Improving statistical inference on pathogen densities estimated by quantitative molecular methods: malaria gametocytaemia as a case study

Seasonality and heterogeneity of malaria transmission determine success of interventions in high-endemic settings: a modeling study

Background

Malaria transmission is both seasonal and heterogeneous, and mathematical models that seek to predict the effects of possible intervention strategies should accurately capture realistic seasonality of vector abundance, seasonal dynamics of within-host effects, and heterogeneity of exposure, which may also vary seasonally.

Methods

Prevalence, incidence, asexual parasite and gametocyte densities, and infectiousness measurements from eight study sites in sub-Saharan Africa were used to calibrate an individual-based model with innate and adaptive immunity. Data from the Garki Project was used to fit exposure rates and parasite densities with month-resolution. A model capturing Garki seasonality and seasonal heterogeneity of exposure was used as a framework for characterizing the infectious reservoir of malaria, testing optimal timing of indoor residual spraying, and comparing four possible mass drug campaign implementations for malaria control.

Results

Seasonality as observed in Garki sites is neither sinusoidal nor box-like, and substantial heterogeneity in exposure arises from dry-season biting. Individuals with dry-season exposure likely account for the bulk of the infectious reservoir during the dry season even when they are a minority in the overall population. Spray campaigns offer the most benefit in prevalence reduction when implemented just prior to peak vector abundance, which may occur as late as a couple months into the wet season, and targeting spraying to homes of individuals with dry-season exposure can be particularly effective. Expanding seasonal malaria chemoprevention programs to cover older children is predicted to increase the number of cases averted per treatment and is therefore recommended for settings of seasonal and intense transmission.

Conclusions

Accounting for heterogeneity and seasonality in malaria transmission is critical for understanding transmission dynamics and predicting optimal timing and targeting of control and elimination interventions.

Electronic supplementary material

The online version of this article (10.1186/s12879-018-3319-y) contains supplementary material, which is available to authorized users.

Predicting the likelihood and intensity of mosquito infection from sex specific Plasmodium falciparum gametocyte density

Understanding the importance of gametocyte density on human-to-mosquito transmission is of immediate relevance to malaria control. Previous work (Churcher et al., 2013) indicated a complex relationship between gametocyte density and mosquito infection. Here we use data from 148 feeding experiments on naturally infected gametocyte carriers to show that the relationship is much simpler and depends on both female and male parasite density. The proportion of mosquitoes infected is primarily determined by the density of female gametocytes though transmission from low gametocyte densities may be impeded by a lack of male parasites. Improved precision of gametocyte quantification simplifies the shape of the relationship with infection increasing rapidly before plateauing at higher densities. The mean number of oocysts per mosquito rises quickly with gametocyte density but continues to increase across densities examined. The work highlights the importance of measuring both female and male gametocyte density when estimating the human reservoir of infection.

Modeling the impact of Plasmodium falciparum sexual stage immunity on the composition and dynamics of the human infectious reservoir for malaria in natural settings

Malaria transmission remains high in Sub-Saharan Africa despite large-scale implementation of malaria control interventions. A comprehensive understanding of the transmissibility of infections to mosquitoes may guide the design of more effective transmission reducing strategies. The impact of P. falciparum sexual stage immunity on the infectious reservoir for malaria has never been studied in natural settings. Repeated measurements were carried out at start-wet, peak-wet and dry season, and provided data on antibody responses against gametocyte/gamete antigens Pfs48/45 and Pfs230 as anti-gametocyte immunity. Data on high and low-density infections and their infectiousness to anopheline mosquitoes were obtained using quantitative molecular methods and mosquito feeding assays, respectively. An event-driven model for P. falciparum sexual stage immunity was developed and fit to data using an agent based malaria model infrastructure. We found that Pfs48/45 and Pfs230 antibody densities increased with increasing concurrent gametocyte densities; associated with 55–70% reduction in oocyst intensity and achieved up to 44% reduction in proportions of infected mosquitoes. We showed that P. falciparum sexual stage immunity significantly reduces transmission of microscopic (p < 0.001) but not submicroscopic (p = 0.937) gametocyte infections to mosquitoes and that incorporating sexual stage immunity into mathematical models had a considerable impact on the contribution of different age groups to the infectious reservoir of malaria. Human antibody responses to gametocyte antigens are likely to be dependent on recent and concurrent high-density gametocyte exposure and have a pronounced impact on the likelihood of onward transmission of microscopic gametocyte densities compared to low density infections. Our mathematical simulations indicate that anti-gametocyte immunity is an important factor for predicting and understanding the composition and dynamics of the human infectious reservoir for malaria.

