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Dekaj E, Gjini E. Pneumococcus and the stress-gradient hypothesis: A trade-off links R 0 and susceptibility to co-colonization across countries. Theor Popul Biol 2024; 156:77-92. [PMID: 38331222 DOI: 10.1016/j.tpb.2024.02.001] [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: 05/30/2022] [Revised: 10/06/2023] [Accepted: 02/01/2024] [Indexed: 02/10/2024]
Abstract
Modern molecular technologies have revolutionized our understanding of bacterial epidemiology, but reported data across studies and different geographic endemic settings remain under-integrated in common theoretical frameworks. Pneumococcus serotype co-colonization, caused by the polymorphic bacteria Streptococcus pneumoniae, has been increasingly investigated and reported in recent years. While the global genomic diversity and serotype distribution of S. pneumoniae have been well-characterized, there is limited information on how co-colonization patterns vary globally, critical for understanding the evolution and transmission dynamics of the bacteria. Gathering a rich dataset of cross-sectional pneumococcal colonization studies in the literature, we quantified patterns of transmission intensity and co-colonization prevalence variation in children populations across 17 geographic locations. Linking these data to an SIS model with cocolonization under the assumption of quasi-neutrality among multiple interacting strains, our analysis reveals strong patterns of negative co-variation between transmission intensity (R0) and susceptibility to co-colonization (k). In line with expectations from the stress-gradient-hypothesis in ecology (SGH), pneumococcus serotypes appear to compete more in co-colonization in high-transmission settings and compete less in low-transmission settings, a trade-off which ultimately leads to a conserved ratio of single to co-colonization μ=1/(R0-1)k. From the mathematical model's behavior, such conservation suggests preservation of 'stability-diversity-complexity' regimes in coexistence of similar co-colonizing strains. We find no major differences in serotype compositions across studies, pointing to adaptation of the same set of serotypes across variable environments as an explanation for their differential interaction in different transmission settings. Our work highlights that the understanding of transmission patterns of Streptococcus pneumoniae from global scale epidemiological data can benefit from simple analytical approaches that account for quasi-neutrality among strains, co-colonization, as well as variable environmental adaptation.
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Affiliation(s)
- Ermanda Dekaj
- Center for Computational and Stochastic Mathematics, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Erida Gjini
- Center for Computational and Stochastic Mathematics, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal.
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2
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Nkemngo FN, W G Raissa L, Nebangwa DN, Nkeng AM, Kengne A, Mugenzi LMJ, Fotso-Toguem YG, Wondji MJ, Shey RA, Nguiffo-Nguete D, Fru-Cho J, Ndo C, Njiokou F, Webster JP, Wanji S, Wondji CS. Epidemiology of malaria, schistosomiasis, and geohelminthiasis amongst children 3-15 years of age during the dry season in Northern Cameroon. PLoS One 2023; 18:e0288560. [PMID: 37523402 PMCID: PMC10389741 DOI: 10.1371/journal.pone.0288560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 06/29/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND The double burden of malaria and helminthiasis in children poses an obvious public health challenge, particularly in terms of anemia morbidity. While both diseases frequently geographically overlap, most studies focus on mono-infection and general prevalence surveys without molecular analysis. The current study investigated the epidemiological determinants of malaria, schistosomiasis, and geohelminthiasis transmission among children in the North Region of Cameroon. METHODOLOGY School and pre-school children aged 3-15 year-of-age were enrolled from three communities in March 2021 using a community cross-sectional design. Capillary-blood samples were obtained, and each