Tag Archives: malaria

Interview with the authors: does indoor spraying alter the genetic diversity of malaria-causing parasites and what does this mean for long-term control?

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In a recent paper in Molecular Ecology, Argyropoulos and Ruybal-Pesántez et al. (2021) investigated the effects of indoor spraying on Plasmodium falciparum, the human malaria-causing protist. They find that 3 consecutive years of indoor spraying reduced transmission and prevalence of malaria by 90% and 35%, respectively, in the high malaria transmission site they surveyed. Despite these large reductions, a change in genetic diversity in P. falciparum that would indicate a large reduction in population size was not detected, illustrating the incredible resiliency of this parasite. Based on these data, the authors suggest that limiting malaria transmission in high transmission areas will require continued indoor spraying or other interventions such as mass drug administration. See the full article and interview with first authors Argyropoulos and Ruybal-Pesántez below for more details of this exciting work.

Images of the local terrain in Bongo District, Ghana taken at the same location at the end of the wet season in October (top) and at the end of the dry season in June (bottom). Photo Credit: Kathryn Tiedje

What led to your interest in this topic / what was the motivation for this study? Global efforts over the past 20 years have significantly reduced malaria mortality and morbidity around the world, but malaria transmission remains high in many countries in sub-Saharan Africa. A major challenge is the fact that most Plasmodium falciparum infections are asymptomatic creating a persistent parasite reservoir that continually fuels transmission to mosquitos. Our group has a long-standing collaboration with colleagues at the Navrongo Health Research Centre and Noguchi Memorial Institute of Medical Research in Ghana, and the University of Chicago in the US, to conduct longitudinal field-based epidemiological studies of the P. falciparumreservoir in Bongo District, Ghana (Tiedje et al., 2017). Our motivation for this study was to understand P. falciparum transmission dynamics in the context of the roll-out of a malaria control intervention by combining population genetics with more traditional epidemiological and entomological parameters. Our previous research in Bongo District established there was high levels of P. falciparum genetic diversity with no population structure (Ruybal‐Pesántez et al., 2017). We were therefore interested in exploring whether the addition of a short-term indoor residual spraying (IRS) programme against a background of widespread long-lasting insecticidal nets (LLINs) would bottleneck this P. falciparum population in Bongo and lead to reductions in diversity and changes in population structure. 

What difficulties did you run into along the way? One of the major technical limitations in P. falciparum genotyping is phasing multi-genome infections to assign multilocus haplotypes. Eighty per cent of the population of all ages where we work in Ghana have multiple diverse parasite genomes. This is  also a problem for whole genome sequencing of isolates. To get around this problem, we focus on genotyping monoclonal infections using panels of multi-allelic microsatellite markers or biallelic SNPs. In high-transmission settings like our study site in Ghana microsatellite genotyping of P. falciparum provides increased power of inference and higher resolution than biallelic SNPs (Anderson et al., 2000; Ellegren, 2004; Selkoe and Toonen, 2006).

What is the biggest or most surprising innovation highlighted in this study? In our paper, we find that despite the addition of three-rounds of IRS against a background of LLINs between 2013 – 2015, it did not lead to a population bottleneck or dramatic change in parasite genetic diversity. This was striking because IRS did achieve a >90% reduction in local malaria transmission intensity and 37.5% fewer malaria infections in the community. The potential for rebound of P. falciparum transmission is therefore highly likely if these control programmes are not implemented long-term. 

Moving forward, what are the next steps in this area of research? Population genomic approaches are increasingly being applied to enhance our understanding of epidemiology, transmission dynamics, and public health strategies for a variety of pathogens. In the malaria field, the potential of genomic data to guide control and elimination strategies has been recognized but is still in early stages with respect to its translation into general practice. In our paper, we highlight that genomic surveillance is pivotal to assess progress towards achieving the World Health Organisation Global Technical Strategy for Malaria 2016-2030 targets. Along with our collaborators in Ghana, we have conducted follow-up surveys in our study site to track the long-term implications of this IRS intervention, as well as other interventions that have been rolled out across Bongo District since 2015. We are also applying phylodynamic approaches to characterize variant antigen genes to further explore the impact of interventions on P. falciparum adaptation and fitness, as alternate but complementary surveillance metrics in this high-transmission setting. 

