-Katz was 85.4% for A. lumbricoides, 34.9% for T. trichiura, and 40.5% for N. americanus. Putative benzimidazole resistance SNPs in the β-tubulin gene were detected in T. trichiura (23%) and N. americanus (21%) infected participants at pretreatment. No statistical difference was observed between pretreatment and posttreatment frequencies for none of the SNPs. Although treatment response to albendazole was low, particularly in T. trichiura, the putative benzimidazole resistance SNPs were not higher after treatment in the population studied. New insights are needed for a better understanding and monitoring of human anthelmintic resistance.
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Affiliation(s)
- Berta Grau-Pujol
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic – University of Barcelona, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Mundo Sano Foundation, Buenos Aires, Argentina
| | - Javier Gandasegui
- Instituto de Ganadería de Montaña (CSIC-Universidad de León), Grulleros, León, Spain
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana, León, Spain
| | - Valdemiro Escola
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Helena Marti-Soler
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic – University of Barcelona, Barcelona, Spain
| | - Maria Cambra-Pellejà
- Instituto de Ganadería de Montaña (CSIC-Universidad de León), Grulleros, León, Spain
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana, León, Spain
| | - Maria Demontis
- Department of Parasitology, Centre of Infectious Diseases, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Eric A. T. Brienen
- Department of Parasitology, Centre of Infectious Diseases, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | | | - Osvaldo Muchisse
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Anelsio Cossa
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Charfudin Sacoor
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Jorge Cano
- Expanded Special Project for Elimination of NTDs, World Health Organization Regional Office for Africa, Brazzaville, The Republic of the Congo
| | - Lisette Van Lieshout
- Department of Parasitology, Centre of Infectious Diseases, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Maria Martinez-Valladares
- Instituto de Ganadería de Montaña (CSIC-Universidad de León), Grulleros, León, Spain
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana, León, Spain
| | - Jose Muñoz
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic – University of Barcelona, Barcelona, Spain
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Ullah H, Arbab S, Li K, Khan MIU, Qadeer A, Muhammad N. Schistosomiasis related circulating cell-free DNA: A useful biomarker in diagnostics. Mol Biochem Parasitol 2022; 251:111495. [PMID: 35835258 DOI: 10.1016/j.molbiopara.2022.111495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/01/2022] [Accepted: 07/08/2022] [Indexed: 12/26/2022]
Abstract
Schistosoma is a genus of trematodes causing schistosomiasis, a major neglected tropical disease infecting more than 240 million people and with 700 million people at the risk of infection in the tropical and subtropical regions of the world, especially low-income countries. For the elimination of the disease, accurate diagnostic tools are needed. Besides allowing early treatment, early detection prevents environmental contamination and in turn ensures safe water sources in the endemic areas. Cell-free DNA (cfDNA) biomarker detection is a relatively new tool, used for the diagnosis of schistosomiasis in the early stages of infection from non-invasive clinical or experimental samples. cfDNA can be detected in Schistosoma infected host body fluids such as urine, serum, saliva and tissues, mainly in blood offering significant benefits for accurate diagnosis. In the current review, we described different characteristics of cfDNA, evidencing and supporting its potential uses in Schistosoma diagnosis and the improvement of treatment effectiveness.
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Affiliation(s)
- Hanif Ullah
- West China School of Nursing, Sichuan University, Chengdu, China.
| | - Safia Arbab
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China; Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ka Li
- West China School of Nursing, Sichuan University, Chengdu, China.
| | - Muhammad Inayat Ullah Khan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Abdul Qadeer
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology of Ministry of Agriculture and Rural Affairs, Shanghai 200241, China
| | - Nehaz Muhammad
- Department of Zoology, University of Swabi, Swabi 23561, Khyber Pakhtunkhwa, Pakistan
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16
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Loop mediated isothermal amplification for detection of foodborne parasites: A journey from lab to lab-on-a-chip. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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17
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Using quantitative PCR to identify opportunities to strengthen soil-transmitted helminth control in Solomon Islands: A cross-sectional epidemiological survey. PLoS Negl Trop Dis 2022; 16:e0010350. [PMID: 35604904 PMCID: PMC9126411 DOI: 10.1371/journal.pntd.0010350] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 03/22/2022] [Indexed: 11/19/2022] Open
Abstract
Background The Kato-Katz microscopy technique is the global standard for assessment of soil-transmitted helminth (STH) burden. However, major limitations include its poor sensitivity, requirement for rapid sample processing, and inability to differentiate hookworm species nor detect Strongyloides spp. infections. We assessed the prevalence and intensity of STH species in Solomon Islands by conducting a province-wide survey using quantitative PCR (qPCR) for diagnosis, which can provide much better characterisation of STH burden than microscopy. Methodology/Principal findings We conducted a cross-sectional survey in 18 villages in Western Province to detect infections with six STH species and quantify intensity with three. We used linear mixed model regression to identify potential water, sanitation, and hygiene (WASH) and environmental risk factors for infection. We collected stool specimens from 830 village residents. Overall STH prevalence was 63.3% (range 27.5 to 91.5% across villages), led by Necator americanus (54.5% [range 17.5–89.4%]), followed by Ancylostoma ceylanicum (15.5% [range 2.8–45.8%]), Trichuris trichiura (9.1% [range 0–79.2%]), and Strongyloides spp. (3.2% [range 0–29.2%]). Most infections were of light intensity for N. americanus (85.7%) and T. trichiura (90.7%). Owning a household latrine was associated with a lower risk of N. americanus infection (AOR 0.41, 95% CI 0.24–0.68) while greater precipitation was linked to more common T. trichiura infection (AOR 1.14, 95% CI 1.04–1.25). Conclusion/Significance In this first large-scale population survey of STH in the Pacific using qPCR, we found evidence that ivermectin should be incorporated into STH control programmes because of the presence of T. trichiura and Strongyloides spp., both of which are poorly responsive to albendazole. Furthermore, One Health strategies are needed for improved A. ceylanicum and Strongyloides spp. control, WASH access and use should be improved to complement deworming programmes, and control efforts should ideally be expanded to entire communities. Trial registration ClinicalTrials.gov Australian and New Zealand Clinical Trials Registry ACTRN12618001086257. Routine assessments of the burden of intestinal worm infections rely on microscopy-based diagnostic methods, such as the Kato-Katz technique. However major limitations include its poor sensitivity, requirement for rapid sample processing, and inability to differentiate individual hookworm species and detect Strongyloides spp. infections. It is important to assess the burden of each of these infections to design control approaches beyond the current core strategy of albendazole preventive chemotherapy. Use of qPCR for diagnosis could address these gaps because it can distinguish all relevant intestinal worm species. We completed a province-wide intestinal worm infections prevalence survey using qPCR in Western Province, Solomon Islands. Overall prevalence was extremely high (62.5%). We identified a high burden of Necator americanus (54.5%) and detected Ancylostoma ceylanicum (15.5%), Trichuris trichiura (9.1%), and Strongyloides spp. (3.2%) infections. Increased age and precipitation were associated with higher prevalence of infection, while owning a household latrine was associated with lower odds of N. americanus infection. Our findings support the need to incorporate ivermectin into deworming programmes for Strongyloides spp. and T. trichiura control as these species are poorly responsive to albendazole, implement One Health strategies to address the zoonotic A. ceylanicum and Strongyloides spp., and expand control efforts to reach entire communities. WASH access should also be improved to complement deworming programmes.
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18
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Scope and limitations of a multiplex conventional PCR for the diagnosis of S. stercoralis and hookworms. Braz J Infect Dis 2021; 25:101649. [PMID: 34774469 PMCID: PMC9392200 DOI: 10.1016/j.bjid.2021.101649] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/23/2021] [Accepted: 10/17/2021] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVES Describe the diagnostic characteristics of a conventional multiplex PCR for the diagnosis of S. stercoralis, N. americanus and Ancylostomas spp. METHODS Fecal samples were collected from a cross-sectional study in Orán department, Salta province, Argentina. The stool samples were analyzed using concentration-sedimentation, Harada Mori, McMaster, and Baermann techniques. DNA was extracted from 50 mg fecal sample using the FastPrep® Spin Kit for Soil. Three pairs of primers were used for the amplification of three products of 101, 330, and 577 base pairs (bp) for S. stercoralis, N. americanus and Ancylostoma spp, respectively. The sensitivity and analytical specificity of multiplex PCR were evaluated, as well as the sensitivity and diagnostic specificity, using a composite standard and Bayesian approach. RESULTS AND CONCLUSIONS Multiplex PCR did not present cross-reaction with other intestinal parasites, and the detection limit for multiplex PCR was between 2 and 20 pg of genomic DNA. In addition it presented a diagnostic sensitivity of 97.4% for S. stercoralis and 90.3% for hookworms with a specificity of 100% and 87.6%, respectively. PCR identified a higher proportion (p <0.01) of coinfections (15.3%) than microscopic techniques (3.5%). Also, multiplex PCR showed that there was a positive association between S. stercoralis and hookworms (odds ratio = 2.12). However, this association was due to N. americanus (odds ratio= 3.22), since no association was observed between S. stercoralis and Ancylostoma spp. Neither was an association observed between the two species of hookworms.
