20
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Multiplicity and molecular epidemiology of Plasmodium vivax and Plasmodium falciparum infections in East Africa

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Background

          Parasite genetic diversity and multiplicity of infection (MOI) affect clinical outcomes, response to drug treatment and naturally-acquired or vaccine-induced immunity. Traditional methods often underestimate the frequency and diversity of multiclonal infections due to technical sensitivity and specificity. Next-generation sequencing techniques provide a novel opportunity to study complexity of parasite populations and molecular epidemiology.

          Methods

          Symptomatic and asymptomatic Plasmodium vivax samples were collected from health centres/hospitals and schools, respectively, from 2011 to 2015 in Ethiopia. Similarly, both symptomatic and asymptomatic Plasmodium falciparum samples were collected, respectively, from hospitals and schools in 2005 and 2015 in Kenya. Finger-pricked blood samples were collected and dried on filter paper. Long amplicon (> 400 bp) deep sequencing of merozoite surface protein 1 ( msp1) gene was conducted to determine multiplicity and molecular epidemiology of P. vivax and P. falciparum infections. The results were compared with those based on short amplicon (117 bp) deep sequencing.

          Results

          A total of 139 P. vivax and 222 P. falciparum samples were pyro-sequenced for pvmsp1 and pfmsp1, yielding a total of 21 P. vivax and 99 P. falciparum predominant haplotypes. The average MOI for P. vivax and P. falciparum were 2.16 and 2.68, respectively, which were significantly higher than that of microsatellite markers and short amplicon (117 bp) deep sequencing. Multiclonal infections were detected in 62.2% of the samples for P. vivax and 74.8% of the samples for P. falciparum. Four out of the five subjects with recurrent P. vivax malaria were found to be a relapse 44–65 days after clearance of parasites. No difference was observed in MOI among P. vivax patients of different symptoms, ages and genders. Similar patterns were also observed in P. falciparum except for one study site in Kenyan lowland areas with significantly higher MOI.

          Conclusions

          The study used a novel method to evaluate Plasmodium MOI and molecular epidemiological patterns by long amplicon ultra-deep sequencing. The complexity of infections were similar among age groups, symptoms, genders, transmission settings (spatial heterogeneity), as well as over years (pre- vs. post-scale-up interventions). This study demonstrated that long amplicon deep sequencing is a useful tool to investigate multiplicity and molecular epidemiology of Plasmodium parasite infections.

          Electronic supplementary material

          The online version of this article (10.1186/s12936-018-2337-y) contains supplementary material, which is available to authorized users.

          Related collections

          Most cited references74

          • Record: found
          • Abstract: found
          • Article: not found

          Microsatellite markers reveal a spectrum of population structures in the malaria parasite Plasmodium falciparum.

          Multilocus genotyping of microbial pathogens has revealed a range of population structures, with some bacteria showing extensive recombination and others showing almost complete clonality. The population structure of the protozoan parasite Plasmodium falciparum has been harder to evaluate, since most studies have used a limited number of antigen-encoding loci that are known to be under strong selection. We describe length variation at 12 microsatellite loci in 465 infections collected from 9 locations worldwide. These data reveal dramatic differences in parasite population structure in different locations. Strong linkage disequilibrium (LD) was observed in six of nine populations. Significant LD occurred in all locations with prevalence <1% and in only two of five of the populations from regions with higher transmission intensities. Where present, LD results largely from the presence of identical multilocus genotypes within populations, suggesting high levels of self-fertilization in populations with low levels of transmission. We also observed dramatic variation in diversity and geographical differentiation in different regions. Mean heterozygosities in South American countries (0.3-0.4) were less than half those observed in African locations (0. 76-0.8), with intermediate heterozygosities in the Southeast Asia/Pacific samples (0.51-0.65). Furthermore, variation was distributed among locations in South America (F:(ST) = 0.364) and within locations in Africa (F:(ST) = 0.007). The intraspecific patterns of diversity and genetic differentiation observed in P. falciparum are strikingly similar to those seen in interspecific comparisons of plants and animals with differing levels of outcrossing, suggesting that similar processes may be involved. The differences observed may also reflect the recent colonization of non-African populations from an African source, and the relative influences of epidemiology and population history are difficult to disentangle. These data reveal a range of population structures within a single pathogen species and suggest intimate links between patterns of epidemiology and genetic structure in this organism.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            A genus- and species-specific nested polymerase chain reaction malaria detection assay for epidemiologic studies.

