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Papaiakovou M, Maclean K, Zwanenburg L, Ajakaye OG, Chakraborty S, Costain A, Souza COS, Cunningham K, Cobb SA, Moescheid MF, Mora J, Amaral MS. Hydra at 21, key to the door for helminth researchers. Trends Parasitol 2023; 39:973-981. [PMID: 37833165 DOI: 10.1016/j.pt.2023.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023]
Affiliation(s)
- Marina Papaiakovou
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
| | - Kate Maclean
- Malaghan Institute of Medical Research, Wellington, New Zealand.
| | | | | | | | - Alice Costain
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK.
| | - Camila Oliveira Silva Souza
- Type 2 Immunity Section, Laboratory of Parasitic Disease, National Institute of Allergy and Infectious Diseases (NIAID), National Institute of Health, Bethesda, MD, USA.
| | | | - Sarah A Cobb
- University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Max F Moescheid
- Institute of Parasitology, Biomedical Research Center Seltersberg (BFS), Justus Liebig University Giessen, Giessen, Germany.
| | - Javier Mora
- Centro de Investigación de Enfermedades Tropicales, Centro de Investigación en Cirugía y Cáncer, and Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Papaiakovou M, Littlewood DTJ, Doyle SR, Gasser RB, Cantacessi C. Worms and bugs of the gut: the search for diagnostic signatures using barcoding, and metagenomics-metabolomics. Parasit Vectors 2022; 15:118. [PMID: 35365192 PMCID: PMC8973539 DOI: 10.1186/s13071-022-05225-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/25/2022] [Indexed: 02/07/2023] Open
Abstract
Gastrointestinal (GI) helminth infections cause significant morbidity in both humans and animals worldwide. Specific and sensitive diagnosis is central to the surveillance of such infections and to determine the effectiveness of treatment strategies used to control them. In this article, we: (i) assess the strengths and limitations of existing methods applied to the diagnosis of GI helminth infections of humans and livestock; (ii) examine high-throughput sequencing approaches, such as targeted molecular barcoding and shotgun sequencing, as tools to define the taxonomic composition of helminth infections; and (iii) discuss the current understanding of the interactions between helminths and microbiota in the host gut. Stool-based diagnostics are likely to serve as an important tool well into the future; improved diagnostics of helminths and their environment in the gut may assist the identification of biomarkers with the potential to define the health/disease status of individuals and populations, and to identify existing or emerging anthelmintic resistance.
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Affiliation(s)
- Marina Papaiakovou
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES UK
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | | | | | - Robin B. Gasser
- Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Cinzia Cantacessi
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES UK
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Jenkins TP, Pritchard DI, Tanasescu R, Telford G, Papaiakovou M, Scotti R, Cortés A, Constantinescu CS, Cantacessi C. Experimental infection with the hookworm, Necator americanus, is associated with stable gut microbial diversity in human volunteers with relapsing multiple sclerosis. BMC Biol 2021; 19:74. [PMID: 33853585 PMCID: PMC8048248 DOI: 10.1186/s12915-021-01003-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/12/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Helminth-associated changes in gut microbiota composition have been hypothesised to contribute to the immune-suppressive properties of parasitic worms. Multiple sclerosis is an immune-mediated autoimmune disease of the central nervous system whose pathophysiology has been linked to imbalances in gut microbial communities. RESULTS In the present study, we investigated, for the first time, qualitative and quantitative changes in the faecal bacterial composition of human volunteers with remitting multiple sclerosis (RMS) prior to and following experimental infection with the human hookworm, Necator americanus (N+), and following anthelmintic treatment, and compared the findings with data obtained from a cohort of RMS patients subjected to placebo treatment (PBO). Bacterial 16S rRNA high-throughput sequencing data revealed significantly decreased alpha diversity in the faecal microbiota of PBO compared to N+ subjects over the course of the trial; additionally, we observed significant differences in the abundances of several bacterial taxa with putative immune-modulatory functions between study cohorts. Parabacteroides were significantly expanded in the faecal microbiota of N+ individuals for which no clinical and/or radiological relapses were recorded at the end of the trial. CONCLUSIONS Overall, our data lend support to the hypothesis of a contributory role of parasite-associated alterations in gut microbial composition to the immune-modulatory properties of hookworm parasites.