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19
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Colella V, Khieu V, Worsley A, Senevirathna D, Muth S, Huy R, Odermatt P, Traub RJ. Risk profiling and efficacy of albendazole against the hookworms Necator americanus and Ancylostoma ceylanicum in Cambodia to support control programs in Southeast Asia and the Western Pacific. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2021; 16:100258. [PMID: 34590062 PMCID: PMC8403762 DOI: 10.1016/j.lanwpc.2021.100258] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/17/2021] [Accepted: 07/26/2021] [Indexed: 11/18/2022]
Abstract
Background: Hookworm disease is endemic throughout many parts of the Asia Pacific, despite targeted control programs of at-risk populations. The success of these programs has been hindered by the limited efficacy of widely-used mebendazole, rapid re-infection rates linked to persistent reservoirs of untreated people and dogs, and the low sensitivity of conventional coprodiagnostic techniques employed. Methods: Here, we used standard faecal flotation (SFF) and a multiplex qPCR (mqPCR) assay to calculate and compare species-specific cure and egg reduction rates of single dose albendazole (400 mg) against hookworm infections at community level. Data from a cross-sectional survey in 1,232 people from Cambodia were used to inform a generalised linear mixed model to identify risk factors linked to hookworm infection(s) at baseline. Furthermore, we calculated risk factors associated to the probability of being cured after albendazole administration. Findings: Overall, 13·5% of all 1,232 people tested by SFF were positive for hookworm infection(s). Most (80·1%) infected people were >12 years of age, hence above the age targeted by the WHO control program. We estimate that as age increases, the odds of being infected increases at a faster rate for females than for males. We revealed a substantial difference in cure rate of hookworm infection(s) following albendazole treatment using the SFF (81·5%) and mqPCR (46·4%) assays, and provide the first data on the efficacy of this drug against the zoonotic hookworm Ancylostoma ceylanicum. We estimated that as age increases by one year, the odds of being cured decreases by 0·4%-3·7%. Similarly, the odds of being cured for people who boiled drinking water was estimated to be between 1·02 and 6·82. Interpretation: These findings show that the adoption of refined diagnostic techniques is central to monitoring hookworm infection(s) and the success of control strategies, which can ultimately aid in reducing associated morbidity in human populations. The approach taken is likely to be directly applicable to other parts of Southeast Asia and the Western Pacific, where specific epidemiological conditions might hamper the success of targeted treatment programs. Funding: Faculty of Veterinary and Agricultural Sciences Strategic Research Funds, The University of Melbourne.
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Affiliation(s)
- Vito Colella
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Australia
| | - Virak Khieu
- National Centre for Parasitology, Entomology and Malaria Control, Ministry of Health, Phnom Penh, Cambodia
| | | | - Dammika Senevirathna
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Australia
| | - Sinuon Muth
- National Centre for Parasitology, Entomology and Malaria Control, Ministry of Health, Phnom Penh, Cambodia
| | - Rekol Huy
- National Centre for Parasitology, Entomology and Malaria Control, Ministry of Health, Phnom Penh, Cambodia
| | - Peter Odermatt
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Rebecca J. Traub
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Australia
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20
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Grau-Pujol B, Martí-Soler H, Escola V, Demontis M, Jamine JC, Gandasegui J, Muchisse O, Cambra-Pellejà M, Cossa A, Martinez-Valladares M, Sacoor C, Van Lieshout L, Cano J, Giorgi E, Muñoz J. Towards soil-transmitted helminths transmission interruption: The impact of diagnostic tools on infection prediction in a low intensity setting in Southern Mozambique. PLoS Negl Trop Dis 2021; 15:e0009803. [PMID: 34695108 PMCID: PMC8568186 DOI: 10.1371/journal.pntd.0009803] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 11/04/2021] [Accepted: 09/09/2021] [Indexed: 11/19/2022] Open
Abstract
World Health Organization goals against soil-transmitted helminthiases (STH) are pointing towards seeking their elimination as a public health problem: reducing to less than 2% the proportion of moderate and heavy infections. Some regions are reaching WHO goals, but transmission could rebound if strategies are discontinued without an epidemiological evaluation. For that, sensitive diagnostic methods to detect low intensity infections and localization of ongoing transmission are crucial. In this work, we estimated and compared the STH infection as obtained by different diagnostic methods in a low intensity setting. We conducted a cross-sectional study enrolling 792 participants from a district in Mozambique. Two stool samples from two consecutive days were collected from each participant. Samples were analysed by Telemann, Kato-Katz and qPCR for STH detection. We evaluated diagnostic sensitivity using a composite reference standard. By geostatistical methods, we estimated neighbourhood prevalence of at least one STH infection for each diagnostic method. We used environmental, demographical and socioeconomical indicators to account for any existing spatial heterogeneity in infection. qPCR was the most sensitive technique compared to composite reference standard: 92% (CI: 83%- 97%) for A. lumbricoides, 95% (CI: 88%- 98%) for T. trichiura and 95% (CI: 91%- 97%) for hookworm. qPCR also estimated the highest neighbourhood prevalences for at least one STH infection in a low intensity setting. While 10% of the neighbourhoods showed a prevalence above 20% when estimating with single Kato-Katz from one stool and Telemann from one stool, 86% of the neighbourhoods had a prevalence above 20% when estimating with qPCR. In low intensity settings, STH estimated prevalence of infection may be underestimated if based on Kato-Katz. qPCR diagnosis outperformed the microscopy methods. Thus, implementation of qPCR based predictive maps at STH control and elimination programmes would disclose hidden transmission and facilitate targeted interventions for transmission interruption.
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Affiliation(s)
- Berta Grau-Pujol
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic—University of Barcelona, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Mundo Sano Foundation, Buenos Aires, Argentina
- * E-mail:
| | - Helena Martí-Soler
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic—University of Barcelona, Barcelona, Spain
| | - Valdemiro Escola
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Maria Demontis
- Department of Parasitology, Centre of Infectious Diseases, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | | | - Javier Gandasegui
- Instituto de Ganadería de Montaña (CSIC-Universidad de León), Grulleros, León, Spain
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana, León, Spain
| | - Osvaldo Muchisse
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Maria Cambra-Pellejà
- Instituto de Ganadería de Montaña (CSIC-Universidad de León), Grulleros, León, Spain
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana, León, Spain
| | - Anelsio Cossa
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Maria Martinez-Valladares
- Instituto de Ganadería de Montaña (CSIC-Universidad de León), Grulleros, León, Spain
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana, León, Spain
| | - Charfudin Sacoor
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Lisette Van Lieshout
- Department of Parasitology, Centre of Infectious Diseases, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Jorge Cano
- Expanded Special Project for Elimination of NTDs, World Health Organization Regional Office for Africa, Brazzaville, The Republic of the Congo
| | - Emanuele Giorgi
- Centre for Health Informatics, Computing and Statistics, Lancaster Medical School, Faculty of Health and Medicine, Lancaster University, United Kingdom
| | - Jose Muñoz
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic—University of Barcelona, Barcelona, Spain
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21
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Detection of six soil-transmitted helminths in human stool by qPCR- a systematic workflow. PLoS One 2021; 16:e0258039. [PMID: 34591904 PMCID: PMC8483301 DOI: 10.1371/journal.pone.0258039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/16/2021] [Indexed: 11/19/2022] Open
Abstract
Soil-transmitted helminths (STH) infect up to one-quarter of the global population, with a significant associated disease burden. The main human STH are: Ancylostoma spp. and Necator americanus (hookworms); Ascaris lumbricoides, Trichuris trichiura, and Strongyloides stercoralis. The aim of this study was to establish a scalable system for stool STH multiplex quantitative real-time polymerase chain reactions (qPCR). Stool samples collected in Fiji and preserved in potassium dichromate were transferred to Melbourne at ambient temperature. Samples were washed to remove potassium dichromate and DNA was extracted with the Mini-Beadbeater-24 and a column-based kit. A SYBR green qPCR to detect the vertebrate mitochondrial gene was used as a DNA extraction control. Samples were tested using a probe-based multiplex qPCR targeting A. lumbricoides, T. trichiura and S. stercoralis, and in a second multiplex reaction to detect hookworms to the species level (A. duodenale, A. ceylanicum, N. americanus). An internal amplification control in both multiplex assays was included to prevent false-negative results due to PCR inhibitors. Samples were homogenised for a single cycle of 40 seconds to release STH DNA and washed stool was stored for up to 15 weeks at -30°C without compromising DNA. Our multiplex qPCR detected multiple species of STH without reduced sensitivity compared to singleplex. qPCR data from 40 stools was validated against STH-positive stools determined by microscopy. We have developed and validated an efficient and staged system for detecting six clinically important STH affecting humans that could be easily implemented without advanced automation in any qPCR-capable laboratory.
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Byrne A, Manalo G, Clarke NE, Vaz Nery S. Impact of hookworm infection and preventive chemotherapy on haemoglobin in non-pregnant populations. Trop Med Int Health 2021; 26:1568-1592. [PMID: 34587315 DOI: 10.1111/tmi.13681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE To assess the impact of hookworm infection and preventive chemotherapy on haemoglobin levels in non-pregnant populations in endemic areas. METHOD Systematic review and meta-analysis searching PubMed and Web of Science for articles published since 2010 reporting either hookworm prevalence and Hb concentration (cross-sectional studies) or Hb concentration before and after the implementation of preventive chemotherapy (before-after studies and randomised controlled trials [RCTs]). For papers published before 2010, data were extracted from a previously published systematic review. Random effects meta-analyses were conducted to examine the relationship between Hb concentration and hookworm infection intensity (from cross-sectional studies) and the effect of preventive chemotherapy on Hb concentration (from before-after studies and RCTs). Sensitivity analyses investigated the impact of malaria endemicity and combined interventions for schistosomiasis and nutrition status on Hb concentration. RESULTS Among cross-sectional studies, both light- and heavy-intensity hookworm infections were associated with lower Hb in school-aged children. School-aged children with heavy hookworm infection in settings of high malaria endemicity had lower mean Hb than those in settings of low malaria endemicity. In non-pregnant populations, deworming with albendazole was associated with an increase in Hb of 3.02 g/L (95% CI 0.1, 6.0 g/L). No additional benefit was seen with deworming using albendazole co-administered with praziquantel for schistosomiasis infection or iron supplementation for nutrition status. CONCLUSION Our findings confirm the benefits of preventive chemotherapy as a public health intervention.
