1
|
Ruybal-Pesántez S, McCann K, Vibin J, Siegel S, Auburn S, Barry AE. Molecular markers for malaria genetic epidemiology: progress and pitfalls. Trends Parasitol 2024; 40:147-163. [PMID: 38129280 DOI: 10.1016/j.pt.2023.11.006] [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] [Received: 09/06/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
Over recent years, progress in molecular markers for genotyping malaria parasites has enabled informative studies of epidemiology and transmission dynamics. Results have highlighted the value of these tools for surveillance to support malaria control and elimination strategies. There are many different types and panels of markers available for malaria parasite genotyping, and for end users, the nuances of these markers with respect to 'use case', resolution, and accuracy, are not well defined. This review clarifies issues surrounding different molecular markers and their application to malaria control and elimination. We describe available marker panels, use cases, implications for different transmission settings, limitations, access, cost, and data accuracy. The information provided can be used as a guide for molecular epidemiology and surveillance of malaria.
Collapse
Affiliation(s)
- Shazia Ruybal-Pesántez
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK; Institute of Microbiology, Universidad San Francisco de Quito, Quito, Ecuador
| | - Kirsty McCann
- Life Sciences Discipline, Burnet Institute, Melbourne, Victoria, Australia; Centre for Innovation in Infectious Disease and Immunology Research (CIIDIR), Institute for Mental and Physical Health and Clinical Translation (IMPACT) and School of Medicine, Deakin University, Geelong, Victoria, Australia
| | - Jessy Vibin
- Life Sciences Discipline, Burnet Institute, Melbourne, Victoria, Australia; Centre for Innovation in Infectious Disease and Immunology Research (CIIDIR), Institute for Mental and Physical Health and Clinical Translation (IMPACT) and School of Medicine, Deakin University, Geelong, Victoria, Australia
| | | | - Sarah Auburn
- Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia; Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Alyssa E Barry
- Life Sciences Discipline, Burnet Institute, Melbourne, Victoria, Australia; Centre for Innovation in Infectious Disease and Immunology Research (CIIDIR), Institute for Mental and Physical Health and Clinical Translation (IMPACT) and School of Medicine, Deakin University, Geelong, Victoria, Australia.
| |
Collapse
|
2
|
Sy M, Deme AB, Warren JL, Early A, Schaffner S, Daniels RF, Dieye B, Ndiaye IM, Diedhiou Y, Mbaye AM, Volkman SK, Hartl DL, Wirth DF, Ndiaye D, Bei AK. Plasmodium falciparum genomic surveillance reveals spatial and temporal trends, association of genetic and physical distance, and household clustering. Sci Rep 2022; 12:938. [PMID: 35042879 PMCID: PMC8766587 DOI: 10.1038/s41598-021-04572-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 12/24/2021] [Indexed: 11/15/2022] Open
Abstract
Molecular epidemiology using genomic data can help identify relationships between malaria parasite population structure, malaria transmission intensity, and ultimately help generate actionable data to assess the effectiveness of malaria control strategies. Genomic data, coupled with geographic information systems data, can further identify clusters or hotspots of malaria transmission, parasite genetic and spatial connectivity, and parasite movement by human or mosquito mobility over time and space. In this study, we performed longitudinal genomic surveillance in a cohort of 70 participants over four years from different neighborhoods and households in Thiès, Senegal—a region of exceptionally low malaria transmission (entomological inoculation rate less than 1). Genetic identity (identity by state, IBS) was established using a 24-single nucleotide polymorphism molecular barcode, identity by descent was calculated from whole genome sequence data, and a hierarchical Bayesian regression model was used to establish genetic and spatial relationships. Our results show clustering of genetically similar parasites within households and a decline in genetic similarity of parasites with increasing distance. One household showed extremely high diversity and warrants further investigation as to the source of these diverse genetic types. This study illustrates the utility of genomic data with traditional epidemiological approaches for surveillance and detection of trends and patterns in malaria transmission not only by neighborhood but also by household. This approach can be implemented regionally and countrywide to strengthen and support malaria control and elimination efforts.