Submicroscopic gametocyte infections are efficiently transmitted from humans to mosquitoes in settings with efficient malaria vectors and may pose challenges for malaria control and elimination efforts. Our understanding of what mechanisms contribute to submicroscopic gametocytes infectiousness remains limited. Here we assess the impact of naturally acquired anti-gametocyte antibodies on malaria transmission to mosquitoes and on the age-dependent composition of the infectious reservoir and seasonal dynamics. Anti-gametocyte immunity significantly reduces the infectiousness of high gametocyte density infections, contributes to explain the age-related profiles of the infectious reservoir in the study area, whilst submicroscopic gametocyte infections that present with lower anti-Pfs48/45 and anti-Pfs230 antibody responses commonly remain transmissible to mosquitoes. Our findings indicate that sexual stage immunity needs to be incorporated in transmission models to better understand transmission dynamics. Furthermore, tools that boost sexual stage immunity may reduce transmission to mosquitoes and thus aid elimination strategies.

Plasmodium Gametocytes in Field Studies: Do We Measure Commitment to Transmission or Detectability?

The proportion of Plasmodium spp. infections carrying gametocytes, and gametocyte densities, are often reported as surrogate markers for transmission potential. It remains unclear whether parasites under natural conditions adjust commitment to transmission depending on external factors. Population-based surveys comprising mostly asymptomatic low-density infections are always impacted by the sensitivity of the assays used to diagnose infections and detect gametocytes. Asexual parasite density is an important predictor for the probability of detecting gametocytes, and in many cases it can explain patterns in gametocyte carriage without the need for an adjustment of the gametocyte conversion rate. When reporting gametocyte data, quantification of blood-stage parasitemia and its inclusion as a confounder in multivariable analyses is essential.

A Molecular Assay to Quantify Male and Female Plasmodium falciparum Gametocytes: Results From 2 Randomized Controlled Trials Using Primaquine for Gametocyte Clearance

Background

Single low-dose primaquine (PQ) reduces Plasmodium falciparum infectivity before it impacts gametocyte density. Here, we examined the effect of PQ on gametocyte sex ratio as a possible explanation for this early sterilizing effect.

Methods

Quantitative reverse-transcription polymerase chain reaction assays were developed to quantify female gametocytes (targeting Pfs25 messenger RNA [mRNA]) and male gametocytes (targeting Pf3D7_1469900 mRNA) in 2 randomized trials in Kenya and Mali, comparing dihydroartemisinin-piperaquine (DP) alone to DP with PQ. Gametocyte sex ratio was examined in relation to time since treatment and infectivity to mosquitoes.

Results

In Kenya, the median proportion of male gametocytes was 0.33 at baseline. Seven days after treatment, gametocyte density was significantly reduced in the DP-PQ arm relative to the DP arm (females: 0.05% [interquartile range {IQR}, 0.0–0.7%] of baseline; males: 3.4% [IQR, 0.4%–32.9%] of baseline; P < .001). Twenty-four hours after treatment, gametocyte sex ratio became male-biased and was not significantly different between the DP and DP-PQ groups. In Mali, there was no significant difference in sex ratio between the DP and DP-PQ groups (>0.125 mg/kg) 48 hours after treatment, and gametocyte sex ratio was not associated with mosquito infection rates.

Conclusions

The early sterilizing effects of PQ may not be explained by the preferential clearance of male gametocytes and may be due to an effect on gametocyte fitness.

Probability of Transmission of Malaria from Mosquito to Human Is Regulated by Mosquito Parasite Density in Naïve and Vaccinated Hosts

Over a century since Ronald Ross discovered that malaria is caused by the bite of an infectious mosquito it is still unclear how the number of parasites injected influences disease transmission. Currently it is assumed that all mosquitoes with salivary gland sporozoites are equally infectious irrespective of the number of parasites they harbour, though this has never been rigorously tested. Here we analyse >1000 experimental infections of humans and mice and demonstrate a dose-dependency for probability of infection and the length of the host pre-patent period. Mosquitoes with a higher numbers of sporozoites in their salivary glands following blood-feeding are more likely to have caused infection (and have done so quicker) than mosquitoes with fewer parasites. A similar dose response for the probability of infection was seen for humans given a pre-erythrocytic vaccine candidate targeting circumsporozoite protein (CSP), and in mice with and without transfusion of anti-CSP antibodies. These interventions prevented infection more efficiently from bites made by mosquitoes with fewer parasites. The importance of parasite number has widespread implications across malariology, ranging from our basic understanding of the parasite, how vaccines are evaluated and the way in which transmission should be measured in the field. It also provides direct evidence for why the only registered malaria vaccine RTS,S was partially effective in recent clinical trials.