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Affiliation(s)
- Aisling Byrne
- Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Giselle Manalo
- School of Public Health, University of Sydney, Sydney, NSW, Australia
| | - Naomi E Clarke
- Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Susana Vaz Nery
- Kirby Institute, University of New South Wales, Sydney, NSW, Australia
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23
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Assessment of the required performance and the development of corresponding program decision rules for neglected tropical diseases diagnostic tests: Monitoring and evaluation of soil-transmitted helminthiasis control programs as a case study. PLoS Negl Trop Dis 2021; 15:e0009740. [PMID: 34520474 PMCID: PMC8480900 DOI: 10.1371/journal.pntd.0009740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 09/29/2021] [Accepted: 08/17/2021] [Indexed: 12/02/2022] Open
Abstract
Recently, the World Health Organization established the Diagnostic Technical Advisory Group to identify and prioritize diagnostic needs for neglected tropical diseases, and to ultimately describe the minimal and ideal characteristics for new diagnostic tests (the so-called target product profiles (TPPs)). We developed two generic frameworks: one to explore and determine the required sensitivity (probability to correctly detect diseased persons) and specificity (probability to correctly detect persons free of disease), and another one to determine the corresponding samples sizes and the decision rules based on a multi-category lot quality assurance sampling (MC-LQAS) approach that accounts for imperfect tests. We applied both frameworks for monitoring and evaluation of soil-transmitted helminthiasis control programs. Our study indicates that specificity rather than sensitivity will become more important when the program approaches the endgame of elimination and that the requirements for both parameters are inversely correlated, resulting in multiple combinations of sensitivity and specificity that allow for reliable decision making. The MC-LQAS framework highlighted that improving diagnostic performance results in a smaller sample size for the same level of program decision making. In other words, the additional costs per diagnostic tests with improved diagnostic performance may be compensated by lower operational costs in the field. Based on our results we proposed the required minimal and ideal diagnostic sensitivity and specificity for diagnostic tests applied in monitoring and evaluating of soil-transmitted helminthiasis control programs. The World Health Organization established an advisory group to identify and prioritize diagnostic needs for neglected tropical diseases, and to ultimately describe the minimal and ideal characteristics for new diagnostic tests. To support this advisory group, we developed two generic frameworks, which we applied to soil-transmitted helminthiases: one to explore and determine the required sensitivity (probability to correctly detect a diseased person) and specificity (probability to correctly detect a person free of disease), and another one to determine the corresponding samples size and decision rules during surveys. We showed that specificity rather than sensitivity will become more important when the program approaches the endgame of elimination and that the requirements for both parameters are inversely correlated, resulting in multiple combinations of sensitivity and specificity that allow for reliable decision making. We also highlighted that improving diagnostic performance results in smaller sample sizes for the same level of program decision making. In other words, the additional costs per diagnostic tests with improved diagnostic performance can be compensated by the lower operational costs in the field. Based on our results we proposed to the advisory group the required performance characteristics of diagnostic tests for soil-transmitted helminthiasis control programs.
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24
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Khurana S, Singh S, Mewara A. Diagnostic Techniques for Soil-Transmitted Helminths - Recent Advances. Res Rep Trop Med 2021; 12:181-196. [PMID: 34377048 PMCID: PMC8349539 DOI: 10.2147/rrtm.s278140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 07/01/2021] [Indexed: 12/26/2022] Open
Abstract
Soil-transmitted helminth (STH) infections (hookworms, Trichuris, Ascaris) and Strongyloides spp. are associated with a substantial global burden and high morbidity. Sensitive and specific methods for diagnosis of these infections are essential for mapping the burden in communities, accurate assessment of infection levels, to guide interventions and monitoring the success of STH control programs. Despite considerable progress to control STH over several decades, we are still far from identifying a fully adequate diagnostic test. Conventional microscopy-based methods such as direct Kato–Katz smear or mounts after stool centrifugation/flotation-based concentration techniques have been the mainstay of diagnosis, especially in resource-poor countries where these infections abound. However, recently, these are being adapted to closed, easy to perform, digital formats, thereby improving the sensitivity as well as applicability in a remote, resource-limited setting. The use of image analysis systems to identify and quantify helminth eggs, with potential adaptation to smartphones, is also promising. Antibody detection tests have a limited role mostly in the case of Strongyloides hyperinfection. Coproantigen detection tests have been developed and used in veterinary practice for detection of STH, but these have not been evaluated for use in humans. More sensitive molecular diagnostics, including assays developed with new bioinformatic tools and techniques such as polymerase chain reaction (PCR), quantitative PCR (qPCR) and loop-mediated amplification assay, can help in the clear and precise assessment of STH burden during elimination phase and are of immense value for diagnosis in areas with low endemicity and in travelers to endemic regions. Moreover, the molecular techniques will help detect new species that may emerge. Sample preservation and efficient DNA extraction are critical and significantly affect the efficiency of molecular diagnostic tests. In addition to the diagnosis of clinical or asymptomatic infection in humans, detection of STH eggs in environmental samples is imperative to boost STH control efforts. Overall the diagnostic performance, cost-effectiveness, ease of performance, rapidity and in-field applicability of any test should be considered when choosing from the various diagnostic assays in areas with different endemicity, in addition to striving towards the development of novel technologies and optimization of existing methods.
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Affiliation(s)
- Sumeeta Khurana
- Department of Medical Parasitology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Shreya Singh
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Abhishek Mewara
- Department of Medical Parasitology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
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25
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Grau-Pujol B, Cuamba I, Jairoce C, Cossa A, Da Silva J, Sacoor C, Dobaño C, Nhabomba A, Mejia R, Muñoz J. Molecular Detection of Soil-Transmitted Helminths and Enteric Protozoa Infection in Children and Its Association with Household Water and Sanitation in Manhiça District, Southern Mozambique. Pathogens 2021; 10:pathogens10070838. [PMID: 34357988 PMCID: PMC8308871 DOI: 10.3390/pathogens10070838] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/26/2021] [Accepted: 06/30/2021] [Indexed: 11/16/2022] Open
Abstract
Intestinal parasite infections can have detrimental health consequences in children. In Mozambique, soil-transmitted helminth (STH) infections are controlled through mass drug administration since 2011, but no specific control program exists for enteric protozoa. This study evaluates STH and protozoan infections in children attending healthcare in Manhiça district, Southern Mozambique, and its association with water and sanitation conditions. We conducted a cross-sectional study in children between 2 and 10 years old in two health centers (n = 405). A stool sample and metadata were collected from each child. Samples were analyzed by multi-parallel real-time quantitative PCR (qPCR). We fitted logistic regression-adjusted models to assess the association between STH or protozoan infection with household water and sanitation use. Nineteen percent were infected with at least one STH and 77.5% with at least one enteric protozoon. qPCR detected 18.8% of participants with intestinal polyparasitism. Protected or unprotected water well use showed a higher risk for at least one protozoan infection in children (OR: 2.59, CI: 1.01-6.65, p-value = 0.010; OR: 5.21, CI: 1.56-17.46, p-value = 0.010, respectively) compared to household piped water. A high proportion of children had enteric protozoan infections. Well consumable water displayed high risk for that.
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Affiliation(s)
- Berta Grau-Pujol
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic—University of Barcelona, 08036 Barcelona, Spain; (C.D.); (J.M.)
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo 1929, Mozambique; (I.C.); (C.J.); (A.C.); (C.S.); (A.N.)
- Mundo Sano Foundation, Buenos Aires 1535, Argentina
- Correspondence: ; Tel.: +34-9322-75400
| | - Inocencia Cuamba
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo 1929, Mozambique; (I.C.); (C.J.); (A.C.); (C.S.); (A.N.)
| | - Chenjerai Jairoce
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo 1929, Mozambique; (I.C.); (C.J.); (A.C.); (C.S.); (A.N.)
| | - Anelsio Cossa
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo 1929, Mozambique; (I.C.); (C.J.); (A.C.); (C.S.); (A.N.)
| | - Juliana Da Silva
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Charfudin Sacoor
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo 1929, Mozambique; (I.C.); (C.J.); (A.C.); (C.S.); (A.N.)
| | - Carlota Dobaño
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic—University of Barcelona, 08036 Barcelona, Spain; (C.D.); (J.M.)
| | - Augusto Nhabomba
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo 1929, Mozambique; (I.C.); (C.J.); (A.C.); (C.S.); (A.N.)
| | - Rojelio Mejia
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Jose Muñoz
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic—University of Barcelona, 08036 Barcelona, Spain; (C.D.); (J.M.)