Collapse
Affiliation(s)
- Mouhamad Sy
- Laboratory of Parasitology and Mycology, Cheikh Anta Diop University, Aristide le Dantec Hospital, Dakar, Senegal
| | - Awa B Deme
- Laboratory of Parasitology and Mycology, Cheikh Anta Diop University, Aristide le Dantec Hospital, Dakar, Senegal.,Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Joshua L Warren
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Angela Early
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephen Schaffner
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rachel F Daniels
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Baba Dieye
- Laboratory of Parasitology and Mycology, Cheikh Anta Diop University, Aristide le Dantec Hospital, Dakar, Senegal
| | - Ibrahima Mbaye Ndiaye
- Laboratory of Parasitology and Mycology, Cheikh Anta Diop University, Aristide le Dantec Hospital, Dakar, Senegal
| | - Younous Diedhiou
- Laboratory of Parasitology and Mycology, Cheikh Anta Diop University, Aristide le Dantec Hospital, Dakar, Senegal
| | - Amadou Moctar Mbaye
- Laboratory of Parasitology and Mycology, Cheikh Anta Diop University, Aristide le Dantec Hospital, Dakar, Senegal
| | - Sarah K Volkman
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,College of Natural, Behavioral and Health Sciences, Simmons University, Boston, MA, USA
| | - Daniel L Hartl
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daouda Ndiaye
- Laboratory of Parasitology and Mycology, Cheikh Anta Diop University, Aristide le Dantec Hospital, Dakar, Senegal
| | - Amy K Bei
- Laboratory of Parasitology and Mycology, Cheikh Anta Diop University, Aristide le Dantec Hospital, Dakar, Senegal. .,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA. .,Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
| |
Collapse
|
3
|
Kattenberg JH, Razook Z, Keo R, Koepfli C, Jennison C, Lautu-Gumal D, Fola AA, Ome-Kaius M, Barnadas C, Siba P, Felger I, Kazura J, Mueller I, Robinson LJ, Barry AE. Monitoring Plasmodium falciparum and Plasmodium vivax using microsatellite markers indicates limited changes in population structure after substantial transmission decline in Papua New Guinea. Mol Ecol 2020; 29:4525-4541. [PMID: 32985031 PMCID: PMC10008436 DOI: 10.1111/mec.15654] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 07/27/2020] [Indexed: 02/01/2023]
Abstract
Monitoring the genetic structure of pathogen populations may be an economical and sensitive approach to quantify the impact of control on transmission dynamics, highlighting the need for a better understanding of changes in population genetic parameters as transmission declines. Here we describe the first population genetic analysis of two major human malaria parasites, Plasmodium falciparum (Pf) and Plasmodium vivax (Pv), following nationwide distribution of long-lasting insecticide-treated nets (LLINs) in Papua New Guinea (PNG). Parasite isolates from pre- (2005-2006) and post-LLIN (2010-2014) were genotyped using microsatellite markers. Despite parasite prevalence declining substantially (East Sepik Province: Pf = 54.9%-8.5%, Pv = 35.7%-5.6%, Madang Province: Pf = 38.0%-9.0%, Pv: 31.8%-19.7%), genetically diverse and intermixing parasite populations remained. Pf diversity declined modestly post-LLIN relative to pre-LLIN (East Sepik: Rs = 7.1-6.4, HE = 0.77-0.71; Madang: Rs = 8.2-6.1, HE = 0.79-0.71). Unexpectedly, population structure present in pre-LLIN populations was lost post-LLIN, suggesting that more frequent human movement between provinces may have contributed to higher gene flow. Pv prevalence initially declined but increased again in one province, yet diversity remained high throughout the study period (East Sepik: Rs = 11.4-9.3, HE = 0.83-0.80; Madang: Rs = 12.2-14.5, HE = 0.85-0.88). Although genetic differentiation values increased between provinces over time, no significant population structure was observed at any time point. For both species, a decline in multiple infections and increasing clonal transmission and significant multilocus linkage disequilibrium post-LLIN were positive indicators of impact on the parasite population using microsatellite markers. These parameters may be useful adjuncts to traditional epidemiological tools in the early stages of transmission reduction.