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Affiliation(s)
- Timothy P. Jenkins
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Present address: Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Radu Tanasescu
- Division of Clinical Neurology, School of Clinical Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, UK
| | - Gary Telford
- Department of Pharmacy, University of Nottingham, Nottingham, UK
| | - Marina Papaiakovou
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- National History Museum, London, UK
| | - Riccardo Scotti
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Alba Cortés
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Departament de Farmàcia i Tecnologia Farmacèutica i Parasitologia, Facultat de Farmàcia, Universitat de València, València, Spain
| | - Cris S. Constantinescu
- Division of Clinical Neurology, School of Clinical Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, UK
| | - Cinzia Cantacessi
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Werkman M, Wright JE, Truscott JE, Oswald WE, Halliday KE, Papaiakovou M, Farrell SH, Pullan RL, Anderson RM. The impact of community-wide, mass drug administration on aggregation of soil-transmitted helminth infection in human host populations. Parasit Vectors 2020; 13:290. [PMID: 32513254 PMCID: PMC7278197 DOI: 10.1186/s13071-020-04149-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/25/2020] [Indexed: 11/21/2022] Open
Abstract
Background Soil-transmitted helminths (STH) are intestinal parasites estimated to infect over 1.5 billion people. Current treatment programmes are aimed at morbidity control through school-based deworming programmes (targeting school-aged children, SAC) and treating women of reproductive age (WRA), as these two groups are believed to record the highest morbidity. More recently, however, the potential for interrupting transmission by treating entire communities has been receiving greater emphasis and the feasibility of such programmes are now under investigation in randomised clinical trials through the Bill & Melinda Gates Foundation funded DeWorm3 studies. Helminth parasites are known to be highly aggregated within human populations, with a small minority of individuals harbouring most worms. Empirical evidence from the TUMIKIA project in Kenya suggests that aggregation may increase significantly after anthelminthic treatment. Methods A stochastic, age-structured, individual-based simulation model of parasite transmission is employed to better understand the factors that might induce this pattern. A simple probabilistic model based on compounded negative binomial distributions caused by age-dependencies in both treatment coverage and exposure to infection is also employed to further this understanding. Results Both approaches confirm helminth aggregation is likely to increase post-mass drug administration as measured by a decrease in the value of the negative binomial aggregation parameter, k. Simple analytical models of distribution compounding describe the observed patterns well. Conclusions The helminth aggregation that was observed in the field was replicated with our stochastic individual-based model. Further work is required to generalise the probabilistic model to take account of the respective sensitivities of different diagnostics on the presence or absence of infection.![]()
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Affiliation(s)
- Marleen Werkman
- London Centre for Neglected Tropical Disease Research (LCNTDR), Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College London, London, UK. .,The DeWorm3 Project, The Natural History Museum of London, London, UK. .,MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.
| | - James E Wright
- London Centre for Neglected Tropical Disease Research (LCNTDR), Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College London, London, UK.,The DeWorm3 Project, The Natural History Museum of London, London, UK.,MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.,Centre for Global Child Health, Hospital for Sick Children, Toronto, Canada
| | - James E Truscott
- London Centre for Neglected Tropical Disease Research (LCNTDR), Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College London, London, UK.,The DeWorm3 Project, The Natural History Museum of London, London, UK.,MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | - William E Oswald
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Katherine E Halliday
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Marina Papaiakovou
- London Centre for Neglected Tropical Disease Research (LCNTDR), Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College London, London, UK.,MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.,Department of Life Sciences, Natural History Museum, London, UK
| | - Sam H Farrell
- London Centre for Neglected Tropical Disease Research (LCNTDR), Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College London, London, UK
| | - Rachel L Pullan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Roy M Anderson
- London Centre for Neglected Tropical Disease Research (LCNTDR), Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College London, London, UK.,The DeWorm3 Project, The Natural History Museum of London, London, UK.,MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Papaiakovou M, Gasser RB, Littlewood DTJ. Quantitative PCR-Based Diagnosis of Soil-Transmitted Helminth Infections: Faecal or Fickle? Trends Parasitol 2019; 35:491-500. [PMID: 31126720 DOI: 10.1016/j.pt.2019.04.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/16/2019] [Accepted: 04/19/2019] [Indexed: 11/19/2022]
Abstract
Treatment and control programmes tackling soil-transmitted helminth (STH) infections require sensitive, reliable, and accurate diagnostic tools. There is a growing need for measures of infection intensity as programmes approach STH control. Quantitative real-time PCR (qPCR) is well suited to the detection of DNA targets present in stool, even in low-prevalence settings. Detecting low levels of infection becomes increasingly important when the breakpoint of transmission is approached, and is vital when monitoring for recrudescence once control, or possibly 'elimination', is achieved. We address key challenges and questions that remain as barriers to incorporating qPCR as a cornerstone diagnostic tool for STH infections.
