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Fola AA, He Q, Xie S, Thimmapuram J, Bhide KP, Dorman J, Ciubotariu II, Mwenda MC, Mambwe B, Mulube C, Hawela M, Norris DE, Moss WJ, Bridges DJ, Carpi G. Genomics reveals heterogeneous Plasmodium falciparum transmission and selection signals in Zambia. Commun Med (Lond) 2024; 4:67. [PMID: 38582941 PMCID: PMC10998850 DOI: 10.1038/s43856-024-00498-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 03/28/2024] [Indexed: 04/08/2024] Open
Abstract
BACKGROUND Genomic surveillance is crucial for monitoring malaria transmission and understanding parasite adaptation to interventions. Zambia lacks prior nationwide efforts in malaria genomic surveillance among African countries. METHODS We conducted genomic surveillance of Plasmodium falciparum parasites from the 2018 Malaria Indicator Survey in Zambia, a nationally representative household survey of children under five years of age. We whole-genome sequenced and analyzed 241 P. falciparum genomes from regions with varying levels of malaria transmission across Zambia and estimated genetic metrics that are informative about transmission intensity, genetic relatedness between parasites, and selection. RESULTS We provide genomic evidence of widespread within-host polygenomic infections, regardless of epidemiological characteristics, underscoring the extensive and ongoing endemic malaria transmission in Zambia. Our analysis reveals country-level clustering of parasites from Zambia and neighboring regions, with distinct separation in West Africa. Within Zambia, identity by descent (IBD) relatedness analysis uncovers local spatial clustering and rare cases of long-distance sharing of closely related parasite pairs. Genomic regions with large shared IBD segments and strong positive selection signatures implicate genes involved in sulfadoxine-pyrimethamine and artemisinin combination therapies drug resistance, but no signature related to chloroquine resistance. Furthermore, differences in selection signatures, including drug resistance loci, are observed between eastern and western Zambian parasite populations, suggesting variable transmission intensity and ongoing drug pressure. CONCLUSIONS Our findings enhance our understanding of nationwide P. falciparum transmission in Zambia, establishing a baseline for analyzing parasite genetic metrics as they vary over time and space. These insights highlight the urgency of strengthening malaria control programs and surveillance of antimalarial drug resistance.
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Affiliation(s)
- Abebe A Fola
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Qixin He
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Shaojun Xie
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jyothi Thimmapuram
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Ketaki P Bhide
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jack Dorman
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Ilinca I Ciubotariu
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Mulenga C Mwenda
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Brenda Mambwe
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Conceptor Mulube
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Moonga Hawela
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Douglas E Norris
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - William J Moss
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Purdue Institute for Inflammation, Immunology, & Infectious Disease, Purdue University, West Lafayette, IN, USA.
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Heilmann E, Tembo T, Fwoloshi S, Kabamba B, Chilambe F, Kalenga K, Siwingwa M, Mulube C, Seffren V, Bolton-Moore C, Simwanza J, Yingst S, Yadav R, Rogier E, Auld AF, Agolory S, Kapina M, Gutman JR, Savory T, Kangale C, Mulenga LB, Sikazwe I, Hines JZ. Trends in SARS-CoV-2 seroprevalence among pregnant women attending first antenatal care visits in Zambia: A repeated cross-sectional survey, 2021-2022. PLOS Glob Public Health 2024; 4:e0003073. [PMID: 38568905 PMCID: PMC10990173 DOI: 10.1371/journal.pgph.0003073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/11/2024] [Indexed: 04/05/2024]
Abstract
SARS-CoV-2 serosurveys help estimate the extent of transmission and guide the allocation of COVID-19 vaccines. We measured SARS-CoV-2 seroprevalence among women attending ANC clinics to assess exposure trends over time in Zambia. We conducted repeated cross-sectional SARS-CoV-2 seroprevalence surveys among pregnant women aged 15-49 years attending their first ANC visits in four districts of Zambia (two urban and two rural) during September 2021-September 2022. Serologic testing was done using a multiplex bead assay which detects IgG antibodies to the nucleocapsid protein and the spike protein receptor-binding domain (RBD). We calculated monthly SARS-CoV-2 seroprevalence by district. We also categorized seropositive results as infection alone, infection and vaccination, or vaccination alone based on anti-RBD and anti-nucleocapsid test results and self-reported COVID-19 vaccination status (vaccinated was having received ≥1 dose). Among 8,304 participants, 5,296 (63.8%) were