Dual-scRNA-seq analysis reveals rare and uncommon parasitized cell populations in chronic L. donovani infection

Droplet microfluidics: unveiling the hidden complexity of the human microbiome

The human body harbors diverse microbial communities essential for maintaining health and influencing disease processes. Droplet microfluidics, a precise and high-throughput platform for manipulating microscale droplets, has become vital in advancing microbiome research. This review introduces the foundational principles of droplet microfluidics, its operational capabilities, and wide-ranging applications. We emphasize its role in enhancing single-cell sequencing technologies, particularly genome and RNA sequencing, transforming our understanding of microbial diversity, gene expression, and community dynamics. We explore its critical function in isolating and cultivating traditionally unculturable microbes and investigating microbial activity and interactions, facilitating deeper insight into community behavior and metabolic functions. Lastly, we highlight its broader applications in microbial analysis and its potential to revolutionize human health research by driving innovations in diagnostics, therapeutic development, and personalized medicine. This review provides a comprehensive overview of droplet microfluidics' impact on microbiome research, underscoring its potential to transform our understanding of microbial dynamics and their relevance to health and disease.

paraCell: a novel software tool for the interactive analysis and visualization of standard and dual host-parasite single-cell RNA-seq data

Advances in sequencing technology have led to a dramatic increase in the number of single-cell transcriptomic datasets. In the field of parasitology, these datasets typically describe the gene expression patterns of a given parasite species at the single-cell level under experimental conditions, in specific hosts or tissues, or at different life cycle stages. However, while this wealth of available data represents a significant resource, analysing these datasets often requires expert computational skills, preventing a considerable proportion of the parasitology community from meaningfully integrating existing single-cell data into their work. Here, we present paraCell, a novel software tool that allows the user to visualize and analyse pre-loaded single-cell data without requiring any programming ability. The source code is free to allow remote installation. On our web server, we demonstrated how to visualize and re-analyse published Plasmodium and Trypanosoma datasets. We have also generated Toxoplasma-mouse and Theileria-cow scRNA-seq datasets to highlight the functionality of paraCell for pathogen-host interaction. The analysis of the data highlights the impact of the host interferon-γ response and gene expression profiles associated with disease susceptibility by these intracellular parasites, respectively.

Macrophage Polarisation During Leishmania (Viannia) braziliensis Infection in Mice

Leishmania (Viannia) braziliensis causes cutaneous and mucocutaneous leishmaniasis. Macrophages are host cells for parasite replication and act as effector cells against the parasite. The two main macrophage phenotypes (M1 and M2) and their polarisation states have been implicated in Leishmania infection despite scarce data on L. (V.) braziliensis. In this study, we investigated the temporal and spatial distribution and predominance of M1 and M2 macrophages during L. (V.) braziliensis infection in Balb/c mice. Animals were infected with L. (V.) braziliensis promastigotes and were monitored for 25 weeks. Histopathological evaluation of footpad lesions, regional lymph nodes, and spleen; cellularity; and macrophage population quantification of M1, and M2 macrophages by flow cytometry were performed in different tissues. The results showed that after infection with either strain of L. (V.) braziliensis the lesions were small and non-ulcerated. The dissemination of parasites to tissues reinforced the characteristic visualisation of dermotropicL. (V.) braziliensis. The proportion of M2 macrophages in different tissues was significantly higher than that of M1 macrophages. Overall, the results reported here confirm that Leishmania an intracellular parasite, promotes and influences macrophage phenotype polarisation in different tissues over time, and researchers testing therapies based on macrophage phenotype regulation should consider this evidence.

Teratogenic parasites: disease mechanisms and emerging study models

Congenital infections are a leading preventable cause of pregnancy complications impacting both mother and fetus. Although advancements have been made in understanding various congenital infections, the mechanisms of parasitic infections during pregnancy remain poorly understood. This review covers the global incidence of three parasites capable of congenital transmission - Trypanosoma cruzi, Plasmodium spp., and Toxoplasma gondii - and the state of research into their transplacental transmission strategies. We highlight technological advancements in placental modeling that offer opportunities to reveal how parasites cause gestational pathology. Additionally, we discuss the likelihood that selective adaptation contributed to the evolution of mechanisms that facilitate placental infection. These insights provide a foundation for understanding the progression and pathology of congenital parasitic diseases and identifying future research directions.

