Mosquito microevolution drives Plasmodium falciparum dynamics.

Malaria, a major cause of child mortality in Africa, is engendered by Plasmodium parasites that are transmitted by anopheline mosquitoes. Fitness of Plasmodium parasites is closely linked to the ecology and evolution of its anopheline vector. However, whether the genetic structure of vector populations impacts malaria transmission remains unknown. Here, we describe a partitioning of the African malaria vectors into generalists and specialists that evolve along ecological boundaries. We next identify the contribution of mosquito species to Plasmodium abundance using Granger causality tests for time-series data collected over two rainy seasons in Mali. We find that mosquito microevolution, defined by changes in the genetic structure of a population over short ecological timescales, drives Plasmodium dynamics in nature, whereas vector abundance, infection prevalence, temperature and rain have low predictive values. Our study demonstrates the power of time-series approaches in vector biology and highlights the importance of focusing local vector control strategies on mosquito species that drive malaria dynamics.

A village level cluster-randomized entomological evaluation of combination long-lasting insecticidal nets containing pyrethroid plus PBO synergist in Southern Mali.

BACKGROUND: There is growing concern that malaria vector resistance to pyrethroid insecticides may reduce the effectiveness of long-lasting insecticidal nets (LLINs). Combination LLINs are designed to control susceptible and pyrethroid-resistant mosquito populations through a mixture of pyrethroid with piperonyl butoxide (PBO) synergist. A cluster randomized trial with entomology outcome measures was conducted in Mali to determine the added benefit over mono-treated pyrethroid predecessors. Four LLIN treatments; permethrin + PBO, permethrin, deltamethrin + PBO, and deltamethrin, were randomly allocated to four villages each (16 villages total) and distributed to cover every sleeping place. Entomological monitoring of indoor Anopheles resting densities, host preference, vector longevity, and sporozoite rates were monitored every 2 months over 2 years in 2014 and 2015. RESULTS: Bottle bioassays confirmed permethrin and deltamethrin resistance in Anopheles gambiae sensu lato (s.l.), (the predominant species throughout the study) with pre-exposure to PBO indicating partial involvement of oxidases. Between 2014 and 2015 the mean indoor resting density was greater in the deltamethrin + PBO LLIN arm than the deltamethrin LLIN arm at 3.05 (95% CI 3.00-3.10) An. gambiae s.l. per room per day compared with 1.9 (95% CI 1.87-1.97). There was no significant difference in sporozoite rate at 3.97% (95% CI 2.91-5.02) for the deltamethrin LLIN arm and 3.04% (95% CI 2.21-3.87) for deltamethrin + PBO LLIN arm (P = 0.17). However, when analysed by season there was some evidence that the sporozoite rate was lower in the deltamethrin + PBO LLIN arm than deltamethrin LLIN arm during the rainy/high malaria transmission seasons at 1.95% (95% CI 1.18-2.72) and 3.70% (95% CI 2.56-4.84) respectively (P = 0.01). CONCLUSIONS: While there was some evidence that An. gambiae s.l. sporozoite rates were lower in villages with deltamethrin + PBO LLINs during the high malaria transmission seasons of 2014-2015, there was no reduction in parity rates or indoor resting densities. There was also no evidence that permethrin + PBO LLINs provided any improved control when compared with permethrin LLINs. Combination nets may have a greater impact in areas where mixed function oxidases play a more important role in pyrethroid resistance.

[Study of the impact of breeding sites on the infectivity of P. falciparum gametocytes to An. gambiae s.l in malaria-endemic area of Nanguilabougou.-Mali]. / Etude de l'impact des gites larvaires sur l'infectivite des gametocytes de Plasmodium Falciparum chez Anopheles Gambiae s.l en zone d'endemie palustre de Nanguilabougou - Mali.

Numerous studies have shown the influence of some bacteria colonizing the breeding sites on the development of the parasite in Anopheles malaria vectors. The aim of this study was to evaluate the impact of the breeding sites of Plasmodium falciparum on the gametocytes infectivity of Anopheles gambiae sl using the membrane feeding method. We carried out an experimental infestation study from September 2010 to January 2011 in a village located in the southern savanna of Mali. Cross sectional surveys were conducted to collect larvae and to select gametocyte carriers. Female offspring of L3 and L4 stage larvae were used for the experimental infestation. The gametocyte carriers were children aged within 4 to 12 years. Bacteria identified in breeding water of larvae and adult mosquitoes were: Escherichia coli, Salmonella spp, Klebsiella oxytoca, Pseudomonas spp, Staphylococcus spp, Shigella sp. The oocyst load of infected mosquitoes did not significantly vary according to the samples (F = 1.517, P = 0.230). Low infection rates (5.4% and 2.8%) were observed in the larval bedding and in mosquitoes containing K. oxytoca and Shigella. The blood feeding rates (62.4%; 60.9%; 67.7%) and mortality (66.4%; 64.9%; 61.9%) of An. gambiae did not significantly vary depending on the breeding sites [(P = 0.15); (P = 0.22)].

