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da Silva C, Boene S, Datta D, Rovira-Vallbona E, Aranda-Díaz A, Cisteró P, Hathaway N, Tessema S, Chidimatembue A, Matambisso G, Nhama A, Macete E, Pujol A, Nhamussua L, Galatas B, Guinovart C, Enosse S, De Carvalho E, Rogier E, Plucinski MM, Colborn J, Zulliger R, Saifodine A, Alonso PL, Candrinho B, Greenhouse B, Aide P, Saute F, Mayor A. Targeted and whole-genome sequencing reveal a north-south divide in P. falciparum drug resistance markers and genetic structure in Mozambique. Commun Biol 2023; 6:619. [PMID: 37291425 PMCID: PMC10250372 DOI: 10.1038/s42003-023-04997-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/30/2023] [Indexed: 06/10/2023] Open
Abstract
Mozambique is one of the four African countries which account for over half of all malaria deaths worldwide, yet little is known about the parasite genetic structure in that country. We performed P. falciparum amplicon and whole genome sequencing on 2251 malaria-infected blood samples collected in 2015 and 2018 in seven provinces of Mozambique to genotype antimalarial resistance markers and interrogate parasite population structure using genome-wide microhaplotyes. Here we show that the only resistance-associated markers observed at frequencies above 5% were pfmdr1-184F (59%), pfdhfr-51I/59 R/108 N (99%) and pfdhps-437G/540E (89%). The frequency of pfdhfr/pfdhps quintuple mutants associated with sulfadoxine-pyrimethamine resistance increased from 80% in 2015 to 89% in 2018 (p < 0.001), with a lower expected heterozygosity and higher relatedness of microhaplotypes surrounding pfdhps mutants than wild-type parasites suggestive of recent selection. pfdhfr/pfdhps quintuple mutants also increased from 72% in the north to 95% in the south (2018; p < 0.001). This resistance gradient was accompanied by a concentration of mutations at pfdhps-436 (17%) in the north, a south-to-north increase in the genetic complexity of P. falciparum infections (p = 0.001) and a microhaplotype signature of regional differentiation. The parasite population structure identified here offers insights to guide antimalarial interventions and epidemiological surveys.
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Affiliation(s)
- Clemente da Silva
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Simone Boene
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Debayan Datta
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | | | - Andrés Aranda-Díaz
- EPPIcenter Research Program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Pau Cisteró
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | | | - Sofonias Tessema
- EPPIcenter Research Program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | | | - Glória Matambisso
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Abel Nhama
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Instituto Nacional de Saúde (INS), Ministério da Saúde, Maputo, Mozambique
| | - Eusebio Macete
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Arnau Pujol
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Lidia Nhamussua
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Beatriz Galatas
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | | | - Sónia Enosse
- Instituto Nacional de Saúde (INS), Ministério da Saúde, Maputo, Mozambique
| | - Eva De Carvalho
- World Health Organization, WHO Country Office Maputo, Maputo, Mozambique
| | - Eric Rogier
- Malaria Branch, Division of Parasitic Diseases and Malaria, United States Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mateusz M Plucinski
- United States President's Malaria Initiative, Malaria Branch, Division of Parasitic Diseases and Malaria, United States Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - James Colborn
- Clinton Health Access Initiative, Maputo, Mozambique
| | - Rose Zulliger
- U.S. President's Malaria Initiative, USAID, Washington, DC, USA
| | | | - Pedro L Alonso
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Hospital Clinic-Universitat de Barcelona, Barcelona, Spain
| | - Baltazar Candrinho
- National Malaria Control Programme, Ministry of Health, Maputo, Mozambique
| | - Bryan Greenhouse
- EPPIcenter Research Program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Pedro Aide
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Instituto Nacional de Saúde (INS), Ministério da Saúde, Maputo, Mozambique
| | - Francisco Saute
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Alfredo Mayor
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique.
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.
- Spanish Consortium for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain.
- Department of Physiologic Sciences, Faculty of Medicine, Universidade Eduardo Mondlane, Maputo, Mozambique.
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Paschalidis A, Watson OJ, Aydemir O, Verity R, Bailey JA. coiaf: Directly estimating complexity of infection with allele frequencies. PLoS Comput Biol 2023; 19:e1010247. [PMID: 37294835 PMCID: PMC10310041 DOI: 10.1371/journal.pcbi.1010247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/29/2023] [Accepted: 05/01/2023] [Indexed: 06/11/2023] Open
Abstract
In malaria, individuals are often infected with different parasite strains. The complexity of infection (COI) is defined as the number of genetically distinct parasite strains in an individual. Changes in the mean COI in a population have been shown to be informative of changes in transmission intensity with a number of probabilistic likelihood and Bayesian models now developed to estimate the COI. However, rapid, direct measures based on heterozygosity or FwS do not properly represent the COI. In this work, we present two new methods that use easily calculated measures to directly estimate the COI from allele frequency data. Using a simulation framework, we show that our methods are computationally efficient and comparably accurate to current approaches in the literature. Through a sensitivity analysis, we characterize how the distribution of parasite densities, the assumed sequencing depth, and the number of sampled loci impact the bias and accuracy of our two methods. Using our developed methods, we further estimate the COI globally from Plasmodium falciparum sequencing data and compare the results against the literature. We show significant differences in the estimated COI globally between continents and a weak relationship between malaria prevalence and COI.
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Affiliation(s)
- Aris Paschalidis
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, United States of America
| | - Oliver J. Watson
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, United States of America
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Ozkan Aydemir
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, United States of America
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Robert Verity
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Jeffrey A. Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, United States of America
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3
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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.
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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
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Angeli A, Del Prete S, Alasmary FAS, Alqahtani LS, AlOthman Z, Donald WA, Capasso C, Supuran CT. The first activation studies of the η-carbonic anhydrase from the malaria parasite Plasmodium falciparum with amines and amino acids. Bioorg Chem 2018; 80:94-98. [PMID: 29894892 DOI: 10.1016/j.bioorg.2018.06.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/30/2018] [Accepted: 06/01/2018] [Indexed: 02/06/2023]
Abstract
The first activation study of a η-class carbonic anhydrase (CAs, EC 4.2.1.1) is reported. A panel of 24 natural and non-natural amino acids and amines was used to explore the activation profile of Plasmodium falciparum CA (PfACA). The most effective activators belonged to the amino acid chemotype, with d-Glu, l-Asp, l-/d-Phe and l-/d-DOPA possessing activation constant in the range of 82 nM-0.75 µM, whereas l-/d-His, l-Tyr, 4-amino-l-Phe and l-Gln were slightly less effective (KA in the range of 1.00-2.51 µM. The only amine with submicromolar activating properties was 1-(2-aminoethyl-piperazine) with a KA of 0.71 µM, whereas histamine, dopamine and serotonin showed KA ranging between 7.18 and 9.97 µM. As CA activators have scarcely been investigated for their interaction with protozoan CAs, this study may be relevant for an improved understanding of the role of this enzyme in the life cycle of the malaria producing organisms belonging to the genus Plasmodium.
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Affiliation(s)
- Andrea Angeli
- Università degli Studi di Firenze, Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Sonia Del Prete
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Fatmah A S Alasmary
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Linah S Alqahtani
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; Department of Chemistry, King Faisal University, Alahsa, Saudi Arabia
| | - Zeid AlOthman
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - William A Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Clemente Capasso
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 111, 80131 Napoli, Italy.
| | - Claudiu T Supuran
- Università degli Studi di Firenze, Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy; Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia.
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