Dionne Argyropoulos, co-first author on this paper, is investigating the neutral and adaptive genetic diversity of P. falciparum in these follow-up surveys and in the context of other control interventions as part of her PhD research. Shazia Ruybal-Pesántez, co-first author on this paper, is now currently applying a suite of genomic epidemiology approaches to better understand residual and resurgent malaria transmission dynamics in the Asia-Pacific and Americas regions as part of her post-doctoral research.

What have you learned about methods and resources development over the course of this project? Firstly, it is important that you understand the basic principles of the concepts that you are using. It may seem rudimentary, but these principles will ensure that you are answering the scientific question that you are interested in and are maintaining scientific integrity throughout the research process. Asking for help or support from others in your field is also useful to bounce ideas and enhance your understanding of your research findings. The most exciting part of Molecular Ecology is how we utilise the insights molecular techniques to answer big picture questions. Our study integrated population genetics and genomic surveillance to address key research questions about malaria transmission and control interventions. To do this, we used existing molecular techniques (i.e., microsatellites) in new ways (i.e., to evaluate IRS over time). We also believe that it is important to not be afraid to apply novel techniques to new research questions, such as using bioinformatic tools and various packages in R.

What would your message be for students about to start developing or using novel techniques in Molecular Ecology? This project was unique as it involved field sample collection and processing, parasite genotyping, data generation and for the analysis required combining traditional epidemiological methods with population genetics and genomics approaches. When working with large sample sets and datasets, it is critical to pay attention to detail during data generation, curation and downstream analyses. Developing and strengthening coding skills was instrumental in enabling us to execute the necessary analyses of these data. We found R to be an incredibly useful resource to document our analyses and facilitate discussion and interpretation of the data with colleagues, while ensuring reproducibility of our work. We used several well-established R packages for data management and the population genetics analyses. Overall, this multidisciplinary project would not have been possible without being part of a multi-disciplinary team with a wealth of knowledge and the strong collaborations with experienced researchers in Ghana. 

Describe the significance of this research for the general scientific community in one sentence. We show how parasite genetics can be harnessed to better understand the efficacy of malaria control interventions, particularly by identifying key factors leading to parasite resilience that may not be reflected in other commonly used evaluation metrics. 

Describe the significance of this research for your scientific community in one sentence. Short-term indoor residual spraying with insecticides did not cause a dramatic change on the genetic diversity of P. falciparum in Bongo District, Ghana, therefore long-term strategies are necessary to genetically bottleneck the parasite population. 

Argyropoulos DC*, Ruybal-Pesántez S*, Deed SL, Oduro AR, Dadzie SK, Apparu MA, Asoala V, Pascual M, Koram KA, Day KP, Tredje KE. THe impact of indoor residual spraying on Plasmodium falciparum microsatellite variation in an area of high seasonal malaria transmission in Ghana, West Africa. Molecular Ecology. https://doi.org/10.1111/mec.16029. (*joint lead authors)

Joint lead authors Dionne Argyropoulos (left) and Shazia Ruybal-Pésantez (right). Photo Credits: The Stockholm International Youth Science Seminar, Unga Forskare; http://www.ungaforskare.se (left) and The Walter and Eliza Hall Institute of Medical Research; www.wehi.edu.au (right). 

Interview with the author: Using host transcriptomics to sample blood parasites

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Hosts offer diverse habitat for an incredibly rich array of microbial groups. Genomic resources for many groups residing within hosts (‘infra-communities’) are poor often due to the difficulty in isolating the DNA from the microbe from that of the host, particularly for species living within host cells. In this interview we go behind the scenes with Spencer Galen as he guides us through his transcriptomic approach he developed with colleagues to sample blood parasites such as malaria. Given how ubiquitous and important these parasites can be for animal health, this resource has the potential to pave the way for important advances in disease ecology. Read the paper here.