cumulatively seropositive for SARS-CoV-2 antibodies from September 2021 through September 2022. SARS-CoV-2 seroprevalence primarily increased from September 2021 to September 2022 in three districts (Lusaka: 61.8-100.0%, Chongwe: 39.6-94.7%, Chipata: 56.5-95.0%), but in Chadiza, seroprevalence increased from 27.8% in September 2021 to 77.2% in April 2022 before gradually dropping to 56.6% in July 2022. Among 5,906 participants with a valid COVID-19 vaccination status, infection alone accounted for antibody responses in 77.7% (4,590) of participants. Most women attending ANC had evidence of prior SARS-CoV-2 infection and most SARS-CoV-2 seropositivity was infection-induced. Capturing COVID-19 vaccination status and using a multiplex bead assay with anti-nucleocapsid and anti-RBD targets facilitated distinguishing infection-induced versus vaccine-induced antibody responses during a period of increasing COVID-19 vaccine coverage in Zambia. Declining seroprevalence in Chadiza may indicate waning antibodies and a need for booster vaccines. ANC clinics have a potential role in ongoing SARS-CoV-2 serosurveillance and can continue to provide insights into SARS-CoV-2 antibody dynamics to inform near real-time public health responses.
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Affiliation(s)
- Elizabeth Heilmann
- Public Health Institute, Oakland, California, United States of America
- Division of Global HIV and Tuberculosis, U.S. Centers for Disease Control and Prevention, Lusaka, Zambia
| | - Tannia Tembo
- Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Sombo Fwoloshi
- Division of Infectious Diseases, Ministry of Health, Lusaka, Zambia
| | | | - Felix Chilambe
- Adult Centre of Excellence, University Teaching Hospital, Lusaka, Zambia
| | - Kalubi Kalenga
- Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Mpanji Siwingwa
- Adult Centre of Excellence, University Teaching Hospital, Lusaka, Zambia
| | | | - Victoria Seffren
- Division of Parasitic Diseases and Malaria, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | | | - John Simwanza
- Surveillance and Disease Intelligence, Zambia National Public Health Institute, Lusaka, Zambia
| | - Samuel Yingst
- Division of Global HIV and Tuberculosis, U.S. Centers for Disease Control and Prevention, Lusaka, Zambia
| | - Ruchi Yadav
- Division of Parasitic Diseases and Malaria, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Eric Rogier
- Division of Parasitic Diseases and Malaria, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Andrew F. Auld
- Division of Global HIV and Tuberculosis, U.S. Centers for Disease Control and Prevention, Lusaka, Zambia
| | - Simon Agolory
- Division of Global HIV and Tuberculosis, U.S. Centers for Disease Control and Prevention, Lusaka, Zambia
| | - Muzala Kapina
- Surveillance and Disease Intelligence, Zambia National Public Health Institute, Lusaka, Zambia
| | - Julie R. Gutman
- Division of Parasitic Diseases and Malaria, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Theodora Savory
- Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | | | - Lloyd B. Mulenga
- Division of Infectious Diseases, Ministry of Health, Lusaka, Zambia
| | - Izukanji Sikazwe
- Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Jonas Z. Hines
- Division of Global HIV and Tuberculosis, U.S. Centers for Disease Control and Prevention, Lusaka, Zambia
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3
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Fola AA, He Q, Xie S, Thimmapuram J, Bhide KP, Dorman J, Ciubotariu II, Mwenda MC, Mambwe B, Mulube C, Hawela M, Norris DE, Moss WJ, Bridges DJ, Carpi G. Genomics reveals heterogeneous Plasmodium falciparum transmission and population differentiation in Zambia and bordering countries. medRxiv 2024:2024.02.09.24302570. [PMID: 38370674 PMCID: PMC10871455 DOI: 10.1101/2024.02.09.24302570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Genomic surveillance plays a critical role in monitoring malaria transmission and understanding how the parasite adapts in response to interventions. We conducted genomic surveillance of malaria by sequencing 241 Plasmodium falciparum genomes from regions with varying levels of malaria transmission across Zambia. We found genomic evidence of high levels of within-host polygenomic infections, regardless of epidemiological characteristics, underscoring the extensive and ongoing endemic malaria transmission in the country. We identified country-level clustering of parasites from Zambia and neighboring countries, and distinct clustering of parasites from West Africa. Within Zambia, our identity by descent (IBD) relatedness analysis uncovered spatial clustering of closely related parasite pairs at the local level and rare cases of long-distance sharing. Genomic regions with large shared IBD segments and strong positive selection signatures identified genes involved in sulfadoxine-pyrimethamine and artemisinin combination therapies drug resistance, but no signature related to chloroquine resistance. Together, our findings enhance our understanding of P. falciparum transmission nationwide in Zambia and highlight the urgency of strengthening malaria control programs and surveillance of antimalarial drug resistance.