was examined for malaria parasites using rapid-diagnostic-test (RDT), microscopy, and PCR while hemoglobin level was measured using a hemoglobinometer. Stool samples were analyzed for Schistosoma mansoni, S. guineensis, and soil-transmitted-helminthiasis (STH) infections using the Kato Katz method, and urine samples were assessed for the presence of S. haematobium eggs (including hybrids) using the standard urine filtration technique. RESULT A malaria prevalence of 56% (277/495) was recorded by PCR as opposed to 31.5% (156/495) by microscopy and 37.8% (186/495) by RDT. Similarly, schistosomiasis was observed at prevalence levels of up to 13.3% (66/495) overall [S. haematobium (8.7%); S. mansoni (3.8%); mixed Sh/Sm (0.6%); mixed Sh/Sm/Sg (0.2%). Both infections were higher in males and the 3-9 year-of-age groups. A high frequency of PCR reported P. falciparum mono-infection of 81.9% (227/277) and mixed P. falciparum/P. malariae infection of 17.3% (48/277) was observed. Malaria-helminths co-infections were observed at 13.1% (65/495) with marked variation between P. falciparum/S. haematobium (50.8%, 33/65); P. falciparum/S. mansoni (16.9%, 11/65) and P. falciparum/Ascaris (9.2%, 6/65) (χ2 = 17.5, p = 0.00003). Anemia prevalence was 32.9% (163/495), categorically associated with P. falciparum (45.8%, 104/227), Pf/Sh (11.5%, 26/227), and Pf/Sm (3.9%, 9/227) polyparasitism. CONCLUSION Polyparasitism with malaria and helminth infections is common in school-aged children despite periodic long-lasting insecticide-treated nets (LLINs) distribution and regular school-based praziquantel (for schistosomiasis) and albendazole (for STH) campaigns. Co-existence of Plasmodium parasites and helminths infections notably Schistosoma species among children may concurrently lead to an increase in Plasmodium infection with an enhanced risk of anemia, highlighting the necessity of an integrated approach for disease control interventions.
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Affiliation(s)
- Francis N Nkemngo
- Centre for Research in Infectious Diseases (CRID), Yaoundé, Cameroon
- Department of Microbiology and Parasitology, Faculty of Science, University of Buea, Buea, Cameroon
| | - Lymen W G Raissa
- Centre for Research in Infectious Diseases (CRID), Yaoundé, Cameroon
| | - Derrick N Nebangwa
- Faculty of Life Science and Medicine, King's College London, New Hunt's House, London, United Kingdom
| | - Asongha M Nkeng
- Centre for Infection Biology and Translational Research (CIBiT), Forzi Institute, Buea, Cameroon
- Department of Sociology & Anthropology, Faculty of Social and Management Sciences, University of Buea, Buea, Cameroon
| | - Alvine Kengne
- Department of Animal Biology and Physiology, Parasitology and Ecology Laboratory, Faculty of Science, University of Yaoundé I, Yaoundé, Cameroon
| | - Leon M J Mugenzi
- Centre for Research in Infectious Diseases (CRID), Yaoundé, Cameroon
| | | | - Murielle J Wondji
- Centre for Research in Infectious Diseases (CRID), Yaoundé, Cameroon
- Vector Biology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, United Kingdom
| | - Robert A Shey
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Buea, Buea, Cameroon
| | | | - Jerome Fru-Cho
- Department of Microbiology and Parasitology, Faculty of Science, University of Buea, Buea, Cameroon
- Research Foundation in Tropical Diseases and Environment (REFOTDE), Buea, Cameroon
| | - Cyrille Ndo
- Centre for Research in Infectious Diseases (CRID), Yaoundé, Cameroon
- Department of Biological Sciences, Faculty of Medicine and Pharmaceutical Sciences, University of Douala, Douala, Cameroon
| | - Flobert Njiokou
- Department of Animal Biology and Physiology, Parasitology and Ecology Laboratory, Faculty of Science, University of Yaoundé I, Yaoundé, Cameroon
| | - Joanne P Webster
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, Herts, United Kingdom
| | - Samuel Wanji
- Department of Microbiology and Parasitology, Faculty of Science, University of Buea, Buea, Cameroon
- Research Foundation in Tropical Diseases and Environment (REFOTDE), Buea, Cameroon
| | - Charles S Wondji
- Centre for Research in Infectious Diseases (CRID), Yaoundé, Cameroon
- Vector Biology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, United Kingdom