            A nested polymerase chain reaction (PCR) assay that uses Plasmodium genus-specific primers for the initial PCR (nest 1) amplification and either genus- or species-specific primers for the nest 2 amplifications was tested on laboratory and field samples. With in vitro cultured Plasmodium falciparum-infected blood samples, it was capable of detecting six parasites/microl of blood using DNA prepared from 25-microl blood spots on filter paper. The assay was evaluated on fingerprick blood samples collected on filter paper from 129 individuals living in a malaria-endemic area in Malaysia. Malaria prevalence by genus-specific nested PCR was 35.6% (46 of 129) compared with 28.7% (37 of 129) by microscopy. The nested PCR detected seven more malaria samples than microscopy in the first round of microscopic examination, malaria in three microscopically negative samples, six double infections identified as single infections by microscopy and one triple infection identified as a double infection by microscopy. The nested PCR assay described is a sensitive technique for collecting accurate malaria epidemiologic data. When coupled with simple blood spot sampling, it is particularly useful for screening communities in remote regions of the world.
              Bookmark
              • Record: found
              • Abstract: not found
              • Article: not found

              High sensitivity of detection of human malaria parasites by the use of nested polymerase chain reaction

                Bookmark

                Author and article information

                Contributors
                dzhong@uci.edu
                guiyuny@uci.edu
                Journal
                Malar J
                Malar. J
                Malaria Journal
                BioMed Central (London )
                1475-2875
                2 May 2018
                2 May 2018
                2018
                : 17
                : 185
                Affiliations
                [1 ]ISNI 0000 0001 0668 7243, GRID grid.266093.8, Program in Public Health, , University of California at Irvine, ; Irvine, CA 92617 USA
                [2 ]ISNI 0000 0000 8598 2218, GRID grid.266859.6, Department of Biological Sciences, , University of North Carolina at Charlotte, ; Charlotte, NC 28223 USA
                [3 ]ISNI 0000 0001 2034 9160, GRID grid.411903.e, Department of Medical Laboratory Sciences, Faculty of Health Sciences, , Jimma University, ; Jimma, Ethiopia
                [4 ]ISNI 0000 0001 2034 9160, GRID grid.411903.e, Tropical and Infectious Diseases Research Center, , Jimma University, ; Jimma, Ethiopia
                [5 ]ISNI 0000 0001 0155 5938, GRID grid.33058.3d, Centre for Global Health Research, Kenya Medical Research Institute, ; Kisumu, Kenya
                [6 ]ISNI 0000 0004 1937 1485, GRID grid.8652.9, Department of Medical Microbiology, College of Health Sciences, , University of Ghana, ; Accra, Ghana
                Author information
                http://orcid.org/0000-0002-2771-9598
                Article
                2337
                10.1186/s12936-018-2337-y
                5932820
                29720181
                5a08d0e7-67ea-417e-ac9e-b223182df580
                © The Author(s) 2018

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 13 December 2017
                : 26 April 2018
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: R01 AI050243
                Award ID: U19 AI129326
                Award ID: D43 TW001505
                Award Recipient :
                Categories
                Research
                Custom metadata
                © The Author(s) 2018

                Infectious disease & Microbiology
                multiplicity of infection,merozoite surface protein 1,amplicon deep sequencing,molecular epidemiology,plasmodium,within-host diversity

                Comments

                Comment on this article