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Affiliation(s)
- Abebe A. Fola
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Qixin He
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Shaojun Xie
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jyothi Thimmapuram
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Ketaki P. Bhide
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jack Dorman
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | | | | | - Brenda Mambwe
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Conceptor Mulube
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Moonga Hawela
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Douglas E. Norris
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - William J. Moss
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Purdue Institute for Inflammation, Immunology, & Infectious Disease, Purdue University, West Lafayette, IN, USA
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4
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Bridges DJ, Miller JM, Chalwe V, Moonga H, Hamainza B, Steketee RW, Mambwe B, Mulube C, Wu L, Tetteh KKA, Drakeley C, Chishimba S, Mwenda M, Silumbe K, Larsen DA. Reactive focal drug administration associated with decreased malaria transmission in an elimination setting: Serological evidence from the cluster-randomized CoRE study. PLOS Glob Public Health 2022; 2:e0001295. [PMID: 36962857 PMCID: PMC10021141 DOI: 10.1371/journal.pgph.0001295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/26/2022] [Indexed: 12/12/2022]
Abstract
Efforts to eliminate malaria transmission need evidence-based strategies. However, accurately assessing end-game malaria elimination strategies is challenging due to the low level of transmission and the rarity of infections. We hypothesised that presumptively treating individuals during reactive case detection (RCD) would reduce transmission and that serology would more sensitively detect this change over standard approaches. We conducted a cluster randomised control trial (NCT02654912) of presumptive reactive focal drug administration (RFDA-intervention) compared to the standard of care, reactive focal test and treat (RFTAT-control) in Southern Province, Zambia-an area of low seasonal transmission (overall incidence of ~3 per 1,000). We measured routine malaria incidence from health facilities as well as PCR parasite prevalence / antimalarial seroprevalence in an endline cross-sectional population survey. No significant difference was identified from routine incidence data and endline prevalence by polymerase chain reaction (PCR) had insufficient numbers of malaria infections (i.e., 16 infections among 6,276 children) to assess the intervention. Comparing long-term serological markers, we found a 19% (95% CI = 4-32%) reduction in seropositivity for the RFDA intervention using a difference in differences approach incorporating serological positivity and age. We also found a 37% (95% CI = 2-59%) reduction in seropositivity to short-term serological markers in a post-only comparison. These serological analyses provide compelling evidence that RFDA both has an impact on malaria transmission and is an appropriate end-game malaria elimination strategy. Furthermore, serology provides a more sensitive approach to measure changes in transmission that other approaches miss, particularly in very low transmission settings. Trial Registration: Registered at www.clinicaltrials.gov (NCT02654912, 13/1/2016).