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3
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Ahmad A, Mohammed NI, Joof F, Affara M, Jawara M, Abubakar I, Okebe J, Ceesay S, Hamid-Adiamoh M, Bradley J, Amambua-Ngwa A, Nwakanma D, D'Alessandro U. Asymptomatic Plasmodium falciparum carriage and clinical disease: a 5-year community-based longitudinal study in The Gambia. Malar J 2023; 22:82. [PMID: 36882754 PMCID: PMC9993664 DOI: 10.1186/s12936-023-04519-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 02/28/2023] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND Carriers of persistent asymptomatic Plasmodium falciparum infections constitute an infectious reservoir that maintains malaria transmission. Understanding the extent of carriage and characteristics of carriers specific to endemic areas could guide use of interventions to reduce infectious reservoir. METHODS In eastern Gambia, an all-age cohort from four villages was followed up from 2012 to 2016. Each year, cross-sectional surveys were conducted at the end of the malaria transmission season (January) and just before the start of the next one (June) to determine asymptomatic P. falciparum carriage. Passive case detection was conducted during each transmission season (August to January) to determine incidence of clinical malaria. Association between carriage at the end of the season and at start of the next one and the risk factors for this were assessed. Effect of carriage before start of the season on risk of clinical malaria during the season was also examined. RESULTS A total of 1403 individuals-1154 from a semi-urban village and 249 from three rural villages were enrolled; median age was 12 years (interquartile range [IQR] 6, 30) and 12 years (IQR 7, 27) respectively. In adjusted analysis, asymptomatic P. falciparum carriage at the end of a transmission season and carriage just before start of the next one were strongly associated (adjusted odds ratio [aOR] = 19.99; 95% CI 12.57-31.77, p < 0.001). The odds of persistent carriage (i.e. infected both in January and in June) were higher in rural villages (aOR = 13.0; 95% CI 6.33-26.88, p < 0.001) and in children aged 5-15 years (aOR = 5.03; 95% CI 2.47-10.23, p = < 0.001). In the rural villages, carriage before start of the season was associated with a lower risk of clinical malaria during the season (incidence risk ratio [IRR] 0.48, 95% CI 0.27-0.81, p = 0.007). CONCLUSIONS Asymptomatic P. falciparum carriage at the end of a transmission season strongly predicted carriage just before start of the next one. Interventions that clear persistent asymptomatic infections when targeted at the subpopulation with high risk of carriage may reduce the infectious reservoir responsible for launching seasonal transmission.
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Affiliation(s)
- Abdullahi Ahmad
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O Box 273, Banjul, The Gambia.
- Global Health Institute, University of Antwerp, Gouverneur Kinsbergencentrum, Campus Drie Eiken, Doornstraat 331, 2610, Wilrijk, Belgium.
| | - Nuredin Ibrahim Mohammed
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O Box 273, Banjul, The Gambia
| | - Fatou Joof
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O Box 273, Banjul, The Gambia
| | - Muna Affara
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O Box 273, Banjul, The Gambia
| | - Musa Jawara
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O Box 273, Banjul, The Gambia
| | - Ismaela Abubakar
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O Box 273, Banjul, The Gambia
| | - Joseph Okebe
- International Public Health Department, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Serign Ceesay
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O Box 273, Banjul, The Gambia
| | - Majidah Hamid-Adiamoh
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O Box 273, Banjul, The Gambia
| | - John Bradley
- MRC International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Alfred Amambua-Ngwa
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O Box 273, Banjul, The Gambia
| | - Davis Nwakanma
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O Box 273, Banjul, The Gambia.