Collapse
Affiliation(s)
- Johanna Helena Kattenberg
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Yagaum, Papua New Guinea
| | - Zahra Razook
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Raksmei Keo
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Cristian Koepfli
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Charlie Jennison
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Dulcie Lautu-Gumal
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Yagaum, Papua New Guinea.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Abebe A Fola
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Maria Ome-Kaius
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Yagaum, Papua New Guinea.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Céline Barnadas
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Yagaum, Papua New Guinea.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Ingrid Felger
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - James Kazura
- Centre for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, USA
| | - Ivo Mueller
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.,Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - Leanne J Robinson
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Yagaum, Papua New Guinea.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.,Disease Elimination, Burnet Institute, Melbourne, VIC, Australia
| | - Alyssa E Barry
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| |
Collapse
|
4
|
Webster J, Mishra VK, Anvikar AR, Kuepfer I, Hoyt J, Bruce J, Greenwood B, Chandramohan D, Valecha N, Mishra N. Evaluation of Implementation of Intermittent Screening and Treatment for Control of Malaria in Pregnancy in Jharkhand, India. Am J Trop Med Hyg 2020; 102:1343-1350. [PMID: 32157995 PMCID: PMC7253127 DOI: 10.4269/ajtmh.19-0514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
This study evaluated intermittent screening and treatment during pregnancy (ISTp) for malaria using rapid diagnostic tests (RDTs) at antenatal care (ANC) compared with passive case detection within the routine health system. The mixed-method evaluation included two cross-sectional household surveys (pre- and post-implementation of ISTp), in-depth interviews with health workers, and focus group discussions (FGDs) with pregnant women. Differences in proportions between surveys for a number of outcomes were tested; 553 and 534 current and recently pregnant women were surveyed (pre- and post-implementation, respectively). In-depth interviews were conducted with 29 health providers, and 13 FGDs were held with pregnant women. The proportion of pregnant women who received an RDT for malaria at ANC at least once during their pregnancy increased from pre- to post-implementation (19.2%; 95% CI: 14.9, 24.3 versus 42.5%; 95% CI: 36.6, 48.7; P < 0.0001), and the proportion of women who had more than one RDT also increased (16.5%; 95% CI: 13.1, 20.5 versus 27.7%; 95% CI: 23.0, 33.0; P = 0.0008). Post-implementation, however, only 8% of women who had completed their pregnancy received an RDT on three visits to ANC. Health workers were positive about ISTp mainly because of their perception that many pregnant women with malaria were asymptomatic. Health workers perceived pregnant women to have reservations about ISTp because of their dislike of frequent blood withdrawal, but pregnant women themselves were more positive. Intermittent screening and treatment during pregnancy was not sufficiently adopted by health workers to ensure the increased detection of malaria infections achievable with this strategy in this setting.
Collapse
Affiliation(s)
- Jayne Webster
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | | | - Irene Kuepfer
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Jenna Hoyt
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Jane Bruce
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Brian Greenwood
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Neena Valecha
- National Institute for Malaria Research, Delhi, India
| | | |
Collapse
|
5
|
Pava Z, Puspitasari AM, Rumaseb A, Handayuni I, Trianty L, Utami RAS, Tirta YK, Burdam F, Kenangalem E, Wirjanata G, Kho S, Trimarsanto H, Anstey NM, Poespoprodjo JR, Noviyanti R, Price RN, Marfurt J, Auburn S. Molecular surveillance over 14 years confirms reduction of Plasmodium vivax and falciparum transmission after implementation of Artemisinin-based combination therapy in Papua, Indonesia. PLoS Negl Trop Dis 2020; 14:e0008295. [PMID: 32379762 PMCID: PMC7237043 DOI: 10.1371/journal.pntd.0008295] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 05/19/2020] [Accepted: 04/15/2020] [Indexed: 01/13/2023] Open
Abstract
Genetic epidemiology can provide important insights into parasite transmission that can inform public health interventions. The current study compared long-term changes in the genetic diversity and structure of co-endemic Plasmodium falciparum and P. vivax populations. The study was conducted in Papua Indonesia, where high-grade chloroquine resistance in P. falciparum and P. vivax led to a universal policy of Artemisinin-based Combination Therapy (ACT) in 2006. Microsatellite typing and population genetic analyses were undertaken on available isolates collected between 2004 and 2017 from patients with uncomplicated malaria (n = 666 P. falciparum and n = 615 P. vivax). The proportion of polyclonal P. falciparum infections fell from 28% (38/135) before policy change (2004-2006) to 18% (22/125) at the end of the study (2015-2017); p<0.001. Over the same period, polyclonal P. vivax infections fell from 67% (80/119) to 35% (33/93); p<0.001. P. falciparum strains persisted for up to 9 years compared to 3 months for P. vivax, reflecting higher rates of outbreeding in the latter. Sub-structure was observed in the P. falciparum population, but not in P. vivax, confirming different patterns of outbreeding. The P. falciparum population exhibited 4 subpopulations that changed in frequency over time. Notably, a sharp rise was observed in the frequency of a minor subpopulation (K2) in the late post-ACT period, accounting for 100% of infections in late 2016-2017. The results confirm epidemiological evidence of reduced P. falciparum and P. vivax transmission over time. The smaller change in P. vivax population structure is consistent with greater outbreeding associated with relapsing infections and highlights the need for radical cure to reduce recurrent infections. The study emphasizes the challenge in disrupting P. vivax transmission and demonstrates the potential of molecular data to inform on the impact of public health interventions.