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26
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Zendejas-Heredia PA, Colella V, Hii SF, Traub RJ. Comparison of the egg recovery rates and limit of detection for soil-transmitted helminths using the Kato-Katz thick smear, faecal flotation and quantitative real-time PCR in human stool. PLoS Negl Trop Dis 2021; 15:e0009395. [PMID: 34038411 PMCID: PMC8153506 DOI: 10.1371/journal.pntd.0009395] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/17/2021] [Indexed: 01/02/2023] Open
Abstract
Background Monitoring the success of soil-transmitted helminth (STH) control programs relies on accurate diagnosis and quantitative assessment of infection prevalence and intensity. As preventative chemotherapeutic program coverage for STH expands, the necessity of gaining insights into the relative or comparative sensitivities, in terms of limits of detection (LOD) and egg-recovery-rates (ERR) for microscopy and quantitative polymerase chain reaction qPCR-based diagnostic techniques becomes imperative to inform suitability for their intended use for large scale STH monitoring and treatment efficacy studies. Methodology/Principal findings The diagnostic performance in terms of ERR and LOD of the Kato-Katz (KK) thick smear technique, sodium nitrate (NaNO3) faecal floatation (FF) and qPCR for the accurate detection and enumeration of STH eggs were calculated and expressed in eggs per gram (EPG), by experimentally seeding parasite-free human faeces with Ascaris spp., Trichuris spp. and Necator americanus eggs representing low, medium and high intensity infections. The efficiency of NaNO3 flotation was also calculated over a range of specific gravities (SpGr) for the optimum recovery of STH eggs. FF of SpGr 1.30 recovered 62.7%, 11% and 8.7% more Trichuris spp., Necator americanus and Ascaris spp. eggs respectively, than the recommended SpGr of 1.20. All diagnostic methods demonstrated strong direct correlation to the intensity of seeded EPG. KK and FF (SpGr 1.30) resulted in significant lower ERRs compared to qPCR (p <0.05). qPCR demonstrated significantly (p <0.05) greater sensitivity with an ability to detect as little as 5 EPG for all three STH, compared to 50 EPG by KK and FF (SpGr 1.30). Conclusions/Significance This study compares the diagnostic parameters in terms of LOD and ERRs of STHs for the KK, FF and qPCR. These results indicate that the diagnostic performance of qPCR assays should be considered by control programs in the phase that aims to seek confirmation of transmission break and cessation of preventive chemotherapy in low-transmission settings, in line with the control targets of the WHO neglected tropical diseases 2030 Roadmap. STH infections predominately affect resource-poor communities and negatively impact on child and maternal health. Diagnostics play a critical role in guiding and informing existing STH control programs and the implementation and evaluation of intervention strategies. The KK technique is most commonly used as per WHO guidelines and is the basis for determining quantitative thresholds for low, moderate and heavy infections. More recently, FF and laboratory-based quantitative PCR techniques have provided alternative options of diagnosing STH infections. A number of studies correlating the relative sensitivity, diagnostic agreement, and egg enumeration of these techniques by comparing field-generated diagnostic data have attempted to correlate quantitative outputs to those defined by the WHO, with little resolution. Moreover, as large-scale deworming programs levels scale up, the necessity to apply techniques that can precisely detect light infections is of outmost importance to establish preventive chemotherapy end-points using more accurate means. In this study we compared the LOD and ERR of seeded non-infected human faecal samples with Ascaris, Trichuris and Necator spp. eggs using KK, FF and qPCR. When compared to copro-microscopy methods, qPCR showed the highest sensitivity for the detection of light-intensity infections and was more accurate in enumerating the original number of eggs per gram of seeded faeces. In addition to this, the results indicated that the diagnostic performance of both KK and FF (using solution at a SpGr of 1.30) were equally efficient and should be considered with their diagnostic limitations in mind, when aiming to monitor STH infections in low-transmission settings.
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Affiliation(s)
- Patsy A. Zendejas-Heredia
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
- * E-mail:
| | - Vito Colella
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Sze Fui Hii
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Rebecca J. Traub
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
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27
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Papaiakovou M, Littlewood DTJ, Gasser RB, Anderson RM. How qPCR complements the WHO roadmap (2021-2030) for soil-transmitted helminths. Trends Parasitol 2021; 37:698-708. [PMID: 33931342 DOI: 10.1016/j.pt.2021.04.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/02/2021] [Accepted: 04/08/2021] [Indexed: 12/19/2022]
Abstract
Complementing the launch of the World Health Organization (WHO) roadmap (2021-2030) we explore key elements needing attention before recruitment of qPCR as the main diagnostics tool to confirm reduction or elimination of soil-transmitted helminth (STH) transmission in both control and elimination programmes. Given the performance limitations of conventional methods, a proposed harmonised qPCR will provide a diagnostic tool, with the sensitivity and specificity required to monitor low-intensity infections, following mass drug administration (MDA). Technical and logistical challenges associated with introducing qPCR as a stand-alone tool are highlighted, and a decision-making scheme on how qPCR can support surveillance, resistance detection, and elimination is presented. An accurate point-of-care (POC) diagnostic test needs to be developed to support STH control in the field, and STH biorepositories need to be established and maintained to ensure that reference materials are available for research and validation.
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Affiliation(s)
- Marina Papaiakovou
- Department of Infectious Disease Epidemiology, St Mary's Campus, Imperial College London, London, UK; London Centre for Neglected Tropical Disease Research (LCNTDR), Imperial College London, London, UK.
| | - D Timothy J Littlewood
- Science Directorate, Natural History Museum, London, UK; London Centre for Neglected Tropical Disease Research (LCNTDR), Imperial College London, London, UK
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Roy M Anderson
- Department of Infectious Disease Epidemiology, St Mary's Campus, Imperial College London, London, UK; London Centre for Neglected Tropical Disease Research (LCNTDR), Imperial College London, London, UK
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28
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Quantitative PCR in soil-transmitted helminth epidemiology and control programs: Toward a universal standard. PLoS Negl Trop Dis 2021; 15:e0009134. [PMID: 33661910 PMCID: PMC7932098 DOI: 10.1371/journal.pntd.0009134] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
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29
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Loop-Mediated Isothermal Amplification in Schistosomiasis. J Clin Med 2021; 10:jcm10030511. [PMID: 33535489 PMCID: PMC7867102 DOI: 10.3390/jcm10030511] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/21/2021] [Accepted: 01/28/2021] [Indexed: 12/17/2022] Open
Abstract
Human schistosomiasis is one of the most important parasitic diseases, causing around 250 million cases (mostly in Africa) and 280,000–500,000 deaths every year. Due to the limited resources and the far-removed nature of many endemic areas, the implementation of new, sensitive and specific diagnostic tools has had little success. This is particularly true for PCR-based molecular methods that require expensive equipment and trained personnel to be executed. Loop-mediated isothermal amplification (LAMP) along with other isothermal techniques appeared in the early 21st century as an alternative to those methods, overcoming some of the aforementioned limitations and achieving a more inexpensive diagnostic. However, to this date, neither LAMP nor any other isothermal technique have signified a meaningful change in the way schistosomiasis diagnosis is routinely performed. Here, we present the recent developments in LAMP-based schistosomiasis diagnosis. We expose the main advantages and disadvantages of LAMP technology over PCR and other classical diagnostic methods focusing in various research approaches on intermediate hosts, animal models and patients. We also examine its potential clinical application in post-therapy monitoring, as well as its usefulness as a point-of-care test.
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30
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Truscott JE, Hardwick RJ, Werkman M, Saravanakumar PK, Manuel M, Ajjampur SSR, Ásbjörnsdóttir KH, Khumbo K, Witek-McManus S, Simwanza J, Cottrell G, Houngbégnon P, Ibikounlé M, Walson JL, Anderson RM. Forecasting the effectiveness of the DeWorm3 trial in interrupting the transmission of soil-transmitted helminths in three study sites in Benin, India and Malawi. Parasit Vectors 2021; 14:67. [PMID: 33472677 PMCID: PMC7818558 DOI: 10.1186/s13071-020-04572-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/29/2020] [Indexed: 11/17/2022] Open
Abstract
Background The DeWorm3 project is an ongoing cluster-randomised trial assessing the feasibility of interrupting the transmission of soil-transmitted helminths (STH) through mass drug administration (MDA) using study sites in India, Malawi and Benin. In this article, we describe an approach which uses a combination of statistical and mathematical methods to forecast the outcome of the trial with respect to its stated goal of reducing the prevalence of infection to below 2%. Methods Our approach is first to define the local patterns of transmission within each study site, which is achieved by statistical inference of key epidemiological parameters using the baseline epidemiological measures of age-related prevalence and intensity of STH infection which have been collected by the DeWorm3 trials team. We use these inferred parameters to calibrate an individual-based stochastic simulation of the trial at the cluster and study site level, which is subsequently run to forecast the future prevalence of STH infections. The simulator takes into account both the uncertainties in parameter estimation and the variability inherent in epidemiological and demographic processes in the simulator. We interpret the forecast results from our simulation with reference to the stated goal of the DeWorm3 trial, to achieve a target of \documentclass[12pt]{minimal}
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\begin{document}$$\le 2\%$$\end{document}≤2% prevalence at a point 24 months post-cessation of MDA. Results Simulated output predicts that the two arms will be distinguishable from each other in all three country sites at the study end point. In India and Malawi, measured prevalence in the intervention arm is below the threshold with a high probability (90% and 95%, respectively), but in Benin the heterogeneity between clusters prevents the arm prevalence from being reduced below the threshold value. At the level of individual study arms within each site, heterogeneity among clusters leads to a very low probability of achieving complete elimination in an intervention arm, yielding a post-study scenario with widespread elimination but a few ‘hot spot’ areas of persisting STH transmission. Conclusions Our results suggest that geographical heterogeneities in transmission intensity and worm aggregation have a large impact on the effect of MDA. It is important to accurately assess cluster-level, or even smaller scale, heterogeneities in factors which influence transmission and aggregation for a clearer perspective on projecting the outcomes of MDA control of STH and other neglected tropical diseases. ![]()
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Affiliation(s)
- James E Truscott
- London Centre for Neglected Tropical Disease Research, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, W2 1PG, UK. .,MRC Centre for Global Infectious Disease Analysis, Imperial College London, St Mary's Campus, London, W2 1PG, UK. .,The DeWorm3 Project, The Natural History Museum, London, SW7 5BD, UK.