| | - Umberto D'Alessandro
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O Box 273, Banjul, The Gambia
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4
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Opoku Afriyie S, Addison TK, Gebre Y, Mutala AH, Antwi KB, Abbas DA, Addo KA, Tweneboah A, Ayisi-Boateng NK, Koepfli C, Badu K. Accuracy of diagnosis among clinical malaria patients: comparing microscopy, RDT and a highly sensitive quantitative PCR looking at the implications for submicroscopic infections. Malar J 2023; 22:76. [PMID: 36870966 PMCID: PMC9985253 DOI: 10.1186/s12936-023-04506-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 02/18/2023] [Indexed: 03/06/2023] Open
Abstract
BACKGROUND The World Health Organization recommends parasitological confirmation of all suspected malaria cases by microscopy or rapid diagnostic tests (RDTs) before treatment. These conventional tools are widely used for point-of-care diagnosis in spite of their poor sensitivity at low parasite density. Previous studies in Ghana have compared microscopy and RDT using standard 18S rRNA PCR as reference with varying outcomes. However, how these conventional tools compare with ultrasensitive varATS qPCR has not been studied. This study, therefore, sought to investigate the clinical performance of microscopy and RDT assuming highly sensitive varATS qPCR as gold standard. METHODS 1040 suspected malaria patients were recruited from two primary health care centers in the Ashanti Region of Ghana and tested for malaria by microscopy, RDT, and varATS qPCR. The sensitivity, specificity, and predictive values were assessed using varATS qPCR as gold standard. RESULTS Parasite prevalence was 17.5%, 24.5%, and 42.1% by microscopy, RDT, and varATS qPCR respectively. Using varATS qPCR as the standard, RDT was more sensitive (55.7% vs 39.3%), equally specific (98.2% vs 98.3%), and reported higher positive (95.7% vs 94.5%) and negative predictive values (75.3% vs 69.0%) than microscopy. Consequently, RDT recorded better diagnostic agreement (kappa = 0.571) with varATS qPCR than microscopy (kappa = 0.409) for clinical detection of malaria. CONCLUSIONS RDT outperformed microscopy for the diagnosis of Plasmodium falciparum malaria in the study. However, both tests missed over 40% of infections that were detected by varATS qPCR. Novel tools are needed to ensure prompt diagnosis of all clinical malaria cases.
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Affiliation(s)
- Stephen Opoku Afriyie
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Thomas Kwame Addison
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Yilekal Gebre
- Department of Biological Sciences, University of Notre Dame, South Bend, IN, USA
| | - Abdul-Hakim Mutala
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Kwasi Baako Antwi
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Dawood Ackom Abbas
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Kofi Agyapong Addo
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Austine Tweneboah
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | | | - Cristian Koepfli
- Department of Biological Sciences, University of Notre Dame, South Bend, IN, USA.
| | - Kingsley Badu
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana.
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Oduma CO, Ombok M, Zhao X, Huwe T, Ondigo BN, Kazura JW, Grieco J, Achee N, Liu F, Ochomo E, Koepfli C. Altitude, not potential larval habitat availability, explains pronounced variation in Plasmodium falciparum infection prevalence in the western Kenya highlands. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0001505. [PMID: 37068071 PMCID: PMC10109483 DOI: 10.1371/journal.pgph.0001505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/03/2023] [Indexed: 04/18/2023]
Abstract
Progress in malaria control has stalled over the recent years. Knowledge on main drivers of transmission explaining small-scale variation in prevalence can inform targeted control measures. We collected finger-prick blood samples from 3061 individuals irrespective of clinical symptoms in 20 clusters in Busia in western Kenya and screened for Plasmodium falciparum parasites using qPCR and microscopy. Clusters spanned an altitude range of 207 meters (1077-1284 m). We mapped potential mosquito larval habitats and determined their number within 250 m of a household and distances to households using ArcMap. Across all clusters, P. falciparum parasites were detected in 49.8% (1524/3061) of individuals by qPCR and 19.5% (596/3061) by microscopy. Across the clusters, prevalence ranged from 26% to 70% by qPCR. Three to 34 larval habitats per cluster and 0-17 habitats within a 250m radius around households were observed. Using a generalized linear mixed effect model (GLMM), a 5% decrease in the odds of getting infected per each 10m increase in altitude was observed, while the number of larval habitats and their proximity to households were not statistically significant predictors for prevalence. Kitchen located indoors, open eaves, a lower level of education of the household head, older age, and being male were significantly associated with higher prevalence. Pronounced variation in prevalence at small scales was observed and needs to be taken into account for malaria surveillance and control. Potential larval habitat frequency had no direct impact on prevalence.