De nombreuses études ont montré l'influence de certaines bactéries vivant dans les gites larvaires sur le développement du parasite chez les anophèles vecteurs du paludisme. Le but du présent travail consistait à étudier l'impact des gites larvaires sur l'infectivité des gamétocytes de Plasmodium falciparum chez Anopheles gambiae s.l par la technique d'infestation sur membrane. Pour réaliser ce travail, une étude d'infestation expérimentale a été conduite de septembre 2010 à janvier 2011 dans un village de savane sud soudanienne du Mali. Des passages transversaux ont été effectués pour la collecte des larves et la sélection des porteurs de gamétocytes. Les femelles issues des larves de stades L3 et L4 ont été utilisées pour les séances d'infestation expérimentale. Les enfants porteurs de gamétocytes étaient âgés de 4 à 12 ans. Les bactéries identifiées dans l'eau des gites chez les larves et les adultes de moustiques étaient : Escherichia coli, Salmonella s.p., Klebsiella oxytoca, Pseudomonas s.p., Staphylococcus s.p., Shigella sp. La charge oocystique des moustiques infectés n'avait pas varié de façon significative en fonction des gites (F=1,517 ; P=0,230). De faibles taux d'infection (5,4% et 2,8%) ont été observés dans les gites et chez les moustiques contenant K. oxytoca et Shigella. Le taux d'engorgement (62,4% ; 60,9% ; 67,7%) et le taux de mortalité (66,4% ; 64,9% ; 61,9%) d'An. gambiae n'ont pas varié significativement en fonction des gites larvaires,[(P= 0,15) ; (P= 0,22)].

A python module to normalize microarray data by the quantile adjustment method.

Microarray technology is widely used for gene expression research targeting the development of new drug treatments. In the case of a two-color microarray, the process starts with labeling DNA samples with fluorescent markers (cyanine 635 or Cy5 and cyanine 532 or Cy3), then mixing and hybridizing them on a chemically treated glass printed with probes, or fragments of genes. The level of hybridization between a strand of labeled DNA and a probe present on the array is measured by scanning the fluorescence of spots in order to quantify the expression based on the quality and number of pixels for each spot. The intensity data generated from these scans are subject to errors due to differences in fluorescence efficiency between Cy5 and Cy3, as well as variation in human handling and quality of the sample. Consequently, data have to be normalized to correct for variations which are not related to the biological phenomena under investigation. Among many existing normalization procedures, we have implemented the quantile adjustment method using the python computer language, and produced a module which can be run via an HTML dynamic form. This module is composed of different functions for data files reading, intensity and ratio computations and visualization. The current version of the HTML form allows the user to visualize the data before and after normalization. It also gives the option to subtract background noise before normalizing the data. The output results of this module are in agreement with the results of other normalization tools.

Breakpoint structure of the Anopheles gambiae 2Rb chromosomal inversion.

BACKGROUND: Alternative arrangements of chromosome 2 inversions in Anopheles gambiae are important sources of population structure, and are associated with adaptation to environmental heterogeneity. The forces responsible for their origin and maintenance are incompletely understood. Molecular characterization of inversion breakpoints provides insight into how they arose, and provides the basis for development of molecular karyotyping methods useful in future studies. METHODS: Sequence comparison of regions near the cytological breakpoints of 2Rb allowed the molecular delineation of breakpoint boundaries. Comparisons were made between the standard 2R+b arrangement in the An. gambiae PEST reference genome and the inverted 2Rb arrangements in the An. gambiae M and S genome assemblies. Sequence differences between alternative 2Rb arrangements were exploited in the design of a PCR diagnostic assay, which was evaluated against the known chromosomal banding pattern of laboratory colonies and field-collected samples from Mali and Cameroon. RESULTS: The breakpoints of the 7.55 Mb 2Rb inversion are flanked by extensive runs of the same short (72 bp) tandemly organized sequence, which was likely responsible for chromosomal breakage and rearrangement. Application of the molecular diagnostic assay suggested that 2Rb has a single common origin in An. gambiae and its sibling species, Anopheles arabiensis, and also that the standard arrangement (2R+b) may have arisen twice through breakpoint reuse. The molecular diagnostic was reliable when applied to laboratory colonies, but its accuracy was lower in natural populations. CONCLUSIONS: The complex repetitive sequence flanking the 2Rb breakpoint region may be prone to structural and sequence-level instability. The 2Rb molecular diagnostic has immediate application in studies based on laboratory colonies, but its usefulness in natural populations awaits development of complementary molecular tools.

The population genomics of trans-specific inversion polymorphisms in Anopheles gambiae.

