Transcriptome analysis based detection of Plasmodium falciparum development in Anopheles stephensi mosquitoes

Effects of sample preservation methods and duration of storage on the performance of mid-infrared spectroscopy for predicting the age of malaria vectors

BACKGROUND

Monitoring the biological attributes of mosquitoes is critical for understanding pathogen transmission and estimating the impacts of vector control interventions on the survival of vector species. Infrared spectroscopy and machine learning techniques are increasingly being tested for this purpose and have been proven to accurately predict the age, species, blood-meal sources, and pathogen infections in Anopheles and Aedes mosquitoes. However, as these techniques are still in early-stage implementation, there are no standardized procedures for handling samples prior to the infrared scanning. This study investigated the effects of different preservation methods and storage duration on the performance of mid-infrared spectroscopy for age-grading females of the malaria vector, Anopheles arabiensis.

METHODS

Laboratory-reared An. arabiensis (N = 3681) were collected at 5 and 17 days post-emergence, killed with ethanol, and then preserved using silica desiccant at 5 °C, freezing at - 20 °C, or absolute ethanol at room temperature. For each preservation method, the mosquitoes were divided into three groups, stored for 1, 4, or 8 weeks, and then scanned using a mid-infrared spectrometer. Supervised machine learning classifiers were trained with the infrared spectra, and the support vector machine (SVM) emerged as the best model for predicting the mosquito ages.

RESULTS

The model trained using silica-preserved mosquitoes achieved 95% accuracy when predicting the ages of other silica-preserved mosquitoes, but declined to 72% and 66% when age-classifying mosquitoes preserved using ethanol and freezing, respectively. Prediction accuracies of models trained on samples preserved in ethanol and freezing also reduced when these models were applied to samples preserved by other methods. Similarly, models trained on 1-week stored samples had declining accuracies of 97%, 83%, and 72% when predicting the ages of mosquitoes stored for 1, 4, or 8 weeks respectively.

CONCLUSIONS

When using mid-infrared spectroscopy and supervised machine learning to age-grade mosquitoes, the highest accuracies are achieved when the training and test samples are preserved in the same way and stored for similar durations. However, when the test and training samples were handled differently, the classification accuracies declined significantly. Protocols for infrared-based entomological studies should therefore emphasize standardized sample-handling procedures and possibly additional statistical procedures such as transfer learning for greater accuracy.

Contribution of Transcriptome to Elucidate the Biology of Plasmodium spp

In the present review, we discuss some of the new technologies that have been applied to elucidate how Plasmodium spp escape from the immune system and subvert the host physiology to orchestrate the regulation of its biological pathways. Our manuscript describes how techniques such as microarray approaches, RNA-Seq and single-cell RNA sequencing have contributed to the discovery of transcripts and changed the concept of gene expression regulation in closely related malaria parasite species. Moreover, the text highlights the contributions of high-throughput RNA sequencing for the current knowledge of malaria parasite biology, physiology, vaccine target and the revelation of new players in parasite signaling.

Plasmodium falciparum Pf77 and male development gene 1 as vaccine antigens that induce potent transmission-reducing antibodies

Malaria vaccines that disrupt the Plasmodium life cycle in mosquitoes and reduce parasite transmission in endemic areas are termed transmission-blocking vaccines (TBVs). Despite decades of research, there are only a few Plasmodium falciparum antigens that indisputably and reproducibly demonstrate transmission-blocking immunity. So far, only two TBV candidates have advanced to phase 1/2 clinical testing with limited success. By applying an unbiased transcriptomics-based approach, we have identified Pf77 and male development gene 1 (PfMDV-1) as two P. falciparum TBV antigens that, upon immunization, induced antibodies that caused reductions in oocyst counts in Anopheles mosquito midguts in a standard membrane feeding assay. In-depth studies were performed to characterize the genetic diversity of, stage-specific expression by, and natural immunity to these two molecules to evaluate their suitability as TBV candidates. Pf77 and PfMDV-1 display limited antigenic polymorphism, are pan-developmentally expressed within the parasite, and induce naturally occurring antibodies in Ghanaian adults, which raises the prospect of natural boosting of vaccine-induced immune response in endemic regions. Together, these biological properties suggest that Pf77 and PfMDV-1 may warrant further investigation as TBV candidates.