Collapse
Affiliation(s)
- Zuleima Pava
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | | | - Angela Rumaseb
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Irene Handayuni
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Leily Trianty
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | | | | | - Faustina Burdam
- Mimika District Health Authority, Timika, Papua, Indonesia
- Timika Malaria Research Programme, Papuan Health and Community Development Foundation, Timika, Papua, Indonesia
| | - Enny Kenangalem
- Mimika District Health Authority, Timika, Papua, Indonesia
- Timika Malaria Research Programme, Papuan Health and Community Development Foundation, Timika, Papua, Indonesia
| | - Grennady Wirjanata
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Steven Kho
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | | | - Nicholas M. Anstey
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Jeanne Rini Poespoprodjo
- Mimika District Health Authority, Timika, Papua, Indonesia
- Timika Malaria Research Programme, Papuan Health and Community Development Foundation, Timika, Papua, Indonesia
- Pediatric Research Office, Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | | | - Ric N. Price
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Jutta Marfurt
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| |
Collapse
|
6
|
A molecular barcode to inform the geographical origin and transmission dynamics of Plasmodium vivax malaria. PLoS Genet 2020; 16:e1008576. [PMID: 32053607 PMCID: PMC7043780 DOI: 10.1371/journal.pgen.1008576] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 02/26/2020] [Accepted: 12/19/2019] [Indexed: 11/19/2022] Open
Abstract
Although Plasmodium vivax parasites are the predominant cause of malaria outside of sub-Saharan Africa, they not always prioritised by elimination programmes. P. vivax is resilient and poses challenges through its ability to re-emerge from dormancy in the human liver. With observed growing drug-resistance and the increasing reports of life-threatening infections, new tools to inform elimination efforts are needed. In order to halt transmission, we need to better understand the dynamics of transmission, the movement of parasites, and the reservoirs of infection in order to design targeted interventions. The use of molecular genetics and epidemiology for tracking and studying malaria parasite populations has been applied successfully in P. falciparum species and here we sought to develop a molecular genetic tool for P. vivax. By assembling the largest set of P. vivax whole genome sequences (n = 433) spanning 17 countries, and applying a machine learning approach, we created a 71 SNP barcode with high predictive ability to identify geographic origin (91.4%). Further, due to the inclusion of markers for within population variability, the barcode may also distinguish local transmission networks. By using P. vivax data from a low-transmission setting in Malaysia, we demonstrate the potential ability to infer outbreak events. By characterising the barcoding SNP genotypes in P. vivax DNA sourced from UK travellers (n = 132) to ten malaria endemic countries predominantly not used in the barcode construction, we correctly predicted the geographic region of infection origin. Overall, the 71 SNP barcode outperforms previously published genotyping methods and when rolled-out within new portable platforms, is likely to be an invaluable tool for informing targeted interventions towards elimination of this resilient human malaria.