| | - Robert J Hardwick
- London Centre for Neglected Tropical Disease Research, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, W2 1PG, UK.,MRC Centre for Global Infectious Disease Analysis, Imperial College London, St Mary's Campus, London, W2 1PG, UK.,The DeWorm3 Project, The Natural History Museum, London, SW7 5BD, UK
| | - Marleen Werkman
- London Centre for Neglected Tropical Disease Research, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, W2 1PG, UK.,MRC Centre for Global Infectious Disease Analysis, Imperial College London, St Mary's Campus, London, W2 1PG, UK.,Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | | | - Malathi Manuel
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Sitara S R Ajjampur
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Kristjana H Ásbjörnsdóttir
- The DeWorm3 Project, The Natural History Museum, London, SW7 5BD, UK.,Departments of Global Health, Medicine (Infectious Disease), Pediatrics and Epidemiology, University of Washington, Seattle, WA, USA
| | - Kalua Khumbo
- Blantyre Institute for Community Outreach, University of Malawi, College of Medicine, Blantyre, Malawi
| | - Stefan Witek-McManus
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - James Simwanza
- Blantyre Institute for Community Outreach, University of Malawi, College of Medicine, Blantyre, Malawi
| | - Gilles Cottrell
- Institut de Recherche pour le Développement, MERIT, Université de Paris, Paris, France
| | - Parfait Houngbégnon
- Institut de Recherche Clinique du Benin, Université d'Abomey-Calavi, Cotonou, Benin
| | - Moudachirou Ibikounlé
- Institut de Recherche Clinique du Benin, Université d'Abomey-Calavi, Cotonou, Benin.,Département de Zoologie, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Benin
| | - Judd L Walson
- London Centre for Neglected Tropical Disease Research, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, W2 1PG, UK.,The DeWorm3 Project, The Natural History Museum, London, SW7 5BD, UK.,Departments of Global Health, Medicine (Infectious Disease), Pediatrics and Epidemiology, University of Washington, Seattle, WA, USA
| | - Roy M Anderson
- London Centre for Neglected Tropical Disease Research, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, W2 1PG, UK.,MRC Centre for Global Infectious Disease Analysis, Imperial College London, St Mary's Campus, London, W2 1PG, UK.,The DeWorm3 Project, The Natural History Museum, London, SW7 5BD, UK
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Circulating cell-free mitochondrial DNA fragment: A possible marker for early detection of Schistosoma japonicum. INFECTION GENETICS AND EVOLUTION 2020; 88:104683. [PMID: 33348056 DOI: 10.1016/j.meegid.2020.104683] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 12/04/2020] [Accepted: 12/16/2020] [Indexed: 02/05/2023]
Abstract
Schistosomiasis is a major public health problem that is included in the neglected tropical diseases. The early diagnosis and detection of the pathogen are of critical importance in the control of the disease. The diagnostic techniques in use include the detection of worm's eggs in fecal examination or detection of circulating antigens in immunological based assays. These traditional strategies lack sensitivity in earlier detection of the schistosomiasis. Cell-free DNA (cfDNA) that includes the fragments of parasitic DNA circulating in the body fluids of host offers an alternative mean for the rapid pathogen detection and thus is a useful diagnostic tool. In this study, we explored the usefulness of the mitochondrial cfDNA markers for the diagnosis of schistosomiasis from the experimentally infected hosts (rabbits and mice). In this study we found mitochondrial DNA fragment cytochrome B gene as persistent and useful cfDNA marker for the early detection of schistosomiasis. We evaluated the sensitivity of cfDNA marker with varying numbers of cercaria. Overall, our results suggest that cfDNA markers can be useful for developing a diagnostic tool for the detection of S. japonicum infection.
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Hoogerwerf MA, Koopman JPR, Janse JJ, Langenberg MCC, van Schuijlenburg R, Kruize YCM, Brienen EAT, Manurung MD, Verbeek-Menken P, van der Beek MT, Westra IM, Meij P, Visser LG, van Lieshout L, de Vlas SJ, Yazdanbakhsh M, Coffeng LE, Roestenberg M. A Randomized Controlled Trial to Investigate Safety and Variability of Egg Excretion After Repeated Controlled Human Hookworm Infection. J Infect Dis 2020; 223:905-913. [PMID: 32645714 DOI: 10.1093/infdis/jiaa414] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 07/09/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Controlled human hookworm infections could significantly contribute to the development of a hookworm vaccine. However, current models are hampered by low and unstable egg output, reducing generalizability and increasing sample sizes. This study aims to investigate the safety, tolerability, and egg output of repeated exposure to hookworm larvae. METHODS Twenty-four healthy volunteers were randomized, double-blindly, to 1, 2, or 3 doses of 50 Necator americanus L3 larvae at 2-week intervals. Volunteers were monitored weekly and were treated with albendazole at week 20. RESULTS There was no association between larval dose and number or severity of adverse events. Geometric mean egg loads stabilized at 697, 1668, and 1914 eggs per gram feces for the 1 × 50L3, 2 × 50L3, and 3 × 50L3 group, respectively. Bayesian statistical modeling showed that egg count variability relative to the mean was reduced with a second infectious dose; however, the third dose did not increase egg load or decrease variability. We therefore suggest 2 × 50L3 as an improved challenge dose. Model-based simulations indicates increased frequency of stool sampling optimizes the power of hypothetical vaccine trials. CONCLUSIONS Repeated infection with hookworm larvae increased egg counts to levels comparable to the field and reduced relative variability in egg output without aggravating adverse events. CLINICAL TRIALS REGISTRATION NCT03257072.
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Affiliation(s)
| | - Jan Pieter R Koopman
- Department of Parasitology, Leiden University Medical Center, Leiden, the Netherlands
| | - Jacqueline J Janse
- Department of Parasitology, Leiden University Medical Center, Leiden, the Netherlands
| | | | | | - Yvonne C M Kruize
- Department of Parasitology, Leiden University Medical Center, Leiden, the Netherlands
| | - Eric A T Brienen
- Department of Parasitology, Leiden University Medical Center, Leiden, the Netherlands
| | - Mikhael D Manurung
- Department of Parasitology, Leiden University Medical Center, Leiden, the Netherlands
| | - Petra Verbeek-Menken
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Martha T van der Beek
- Clinical Microbiology Laboratory, Leiden University Medical Center, Leiden, the Netherlands
| | - Inge M Westra
- Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, Leiden, the Netherlands
| | - Pauline Meij
- Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, Leiden, the Netherlands
| | - Leo G Visser
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Lisette van Lieshout
- Department of Parasitology, Leiden University Medical Center, Leiden, the Netherlands
| | - Sake J de Vlas
- Department of Public Health, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Maria Yazdanbakhsh
- Department of Parasitology, Leiden University Medical Center, Leiden, the Netherlands
| | - Luc E Coffeng
- Department of Public Health, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Meta Roestenberg
- Department of Parasitology, Leiden University Medical Center, Leiden, the Netherlands.,Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
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33
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Levecke B, Cools P, Albonico M, Ame S, Angebault C, Ayana M, Behnke JM, Bethony JM, Cringoli G, Dana D, Guillard B, Viet Hoa NT, Kang G, Kattula D, Keiser J, Kotze AC, Matoso LF, Maurelli MP, McCarthy JS, Mekonnen Z, Mirams G, Montresor A, Oliveira RC, Periago MV, Pinto SA, Rinaldi L, Sayasone S, Sumo L, Tchuem-Tchuenté LA, Cam Thach DT, Thomas E, Zeynudin A, Verweij JJ, Vlaminck J, Vercruysse J. Identifying thresholds for classifying moderate-to-heavy soil-transmitted helminth intensity infections for FECPAKG2, McMaster, Mini-FLOTAC and qPCR. PLoS Negl Trop Dis 2020; 14:e0008296. [PMID: 32614828 PMCID: PMC7413557 DOI: 10.1371/journal.pntd.0008296] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 08/07/2020] [Accepted: 04/15/2020] [Indexed: 11/18/2022] Open
Abstract
The World Health Organization (WHO) has defined moderate-to-heavy intensity (M&HI) infections with soil-transmitted helminths (Ascaris lumbricoides, Trichuris trichiura and the two hookworms, Ancylostoma duodenale and Necator americanus) based on specific values of eggs per gram of stool, as measured by the Kato-Katz method. There are a variety of novel microscopy and DNA-based methods but it remains unclear whether applying current WHO thresholds on to these methods allows for a reliable classification of M&HI infections. We evaluated both WHO and method-specific thresholds for classifying the M&HI infections for novel microscopic (FECPAKG2, McMaster and Mini-FLOTAC) and DNA-based (qPCR) diagnostic methods. For this, we determined method-specific thresholds that best classified M&HI infections (defined by Kato-Katz and WHO thresholds; reference method) in two multi-country drug efficacy studies. Subsequently, we verified whether applying these method-specific thresholds improved the agreement in classifying M&HI infections compared to the reference method. When we applied the WHO thresholds, the new microscopic methods mainly misclassified M&HI as low intensity, and to a lesser extent low intensity infection as M&HI. For FECPAKG2, applying the method-specific thresholds significantly improved the agreement for Ascaris (moderate → substantial), Trichuris and hookworms (fair → moderate). For Mini-FLOTAC, a significantly improved agreement was observed for hookworms only (fair → moderate). For the other STHs, the agreement was almost perfect and remained unchanged. For McMaster, the method-specific thresholds revealed a fair to a substantial agreement but did not significantly improve the agreement. For qPCR, the method-specific thresholds based on genome equivalents per ml of DNA moderately agreed with the reference method for hookworm and Trichuris infections. For Ascaris, there was a substantial agreement. We defined method-specific thresholds that improved the classification of M&HI infections. Validation studies are required before they can be recommended for general use in assessing M&HI infections in programmatic settings.