Malaria is transmitted to humans by the bite of an infectious mosquito though it is unclear whether a mosquito with a high number of parasites is more infectious than one with only a few. Here we show that the greater the number of parasites within the salivary gland of the mosquito following blood-feeding the more likely it is to have transmitted the disease. A clear dose-response is seen with highly infected mosquitoes being more likely to have caused infection (and to have done so quicker) than lightly infected mosquitoes. This suggesting that mosquito-based methods for measuring transmission in the field need to be refined as they currently only consider whether a mosquito is infected or not (and not how heavily infected the mosquito is). Novel transmission reducing drugs and vaccines are tested by experimentally infecting people using infectious mosquitoes. This work indicates that it is important to further standardise infectious dose in malaria experimental infections to enable the efficacy of new interventions to be accurately compared. The work also provides direct evidence to suggest that the world’s first licenced malaria vaccine may be partially effective because it fails to provide protection against highly infected mosquitoes.

Associations between Season and Gametocyte Dynamics in Chronic Plasmodium falciparum Infections

INTRODUCTION

In a markedly seasonal malaria setting, the transition from the transmission-free dry season to the transmission season depends on the resurgence of the mosquito population following the start of annual rains. The sudden onset of malaria outbreaks at the start of the transmission season suggests that parasites persist during the dry season and respond to either the reappearance of vectors, or correlated events, by increasing the production of transmission stages. Here, we investigate whether Plasmodium falciparum gametocyte density and the correlation between gametocyte density and parasite density show seasonal variation in chronic (largely asymptomatic) carriers in eastern Sudan.

MATERIALS AND METHODS

We recruited and treated 123 malaria patients in the transmission season 2001. We then followed them monthly during four distinct consecutive epidemiological seasons: transmission season 1, transmission-free season, pre-clinical period, and transmission season 2. In samples collected from 25 participants who fulfilled the selection criteria of the current analysis, we used quantitative PCR (qPCR) and RT-qPCR to quantify parasite and gametocyte densities, respectively.

RESULTS AND DISCUSSION

We observed a significant increase in gametocyte density and a significantly steeper positive correlation between gametocyte density and total parasite density during the pre-clinical period compared to the preceding transmission-free season. However, there was no corresponding increase in the density or prevalence of total parasites or gametocyte prevalence. The increase in gametocyte production during the pre-clinical period supports the hypothesis that P. falciparum may respond to environmental cues, such as mosquito biting, to modulate its transmission strategy. Thus, seasonal changes may be important to ignite transmission in unstable-malaria settings.

Onchocerciasis transmission in Ghana: the human blood index of sibling species of the Simulium damnosum complex

Background

Vector-biting behaviour is important for vector-borne disease (VBD) epidemiology. The proportion of blood meals taken on humans (the human blood index, HBI), is a component of the biting rate per vector on humans in VBD transmission models. Humans are the definitive host of Onchocerca volvulus, but the simuliid vectors feed on a range of animals and HBI is a key indicator of the potential for human onchocerciasis transmission. Ghana has a diversity of Simulium damnosum complex members, which are likely to vary in their HBIs, an important consideration for parameterization of onchocerciasis control and elimination models.

Methods

Host-seeking and ovipositing S. damnosum (sensu lato) (s.l.) were collected from seven villages in four Ghanaian regions. Taxa were morphologically and molecularly identified. Blood meals from individually stored blackfly abdomens were used for DNA profiling, to identify previous host choice. Household, domestic animal, wild mammal and bird surveys were performed to estimate the density and diversity of potential blood hosts of blackflies.