In the malaria mosquito Anopheles gambiae polymorphic chromosomal inversions may play an important role in adaptation to environmental variation. Recently, we used microarray-based divergence mapping combined with targeted resequencing to map nucleotide differentiation between alternative arrangements of the 2La inversion. Here, we applied the same technique to four different polymorphic inversions on the 2R chromosome of An. gambiae. Surprisingly, divergence was much lower between alternative arrangements for all 2R inversions when compared to the 2La inversion. For one of the rearrangements, 2Ru, we successfully mapped a very small region (approximately 100 kb) of elevated divergence. For the other three rearrangements, we did not identify any regions of significantly high divergence, despite ample independent evidence from natural populations of geographic clines and seasonal cycling, and stable heterotic polymorphisms in laboratory populations. If these inversions are the targets of selection as hypothesized, we suggest that divergence between rearrangements may have escaped detection due to retained ancestral polymorphism in the case of the youngest 2R rearrangements and to extensive gene flux in the older 2R inversion systems that segregate in both An. gambiae and its sibling species An. arabiensis.

Satellite DNA from the Y chromosome of the malaria vector Anopheles gambiae.

Satellite DNA is an enigmatic component of genomic DNA with unclear function that has been regarded as "junk." Yet, persistence of these tandem highly repetitive sequences in heterochromatic regions of most eukaryotic chromosomes attests to their importance in the genome. We explored the Anopheles gambiae genome for the presence of satellite repeats and identified 12 novel satellite DNA families. Certain families were found in close juxtaposition within the genome. Six satellites, falling into two evolutionarily linked groups, were investigated in detail. Four of them were experimentally confirmed to be linked to the Y chromosome, whereas their relatives occupy centromeric regions of either the X chromosome or the autosomes. A complex evolutionary pattern was revealed among the AgY477-like satellites, suggesting their rapid turnover in the A. gambiae complex and, potentially, recombination between sex chromosomes. The substitution pattern suggested rolling circle replication as an array expansion mechanism in the Y-linked 53-bp satellite families. Despite residing in different portions of the genome, the 53-bp satellites share the same monomer lengths, apparently maintained by molecular drive or structural constraints. Potential functional centromeric DNA structures, consisting of twofold dyad symmetries flanked by a common sequence motif, have been identified in both satellite groups.

Malaria transmission in relation to rice cultivation in the irrigated Sahel of Mali.

Seven cross-sectional entomological surveys were carried out from September 1995 to February 1998 in three irrigated rice growing villages and three villages without irrigated agriculture in the area surrounding Niono, located 350km north-east of Bamako, Mali. The transmission pattern differed markedly between the two zones. In the irrigated zone, the transmission of malaria was fairly constant over the seasons at a low level. In the non-irrigated zone, transmission was mostly below detection level during the dry season, whereas it was high toward the end of the rainy season. In the irrigated zone, high densities of mosquitoes were correlated with low anthropophily, low sporozoite indices and probably low survival rates. In the non-irrigated zone, mosquito densities were lower and these relationships were less pronounced. Differential use of mosquito nets in the two zones may have been an important factor in the observed differences in transmission. The presence of cattle may also have played an important role. Two mosquito-catching methods (human landing catch and spray catch) were compared.

Genetic loci affecting resistance to human malaria parasites in a West African mosquito vector population.

Successful propagation of the malaria parasite Plasmodium falciparum within a susceptible mosquito vector is a prerequisite for the transmission of malaria. A field-based genetic analysis of the major human malaria vector, Anopheles gambiae, has revealed natural factors that reduce the transmission of P. falciparum. Differences in P. falciparum oocyst numbers between mosquito isofemale families fed on the same infected blood indicated a large genetic component affecting resistance to the parasite, and genome-wide scanning in pedigrees of wild mosquitoes detected segregating resistance alleles. The apparently high natural frequency of resistance alleles suggests that malaria parasites (or a similar pathogen) exert a significant selective pressure on vector populations.

A high malaria reinfection rate in children and young adults living under a low entomological inoculation rate in a periurban area of Bamako, Mali.

In areas of intense malaria parasite transmission, preliminary studies of the rate of reinfection after curative therapy suggest that small sample size studies of vaccine efficacy are feasible. However, the effect of transmission rate, which may vary considerably between transmission seasons, on reinfection rate has not been assessed in areas of mesoendemicity with seasonal transmission. To address this question, the Plasmodium falciparum reinfection rate after curative therapy was measured in Sotuba, a Malian village with historically low transmission rates, as estimated by the entomological inoculation rate (EIR). The reinfection rate after curative Fansidar (sulfadoxine-pyrimethamine) treatment was 80.7% (88/109). The EIR during the 13-week study period (seasonal transmission) varied between 1 and 4.5 infected bites/person/month. The finding that reinfection rates were high despite low EIRs suggests that a low EIR may be sufficient to support small sample size vaccine efficacy trials in mesoendemic areas.