Collapse
|
7
|
Webster J, Ansariadi, Burdam FH, Landuwulang CUR, Bruce J, Poespoprodjo JR, Syafruddin D, Ahmed R, Hill J. Evaluation of the implementation of single screening and treatment for the control of malaria in pregnancy in Eastern Indonesia: a systems effectiveness analysis. Malar J 2018; 17:310. [PMID: 30143047 PMCID: PMC6108152 DOI: 10.1186/s12936-018-2448-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/05/2018] [Indexed: 11/10/2022] Open
Abstract
Background Indonesia introduced single screening and treatment (SST) of pregnant women for the control of malaria in pregnancy in 2012. Under this policy pregnant women are screened for malaria at their first antenatal clinic (ANC) visit and on subsequent visits are tested for malaria only if symptomatic. The implementation of this policy in two districts of Indonesia was evaluated. Cross sectional survey structured observations of the ANC visit and exit interviews with pregnant women were conducted to assess health provider compliance with SST guidelines. Systems effectiveness analysis was performed on components of the strategy. Multiple logistic regression was used to test for predictors of women being screened at their first ANC visit. Results A total of 865 and 895 ANC visits in Mimika and West Sumba across seven and ten health facilities (plus managed health posts) respectively, were included in the study. Adherence to malaria screening at first ANC visit among pregnant women was 51.4% (95% CI 11.9, 89.2) in health facilities in Mimika (94.8% in health centres) and 24.8% (95% CI 10.3, 48.9) in West Sumba (60.0% in health centres). Reported fever was low amongst women presenting for their second and above ANC visit (2.8% in Mimika and 3.5% in West Sumba) with 89.5% and 46.2% of these women tested for malaria in Mimka and West Sumba, respectively. Cumulative systems effectiveness for SST on first visit to ANC was 7.6% for Mimika and 0.1% for West Sumba; and for second or above visits to ANC was 0.7% in Mimika and 0% in West Sumba. Being screened on a 1st visit to ANC was associated with level of health facility in both sites. Conclusion Cumulative systems effectiveness of the SST strategy was poor in both sites. Both elements of the SST strategy, screening on first visit and passive case detection on second and above visits, was driven by the difference in implementation of malaria testing in health centres and health posts, and by low malaria transmission levels and reported fever.
Collapse
Affiliation(s)
- Jayne Webster
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
| | - Ansariadi
- Department of Epidemiology, School of Public Health, Hasanuddin University, Makassar, Indonesia
| | - Faustina Helena Burdam
- Timika Research Facility (Papuan Community and Health Development Foundation), Timika, Indonesia
| | | | - Jane Bruce
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Jeanne Rini Poespoprodjo
- Timika Research Facility (Papuan Community and Health Development Foundation), Timika, Indonesia.,Paediatric Research Office, Department of Child Health, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Mimika District Hospital, Timika, Indonesia
| | - Din Syafruddin
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Rukhsana Ahmed
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Jenny Hill
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| |
Collapse
|
8
|
White MT, Walker P, Karl S, Hetzel MW, Freeman T, Waltmann A, Laman M, Robinson LJ, Ghani A, Mueller I. Mathematical modelling of the impact of expanding levels of malaria control interventions on Plasmodium vivax. Nat Commun 2018; 9:3300. [PMID: 30120250 PMCID: PMC6097992 DOI: 10.1038/s41467-018-05860-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 07/23/2018] [Indexed: 01/07/2023] Open
Abstract
Plasmodium vivax poses unique challenges for malaria control and elimination, notably the potential for relapses to maintain transmission in the face of drug-based treatment and vector control strategies. We developed an individual-based mathematical model of P. vivax transmission calibrated to epidemiological data from Papua New Guinea (PNG). In many settings in PNG, increasing bed net coverage is predicted to reduce transmission to less than 0.1% prevalence by light microscopy, however there is substantial risk of rebounds in transmission if interventions are removed prematurely. In several high transmission settings, model simulations predict that combinations of existing interventions are not sufficient to interrupt P. vivax transmission. This analysis highlights the potential options for the future of P. vivax control: maintaining existing public health gains by keeping transmission suppressed through indefinite distribution of interventions; or continued development of strategies based on existing and new interventions to push for further reduction and towards elimination.