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Affiliation(s)
- Daniel J Bridges
- PATH-Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Chainama Hospital College Grounds, Lusaka, Zambia
| | - John M Miller
- PATH-Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Chainama Hospital College Grounds, Lusaka, Zambia
| | - Victor Chalwe
- National Health Research Authority, Paediatric Centre of Excellence, University Teaching Hospital, Lusaka, Zambia
| | - Hawela Moonga
- National Malaria Elimination Centre, Zambia Ministry of Health, Chainama Hospital, Lusaka, Zambia
| | - Busiku Hamainza
- National Malaria Elimination Centre, Zambia Ministry of Health, Chainama Hospital, Lusaka, Zambia
| | - Richard W Steketee
- PATH-Malaria Control and Elimination Partnership in Africa (MACEPA), Seattle, Washington, United States of America
| | - Brenda Mambwe
- PATH-Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Chainama Hospital College Grounds, Lusaka, Zambia
| | - Conceptor Mulube
- PATH-Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Chainama Hospital College Grounds, Lusaka, Zambia
| | - Lindsey Wu
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Kevin K A Tetteh
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Chris Drakeley
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sandra Chishimba
- PATH-Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Chainama Hospital College Grounds, Lusaka, Zambia
| | - Mulenga Mwenda
- PATH-Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Chainama Hospital College Grounds, Lusaka, Zambia
| | - Kafula Silumbe
- PATH-Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Chainama Hospital College Grounds, Lusaka, Zambia
| | - David A Larsen
- Syracuse University Department of Public Health, Syracuse, New York, United States of America
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5
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Mwenda MC, Fola AA, Ciubotariu II, Mulube C, Mambwe B, Kasaro R, Hawela MB, Hamainza B, Miller JM, Carpi G, Bridges DJ. Performance evaluation of RDT, light microscopy, and PET-PCR for detecting Plasmodium falciparum malaria infections in the 2018 Zambia National Malaria Indicator Survey. Malar J 2021; 20:386. [PMID: 34583692 PMCID: PMC8477358 DOI: 10.1186/s12936-021-03917-6] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 09/14/2021] [Indexed: 11/29/2022] Open
Abstract
Background Zambia continues to advance on the path to elimination with significant reductions in malaria morbidity and mortality. Crucial components that have contributed to progress thus far and are necessary for achieving the national malaria elimination goals include properly identifying and treating all malaria cases through accurate diagnosis. This study sought to compare and assess the diagnostic performance of Rapid Diagnostic Tests (RDT) and Light Microscopy (LM) with photo-induced electron transfer polymerase chain reaction (PET-PCR) as the gold standard using 2018 Malaria Indicator Survey (MIS) data across Zambia to better understand diagnostic accuracy metrics and how these vary across a transmission gradient. Methods Cross-sectional samples collected in a nationally representative survey from 7 provinces in Zambia were tested for the presence of malaria parasites by light microscopy (LM), rapid diagnostic test (RDT) and the gold standard PET-PCR. Diagnostic performance was assessed including sensitivity, specificity, negative- and positive-predictive values across a wide malaria transmission spectrum. Diagnostic accuracy metrics were measured, and statistically significant differences were calculated between test methods for different outcome variables. Results From the individuals included in the MIS, the overall prevalence of Plasmodium falciparum malaria was 32.9% by RDT, 19.4% by LM, and 23.2% by PET-PCR. Herein, RDT and LM diagnostic performance was compared against gold standard PET-PCR with LM displaying a higher diagnostic accuracy than RDTs (91.3% vs. 84.6% respectively) across the transmission spectrum in Zambia. However, the performance of both diagnostics was significantly reduced in low parasitaemia samples. Consistent with previous studies, RDT diagnostic accuracy was predominantly affected by a high rate of false positives. Conclusions RDTs and LM both perform well across a range of transmission intensities within their respective target applications, i.e., in the community, for the former, where ease of use and speed of result is critical, and at the health facility, for the latter, where accuracy is prioritized. However, the performance of both diagnostic methods is adversely affected by low parasitaemia infections. As Zambia moves towards elimination more sensitive tools may be required to identify the last cases. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-021-03917-6.
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Affiliation(s)
- Mulenga C Mwenda
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Ministry of Health, Chainama Grounds, Lusaka, Zambia
| | - Abebe A Fola
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Ilinca I Ciubotariu
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Conceptor Mulube
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Ministry of Health, Chainama Grounds, Lusaka, Zambia
| | - Brenda Mambwe
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Ministry of Health, Chainama Grounds, Lusaka, Zambia
| | - Rachael Kasaro
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Ministry of Health, Chainama Grounds, Lusaka, Zambia
| | - Moonga B Hawela
- National Malaria Elimination Centre, Ministry of Health, Chainama Hospital and College Grounds, Lusaka, Zambia
| | - Busiku Hamainza
- National Malaria Elimination Centre, Ministry of Health, Chainama Hospital and College Grounds, Lusaka, Zambia
| | - John M Miller
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Ministry of Health, Chainama Grounds, Lusaka, Zambia
| | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.,Purdue Institute of Inflammation, Immunology and Infectious Disease, Indiana, USA
| | - Daniel J Bridges
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Ministry of Health, Chainama Grounds, Lusaka, Zambia.