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Affiliation(s)
- Bruno Levecke
- Department of Virology, Parasitology and Immunology, Ghent University, Merelbeke, Belgium
- * E-mail:
| | - Piet Cools
- Department of Virology, Parasitology and Immunology, Ghent University, Merelbeke, Belgium
| | - Marco Albonico
- Center for Tropical Diseases, Sacro Cuore Don Calabria Hospital, Negrar, Italy
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Shaali Ame
- Public Health Laboratory-Ivo de Carneri, Chake Chake, United Republic of Tanzania
| | | | - Mio Ayana
- Jimma University Institute of Health, Jimma University, Jimma, Ethiopia
| | - Jerzy M. Behnke
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Jeffrey M. Bethony
- Microbiology, Immunology, and Tropical Medicine, George Washington University Medical Center, Washington D.C., United States of America
| | - Giuseppe Cringoli
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
| | - Daniel Dana
- Jimma University Institute of Health, Jimma University, Jimma, Ethiopia
| | | | - Nguyen Thi Viet Hoa
- Department of Parasitology, National Institute of Malariology, Parasitology and Entomology, Ha Noi, Vietnam
| | - Gagandeep Kang
- Department of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Deepthi Kattula
- Department of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Jennifer Keiser
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland & University of Basel, Basel, Switzerland
| | - Andrew C. Kotze
- Division of Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, St. Lucia, Australia
| | - Leonardo F. Matoso
- Laboratory of Molecular and Cellular Immunology, Research Center René Rachou - FIOCRUZ, Belo Horizonte, Brazil
| | - Maria P. Maurelli
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
| | - James S. McCarthy
- QIMR Berghofer Medical Research Institute, University of Queensland, Brisbane, Australia
| | - Zeleke Mekonnen
- Jimma University Institute of Health, Jimma University, Jimma, Ethiopia
| | | | - Antonio Montresor
- Department of Control of Neglected Tropical Diseases, World Health Organization, Geneva, Switzerland
| | - Rodrigo Corrêa Oliveira
- Laboratory of Molecular and Cellular Immunology, Research Center René Rachou - FIOCRUZ, Belo Horizonte, Brazil
| | - Maria V. Periago
- Laboratory of Molecular and Cellular Immunology, Research Center René Rachou - FIOCRUZ, Belo Horizonte, Brazil
| | - Simone A. Pinto
- Laboratory of Molecular and Cellular Immunology, Research Center René Rachou - FIOCRUZ, Belo Horizonte, Brazil
| | - Laura Rinaldi
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
| | - Somphou Sayasone
- Lao Tropical and Public Health Institute, Ministry of Health, Vientiane Capital, Lao People’s Democratic Republic
| | - Laurentine Sumo
- Centre for Schistosomiasis and Parasitology, University of Yaoundé I, Yaoundé, Cameroon
| | | | - Dang Thi Cam Thach
- Department of Parasitology, National Institute of Malariology, Parasitology and Entomology, Ha Noi, Vietnam
| | | | - Ahmed Zeynudin
- Jimma University Institute of Health, Jimma University, Jimma, Ethiopia
| | - Jaco J. Verweij
- Laboratory for Medical Microbiology and Immunology, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands
| | - Johnny Vlaminck
- Department of Virology, Parasitology and Immunology, Ghent University, Merelbeke, Belgium
| | - Jozef Vercruysse
- Department of Virology, Parasitology and Immunology, Ghent University, Merelbeke, Belgium
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Dunn JC, Papaiakovou M, Han KT, Chooneea D, Bettis AA, Wyine NY, Lwin AMM, Maung NS, Misra R, Littlewood DTJ, Anderson RM. The increased sensitivity of qPCR in comparison to Kato-Katz is required for the accurate assessment of the prevalence of soil-transmitted helminth infection in settings that have received multiple rounds of mass drug administration. Parasit Vectors 2020; 13:324. [PMID: 32580759 PMCID: PMC7315547 DOI: 10.1186/s13071-020-04197-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 06/17/2020] [Indexed: 12/13/2022] Open
Abstract
Background The most commonly used diagnostic tool for soil-transmitted helminths (STH) is the Kato-Katz (KK) thick smear technique. However, numerous studies have suggested that the sensitivity of KK can be problematic, especially in low prevalence and low intensity settings. An emerging alternative is quantitative polymerase chain reaction (qPCR). Methods In this study, both KK and qPCR were conducted on stool samples from 648 participants in an STH epidemiology study conducted in the delta region of Myanmar in June 2016. Results Prevalence of any STH was 20.68% by KK and 45.06% by qPCR. Prevalence of each individual STH was also higher by qPCR than KK, the biggest difference was for hookworm with an approximately 4-fold increase between the two diagnostic techniques. Prevalence of Ancylostoma ceylanicum, a parasite predominately found in dogs, was 4.63%, indicating that there is the possibility of zoonotic transmission in the study setting. In individuals with moderate to high intensity infections there is evidence for a linear relationship between eggs per gram (EPG) of faeces, derived from KK, and DNA copy number, derived from qPCR which is particularly strong for Ascaris lumbricoides. Conclusions The use of qPCR in low prevalence settings is important to accurately assess the epidemiological situation and plan control strategies for the ‘end game’. However, more work is required to accurately assess STH intensity from qPCR results and to reduce the cost of qPCR so that is widely accessible in STH endemic countries.![]()
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Affiliation(s)
- Julia C Dunn
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, Imperial College London, London, W2 1PG, UK. .,London Centre for Neglected Tropical Disease Research, London, UK.
| | - Marina Papaiakovou
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, Imperial College London, London, W2 1PG, UK.,London Centre for Neglected Tropical Disease Research, London, UK.,Department of Life Sciences, Natural History Museum, London, UK
| | - Kay Thwe Han
- Department of Medical Research, Ministry of Health and Sports, Nyapyitaw, Myanmar
| | - Darren Chooneea
- Core Research Laboratories, Natural History Museum, London, UK
| | - Alison A Bettis
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, Imperial College London, London, W2 1PG, UK.,London Centre for Neglected Tropical Disease Research, London, UK
| | - Nay Yee Wyine
- London Centre for Neglected Tropical Disease Research, London, UK
| | - Aye Moe Moe Lwin
- University of Public Health, Myorma Kyaung Street, Yangon, 11131, Myanmar
| | - Nay Soe Maung
- University of Public Health, Myorma Kyaung Street, Yangon, 11131, Myanmar
| | - Raju Misra
- Core Research Laboratories, Natural History Museum, London, UK
| | | | - Roy M Anderson
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, Imperial College London, London, W2 1PG, UK.,London Centre for Neglected Tropical Disease Research, London, UK
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35
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Cools P, van Lieshout L, Koelewijn R, Addiss D, Ajjampur SSR, Ayana M, Bradbury RS, Cantera JL, Dana D, Fischer K, Imtiaz R, Kabagenyi J, Lok J, McCarthy J, Mejia R, Mekonnen Z, Njenga SM, Othman N, Shao H, Traub R, Van Esbroeck M, Vercruysse J, Vlaminck J, Williams SA, Verweij JJ, van Hellemond JJ, Levecke B. First international external quality assessment scheme of nucleic acid amplification tests for the detection of Schistosoma and soil-transmitted helminths, including Strongyloides: A pilot study. PLoS Negl Trop Dis 2020; 14:e0008231. [PMID: 32544158 PMCID: PMC7319349 DOI: 10.1371/journal.pntd.0008231] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 06/26/2020] [Accepted: 03/17/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Nucleic acid amplification tests (NAATs) are increasingly being used as diagnostic tools for soil-transmitted helminths (STHs; Ascaris lumbricoides, Trichuris trichiura, Necator americanus, Ancylostoma duodenale and A. ceylanicum), Strongyloides stercoralis and Schistosoma in human stool. Currently, there is a large diversity of NAATs being applied, but an external quality assessment scheme (EQAS) for these diagnostics is lacking. An EQAS involves a blinded process where test results reported by a laboratory are compared to those reported by reference or expert laboratories, allowing for an objective assessment of the diagnostic performance of a laboratory. In the current study, we piloted an international EQAS for these helminths (i) to investigate the feasibility of designing and delivering an EQAS; (ii) to assess the diagnostic performance of laboratories; and (iii) to gain insights into the different NAAT protocols used. METHODS AND PRINCIPAL FINDINGS A panel of twelve stool samples and eight DNA samples was validated by six expert laboratories for the presence of six helminths (Ascaris, Trichuris, N. americanus, Ancylostoma, Strongyloides and Schistosoma). Subsequently this panel was sent to 15 globally dispersed laboratories. We found a high degree of diversity among the different DNA extraction and NAAT protocols. Although most laboratories performed well, we could clearly identify the laboratories that were poorly performing. CONCLUSIONS/SIGNIFICANCE We showed the technical feasibility of an international EQAS for the NAAT of STHs, Strongyloides and Schistosoma. In addition, we documented that there are clear benefits for participating laboratories, as they can confirm and/or improve the diagnostic performance of their NAATs. Further research should aim to identify factors that explain poor performance of NAATs.