Collapse
Affiliation(s)
- Michael T White
- Malaria: Parasites and Hosts, Department of Parasites and Insect Vectors, Institut Pasteur, 25-28 Rue du Dr Roux, 75015, Paris, France.
| | - Patrick Walker
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College London, London, Norfolk Place, W2 1PG, UK
| | - Stephan Karl
- Vector-borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang 511, Papua New Guinea
- Division of Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, Melbourne University, Melbourne, VIC, 3052, Australia
| | - Manuel W Hetzel
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051, Basel, Switzerland
- University of Basel, Petersplatz 1, 4001, Basel, Switzerland
| | - Tim Freeman
- Rotarians Against Malaria, Port Moresby 121, Papua New Guinea
| | - Andreea Waltmann
- Division of Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, Melbourne University, Melbourne, VIC, 3052, Australia
| | - Moses Laman
- Vector-borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang 511, Papua New Guinea
| | - Leanne J Robinson
- Vector-borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang 511, Papua New Guinea
- Division of Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, Melbourne University, Melbourne, VIC, 3052, Australia
- Burnet Institute, Melbourne, VIC, 3004, Australia
| | - Azra Ghani
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College London, London, Norfolk Place, W2 1PG, UK
| | - Ivo Mueller
- Malaria: Parasites and Hosts, Department of Parasites and Insect Vectors, Institut Pasteur, 25-28 Rue du Dr Roux, 75015, Paris, France
- Division of Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, Melbourne University, Melbourne, VIC, 3052, Australia
| |
Collapse
|
9
|
Auburn S, Benavente ED, Miotto O, Pearson RD, Amato R, Grigg MJ, Barber BE, William T, Handayuni I, Marfurt J, Trimarsanto H, Noviyanti R, Sriprawat K, Nosten F, Campino S, Clark TG, Anstey NM, Kwiatkowski DP, Price RN. Genomic analysis of a pre-elimination Malaysian Plasmodium vivax population reveals selective pressures and changing transmission dynamics. Nat Commun 2018; 9:2585. [PMID: 29968722 PMCID: PMC6030216 DOI: 10.1038/s41467-018-04965-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 06/01/2018] [Indexed: 01/13/2023] Open
Abstract
The incidence of Plasmodium vivax infection has declined markedly in Malaysia over the past decade despite evidence of high-grade chloroquine resistance. Here we investigate the genetic changes in a P. vivax population approaching elimination in 51 isolates from Sabah, Malaysia and compare these with data from 104 isolates from Thailand and 104 isolates from Indonesia. Sabah displays extensive population structure, mirroring that previously seen with the emergence of artemisinin-resistant P. falciparum founder populations in Cambodia. Fifty-four percent of the Sabah isolates have identical genomes, consistent with a rapid clonal expansion. Across Sabah, there is a high prevalence of loci known to be associated with antimalarial drug resistance. Measures of differentiation between the three countries reveal several gene regions under putative selection in Sabah. Our findings highlight important factors pertinent to parasite resurgence and molecular cues that can be used to monitor low-endemic populations at the end stages of P. vivax elimination.