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6
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Daniels RF, Schaffner SF, Bennett A, Porter TR, Yukich JO, Mulube C, Mambwe B, Mwenda MC, Chishimba S, Bridges DJ, Moonga H, Hamainza B, Chizema Kawesha E, Miller JM, Steketee RW, Wirth DF, Eisele TP, Hartl DL, Volkman SK. Evidence for Reduced Malaria Parasite Population after Application of Population-Level Antimalarial Drug Strategies in Southern Province, Zambia. Am J Trop Med Hyg 2020; 103:66-73. [PMID: 32618255 PMCID: PMC7416975 DOI: 10.4269/ajtmh.19-0666] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A mass drug administration trial was carried out in Southern Province, Zambia, between 2014 and 2016, in conjunction with a standard of care package that included improved surveillance, increased access to malaria case management, and sustained high levels of vector control coverage. This was preceded by mass test and treatment in the same area from 2011 to 2013. Concordant decreases in malaria prevalence in Southern Province and deaths attributed to malaria in Zambia over this time suggest that these strategies successfully reduced the malaria burden. Genetic epidemiological studies were used to assess the consequences of these interventions on parasite population structure. Analysis of parasite material derived from 1,620 rapid diagnostic test (RDT)-positive individuals obtained from studies to evaluate trial outcomes revealed a reduction in the average complexity of infection and consequential increase in the proportion of infections that harbored a single parasite genome (monogenomic infections). Highly related parasites, consistent with inbreeding, were detected after interventions were deployed. Geographical analysis indicated that the highly related infections were both clustered focally and dispersed across the study area. These findings provide genetic evidence for a reduced parasite population, with indications of inbreeding following the application of comprehensive interventions, including drug-based campaigns, that reduced the malaria burden in Southern Province. Genetic data additionally revealed the relationship between individual infections in the context of these population-level patterns, which has the potential to provide useful data for stratification and targeting of interventions to reduce the malaria burden.
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Affiliation(s)
- Rachel F Daniels
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Stephen F Schaffner
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Adam Bennett
- Malaria Elimination Initiative, Global Health Group, University of California San Francisco, San Francisco, California
| | - Travis R Porter
- Center for Applied Malaria Research and Evaluation, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana
| | - Joshua O Yukich
- Center for Applied Malaria Research and Evaluation, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana
| | - Conceptor Mulube
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
| | - Brenda Mambwe
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
| | - Mulenga C Mwenda
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
| | - Sandra Chishimba
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
| | - Daniel J Bridges
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
| | - Hawela Moonga
- National Malaria Elimination Centre, Zambia Ministry of Health, Lusaka, Zambia
| | - Busiku Hamainza
- National Malaria Elimination Centre, Zambia Ministry of Health, Lusaka, Zambia
| | | | - John M Miller
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
| | | | - Dyann F Wirth
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Thomas P Eisele
- Center for Applied Malaria Research and Evaluation, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana
| | - Daniel L Hartl
- Harvard University, Cambridge, Massachusetts.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Sarah K Volkman
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Simmons University, Boston, Massachusetts
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7
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Bennett A, Porter TR, Mwenda MC, Yukich JO, Finn TP, Lungu C, Silumbe K, Mambwe B, Chishimba S, Mulube C, Bridges DJ, Hamainza B, Slutsker L, Steketee RW, Miller JM, Eisele TP. A Longitudinal Cohort to Monitor Malaria Infection Incidence during Mass Drug Administration in Southern Province, Zambia. Am J Trop Med Hyg 2020; 103:54-65. [PMID: 32618245 PMCID: PMC7416973 DOI: 10.4269/ajtmh.19-0657] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Rigorous evidence of effectiveness is needed to determine where and when to apply mass drug administration (MDA) or focal MDA (fMDA) as part of a malaria elimination strategy. The Zambia National Malaria Elimination Centre recently completed a community-randomized controlled trial in Southern Province to evaluate MDA and fMDA for transmission reduction. To assess the role of MDA and fMDA on infection incidence, we enrolled a longitudinal cohort for an 18-month period of data collection including monthly malaria parasite infection detection based on polymerase chain reaction and compared time to first infection and cumulative infection incidence outcomes across study arms using Cox proportional hazards and negative binomial models. A total of 2,026 individuals from 733 households were enrolled and completed sufficient follow-up for inclusion in analysis. Infection incidence declined dramatically across all study arms during the period of study, and MDA was associated with reduced risk of first infection (hazards ratio: 0.36; 95% CI: 0.16–0.80) and cumulative infection incidence during the first rainy season (first 5 months of follow-up) (incidence rate ratio: 0.34; 95% CI: 0.12–0.95). No significant effect was found for fMDA or for either arm over the full study period. Polymerase chain reaction infection status at baseline was strongly associated with follow-up infection. The short-term effects of MDA suggest it may be an impactful accelerator of transmission reduction in areas with high coverage of case management and vector control and should be considered as part of a malaria elimination strategy.