Avian blood transcriptomes revealed that hosts often have far more complex parasite communities than traditionally thought. For instance, the transcriptome of this Baltimore oriole (Icterus galbula) revealed at least six malaria parasite infections from three malaria parasite genera. The blood smear image from this bird shows the three genera in close contact within the host bloodstream. L: Leucocytozoon, PL: Plasmodium, PA: Parahaemoproteus.
Credit: Spencer Galen

What led to your interest in this topic / what was the motivation for this study? 

This study began with two classic ingredients of scientific discovery: a lot of frustration mixed with a bit of inspiration from other researchers. The frustration was born from a lack of available genetic resources for malaria parasites and other blood parasites, which I felt was hindering the kind of research that I wanted to do. The inspiration came during the first year of my PhD, when several papers were published within a span of just a few months showing that researchers were passively generating large quantities of blood parasite genomic data by sequencing the transcriptomes of their vertebrate hosts. My PhD advisor Susan Perkins and I thought that designing a study to explore this approach in more detail could solve some of my frustrations and help the field of blood parasite research at large.

What difficulties did you run into along the way? 

When we started this project there was always the looming possibility that we would sequence a number of host transcriptomes that were infected with blood parasites and simply not recover any useful parasite data. Even a small-scale transcriptomic project is not a trivial matter financially, and so I will admit that I lost some sleep wondering if this project was a bad idea. Fortunately, field and lab work went quite smoothly, and the results of my first scan for parasites within our initial test transcriptomes exceeded my wildest expectations. And so in reality the biggest challenge was my own self-doubt – if I had paid too much attention to those thoughts, this project might not have gotten off the ground.

What is the biggest or most surprising innovation highlighted in this study? 

We were astounded by just how prevalent blood parasite transcripts can be within host transcriptomes. For instance, in one bird (Vireo plumbeus sampled in the mountains of New Mexico) we found that nearly 17% of all contigs generated from the initial Trinity assembly were derived from a parasite that was infecting just 0.75% of all blood cells. A second surprising finding was the degree to which many of the birds that we sampled were infected with complex communities of parasites that we did not detect using traditional microscopic and DNA barcoding methods. Across all samples we found that transcriptomes revealed about ~20% more infections than the methods that are typically used to study these parasites. This included one individual bird that was infected by three different genera and at least six species of malaria parasite.

Moving forward, what are the next steps in this area of research?

While it is exciting to find that a transcriptomic approach can improve our ability to study the genomic diversity and abundance of wildlife blood parasites, it still remains a rather inefficient approach – at the end of the day, the majority of transcripts from each sample came from the host organism that was not the focus of our study. The next step will be to apply single-cell and other advanced RNA sequencing techniques that have successfully been applied to model systems to provide greater resolution to studies of blood parasite gene expression and host-parasite interactions.   

What would your message be for students about to start developing or using novel techniques in Molecular Ecology? 

At risk of sounding overly pessimistic, be prepared for things to fail the first time around and have a plan B in place. It is wonderful to have a lot of confidence, but pessimism does tend to favor preparedness. Small actions within this frame of mind can save you a lot of grief in the long run, and can be as simple as testing a new method on a sample that isn’t important before you start your project or taking the time to visit a lab to learn a technique before you try it yourself. I naturally assume everything I try in the lab will fail, so each time things work (and they actually often do!) it is a pleasant surprise.

What have you learned about methods and resources development over the course of this project? 

I think that there is a difference between producing a resource, and producing a resource that is easily accessible to the broader research community in practice. As a result, I spent a lot of time thinking about how my colleagues would most directly benefit from the data that we had generated. In the end we made the data from this study available in as many formats as we thought might be useful to other researchers (raw sequences, assemblies from before and after parasite identification, curated alignments, DNA barcodes, etc.). The amount of time that it took to prepare these datasets was extremely small relative to the length of the entire project, and I think will go a long way towards making these data as useful as possible.

Describe the significance of this research for the general scientific community in one sentence.

This study improves our ability to research the ecology and evolution of wildlife blood parasites, a cosmopolitan and ubiquitous group that is widely relevant to global health.

Describe the significance of this research for your scientific community in one sentence.

The methodological framework that we present in this study profoundly improves the genomic resource base that is available to research understudied blood pathogens of wildlife, as well as better detect multi-species parasite communities within hosts.