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Affiliation(s)
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
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O'Connell EM, Mitchell T, Papaiakovou M, Pilotte N, Lee D, Weinberg M, Sakulrak P, Tongsukh D, Oduro-Boateng G, Harrison S, Williams SA, Stauffer WM, Nutman TB. Ancylostoma ceylanicum Hookworm in Myanmar Refugees, Thailand, 2012-2015. Emerg Infect Dis 2019; 24. [PMID: 30014834 PMCID: PMC6056130 DOI: 10.3201/eid2408.180280] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
This hookworm, uncommonly found in humans, has a higher cure rate than that for Necator americanus hookworm. During 2012–2015, US-bound refugees living in Myanmar–Thailand border camps (n = 1,839) were surveyed for hookworm infection and treatment response by using quantitative PCR. Samples were collected at 3 time points: after each of 2 treatments with albendazole and after resettlement in the United States. Baseline prevalence of Necator americanus hookworm was 25.4%, Ancylostoma duodenale 0%, and Ancylostoma ceylanicum (a zoonosis) 5.4%. Compared with N. americanus prevalence, A. ceylanicum hookworm prevalence peaked in younger age groups, and blood eosinophil concentrations during A. ceylanicum infection were higher than those for N. americanus infection. Female sex was associated with a lower risk for either hookworm infection. Cure rates after 1 dose of albendazole were greater for A. ceylanicum (93.3%) than N. americanus (65.9%) hookworm (p<0.001). Lower N. americanus hookworm cure rates were unrelated to β-tubulin single-nucleotide polymorphisms at codons 200 or 167. A. ceylanicum hookworm infection might be more common in humans than previously recognized.
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Truscott JE, Dunn JC, Papaiakovou M, Schaer F, Werkman M, Littlewood DTJ, Walson JL, Anderson RM. Calculating the prevalence of soil-transmitted helminth infection through pooling of stool samples: Choosing and optimizing the pooling strategy. PLoS Negl Trop Dis 2019; 13:e0007196. [PMID: 30897089 PMCID: PMC6445468 DOI: 10.1371/journal.pntd.0007196] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 04/02/2019] [Accepted: 01/29/2019] [Indexed: 12/31/2022] Open
Abstract
Prevalence is a common epidemiological measure for assessing soil-transmitted helminth burden and forms the basis for much public-health decision-making. Standard diagnostic techniques are based on egg detection in stool samples through microscopy and these techniques are known to have poor sensitivity for individuals with low infection intensity, leading to poor sensitivity in low prevalence populations. PCR diagnostic techniques offer very high sensitivities even at low prevalence, but at a greater cost for each diagnostic test in terms of equipment needed and technician time and training. Pooling of samples can allow prevalence to be estimated while minimizing the number of tests performed. We develop a model of the relative cost of pooling to estimate prevalence, compared to the direct approach of testing all samples individually. Analysis shows how expected relative cost depends on both the underlying prevalence in the population and the size of the pools constructed. A critical prevalence level (approx. 31%) above which pooling is never cost effective, independent of pool size. When no prevalence information is available, there is no basis on which to choose between pooling and testing all samples individually. We recast our model of relative cost in a Bayesian framework in order to investigate how prior information about prevalence in a given population can be used to inform the decision to choose either pooling or full testing. Results suggest that if prevalence is below 10%, a relatively small exploratory prevalence survey (10-15 samples) can be sufficient to give a high degree of certainty that pooling may be relatively cost effective.
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Affiliation(s)
- James E. Truscott
- The DeWorm3 Project, Department of Life Sciences, Natural History Museum, London, United Kingdom
- Department of Infectious Disease Epidemiology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Julia C. Dunn
- Department of Infectious Disease Epidemiology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Marina Papaiakovou
- The DeWorm3 Project, Department of Life Sciences, Natural History Museum, London, United Kingdom
- Parasites & Vectors, Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Fabian Schaer
- The DeWorm3 Project, Department of Life Sciences, Natural History Museum, London, United Kingdom
- Parasites & Vectors, Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Marleen Werkman
- The DeWorm3 Project, Department of Life Sciences, Natural History Museum, London, United Kingdom
- Department of Infectious Disease Epidemiology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - D. Timothy J. Littlewood
- The DeWorm3 Project, Department of Life Sciences, Natural History Museum, London, United Kingdom
- Parasites & Vectors, Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Judd L. Walson
- The DeWorm3 Project, Department of Life Sciences, Natural History Museum, London, United Kingdom
- Parasites & Vectors, Department of Life Sciences, Natural History Museum, London, United Kingdom
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Roy M. Anderson
- The DeWorm3 Project, Department of Life Sciences, Natural History Museum, London, United Kingdom
- Department of Infectious Disease Epidemiology, Faculty of Medicine, Imperial College London, London, United Kingdom