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Affiliation(s)
- Adam Bennett
- Malaria Elimination Initiative, Global Health Group, University of California San Francisco, San Francisco, California
| | - Travis R Porter
- Department of Tropical Medicine, Center for Applied Malaria Research and Evaluation, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana
| | - Mulenga C Mwenda
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
| | - Joshua O Yukich
- Department of Tropical Medicine, Center for Applied Malaria Research and Evaluation, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana
| | - Timothy P Finn
- Department of Tropical Medicine, Center for Applied Malaria Research and Evaluation, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana
| | - Chris Lungu
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
| | - Kafula Silumbe
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
| | - Brenda Mambwe
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
| | - Sandra Chishimba
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
| | - Conceptor Mulube
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
| | - Daniel J Bridges
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
| | - Busiku Hamainza
- National Malaria Elimination Centre, Zambia Ministry of Health, Lusaka, Zambia
| | | | | | - John M Miller
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
| | - Thomas P Eisele
- Department of Tropical Medicine, Center for Applied Malaria Research and Evaluation, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana
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8
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Chishimba S, Mwenda M, Mambwe B, Mulube C, Chalwe V, Moonga H, Hamainza B, Chizema-Kawesha E, Steketee RW, Domingo G, Fraser M, Kahn M, Pal S, Silumbe K, Conner RO, Bennett A, Porter TR, Eisele TP, Miller JM, Bridges DJ. Prevalence of Plasmodium falciparum and Non- falciparum Infections by Photo-Induced Electron Transfer-PCR in a Longitudinal Cohort of Individuals Enrolled in a Mass Drug Administration Trial in Southern Province, Zambia. Am J Trop Med Hyg 2020; 103:82-89. [PMID: 32618252 PMCID: PMC7416980 DOI: 10.4269/ajtmh.19-0668] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Malaria burden in Zambia has significantly declined over the last decade because of improved coverage of several key malaria interventions (e.g., vector control, case management, bed net distributions, and enhanced surveillance/responses). Campaign-based mass drug administration (MDA) and focal MDA (fMDA) were assessed in a trial in Southern Province, Zambia, to identify its utility in elimination efforts. As part of the study, a longitudinal cohort was visited and tested (by PCR targeting the 18s rRNA and a Plasmodium falciparum–specific rapid diagnostic test [RDT] from SD Bioline) every month for the trial duration (18 months). Overall, there was high concordance (> 97%) between the PCR and RDT results, using the PCR as the gold standard. The RDTs had high specificity and negative predictive values (98.5% and 98.6%, respectively) but low sensitivity (53.0%) and a low positive predictive value (53.8%). There was evidence for persistent antigenemia affecting the low specificity of the RDT, while false-negative RDTs were associated with a lower parasite density than true positive RDTs. Plasmodium falciparum was the dominant species identified, with 98.3% of all positive samples containing P. falciparum. Of these, 97.5% were mono-infections and 0.8% coinfections with one other species. Plasmodium malariae was found in 1.4% of all positive samples (50% mono-infections and 50% coinfections with P. falciparum), whereas Plasmodium ovale was found in 1.1% of all positive samples (90% mono-infections and 10% coinfections with P. falciparum). Although MDA/fMDA appeared to reduce P. malariae prevalence, P. ovale prevalence appeared unchanged.