Results

A total of 11,107 abdomens of simuliid females (which would have obtained blood meal(s) previously) were tested, with blood meals successfully amplified in 3,772 (34 %). A single-host species was identified in 2,857 (75.7 %) of the blood meals, of which 2,162 (75.7 %) were human. Simulium soubrense Beffa form, S. squamosum C and S. sanctipauli Pra form were the most anthropophagic (HBI = 0.92, 0.86 and 0.70, respectively); S. squamosum E, S. yahense and S. damnosum (sensu stricto) (s.s.)/S. sirbanum were the most zoophagic (HBI = 0.44, 0.53 and 0.63, respectively). The degree of anthropophagy decreased (but not statistically significantly) with increasing ratio of non-human/human blood hosts. Vector to human ratios ranged from 139 to 1,198 blackflies/person.

Conclusions

DNA profiling can successfully identify blood meals from host-seeking and ovipositing blackflies. Host choice varies according to sibling species, season and capture site/method. There was no evidence that HBI is vector and/or host density dependent. Transmission breakpoints will vary among locations due to differing cytospecies compositions and vector abundances.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-016-1703-2) contains supplementary material, which is available to authorized users.

Assessing the impact of next-generation rapid diagnostic tests on Plasmodium falciparum malaria elimination strategies

Mass-screen-and-treat and targeted mass-drug-administration strategies are being considered as a means to interrupt transmission of Plasmodium falciparum malaria. However, the effectiveness of such strategies will depend on the extent to which current and future diagnostics are able to detect those individuals who are infectious to mosquitoes. We estimate the relationship between parasite density and onward infectivity using sensitive quantitative parasite diagnostics and mosquito feeding assays from Burkina Faso. We find that a diagnostic with a lower detection limit of 200 parasites per microlitre would detect 55% of the infectious reservoir (the combined infectivity to mosquitoes of the whole population weighted by how often each individual is bitten) whereas a test with a limit of 20 parasites per microlitre would detect 83% and 2 parasites per microlitre would detect 95% of the infectious reservoir. Using mathematical models, we show that increasing the diagnostic sensitivity from 200 parasites per microlitre (equivalent to microscopy or current rapid diagnostic tests) to 2 parasites per microlitre would increase the number of regions where transmission could be interrupted with a mass-screen-and-treat programme from an entomological inoculation rate below 1 to one of up to 4. The higher sensitivity diagnostic could reduce the number of treatment rounds required to interrupt transmission in areas of lower prevalence. We predict that mass-screen-and-treat with a highly sensitive diagnostic is less effective than mass drug administration owing to the prophylactic protection provided to uninfected individuals by the latter approach. In low-transmission settings such as those in Southeast Asia, we find that a diagnostic tool with a sensitivity of 20 parasites per microlitre may be sufficient for targeted mass drug administration because this diagnostic is predicted to identify a similar village population prevalence compared with that currently detected using polymerase chain reaction if treatment levels are high and screening is conducted during the dry season. Along with other factors, such as coverage, choice of drug, timing of the intervention, importation of infections, and seasonality, the sensitivity of the diagnostic can play a part in increasing the chance of interrupting transmission.

Characterization of the infectious reservoir of malaria with an agent-based model calibrated to age-stratified parasite densities and infectiousness

Background

Elimination of malaria can only be achieved through removal of all vectors or complete depletion of the infectious reservoir in humans. Mechanistic models can be built to synthesize diverse observations from the field collected under a variety of conditions and subsequently used to query the infectious reservoir in great detail.

Methods

The EMOD model of malaria transmission was calibrated to prevalence, incidence, asexual parasite density, gametocyte density, infection duration, and infectiousness data from nine study sites. The infectious reservoir was characterized by age and parasite detectability with diagnostics of varying sensitivity over a range of transmission intensities with and without case management and vector control. Mass screen-and-treat drug campaigns were tested for likelihood of achieving elimination.

Results

The composition of the infectious reservoir is similar over a range of transmission intensities, and higher intensity settings are biased towards infections in children. Recent ramp-ups in case management and use of insecticide-treated bed nets (ITNs) reduce the infectious reservoir and shift the composition towards sub-microscopic infections. Mass campaigns with anti-malarial drugs are highly effective at interrupting transmission if deployed shortly after ITN campaigns.

Conclusions

Low-density infections comprise a substantial portion of the infectious reservoir. Proper timing of vector control, seasonal variation in transmission intensity and mass drug campaigns allows lingering population immunity to help drive a region towards elimination.

Electronic supplementary material

The online version of this article (doi:10.1186/s12936-015-0751-y) contains supplementary material, which is available to authorized users.