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Affiliation(s)
- Colins O Oduma
- Department of Biochemistry and Molecular Biology, Egerton University, Nakuru, Kenya
- Kenya Medical Research Institute, Centre for Global Health Research, Kisumu, Kenya
| | - Maurice Ombok
- Kenya Medical Research Institute, Centre for Global Health Research, Kisumu, Kenya
| | - Xingyuan Zhao
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, IN, United States of America
| | - Tiffany Huwe
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States of America
| | - Bartholomew N Ondigo
- Department of Biochemistry and Molecular Biology, Egerton University, Nakuru, Kenya
- Kenya Medical Research Institute, Centre for Global Health Research, Kisumu, Kenya
| | - James W Kazura
- Case Western Reserve University, Center for Global Health and Diseases, Cleveland, OH, United States of America
| | - John Grieco
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States of America
| | - Nicole Achee
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States of America
| | - Fang Liu
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, IN, United States of America
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States of America
| | - Eric Ochomo
- Kenya Medical Research Institute, Centre for Global Health Research, Kisumu, Kenya
| | - Cristian Koepfli
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States of America
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Vera-Arias CA, Holzschuh A, Oduma CO, Badu K, Abdul-Hakim M, Yukich J, Hetzel MW, Fakih BS, Ali A, Ferreira MU, Ladeia-Andrade S, Sáenz FE, Afrane Y, Zemene E, Yewhalaw D, Kazura JW, Yan G, Koepfli C. High-throughput Plasmodium falciparum hrp2 and hrp3 gene deletion typing by digital PCR to monitor malaria rapid diagnostic test efficacy. eLife 2022; 11:72083. [PMID: 35762586 PMCID: PMC9246365 DOI: 10.7554/elife.72083] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 06/05/2022] [Indexed: 01/11/2023] Open
Abstract
Most rapid diagnostic tests for Plasmodium falciparum malaria target the Histidine-Rich Proteins 2 and 3 (HRP2 and HRP3). Deletions of the hrp2 and hrp3 genes result in false-negative tests and are a threat for malaria control. A novel assay for molecular surveillance of hrp2/hrp3 deletions was developed based on droplet digital PCR (ddPCR). The assay quantifies hrp2, hrp3, and a control gene with very high accuracy. The theoretical limit of detection was 0.33 parasites/µl. The deletion was reliably detected in mixed infections with wild-type and hrp2-deleted parasites at a density of >100 parasites/reaction. For a side-by-side comparison with the conventional nested PCR (nPCR) assay, 248 samples were screened in triplicate by ddPCR and nPCR. No deletions were observed by ddPCR, while by nPCR hrp2 deletion was observed in 8% of samples. The ddPCR assay was applied to screen 830 samples from Kenya, Zanzibar/Tanzania, Ghana, Ethiopia, Brazil, and Ecuador. Pronounced differences in the prevalence of deletions were observed among sites, with more hrp3 than hrp2 deletions. In conclusion, the novel ddPCR assay minimizes the risk of false-negative results (i.e., hrp2 deletion observed when the sample is wild type), increases sensitivity, and greatly reduces the number of reactions that need to be run.