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Affiliation(s)
- Sandra Chishimba
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
| | - Mulenga Mwenda
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
| | - Brenda Mambwe
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
| | - Conceptor Mulube
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
| | - Victor Chalwe
- Zambia Ministry of Health Provincial Medical Office, Mansa, Zambia
| | - Hawela Moonga
- National Malaria Elimination Centre, Zambia Ministry of Health, Lusaka, Zambia
| | - Busiku Hamainza
- National Malaria Elimination Centre, Zambia Ministry of Health, Lusaka, Zambia
| | | | - Richard W Steketee
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Seattle, Washington
| | - Gonzalo Domingo
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Seattle, Washington
| | - Maya Fraser
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Seattle, Washington
| | - Maria Kahn
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Seattle, Washington
| | - Sampa Pal
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Seattle, Washington
| | - Kafula Silumbe
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
| | - Ruben O Conner
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Seattle, Washington
| | - Adam Bennett
- Malaria Elimination Initiative, Global Health Group, University of California San Francisco, San Francisco, California
| | - Travis R Porter
- Department of Tropical Medicine, Center for Applied Malaria Research and Evaluation, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana
| | - Thomas P Eisele
- Department of Tropical Medicine, Center for Applied Malaria Research and Evaluation, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana
| | - John M Miller
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
| | - Daniel J Bridges
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
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9
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Chanda J, Saili K, Phiri F, Stevenson JC, Mwenda M, Chishimba S, Mulube C, Mambwe B, Lungu C, Earle D, Bennett A, Eisele TP, Kamuliwo M, Steketee RW, Keating J, Miller JM, Sikaala CH. Pyrethroid and Carbamate Resistance in Anopheles funestus Giles along Lake Kariba in Southern Zambia. Am J Trop Med Hyg 2020; 103:90-97. [PMID: 32618244 PMCID: PMC7416976 DOI: 10.4269/ajtmh.19-0664] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Whereas data on insecticide resistance and its underlying mechanisms exist for parts of Zambia, data remain limited in the southern part of the country. This study investigated the status of insecticide resistance, metabolic mechanisms, and parasite infection in Anopheles funestus along Lake Kariba in southern Zambia. Indoor-resting mosquitoes were collected from 20 randomly selected houses within clusters where a mass drug administration trial was conducted and raised to F1 progeny. Non–blood-fed 2- to 5-day-old female An. funestus were exposed to WHO insecticide-impregnated papers with 0.05% deltamethrin, 0.1% bendiocarb, 0.25% pirimiphos-methyl, or 4% dichloro-diphenyl-trichloroethane (DDT). In separate assays, An. funestus were pre-exposed to piperonyl butoxide (PBO) to determine the presence of monooxygenases. Wild-caught An. funestus that had laid eggs for susceptibility assays were screened for circumsporozoite protein of Plasmodium falciparum by ELISA, and sibling species were identified by polymerase chain reaction. Anopheles funestus showed resistance to deltamethrin and bendiocarb but remained susceptible to pirimiphos-methyl and DDT. The pre-exposure of An. funestus to PBO restored full susceptibility to deltamethrin but not to bendiocarb. The overall sporozoite infection rate in An. funestus populations was 5.8%. Detection of pyrethroid and carbamate resistance in An. funestus calls for increased insecticide resistance monitoring to guide planning and selection of effective insecticide resistance management strategies. To prevent the development of resistance and reduce the underlying vectorial capacity of mosquitoes in areas targeted for malaria elimination, an effective integrated vector management strategy is needed.