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Affiliation(s)
- Piet Cools
- Laboratory of Parasitology, Ghent University, Merelbeke, Belgium
| | - Lisette van Lieshout
- Leiden University Medical Center, Leiden, The Netherlands
- Dutch Foundation for Quality Assessment in Medical Laboratories, Nijmegen, The Netherlands
| | - Rob Koelewijn
- Dutch Foundation for Quality Assessment in Medical Laboratories, Nijmegen, The Netherlands
- Erasmus University Medical Center, Rotterdam, The Netherlands
| | - David Addiss
- The Task Force for Global Health, Decatur, Georgia, United States of America
| | | | | | - Richard S. Bradbury
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | | | | | - Kerstin Fischer
- Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Rubina Imtiaz
- Children Without Worms, Decatur, Georgia, United States of America
| | - Joyce Kabagenyi
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - James Lok
- University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - James McCarthy
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Rojelio Mejia
- Baylor College of Medicine, Houston, Texas, United States of America
| | | | | | | | - Hongguang Shao
- University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | | | | | - Jozef Vercruysse
- Laboratory of Parasitology, Ghent University, Merelbeke, Belgium
| | - Johnny Vlaminck
- Laboratory of Parasitology, Ghent University, Merelbeke, Belgium
| | - Steven A. Williams
- Smith College, Northampton, Massachusetts, United States of America
- University of Massachusetts, Amherst, Massachusetts, United States of America
| | | | - Jaap J. van Hellemond
- Dutch Foundation for Quality Assessment in Medical Laboratories, Nijmegen, The Netherlands
- Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bruno Levecke
- Laboratory of Parasitology, Ghent University, Merelbeke, Belgium
- * E-mail:
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36
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Benjamin-Chung J, Pilotte N, Ercumen A, Grant JR, Maasch JRMA, Gonzalez AM, Ester AC, Arnold BF, Rahman M, Haque R, Hubbard AE, Luby SP, Williams SA, Colford JM. Comparison of multi-parallel qPCR and double-slide Kato-Katz for detection of soil-transmitted helminth infection among children in rural Bangladesh. PLoS Negl Trop Dis 2020; 14:e0008087. [PMID: 32330127 PMCID: PMC7202662 DOI: 10.1371/journal.pntd.0008087] [Citation(s) in RCA: 23] [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: 05/01/2019] [Revised: 05/06/2020] [Accepted: 01/24/2020] [Indexed: 01/08/2023] Open
Abstract
There is growing interest in local elimination of soil-transmitted helminth (STH) infection in endemic settings. In such settings, highly sensitive diagnostics are needed to detect STH infection. We compared double-slide Kato-Katz, the most commonly used copromicroscopic detection method, to multi-parallel quantitative polymerase chain reaction (qPCR) in 2,799 stool samples from children aged 2–12 years in a setting in rural Bangladesh with predominantly low STH infection intensity. We estimated the sensitivity and specificity of each diagnostic using Bayesian latent class analysis. Compared to double-slide Kato-Katz, STH prevalence using qPCR was almost 3-fold higher for hookworm species and nearly 2-fold higher for Trichuris trichiura. Ascaris lumbricoides prevalence was lower using qPCR, and 26% of samples classified as A. lumbricoides positive by Kato-Katz were negative by qPCR. Amplicon sequencing of the 18S rDNA from 10 samples confirmed that A. lumbricoides was absent in samples classified as positive by Kato-Katz and negative by qPCR. The sensitivity of Kato-Katz was 49% for A. lumbricoides, 32% for hookworm, and 52% for T. trichiura; the sensitivity of qPCR was 79% for A. lumbricoides, 93% for hookworm, and 90% for T. trichiura. Specificity was ≥ 97% for both tests for all STH except for Kato-Katz for A. lumbricoides (specificity = 68%). There were moderate negative, monotonic correlations between qPCR cycle quantification values and eggs per gram quantified by Kato-Katz. While it is widely assumed that double-slide Kato-Katz has few false positives, our results indicate otherwise and highlight inherent limitations of the Kato-Katz technique. qPCR had higher sensitivity than Kato-Katz in this low intensity infection setting. Soil-transmitted helminth infections (STH) (e.g., Ascaris, hookworm, Trichuris) contribute to a large burden of disease among children in low- and middle-income countries. There is increasing interest in implementing large-scale deworming programs to eliminate STH in certain settings. Efforts to monitor whether local elimination has occurred require sensitive diagnostic tests that will not miss positive cases. Kato-Katz, a microscopy-based diagnostic test, has commonly been used to identify STH eggs in stool, but in settings where infection intensity is low, this method frequently misses positive samples because it requires visual identification of small numbers of eggs, and hookworm eggs may degrade prior to visualization. Quantitative polymerase chain reaction (qPCR) is a molecular diagnostic method for detecting STH. It may detect more low intensity infections than Kato-Katz because it identifies STH DNA in stool; DNA can be detected in very small quantities and is less likely to degrade than STH ova. Thus, qPCR is likely to be more accurate than Kato-Katz. This study compared the performance of double-slide Kato-Katz and qPCR using 2,799 stool samples from children aged 2–12 years in a setting in rural Bangladesh with predominantly low STH infection intensity. qPCR was more sensitive than Kato-Katz for hookworm and Trichuris infections. 26% of samples were classified as Ascaris positive by Kato-Katz and negative by qPCR. DNA sequencing of 10 samples confirmed that Ascaris was absent in samples classified as positive by Kato-Katz and negative by qPCR. We conclude that Kato-Katz likely produced false positive results for Ascaris and that qPCR had a higher sensitivity than double-slide Kato-Katz in this low infection intensity setting.
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Affiliation(s)
- Jade Benjamin-Chung
- Division of Epidemiology & Biostatistics, University of California, Berkeley, Berkeley, California, United States of America
- * E-mail:
| | - Nils Pilotte
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Ayse Ercumen
- Division of Epidemiology & Biostatistics, University of California, Berkeley, Berkeley, California, United States of America
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Jessica R. Grant
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
| | | | - Andrew M. Gonzalez
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
| | - Ashanta C. Ester
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
| | - Benjamin F. Arnold
- Division of Epidemiology & Biostatistics, University of California, Berkeley, Berkeley, California, United States of America
| | - Mahbubur Rahman
- Infectious Disease Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Rashidul Haque
- Infectious Disease Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Alan E. Hubbard
- Division of Epidemiology & Biostatistics, University of California, Berkeley, Berkeley, California, United States of America
| | - Stephen P. Luby
- Infectious Diseases & Geographic Medicine, Stanford University, Stanford, California, United States of America
| | - Steven A. Williams
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - John M. Colford
- Division of Epidemiology & Biostatistics, University of California, Berkeley, Berkeley, California, United States of America
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Abstract
Helminth parasitology is an important discipline, which poses often unique technical challenges. One challenge is that helminth parasites, particularly those in humans, are often difficult to obtain alive and in sufficient quantities for study; another is the challenge of studying these organisms in vitro – no helminth parasite life cycle has been fully recapitulated outside of a host. Arguably, the key issue retarding progress in helminth parasitology has been a lack of experimental tools and resources, certainly relative to the riches that have driven many parasitologists to adopt free-living model organisms as surrogate systems. In response to these needs, the past 10–12 years have seen the beginnings of helminth parasitology's journey into the ‘omics’ era, with the release of abundant sequencing resources, and the functional genomics tools with which to test biological hypotheses. To reflect this progress, the 2019 Autumn Symposium of the British Society for Parasitology was held in Queen's University Belfast on the topic of ‘post-genomic progress in helminth parasitology’. This issue presents examples of the current state of play in the field, while this editorial summarizes how genomic datasets and functional genomic tools have stimulated impressive recent progress in our understanding of parasite biology.
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Calvani NED, Ichikawa-Seki M, Bush RD, Khounsy S, Šlapeta J. Which species is in the faeces at a time of global livestock movements: single nucleotide polymorphism genotyping assays for the differentiation of Fasciola spp. Int J Parasitol 2020; 50:91-101. [PMID: 32006549 DOI: 10.1016/j.ijpara.2019.12.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 12/12/2019] [Accepted: 12/18/2019] [Indexed: 01/08/2023]
Abstract
Fasciolosis, caused by Fasciola hepatica and Fasciola gigantica, is a globally distributed zoonotic disease of livestock. While F. hepatica and F. gigantica have temperate and tropical distributions, respectively, parasite sympatry occurs in parts of Asia and Africa. A growing protein demand has the potential to facilitate the translocation of parasites from endemic to non-endemic areas, via associated international livestock movements. Such is the case in Southeast Asia, where livestock trade from F. hepatica-endemic countries into China and Vietnam may account for detection of F. hepatica hybrid/introgressed forms. Of particular importance is Lao People's Democratic Republic, which acts as a major livestock thoroughfare for the region. Our ability to understand the impacts of livestock-associated Fasciola spp. movements on local animal and human health is hindered by a lack of ante-mortem diagnostic tools allowing species differentiation. Molecular tools have been developed for Fasciola spp. differentiation, however those rely on access to pure DNA from adult specimens, limiting their application to post-mortem use. Our aim was to detect and differentiate F. hepatica from the endemic F. gigantica in local smallholder cattle in a region of Southeast Asia with frequent livestock trafficking. To do this we designed and validated ante-mortem molecular assays for Fasciola spp. differentiation targeting single-nucleotide polymorphisms (SNPs) within ITS1 and lsrRNA. We then deployed these SNP genotyping assays to diagnose Fasciola spp. infection in 153 local cattle from 27 villages in Northern Laos. We demonstrate the presence of F. hepatica DNA, confirmed by qualitative Sanger and quantitative Illumina amplicon sequencing of ITS1 and lsrRNA, and highlight the shortfalls of Sanger sequencing for Fasciola spp. identification due to the preferential amplification of F. gigantica nucleotides in mixed DNA samples. The outlined protocol enables rapid surveillance of faecal samples for the presence of Fasciola species eggs, their co-infection and/or infection with F. hepatica/F. gigantica hybrids.