Collapse
Affiliation(s)
- Sarah Auburn
- 0000 0000 8523 7955grid.271089.5Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT 0811 Australia ,Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, OX3 7LF UK
| | - Ernest D. Benavente
- 0000 0004 0425 469Xgrid.8991.9Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Olivo Miotto
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, OX3 7LF UK ,0000 0004 0606 5382grid.10306.34Wellcome Trust Sanger Institute, Hinxton Cambridge, CB10 1SA UK ,0000 0004 1937 0490grid.10223.32Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, 10400 Thailand
| | - Richard D. Pearson
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, OX3 7LF UK ,0000 0004 0606 5382grid.10306.34Wellcome Trust Sanger Institute, Hinxton Cambridge, CB10 1SA UK
| | - Roberto Amato
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, OX3 7LF UK ,0000 0004 0606 5382grid.10306.34Wellcome Trust Sanger Institute, Hinxton Cambridge, CB10 1SA UK
| | - Matthew J. Grigg
- 0000 0000 8523 7955grid.271089.5Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT 0811 Australia ,Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, 88300 Kota Kinabalu Sabah, Malaysia
| | - Bridget E. Barber
- 0000 0000 8523 7955grid.271089.5Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT 0811 Australia ,Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, 88300 Kota Kinabalu Sabah, Malaysia
| | - Timothy William
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, 88300 Kota Kinabalu Sabah, Malaysia ,0000 0004 1772 8727grid.415560.3Clinical Research Centre, Queen Elizabeth Hospital, 88300 Kota Kinabalu Sabah, Malaysia ,Jesselton Medical Centre, 88300 Kota Kinabalu Sabah, Malaysia
| | - Irene Handayuni
- 0000 0000 8523 7955grid.271089.5Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT 0811 Australia
| | - Jutta Marfurt
- 0000 0000 8523 7955grid.271089.5Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT 0811 Australia
| | - Hidayat Trimarsanto
- 0000 0004 1795 0993grid.418754.bEijkman Institute for Molecular Biology, Jakarta, 10430 Indonesia ,0000 0001 0746 0534grid.432292.cAgency for Assessment and Application of Technology, Jl. MH Thamrin 8, Jakarta, 10340 Indonesia
| | - Rintis Noviyanti
- 0000 0004 1795 0993grid.418754.bEijkman Institute for Molecular Biology, Jakarta, 10430 Indonesia
| | - Kanlaya Sriprawat
- 0000 0004 1937 0490grid.10223.32Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot Tak, 63110 Thailand
| | - Francois Nosten
- 0000 0004 1937 0490grid.10223.32Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot Tak, 63110 Thailand ,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine Research Building, University of Oxford Old Road Campus, Oxford, OX3 7LJ UK
| | - Susana Campino
- 0000 0004 0425 469Xgrid.8991.9Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Taane G. Clark
- 0000 0004 0425 469Xgrid.8991.9Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT UK ,0000 0004 0425 469Xgrid.8991.9Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Nicholas M. Anstey
- 0000 0000 8523 7955grid.271089.5Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT 0811 Australia
| | - Dominic P. Kwiatkowski
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, OX3 7LF UK ,0000 0004 0606 5382grid.10306.34Wellcome Trust Sanger Institute, Hinxton Cambridge, CB10 1SA UK
| | - Ric N. Price
- 0000 0000 8523 7955grid.271089.5Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT 0811 Australia ,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine Research Building, University of Oxford Old Road Campus, Oxford, OX3 7LJ UK
| |
Collapse
|
10
|
Pava Z, Handayuni I, Trianty L, Utami RAS, Tirta YK, Puspitasari AM, Burdam F, Kenangalem E, Wirjanata G, Kho S, Trimarsanto H, Anstey N, Poespoprodjo JR, Noviyanti R, Price RN, Marfurt J, Auburn S. Passively versus Actively Detected Malaria: Similar Genetic Diversity but Different Complexity of Infection. Am J Trop Med Hyg 2017; 97:1788-1796. [PMID: 29016343 PMCID: PMC5790166 DOI: 10.4269/ajtmh.17-0364] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The surveillance of malaria is generally undertaken on the assumption that samples passively collected at health facilities are comparable to or representative of the broader Plasmodium reservoir circulating in the community. Further characterization and comparability of the hidden asymptomatic parasite reservoir are needed to inform on the potential impact of sampling bias. This study explores the impact of sampling strategy on molecular surveillance by comparing the genetic make-up of Plasmodium falciparum and Plasmodium vivax isolates collected by passive versus active case detection. Sympatric isolates of P. falciparum and P. vivax were collected from a large community survey and ongoing clinical surveillance studies undertaken in the hypomesoendemic setting of Mimika District (Papua, Indonesia). Plasmodium falciparum isolates were genotyped at nine microsatellite loci and P. vivax at eight loci. Measures of diversity and differentiation were used to compare different patient and parasitological sample groups. The results demonstrated that passively detected cases (symptomatic) had comparable population diversity to those circulating in the community (asymptomatic) in both species. In addition, asymptomatic patent infections were as diverse as subpatent infections. However, a significant difference in multiplicity of infection (MOI) and percentage of polyclonal infections was observed between actively and passively detected P. vivax cases (mean MOI: 1.7 ± 0.7 versus 1.4 ± 1.4, respectively; P = 0.001). The study findings infer that, in hypomesoendemic settings, passive sampling is appropriate for molecular parasite surveillance strategies using the predominant clone in any given infection; however, the findings suggest caution when analyzing complexity of infection. Further evaluation is required in other endemic settings.