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Affiliation(s)
| | - Aurel Holzschuh
- University of Notre Dame, Notre Dame, United States.,Swiss Tropical and Public Health Institute, Allschwil, Switzerland
| | - Colins O Oduma
- Kenya Medical Research Institute-Centre for Global Health Research, Kisumu, Kenya.,Department of Biochemistry and Molecular Biology, Egerton University, Nakuru, Kenya
| | - Kingsley Badu
- Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | | | - Manuel W Hetzel
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.,University of Basel, Basel, Switzerland
| | - Bakar S Fakih
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.,University of Basel, Basel, Switzerland.,Ifakara Health Institute, Dar es Salaam, United Republic of Tanzania
| | - Abdullah Ali
- Zanzibar Malaria Elimination Programme, Zanzibar, Zanzibar, United Republic of Tanzania
| | | | | | - Fabián E Sáenz
- Centro de Investigación para la Salud en América Latina, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Yaw Afrane
- Department of Medical Microbiology, University of Ghana, Accra, Ghana
| | - Endalew Zemene
- Tropical and Infectious Diseases Research Center, Jimma University, Jimma, Ethiopia
| | - Delenasaw Yewhalaw
- Tropical and Infectious Diseases Research Center, Jimma University, Jimma, Ethiopia
| | - James W Kazura
- Case Western Reserve University, Cleveland, United States
| | - Guiyun Yan
- Program in Public Health, University of California, Irvine, Irvine, United States
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7
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Ochwedo KO, Ariri FO, Otambo WO, Magomere EO, Debrah I, Onyango SA, Orondo PW, Atieli HE, Ogolla SO, Otieno ACA, Mukabana WR, Githeko AK, Lee MC, Yan G, Zhong D, Kazura JW. Rare Alleles and Signatures of Selection on the Immunodominant Domains of Pfs230 and Pfs48/45 in Malaria Parasites From Western Kenya. Front Genet 2022; 13:867906. [PMID: 35656326 PMCID: PMC9152164 DOI: 10.3389/fgene.2022.867906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/25/2022] [Indexed: 01/27/2023] Open
Abstract
Background: Malaria elimination and eradication efforts can be advanced by including transmission-blocking or reducing vaccines (TBVs) alongside existing interventions. Key transmission-blocking vaccine candidates, such as Pfs230 domain one and Pfs48/45 domain 3, should be genetically stable to avoid developing ineffective vaccines due to antigenic polymorphisms. We evaluated genetic polymorphism and temporal stability of Pfs230 domain one and Pfs48/45 domain three in Plasmodium falciparum parasites from western Kenya. Methods: Dry blood spots on filter paper were collected from febrile malaria patients reporting to community health facilities in endemic areas of Homa Bay and Kisumu Counties and an epidemic-prone area of Kisii County in 2018 and 2019. Plasmodium speciation was performed using eluted DNA and real-time PCR. Amplification of the target domains of the two Pfs genes was performed on P. falciparum positive samples. We sequenced Pfs230 domain one on 156 clinical isolates and Pfs48/45 domain three on 118 clinical isolates to infer the levels of genetic variability, signatures of selection, genetic diversity indices and perform other evolutionary analyses. Results: Pfs230 domain one had low nucleotide diversity (π = 0.15 × 10-2) with slight variation per study site. Six polymorphic sites with nonsynonymous mutations and eight haplotypes were discovered. I539T was a novel variant, whereas G605S was nearing fixation. Pfs48/45 domain three had a low π (0.063 × 10-2), high conservation index, and three segregating sites, resulting in nonsynonymous mutation and four haplotypes. Some loci of Pfs230 D1 were in positive or negative linkage disequilibrium, had negative or positive selection signatures, and others (1813, 1955) and (1813, 1983) had a history of recombination. Mutated loci pairs in Pfs48/45 domain three had negative linkage disequilibrium, and some had negative and positive Tajima's D values with no history of recombination events. Conclusion: The two transmission blocking vaccine candidates have low nucleotide diversity, a small number of zone-specific variants, high nucleotide conservation index, and high frequency of rare alleles. With the near fixation a polymorphic site and the proximity of mutated codons to antibody binding epitopes, it will be necessary to continue monitoring sequence modifications of these domains when designing TBVs that include Pfs230 and Pfs48/45 antigens.