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Papaiakovou M, Pilotte N, Grant JR, Traub RJ, Llewellyn S, McCarthy JS, Krolewiecki AJ, Cimino R, Mejia R, Williams SA. A novel, species-specific, real-time PCR assay for the detection of the emerging zoonotic parasite Ancylostoma ceylanicum in human stool. PLoS Negl Trop Dis 2017; 11:e0005734. [PMID: 28692668 PMCID: PMC5519186 DOI: 10.1371/journal.pntd.0005734] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 07/20/2017] [Accepted: 06/21/2017] [Indexed: 11/18/2022] Open
Abstract
Background Molecular-based surveys have indicated that Ancylostoma ceylanicum, a zoonotic hookworm, is likely the second most prevalent hookworm species infecting humans in Asia. Most current PCR-based diagnostic options for the detection of Ancylostoma species target the Internal Transcribed Spacer (ITS) regions of the ribosomal gene cluster. These regions possess a considerable degree of conservation among the species of this genus and this conservation can lead to the misidentification of infecting species or require additional labor for accurate species-level determination. We have developed a novel, real-time PCR-based assay for the sensitive and species-specific detection of A. ceylanicum that targets a non-coding, highly repetitive genomic DNA element. Comparative testing of this PCR assay with an assay that targets ITS sequences was conducted on field-collected samples from Argentina and Timor-Leste to provide further evidence of the sensitivity and species-specificity of this assay. Methods/Principal findings A previously described platform for the design of primers/probe targeting non-coding highly repetitive regions was used for the development of this novel assay. The assay’s limits of detection (sensitivity) and cross-reactivity with other soil-transmitted helminth species (specificity) were assessed with real-time PCR experiments. The assay was successfully used to identify infections caused by A. ceylanicum that were previously only identified to the genus level as Ancylostoma spp. when analyzed using other published primer-probe pairings. Further proof of sensitive, species-specific detection was provided using a published, semi-nested restriction fragment length polymorphism-PCR assay that differentiates between Ancylostoma species. Conclusions/Significance Due to the close proximity of people and domestic/wild animals in many regions of the world, the potential for zoonotic infections is substantial. Sensitive tools enabling the screening for different soil-transmitted helminth infections are essential to the success of mass deworming efforts and facilitate the appropriate interpretation of data. This study describes a novel, species-specific, real-time PCR-based assay for the detection of A. ceylanicum that will help to address the need for such tools in integrated STH deworming programs. Trial registration ANZCTR.org.au ACTRN12614000680662 Historically, Ancylostoma ceylanicum has been viewed as an uncommon cause of human hookworm infection, with minimal public health importance. However, recent reports have indicated that this zoonotic hookworm causes a much greater incidence of infection within certain human populations than was previously believed. Current methods for the species-level detection of A. ceylanicum rely on techniques that involve conventional PCR accompanied by restriction enzyme digestions. These PCR-based assays are not only laborious but they lack sensitivity as they target suboptimal regions on the DNA. As efforts aimed at the eradication of hookworm disease have grown substantially over the last decade, the need for sensitive and specific tools to monitor and evaluate programmatic successes has correspondingly escalated. Since a growing body of evidence suggests that patient responses to drug treatment can vary based upon the species of hookworm that is causing infection, accurate species-level diagnostics are advantageous. Accordingly, the novel real-time PCR-based assay described here provides a sensitive, species-specific diagnostic tool that will facilitate the accurate mapping of disease endemicity and will aid in the evaluation of progress of programmatic deworming efforts.
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Affiliation(s)
- Marina Papaiakovou
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 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
| | - Jessica R. Grant
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, United States of America
| | - Rebecca J. Traub
- Faculty of Veterinary and Agricultural Science, University of Melbourne, Parkville, Australia
| | - Stacey Llewellyn
- Clinical Medical Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - James S. McCarthy
- Clinical Medical Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Alejandro J. Krolewiecki
- Instituto de Investigaciones en Enfermedades Tropicales, Universidad Nacional de Salta/CONICET, Orán, Argentina
- Instituto de Patología Experimental (IPE-CONICET), Facultad de Ciencias de la Salud, Universidad Nacional de Salta, Salta, Argentina
| | - Rubén Cimino
- Instituto de Investigaciones en Enfermedades Tropicales, Universidad Nacional de Salta/CONICET, Orán, Argentina
| | - Rojelio Mejia
- National School of Tropical Medicine, Baylor College of Medicine, Houston, Texas, 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
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Zois CE, Giatromanolaki A, Sivridis E, Papaiakovou M, Kainulainen H, Koukourakis MI. "Autophagic flux" in normal mouse tissues: Focus on endogenous LC3A processing. Autophagy 2014; 7:1371-8. [DOI: 10.4161/auto.7.11.16664] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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