Collapse
Affiliation(s)
- Zuleima Pava
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Irene Handayuni
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Leily Trianty
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | | | | | | | - Faustina Burdam
- Mimika District Health Authority, Timika, Papua, Indonesia;,Timika Malaria Research Programme, Papuan Health and Community Development Foundation, Timika, Papua, Indonesia;,Maternal and Child Health and Reproductive Health, Department of Public Health, Faculty of Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Enny Kenangalem
- Mimika District Health Authority, Timika, Papua, Indonesia;,Timika Malaria Research Programme, Papuan Health and Community Development Foundation, Timika, Papua, Indonesia
| | - Grennady Wirjanata
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Steven Kho
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | | | - Nicholas Anstey
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Jeanne Rini Poespoprodjo
- Mimika District Health Authority, Timika, Papua, Indonesia;,Timika Malaria Research Programme, Papuan Health and Community Development Foundation, Timika, Papua, Indonesia;,Maternal and Child Health and Reproductive Health, Department of Public Health, Faculty of Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | | | - Ric N. Price
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia;,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Jutta Marfurt
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia;,Address correspondence to Sarah Auburn, Menzies School of Health Research, PO Box 41096, Casuarina, Darwin, NT 0811, Australia. E-mail:
| |
Collapse
|
11
|
Nationwide genetic surveillance of Plasmodium vivax in Papua New Guinea reveals heterogeneous transmission dynamics and routes of migration amongst subdivided populations. INFECTION GENETICS AND EVOLUTION 2017; 58:83-95. [PMID: 29313805 DOI: 10.1016/j.meegid.2017.11.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/27/2017] [Accepted: 11/30/2017] [Indexed: 11/20/2022]
Abstract
The Asia Pacific Leaders in Malaria Alliance (APLMA) have committed to eliminate malaria from the region by 2030. Papua New Guinea (PNG) has the highest malaria burden in the Asia-Pacific region but with the intensification of control efforts since 2005, transmission has been dramatically reduced and Plasmodium vivax is now the dominant malaria infection in some parts of the country. To gain a better understanding of the transmission dynamics and migration patterns of P. vivax in PNG, here we investigate population structure in eight geographically and ecologically distinct regions of the country. A total of 219 P. vivax isolates (16-30 per population) were successfully haplotyped using 10 microsatellite markers. A wide range of genetic diversity (He=0.37-0.87, Rs=3.60-7.58) and significant multilocus linkage disequilibrium (LD) was observed in six of the eight populations (IAS=0.08-0.15 p-value<0.05) reflecting a spectrum of transmission intensities across the country. Genetic differentiation between regions was evident (Jost's D=0.07-0.72), with increasing divergence of populations with geographic distance. Overall, P. vivax isolates clustered into three major genetic populations subdividing the Mainland lowland and coastal regions, the Islands and the Highlands. P. vivax gene flow follows major human migration routes, and there was higher gene flow amongst Mainland parasite populations than among Island populations. The Central Province (samples collected in villages close to the capital city, Port Moresby), acts as a sink for imported infections from the three major endemic areas. These insights into P. vivax transmission dynamics and population networks will inform targeted strategies to contain malaria infections and to prevent the spread of drug resistance in PNG.
Collapse
|
12
|
Malaria Epidemiology at the Clone Level. Trends Parasitol 2017; 33:974-985. [PMID: 28966050 DOI: 10.1016/j.pt.2017.08.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/14/2017] [Accepted: 08/30/2017] [Indexed: 01/08/2023]
Abstract
Genotyping to distinguish between parasite clones is nowadays a standard in many molecular epidemiological studies of malaria. It has become crucial in drug trials and to follow individual clones in epidemiological studies, and to understand how drug resistance emerges and spreads. Here, we review the applications of the increasingly available genotyping tools and whole-genome sequencing data, and argue for a better integration of population genetics findings into malaria-control strategies.
Collapse
|