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Affiliation(s)
- Kevin O. Ochwedo
- Department of Biology, Faculty of Science and Technology, University of Nairobi, Nairobi, Kenya,Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya
| | - Fredrick O. Ariri
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya,Department of Zoology, School of Physical and Biological Sciences, Maseno University, Kisumu, Kenya
| | - Wilfred O. Otambo
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya,Department of Zoology, School of Physical and Biological Sciences, Maseno University, Kisumu, Kenya
| | - Edwin O. Magomere
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya,Department of Biochemistry, Egerton University, Nakuru, Kenya
| | - Isaiah Debrah
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya,West Africa Centre for Cell Biology of Infectious Pathogen, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Shirley A. Onyango
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya,School of Zoological Sciences, Kenyatta University, Nairobi, Kenya
| | - Pauline W. Orondo
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya
| | - Harrysone E. Atieli
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya
| | - Sidney O. Ogolla
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Antony C. A. Otieno
- Department of Biology, Faculty of Science and Technology, University of Nairobi, Nairobi, Kenya
| | - Wolfgang R. Mukabana
- Department of Biology, Faculty of Science and Technology, University of Nairobi, Nairobi, Kenya,Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya
| | - Andrew K. Githeko
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya,Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Ming-Chieh Lee
- Program in Public Health, College of Health Sciences, University of California, Irvine, Irvine, CA, United States
| | - Guiyun Yan
- Program in Public Health, College of Health Sciences, University of California, Irvine, Irvine, CA, United States
| | - Daibin Zhong
- Program in Public Health, College of Health Sciences, University of California, Irvine, Irvine, CA, United States,*Correspondence: Daibin Zhong,
| | - James W. Kazura
- Centre for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, United States
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8
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Oduma CO, Koepfli C. Plasmodium falciparum and Plasmodium vivax Adjust Investment in Transmission in Response to Change in Transmission Intensity: A Review of the Current State of Research. Front Cell Infect Microbiol 2021; 11:786317. [PMID: 34956934 PMCID: PMC8692836 DOI: 10.3389/fcimb.2021.786317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/19/2021] [Indexed: 12/02/2022] Open
Abstract
Malaria parasites can adjust the proportion of parasites that develop into gametocytes, and thus the probability for human-to-vector transmission, through changes in the gametocyte conversion rate. Understanding the factors that impact the commitment of malaria parasites to transmission is required to design better control interventions. Plasmodium spp. persist across countries with vast differences in transmission intensities, and in sites where transmission is highly seasonal. Mounting evidence shows that Plasmodium spp. adjusts the investment in transmission according to seasonality of vector abundance, and transmission intensity. Various techniques to determine the investment in transmission are available, i.e., short-term culture, where the conversion rate can be measured most directly, genome and transcriptome studies, quantification of mature gametocytes, and mosquito feeding assays. In sites with seasonal transmission, the proportion of gametocytes, their densities and infectivity are higher during the wet season, when vectors are plentiful. When countries with pronounced differences in transmission intensity were compared, the investment in transmission was higher when transmission was low, thus maximizing the parasite’s chances to be transmitted to mosquitoes. Increased transmissibility of residual infections after a successful reduction of malaria transmission levels need to be considered when designing intervention measures.
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Affiliation(s)
- Colins O Oduma
- Department of Biochemistry and Molecular Biology, Egerton University, Nakuru, Kenya.,Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Cristian Koepfli
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
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9
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Usui M, Williamson KC. Stressed Out About Plasmodium falciparum Gametocytogenesis. Front Cell Infect Microbiol 2021; 11:790067. [PMID: 34926328 PMCID: PMC8674873 DOI: 10.3389/fcimb.2021.790067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/08/2021] [Indexed: 11/21/2022] Open
Abstract
Blocking malaria transmission is critical to malaria control programs but remains a major challenge especially in endemic regions with high levels of asymptomatic infections. New strategies targeting the transmissible sexual stages of the parasite, called gametocytes, are needed. This review focuses on P. falciparum gametocytogenesis in vivo and in vitro. Highlighting advances made elucidating genes required for gametocyte production and identifying key questions that remain unanswered such as the factors and regulatory mechanisms that contribute to gametocyte induction, and the mechanism of sequestration. Tools available to begin to address these issues are also described to facilitate advances in our understanding of this important stage of the life cycle.
