Microbiology

The discovery of broad-spectrum antiparasitic agents relies on the ability to evaluate drug efficacy under harmonized in vitro conditions across related species. However, current drug screening pipelines for intraerythrocytic parasites are constrained by the use of species-specific media with distinct nutrient compositions and serum sources, which hinder direct comparison of compound potency. To address this gap, we describe a unified erythrocytic culture system based on DMEM/F12 supplemented with 20% fetal bovine serum (DFS20), which supports robust asexual growth of multiple Plasmodium falciparum strains (3D7, Dd2, HB3, V1/S), Babesia duncani, Babesia divergens (Rouen 87), and Babesia MO1. Parasite proliferation and morphology in DFS20 are comparable to those observed in established species-specific media such as RPMI-1640 for P. falciparum and B. divergens and HL-1/Claycomb/DMEM/F12/SFM for B. duncani, while eliminating reliance on undefined or discontinued proprietary components. Importantly, this standardized medium enables cross-species growth inhibition assays for direct comparison of drug efficacy under identical conditions. Using this platform, we recently screened dihydrotriazines and biguanides targeting the conserved DHFR-TS enzymes and identified potent antifolate candidates with broad-spectrum activity against Babesia and Plasmodium species. For B. duncani, which is uniquely supported by both a continuous in vitro human erythrocyte culture system and a lethal in vivo mouse infection model, integration with the in-culture and in-mouse (ICIM) pipeline enables systematic validation of pharmacodynamics, pharmacokinetics, resistance, and toxicity. This unified DFS20-based system establishes a scalable and reproducible protocol for harmonized drug efficacy evaluation across intraerythrocytic parasites and provides a foundation for the development and prioritization of pan-antiparasitic therapies.

Babesiosis is a tick-borne disease caused by pathogens belonging to the genus Babesia. In humans, the disease presents as a malaria-like illness and can be fatal in immunocompromised and elderly people. In the past few years, human babesiosis has been a rising concern worldwide. The disease is transmitted through tick bite, blood transfusion, and transplacentally in rare cases, with several species of Babesia causing human infection. Babesia microti, Babesia duncani, and Babesia divergens are of particular interest because of their important health impact and amenability to research inquiries. B. microti, the most commonly reported Babesia pathogen infecting humans, can be propagated in immunocompetent and immunocompromised mice but so far has not been successfully continuously propagated in vitro in human red blood cells (hRBCs). Conversely, B. divergens can be propagated in vitro in hRBCs but lacks a mouse model to study its virulence. Recent studies have highlighted the uniqueness of B. duncani as an ideal model organism to study intraerythrocytic parasitism in vitro and in vivo. An optimized B. duncani in culture and in mouse (ICIM) model has recently been described, combining long-term continuous in vitro culture of the parasite in human red blood cells with an animal model of parasitemia (P) and lethal infection in C3H/HeJ mice. Here, we provide a detailed protocol for the use of the B. duncani ICIM model in research. This model provides a unique and sound foundation to gain further insights into the biology, pathogenesis, and virulence of Babesia and other intraerythrocytic parasites, and has been validated as an efficient system to evaluate novel strategies for the treatment of human babesiosis and possibly other parasitic diseases.

Graphical abstract:

ICIM model [Adapted and modified from Pal et al. (2022)]

Microorganisms have evolved adaptive strategies to respond to the autonomous degradation of their environment. Indeed, a growing culture progressively exhausts nutrients from its media and modifies its composition. Yet, how single cells react to these modifications remains difficult to study since it requires population-scale growth experiments to allow cell proliferation to have a collective impact on the environment, while monitoring the same individuals exposed to this environment for days. For this purpose, we have previously described an integrated microfluidic pipeline, based on continuous separation of the cells from the media and subsequent perfusion of the filtered media in an observation chamber containing isolated single cells. Here, we provide a detailed protocol to implement this methodology, including the setting up of the microfluidic system and the processing of timelapse images.

The relapsing malaria species, Plasmodium vivax, is the most widely distributed and difficult-to-treat cause of human malaria. The merozoites of P. vivax preferentially invade ephemeral human CD71⁺ reticulocytes (nascent reticulocytes), thereby limiting the development of a robust continuous culture in vitro. Fortunately, P. vivax’s sister species, P. cynomolgi Berok, can be cultured continuously, providing the ability to screen novel therapeutics drug and vaccine candidates in a reliable and high-throughput manner. Based on well-established growth inhibition activity (GIA) assays against P. falciparum and P. knowlesi, this protocol adopts the current flow cytometry assay methodology and investigates P. vivax inhibitory antibodies using the P. cynomolgi Berok invasion model based on the thiol-reactivity and DNA abundance of viable parasites in macaque erythrocytes. Established GIA assays screen antibodies at either a single concentration or high/low dose concentrations to provide quick insights for prioritizing potential antibodies capable of specifically interrupting parasite ligand and host receptor binding with minimal concentrations. Hence, this protocol expands on the existing GIA assay by using serially diluted antibodies and generating a dose-response curve to better quantify the inhibitory efficacy amongst selected vaccine candidates.

The diversity of lipid structures, properties, and combinations in biological tissues makes their extraction and analysis an experimental challenge. Accordingly, even for one of the simplest single-cellular fungi, the budding yeast (Saccharomyces cerevisiae), numerous extraction and analysis protocols have been developed to separate and quantitate the different molecular lipid species. Among them, most are quite sophisticated and tricky to follow. Herein, we describe a yeast total lipids extraction procedure with a relatively good yield, which is appropriate for subsequent thin-layer chromatography (TLC) or liquid chromatography-mass (LC-MS) analysis. We then discuss the most widely used solvent systems to separate yeast phospholipids and neutral lipids by TLC. Finally, we describe an easy and rapid method for silica gel staining by a Coomassie Brilliant Blue-methanol mixture. The stained lipid species can then be quantitated using imaging software such as ImageJ. Overall, the methods described in this protocol are time-saving and novice-friendly.

Plasmodium falciparum is a unicellular eukaryotic parasite that causes malaria in humans. The parasite is spread by Anopheles mosquitoes after ingestion of sexual stage parasites known as gametocytes. Malaria transmission depends on parasites switching from the disease-causing asexual blood forms to male and female gametocytes. The current protocol allows the simultaneous isolation of male and female parasites from the same population to study this critical lifecycle stage in a sex-specific manner. We have generated a transgenic P. falciparum cell line that expresses a GFP-tagged parasite protein in female, but not male, parasites. Gametocyte production is stress induced and, through a series of steps, sexual stage parasites are enriched relative to uninfected red blood cells or red blood cells infected with asexual stage parasites. Finally, male and female gametocytes are separated by fluorescence-activated cell sorting. This protocol allows for the separation of up to 12 million live male and female parasites from the same population, which are amenable to further analysis.

Hypnozoites are dormant liver-stage parasites unique to relapsing malarial species, including the important human pathogen Plasmodium vivax, and pose a barrier to the elimination of malaria. Little is known regarding the biology of these stages, largely due to their inaccessible location. Hypnozoites can be cultured in vitro but these cultures always consist of a mixture of hepatocytes, developing forms, and hypnozoites. Here, using a GFP-expressing line of the hypnozoite model parasite Plasmodium cynomolgi, we describe a protocol for the FACS-based isolation of malarial hypnozoites. The purified hypnozoites can be used for a range of ‘-omics’ studies to dissect the biology of this cryptic stage of the malarial life cycle.