Dissecting host-microbe interactions with modern functional genomics

Interrogation of host-microbe interactions has long been a source of both basic discoveries and benefits to human health. Here, we review the role that functional genomics approaches have played in such efforts, with an emphasis on recent examples that have harnessed technological advances to provide mechanistic insight at increased scale and resolution. Finally, we discuss how concurrent innovations in model systems and genetic tools have afforded opportunities to interrogate additional types of host-microbe relationships, such as those in the mammalian gut. Bringing these innovations together promises many exciting discoveries ahead.

Clinical anemia predicts dermal parasitism and reservoir infectiousness during progressive visceral leishmaniosis

Dogs represent the primary reservoir for Leishmania infantum human visceral leishmaniasis (VL) transmitted through phlebotomine sand flies. Public health initiatives targeting zoonotic VL commonly focus on dogs with severe clinical disease, often in renal failure, as they have previously been considered the most infectious to sand flies. However, more recent studies suggest that dogs with mild to moderate clinical disease may be more infectious than dogs with severe disease. The mechanisms of infectiousness from the skin and how this relates to transmissibility as clinical disease progresses is largely unknown. We evaluated dermal parasitism in dogs naturally infected with L. infantum across the four LeishVet clinical stages of disease. We establish the relationship between dermal parasitism, critical, frequently observed, clinical parameters such as anemia and creatinine, and infectiousness. Using RNAscope and confocal microscopy, we found notable variation in dermal parasitism between dogs, particularly within LeishVet II. Dogs with mild disease had significantly less dermal inflammation and parasitism than dogs with moderate or severe disease. We found significant correlations between anemia, dermal parasitism, and infectiousness (p = 0.0098, r = -0.4798; p = 0.0022, r = -0.8364). In contrast, we did not observe significant correlation between creatinine, a measure of renal function, and dermal parasitism or infectiousness. Host blood cell abnormalities, including anemia, correlate with infectiousness to sand flies. As these signs of disease often appear earlier in the course of disease, this indicates that classical measures of disease severity do not necessarily correlate with infectiousness or epidemiological importance. Public health initiatives attempting to break the zoonotic cycle of L. infantum infection should therefore focus on preventing transmission from infectious, anemic dogs, and not those with the most severe disease.

Adaptive and innate immune response of Leishmania infantum infection in Cirneco dell'Etna dog breed

Leishmania spp. are an intracellular protozoa present in many countries around the world. In Europe, both the parasite and the disease it causes, leishmaniasis, are endemic in the Mediterranean basin. Clinical signs and severity of disease are highly variable depending on the host in both humans and dogs, traditionally considered the main reservoir of the parasite. The reason for these differences is not known, but it has been speculated that some hosts present immune response, related to activation of Th1 and Th17, capable of controlling the spread of the parasite, and that these immune responses are related to the genetic background of the host. The Ibizan hound, an autochthonous canine breed of the Mediterranean basin, has been postulated as a breed resistant to infection, but other canine breeds evolutionarily close to it and native to this region have not been studied. One of them is the Cirneco dell'Etna, native to the island of Sicily in southern Italy. In this study, the immune response against L. infantum infection in this canine breed was analysed. The results showed that infected dogs of this breed present high levels of several cytokines related to Th1 and Th17 immune response, and significant correlation between serum levels of cytokines related to disease resistance. Further studies are necessary in this canine breed to determine the mechanisms of immune response and genetic background related to L. infantum infection control.

The immunomicrotope of Leishmania control and persistence

Leishmania is an intracellular protozoan transmitted by sand fly vectors; it causes cutaneous, mucocutaneous, or visceral disease. Its growth and survival are impeded by type 1 T helper cell responses, which entail interferon (IFN)-γ-mediated macrophage activation. Leishmania partially escapes this host defense by triggering immune cell and cytokine responses that favor parasite replication rather than killing. Novel methods for in situ analyses have revealed that the pathways of immune control and microbial evasion are strongly influenced by the tissue context, the micro milieu factors, and the metabolism at the site of infection, which we collectively term the 'immunomicrotope'. Understanding the components and the impact of the immunomicrotope will enable the development of novel strategies for the treatment of chronic leishmaniasis.