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Affiliation(s)
- Miho Usui
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Kim C Williamson
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
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10
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Ochwedo KO, Omondi CJ, Magomere EO, Olumeh JO, Debrah I, Onyango SA, Orondo PW, Ondeto BM, Atieli HE, Ogolla SO, Githure J, Otieno ACA, Githeko AK, Kazura JW, Mukabana WR, Guiyan Y. Hyper-prevalence of submicroscopic Plasmodium falciparum infections in a rural area of western Kenya with declining malaria cases. Malar J 2021; 20:472. [PMID: 34930283 PMCID: PMC8685826 DOI: 10.1186/s12936-021-04012-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 12/07/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The gold standard for diagnosing Plasmodium falciparum infection is microscopic examination of Giemsa-stained peripheral blood smears. The effectiveness of this procedure for infection surveillance and malaria control may be limited by a relatively high parasitaemia detection threshold. Persons with microscopically undetectable infections may go untreated, contributing to ongoing transmission to mosquito vectors. The purpose of this study was to determine the magnitude and determinants of undiagnosed submicroscopic P. falciparum infections in a rural area of western Kenya. METHODS A health facility-based survey was conducted, and 367 patients seeking treatment for symptoms consistent with uncomplicated malaria in Homa Bay County were enrolled. The frequency of submicroscopic P. falciparum infection was measured by comparing the prevalence of infection based on light microscopic inspection of thick blood smears versus real-time polymerase chain reaction (RT-PCR) targeting P. falciparum 18S rRNA gene. Long-lasting insecticidal net (LLIN) use, participation in nocturnal outdoor activities, and gender were considered as potential determinants of submicroscopic infections. RESULTS Microscopic inspection of blood smears was positive for asexual P. falciparum parasites in 14.7% (54/367) of cases. All of these samples were confirmed by RT-PCR. 35.8% (112/313) of blood smear negative cases were positive by RT-PCR, i.e., submicroscopic infection, resulting in an overall prevalence by RT-PCR alone of 45.2% compared to 14.7% for blood smear alone. Females had a higher prevalence of submicroscopic infections (35.6% or 72 out of 202 individuals, 95% CI 28.9-42.3) compared to males (24.2%, 40 of 165 individuals, 95% CI 17.6-30.8). The risk of submicroscopic infections in LLIN users was about half that of non-LLIN users (OR = 0.59). There was no difference in the prevalence of submicroscopic infections of study participants who were active in nocturnal outdoor activities versus those who were not active (OR = 0.91). Patients who participated in nocturnal outdoor activities and use LLINs while indoors had a slightly higher risk of submicroscopic infection than those who did not use LLINs (OR = 1.48). CONCLUSION Microscopic inspection of blood smears from persons with malaria symptoms for asexual stage P. falciparum should be supplemented by more sensitive diagnostic tests in order to reduce ongoing transmission of P. falciparum parasites to local mosquito vectors.
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Affiliation(s)
- Kevin O. Ochwedo
- Department of Biology, Faculty of Science and Technology, University of Nairobi, Nairobi, Kenya
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya
| | - Collince J. Omondi
- Department of Biology, Faculty of Science and Technology, University of Nairobi, Nairobi, Kenya
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya
| | - Edwin O. Magomere
- Department of Biochemistry and Molecular Biology, Egerton University, Njoro, Kenya
| | - Julius O. Olumeh
- Department of Biology, Faculty of Science and Technology, University of Nairobi, Nairobi, Kenya
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya
| | - Isaiah Debrah
- West Africa Centre for Cell Biology of Infectious Pathogen, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Shirley A. Onyango
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya
| | - Pauline W. Orondo
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya
| | - Benyl M. Ondeto
- Department of Biology, Faculty of Science and Technology, University of Nairobi, Nairobi, Kenya
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya
| | - Harrysone E. Atieli
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya
| | - Sidney O. Ogolla
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - John Githure
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya
| | - Antony C. A. Otieno
- Department of Biology, Faculty of Science and Technology, University of Nairobi, Nairobi, Kenya
| | - Andrew K. Githeko
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - James W. Kazura
- Centre for Global Health and Diseases, Case Western Reserve University, Cleveland, OH USA
| | - Wolfgang R. Mukabana
- Department of Biology, Faculty of Science and Technology, University of Nairobi, Nairobi, Kenya
- Sub-Saharan Africa International Centre for Excellence in Malaria Research, Homa Bay, Kenya
| | - Yan Guiyan
- Program in Public Health, College of Health Sciences, University of California, Irvine, USA
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