The impact of within-vector parasite development on the extrinsic incubation period

Mosquito-borne diseases, in particular malaria, have a significant burden worldwide leading to nearly half a million deaths each year. The malaria parasite requires a vertebrate host, such as a human, and a vector host, the Anopheles mosquito, to complete its full life cycle. Here, we focus on the parasite dynamics within the vector to examine the first appearance of sporozoites in the salivary glands, which indicates a first time of infectiousness of mosquitoes. The timing of this period of pathogen development in the mosquito until transmissibility, known as the extrinsic incubation period, remains poorly understood. We develop compartmental models of within-mosquito parasite dynamics fitted with experimental data on oocyst and sporozoite counts. We find that only a fraction of oocysts burst to release sporozoites and bursting must be delayed either via a time-dependent function or a gamma-distributed set of compartments. We use Bayesian inference to estimate distributions of parameters and determine that bursting rate is a key epidemiological parameter. A better understanding of the factors impacting the extrinsic incubation period will aid in the development of interventions to slow or stop the spread of malaria.

Plasmodium falciparum Gametocyte Culture and Mosquito Infection Through Artificial Membrane Feeding

Malaria remains one of the most important public health problems, causing significant morbidity and mortality. Malaria is a mosquito borne disease transmitted through an infectious bite from the female Anopheles mosquito. Malaria control will eventually rely on a multitude of approaches, which includes ways to block transmission to, through and from mosquitoes. To study mosquito stages of malaria parasites in the laboratory, we have optimized a protocol to culture highly infectious Plasmodium falciparum gametocytes, a parasite stage required for transmission from the human host to the mosquito vector. P. falciparum gametocytes mature through five morphologically distinct steps, which takes approximately 1-2 weeks. Gametocyte culture described in this protocol is completed in 15 days and are infectious to mosquitoes from days 15-18. These protocols were developed to maintain a continuous cycle of infection competent gametocytes and to maintain uninterrupted supply of mosquito stages of the parasite. Here, we describe the methodology of gametocyte culture and how to infect mosquitoes with these parasites using glass membrane feeders.

Functional genomics of simian malaria parasites and host-parasite interactions

Two simian malaria parasite species, Plasmodium knowlesi and Plasmodium cynomolgi, cause zoonotic infections in Southeast Asia, and they have therefore gained recognition among scientists and public health officials. Notwithstanding, these species and others including Plasmodium coatneyi have served for decades as sources of knowledge on the biology, genetics and evolution of Plasmodium, and the diverse ramifications and outcomes of malaria in their monkey hosts. Experimental analysis of these species can help to fill gaps in knowledge beyond what may be possible studying the human malaria parasites or rodent parasite species. The genome sequences for these simian malaria parasite species were reported during the last decade, and functional genomics research has since been pursued. Here research on the functional genomics analysis involving these species is summarized and their importance is stressed, particularly for understanding host–parasite interactions, and potentially testing novel interventions. Importantly, while Plasmodium falciparum and Plasmodium vivax can be studied in small New World monkeys, the simian malaria parasites can be studied more effectively in the larger Old World monkey macaque hosts, which are more closely related to humans. In addition to ex vivo analyses, experimental scenarios can include passage through Anopheline mosquito hosts and longitudinal infections in monkeys to study acute and chronic infections, as well as relapses, all in the context of the in vivo host environment. Such experiments provide opportunities for understanding functional genomic elements that govern host–parasite interactions, immunity and pathogenesis in-depth, addressing hypotheses not possible from in vitro cultures or cross-sectional clinical studies with humans.