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Affiliation(s)
- Nichola Eliza Davies Calvani
- Laboratory of Veterinary Parasitology, Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Australia; Mekong Livestock Research Group, Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Australia
| | - Madoka Ichikawa-Seki
- Laboratory of Veterinary Parasitology, Faculty of Agriculture, Iwate University, Japan
| | - Russell David Bush
- Mekong Livestock Research Group, Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Australia
| | - Syseng Khounsy
- Department of Livestock and Fisheries, Lao Democratic People's Republic
| | - Jan Šlapeta
- Laboratory of Veterinary Parasitology, Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Australia.
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Role of DNA-detection-based tools for monitoring the soil-transmitted helminth treatment response in drug-efficacy trials. PLoS Negl Trop Dis 2020; 14:e0007931. [PMID: 32027646 PMCID: PMC7004296 DOI: 10.1371/journal.pntd.0007931] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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Hasegawa M, Pilotte N, Kikuchi M, Means AR, Papaiakovou M, Gonzalez AM, Maasch JRMA, Ikuno H, Sunahara T, Ásbjörnsdóttir KH, Walson JL, Williams SA, Hamano S. What does soil-transmitted helminth elimination look like? Results from a targeted molecular detection survey in Japan. Parasit Vectors 2020; 13:6. [PMID: 31915050 PMCID: PMC6950881 DOI: 10.1186/s13071-019-3875-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 12/30/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Japan is one of the few countries believed to have eliminated soil-transmitted helminths (STHs). In 1949, the national prevalence of Ascaris lumbricoides was 62.9%, which decreased to 0.6% in 1973 due to improvements in infrastructure, socioeconomic status, and the implementation of national STH control measures. The Parasitosis Prevention Law ended in 1994 and population-level screening ceased in Japan; therefore, current transmission status of STH in Japan is not well characterized. Sporadic cases of STH infections continue to be reported, raising the possibility of a larger-scale recrudescence of STH infections. Given that traditional microscopic detection methods are not sensitive to low-intensity STH infections, we conducted targeted prevalence surveys using sensitive PCR-based assays to evaluate the current STH-transmission status and to describe epidemiological characteristics of areas of Japan believed to have achieved historical elimination of STHs. METHODS Stool samples were collected from 682 preschool- and school-aged children from six localities of Japan with previously high prevalence of STH. Caregivers of participants completed a questionnaire to ascertain access to water, sanitation and hygiene (WASH), and potential exposures to environmental contamination. For fecal testing, multi-parallel real-time PCR assays were used to detect infections of Ascaris lumbricoides, Necator americanus, Ancylostoma duodenale and Trichuris trichiura. RESULTS Among the 682 children, no positive samples were identified, and participants reported high standards of WASH. CONCLUSIONS To our knowledge, this is the first STH-surveillance study in Japan to use sensitive molecular techniques for STH detection. The results suggest that recrudescence of STH infections has not occurred, and that declines in prevalence have been sustained in the sampled areas. These findings suggest that reductions in prevalence below the elimination thresholds, suggestive of transmission interruption, are possible. Additionally, this study provides circumstantial evidence that multi-parallel real-time PCR methods are applicable for evaluating elimination status in areas where STH prevalence is extremely low.
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Affiliation(s)
- Mitsuko Hasegawa
- Department of Parasitology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan.,Doctoral Leadership Program, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.,The Joint Usage/Research Center on Tropical Disease, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Nils Pilotte
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, USA.,Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts, USA
| | - Mihoko Kikuchi
- Doctoral Leadership Program, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.,The Joint Usage/Research Center on Tropical Disease, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan.,Department of Immunogenetics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Arianna R Means
- Department of Global Health, University of Washington, Seattle, Washington, USA.,Department of Life Sciences, Natural History Museum, London, UK
| | - Marina Papaiakovou
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, USA.,Department of Life Sciences, Natural History Museum, London, UK
| | - Andrew M Gonzalez
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, USA
| | | | - Hiroshi Ikuno
- Department of Bacteriology, BML, Inc, Saitama, Japan
| | - Toshihiko Sunahara
- The Joint Usage/Research Center on Tropical Disease, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan.,Department of Vector Ecology and Environment, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | | | - Judd L Walson
- Department of Global Health, University of Washington, Seattle, Washington, USA.,Department of Life Sciences, Natural History Museum, London, UK.,Departments of Medicine (Infectious Disease), Pediatrics and Epidemiology, University of Washington, Seattle, Washington, USA
| | - Steven A Williams
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, USA.,Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts, USA
| | - Shinjiro Hamano
- Department of Parasitology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan. .,Doctoral Leadership Program, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan. .,The Joint Usage/Research Center on Tropical Disease, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan.
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Recent advances in nucleic acid-based methods for detection of helminth infections and the perspective of biosensors for future development. Parasitology 2019; 147:383-392. [PMID: 31840627 DOI: 10.1017/s0031182019001665] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Pathogenic helminth infections are responsible for severe health problems and economic losses worldwide. Timely and accurate diagnosis of helminth infections is critical for adopting suitable strategies for pathogen control. Here, we review recent advances in nucleic acid-based diagnostic methods, including polymerase chain reaction, quantitative qPCR, loop-mediated isothermal amplification and recombinase polymerase amplification, and discuss their advantages and disadvantages for diagnosing helminth infections. In addition, we highlight recent advances in biosensors for the detection of nucleic acid biomarkers that can potentially be used for the diagnosis of helminth infection.
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Papaiakovou M, Wright J, Pilotte N, Chooneea D, Schär F, Truscott JE, Dunn JC, Gardiner I, Walson JL, Williams SA, Littlewood DTJ. Pooling as a strategy for the timely diagnosis of soil-transmitted helminths in stool: value and reproducibility. Parasit Vectors 2019; 12:443. [PMID: 31522691 PMCID: PMC6745781 DOI: 10.1186/s13071-019-3693-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/30/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The strategy of pooling stool specimens has been extensively used in the field of parasitology in order to facilitate the screening of large numbers of samples whilst minimizing the prohibitive cost of single sample analysis. The aim of this study was to develop a standardized reproducible pooling protocol for stool samples, validated between two different laboratories, without jeopardizing the sensitivity of the quantitative polymerase chain reaction (qPCR) assays employed for the detection of soil-transmitted helminths (STHs). Two distinct experimental phases were recruited. First, the sensitivity and specificity of the established protocol was assessed by real-time PCR for each one of the STHs. Secondly, agreement and reproducibility of the protocol between the two different laboratories were tested. The need for multiple stool sampling to avoid false negative results was also assessed. Finally, a cost exercise was conducted which included labour cost in low- and high-wage settings, consumable cost, prevalence of a single STH species, and a simple distribution pattern of the positive samples in pools to estimate time and money savings suggested by the strategy. RESULTS The sensitivity of the pooling method was variable among the STH species but consistent between the two laboratories. Estimates of specificity indicate a 'pooling approach' can yield a low frequency of 'missed' infections. There were no significant differences regarding the execution of the protocol and the subsequent STH detection between the two laboratories, which suggests in most cases the protocol is reproducible by adequately trained staff. Finally, given the high degree of agreement, there appears to be little or no need for multiple sampling of either individuals or pools. CONCLUSIONS Our results suggest that the pooling protocol developed herein is a robust and efficient strategy for the detection of STHs in 'pools-of-five'. There is notable complexity of the pool preparation to ensure even distribution of helminth DNA throughout. Therefore, at a given setting, cost of labour among other logistical and epidemiological factors, is the more concerning and determining factor when choosing pooling strategies, rather than losing sensitivity and/or specificity of the molecular assay or the method.
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Affiliation(s)
- Marina Papaiakovou
- Department of Life Sciences, Natural History Museum, London, UK.
- Department of Biological Sciences, Smith College, Northampton, MA, USA.
| | - James Wright
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, Imperial College London, London, UK
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Nils Pilotte
- Department of Biological Sciences, Smith College, Northampton, MA, USA
- Molecular and Cellular Biology Programme, University of Massachusetts, Amherst, MA, USA
| | - Darren Chooneea
- Core Research Laboratories, Natural History Museum, London, UK
| | | | - James E Truscott
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, Imperial College London, London, UK
| | - Julia C Dunn
- Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, Imperial College London, London, UK
| | | | - Judd L Walson
- DeWorm3, Natural History Museum, London, UK
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Steven A Williams
- Department of Biological Sciences, Smith College, Northampton, MA, USA
- Molecular and Cellular Biology Programme, University of Massachusetts, Amherst, MA, USA
| | - D Timothy J Littlewood
- Department of Life Sciences, Natural History Museum, London, UK
- DeWorm3, Natural History Museum, London, UK
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