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Affiliation(s)
- Javan Chanda
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
| | - Kochelani Saili
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
| | - Foustina Phiri
- National Malaria Elimination Centre, Zambia Ministry of Health, Lusaka, Zambia
| | - Jennifer C Stevenson
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Macha Research Trust, Choma, Zambia
| | - Mulenga Mwenda
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
| | - Sandra Chishimba
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
| | - Conceptor Mulube
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
| | - Brenda Mambwe
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
| | - Christopher Lungu
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
| | - Duncan Earle
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
| | - Adam Bennett
- Malaria Elimination Initiative, Global Health Group, University of California San Francisco, San Francisco, California
| | - Thomas P Eisele
- Department of Tropical Medicine, Center for Applied Malaria Research and Evaluation, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana
| | - Mulakwa Kamuliwo
- National Malaria Elimination Centre, Zambia Ministry of Health, Lusaka, Zambia
| | | | - Joseph Keating
- Department of Tropical Medicine, Center for Applied Malaria Research and Evaluation, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana
| | - John M Miller
- PATH Malaria Control and Elimination Partnership in Africa (MACEPA), Lusaka, Zambia
| | - Chadwick H Sikaala
- SADC Malaria Elimination Eight Secretariat, Windhoek, Namibia.,National Malaria Elimination Centre, Zambia Ministry of Health, Lusaka, Zambia
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10
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Bridges DJ, Chishimba S, Mwenda M, Winters AM, Slawsky E, Mambwe B, Mulube C, Searle KM, Hakalima A, Mwenechanya R, Larsen DA. The use of spatial and genetic tools to assess Plasmodium falciparum transmission in Lusaka, Zambia between 2011 and 2015. Malar J 2020; 19:20. [PMID: 31941493 PMCID: PMC6964105 DOI: 10.1186/s12936-020-3101-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 08/07/2019] [Accepted: 01/07/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Zambia has set itself the ambitious target of eliminating malaria by 2021. To continue tracking transmission to zero, new interventions, tools and approaches are required. METHODS Urban reactive case detection (RCD) was performed in Lusaka city from 2011 to 2015 to better understand the location and drivers of malaria transmission. Briefly, index cases were followed to their home and all consenting individuals living in the index house and nine proximal houses were tested with a malaria rapid diagnostic test and treated if positive. A brief survey was performed and for certain responses, a dried blood spot sample collected for genetic analysis. Aggregate health facility data, individual RCD response data and genetic results were analysed spatially and against environmental correlates. RESULTS Total number of malaria cases remained relatively constant, while the average age of incident cases and the proportion of incident cases reporting recent travel both increased. The estimated R0 in Lusaka was < 1 throughout the study period. RCD responses performed within 250 m of uninhabited/vacant land were associated with a higher probability of identifying additional infections. CONCLUSIONS Evidence suggests that the majority of malaria infections are imported from outside Lusaka. However there remains some level of local transmission occurring on the periphery of urban settlements, namely in the wet season. Unfortunately, due to the higher-than-expected complexity of infections and the small number of samples tested, genetic analysis was unable to identify any meaningful trends in the data.
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Affiliation(s)
- Daniel J Bridges
- PATH MACEPA, National Malaria Elimination Centre, Gt East Rd, Lusaka, Zambia. .,Akros, 45A Roan Road, Lusaka, Zambia.
| | - Sandra Chishimba
- PATH MACEPA, National Malaria Elimination Centre, Gt East Rd, Lusaka, Zambia.,Akros, 45A Roan Road, Lusaka, Zambia
| | - Mulenga Mwenda
- PATH MACEPA, National Malaria Elimination Centre, Gt East Rd, Lusaka, Zambia.,Akros, 45A Roan Road, Lusaka, Zambia
| | - Anna M Winters
- Akros, 45A Roan Road, Lusaka, Zambia.,School of Public and Community Health Sciences, University of Montana, Missoula, MT, USA
| | - Erik Slawsky
- Department of Public Health, Syracuse University, Syracuse, NY, USA
| | - Brenda Mambwe
- PATH MACEPA, National Malaria Elimination Centre, Gt East Rd, Lusaka, Zambia
| | - Conceptor Mulube
- PATH MACEPA, National Malaria Elimination Centre, Gt East Rd, Lusaka, Zambia
| | - Kelly M Searle
- School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Aves Hakalima
- Lusaka District Health Management Team, Ministry of Health, Lusaka, Zambia
| | - Roy Mwenechanya
- Akros, 45A Roan Road, Lusaka, Zambia.,Department of Biomedical Sciences, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - David A Larsen
- Akros, 45A Roan Road, Lusaka, Zambia.,Department of Public Health, Syracuse University, Syracuse, NY, USA
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