Connectivity Network Feature Sharing in Single-Cell RNA Sequencing Data Identifies Rare Cells

Single-cell RNA sequencing is a valuable technique for identifying diverse cell subtypes. A key challenge in this process is that the detection of rare cells is often missed by conventional methods due to low abundance and subtle features of these cells. To overcome this, we developed SCLCNF (Local Connectivity Network Feature Sharing in Single-Cell RNA sequencing), a novel approach that identifies rare cells by analyzing features uniquely expressed in these cells. SCLCNF creates a cellular connectivity network, considering how each cell relates to its neighbors. This network helps to pinpoint coexpression patterns unique to rare cells, utilizing a rarity score to confirm their presence. Our method performs better in detecting rare cells than existing techniques, offering enhanced robustness. It has proven to be effective in human gastrula data sets for accurately pinpointing rare cells, and in sepsis data sets where it uncovers previously unidentified rare cell populations.

MAPK/ERK activation in macrophages promotes Leishmania internalization and pathogenesis

The obligate intracellular parasite Leishmania binds several receptors to trigger uptake by phagocytic cells, ultimately resulting in visceral or cutaneous leishmaniasis. A series of signaling pathways in host cells, which are critical for establishment and persistence of infection, are activated during Leishmania internalization. Thus, preventing Leishmania uptake by phagocytes could be a novel therapeutic strategy for leishmaniasis. However, the host cellular machinery mediating promastigote and amastigote uptake is not well understood. Here, using small molecule inhibitors of Mitogen-activated protein/Extracellular signal regulated kinases (MAPK/ERK), we demonstrate that ERK1/2 mediates Leishmania amazonensis uptake and (to a lesser extent) phagocytosis of beads by macrophages. We find that inhibiting host MEK1/2 or ERK1/2 leads to inefficient amastigote uptake. Moreover, using inhibitors and primary macrophages lacking spleen tyrosine kinase (SYK) or Abl family kinases, we show that SYK and Abl family kinases mediate Raf, MEK, and ERK1/2 activity and are necessary for uptake. Finally, we demonstrate that trametinib, a MEK1/2 inhibitor used to treat cancer, reduces disease severity and parasite burden in Leishmania-infected mice, even if it is started after lesions develop. Our results show that maximal Leishmania infection requires MAPK/ERK and highlight potential for MAPK/ERK-mediated signaling pathways to be novel therapeutic targets for leishmaniasis.

Long-term hematopoietic stem cells trigger quiescence in Leishmania parasites

Addressing the challenges of quiescence and post-treatment relapse is of utmost importance in the microbiology field. This study shows that Leishmania infantum and L. donovani parasites rapidly enter into quiescence after an estimated 2-3 divisions in both human and mouse bone marrow stem cells. Interestingly, this behavior is not observed in macrophages, which are the primary host cells of the Leishmania parasite. Transcriptional comparison of the quiescent and non-quiescent metabolic states confirmed the overall decrease of gene expression as a hallmark of quiescence. Quiescent amastigotes display a reduced size and signs of a rapid evolutionary adaptation response with genetic alterations. Our study provides further evidence that this quiescent state significantly enhances resistance to treatment. Moreover, transitioning through quiescence is highly compatible with sand fly transmission and increases the potential of parasites to infect cells. Collectively, this work identified stem cells in the bone marrow as a niche where Leishmania quiescence occurs, with important implications for antiparasitic treatment and acquisition of virulence traits.

No place to hide! A method for revealing hidden loci of infection

The capacity to infect and survive in a wide variety of host cells is amongst the strategies that contribute to pathogen persistence. The recent study by Karagiannis et al. presents an unbiased approach to identify infected cells in a visceral leishmaniasis (VL) infection, which revealed parasites in unexpected host cells.