Biology subjects

Schwabl, P.

Publications and source records attributed to Schwabl, P..

7 recordsLinked to original sources

bioRxiv2026

Additional blood meals increase mosquito infectivity by accelerating the transcriptional development of Plasmodium sporozoites

Sporozoites, the infectious stage of Plasmodium malaria parasites, must invade two different tissues in two very different hosts to ensure transmission: the mosquito salivary glands and the human liver. Whether infectivity to hepatocytes is affected by physiological components, such as the availability of nutrients within the Anopheles female, is not well understood. Here we show that Plasmodium falciparum sporozoite infectivity to hepatocytes is increased if mosquitoes take an additional blood meal while oocysts are developing. Infection rates of HC04.J7 hepatocytes at 24 h were 1.8-fold higher for P. falciparum salivary gland sporozoites isolated from Anopheles gambiae females fed twice (2BF) compared to those which only received the infectious blood meal (1BF). This increase in infectivity was observed at an early infection timepoint (day 11) and was accompanied by a marked shift in the transcriptional profiles of 2BF salivary gland sporozoites, identifying genes likely involved in infection and development in the mammalian host. Overall, our data reveal new factors potentially involved in sporozoite infectivity, and have broad implications for understanding transmission of malaria in endemic areas where multiple blood meals commonly shape available resources for adult female mosquitoes.

microbiology↗

bioRxiv2025

Distinguishing new from persistent infections at the strain level using longitudinal genotyping data

MotivationLongitudinal pathogen genotyping data from individual hosts can uncover strain-specific infection dynamics and their relationships to disease and intervention, especially in the malaria field. An important use case involves distinguishing newly incident from pre-existing (persistent) strains, but implementation faces statistical challenges relating to individual samples containing multiple strains, strains sharing alleles, and markers dropping out stochastically during the genotyping process. Current approaches to distinguish new versus persistent strains therefore rely primarily on simple rules that consider only the time since alleles were last observed. ResultsWe developed DINEMITES (Distinguishing New Malaria Infections in Time Series), a set of statistical methods to estimate, from longitudinal genotyping data, the probability each sequenced allele represents a new infection harboring that allele, the total molecular force of infection (molFOI, the cumulative number of newly acquired strains over time) for each individual, and the total number of new infection events for each individual. DINEMITES can handle time points with missing sequencing data, incorporate treatment history and covariates affecting the rate of new or persistent infections, and can scale to studies with thousands of samples sequenced across multiple loci containing hundreds of possible alleles. In synthetic evaluations, the DINEMITES Bayesian model, which generally outperformed an alternative clustering-based model also developed in this work, accurately estimated key clinical parameters such as molFOI (bias 2.5, compared to -12.2 for a typical simple rule). When applied to three real longitudinal genotyping datasets, the model detected 33%, 112%, and 359% more average infections per participant than would have been detected by applying a typical simple rule to the equivalent datasets without sequencing. Availability and implementationDINEMITES is freely available as an R package, along with documentation, tutorials, and example data, at https://github.com/WillNickols/dinemites.

genomics↗

bioRxiv2024

Temporal and spatial dynamics of Plasmodium falciparum clonal lineages in Guyana

Plasmodium parasites, the causal agents of malaria, are eukaryotic organisms that obligately undergo sexual recombination within mosquitoes. However, in low transmission settings where most mosquitoes become infected with only a single parasite clone, parasites recombine with themselves, and the clonal lineage is propagated rather than broken up by outcrossing. We investigated whether stochastic/neutral factors drive the persistence and abundance of Plasmodium falciparum clonal lineages in Guyana, a country with relatively low malaria transmission, but the only setting in the Americas in which an important artemisinin resistance mutation (pfk13 C580Y) has been observed. To investigate whether this clonality was potentially associated with the persistence and spatial spread of the mutation, we performed whole genome sequencing on 1,727 Plasmodium falciparum samples collected from infected patients across a five-year period (2016- 2021). We characterized the relatedness between each pair of monoclonal infections (n=1,409) through estimation of identity by descent (IBD) and also typed each sample for known or candidate drug resistance mutations. A total of 160 clones (mean IBD [≥] 0.90) were circulating in Guyana during the study period, comprising 13 highly related clusters (mean IBD [≥] 0.40). In the five-year study period, we observed a decrease in frequency of a mutation associated with artemisinin partner drug (piperaquine) resistance (pfcrt C350R) and limited co-occurence of pfcrt C350R with duplications of plasmepsin 2/3, an epistatic interaction associated with piperaquine resistance. We additionally report polymorphisms exhibiting evidence of selection for drug resistance or other phenotypes and reported a novel pfk13 mutation (G718S) as well as 61 nonsynonymous substitutions that increased markedly in frequency. However, P. falciparum clonal dynamics in Guyana appear to be largely driven by stochastic factors, in contrast to other geographic regions. The use of multiple artemisinin combination therapies in Guyana may have contributed to the disappearance of the pfk13 C580Y mutation. Author SummaryMalaria is caused by eukaryotic Plasmodium parasites, which undergo sexual recombination within mosquitoes. In settings with low transmission, such as Guyana, these parasites often recombine with themselves, leading to the propagation of identical clones. We explored the population genomics of Plasmodium falciparum malaria parasites in Guyana over five years to characterize clonal transmission dynamics and understand whether they were influenced by local drug resistance mutations under strong selection, including pfk13 C580Y, which confers resistance to artemisinin, and pfcrt C350R, which confers resistance to piperaquine. Using whole genome sequencing on 1,463 samples, we identified 160 clones, in which all parasites share at least 90% of their genomes through recent common ancestry. We observed a decrease in frequency of the pfcrt C350R mutation, as well as the disappearance of pfk13 C580Y. Our findings contrast with the deterministic rise of drug resistance mutations observed in other geographic regions, sometimes associated with clonality. The simultaneous use of at least two different artemisinin combination therapies may have prevented the spread of an artemisinin-resistant clone in Guyana, suggesting a strategy for resistance management in other geographic regions.

genomics↗

bioRxiv2023

Transcriptomic signatures of progressive and regressive liver fibrosis and portal hypertension

Persistent liver injury triggers a fibrogenic program that causes pathologic remodelling of the hepatic microenvironment (i.e., liver fibrosis) and portal hypertension. The dynamics of gene regulation during liver disease progression and regression remain understudied. Here, we generated hepatic transcriptome profiles in two well-established liver disease models at peak fibrosis and during spontaneous regression after the removal of the inducing agents. We linked the dynamics of key liver disease readouts, such as portal pressure, collagen proportionate area, and transaminase serum levels, to most differentially expressed genes, enabling the identification of transcriptomic signatures of progressive vs. regressive liver fibrosis and portal hypertension. These candidate biomarkers (e.g., Scube1, Tcf4, Src, Hmga1, Trem2, Mafk, Mmp7) were also validated in RNA-seq datasets of patients with cirrhosis and portal hypertension. Finally, deconvolution analysis identified major cell types and suggested an association of macrophage and portal hepatocyte signatures with portal hypertension and fibrosis area in both models.

systems biology↗

bioRxiv2020

Genome-wide locus sequence typing (GLST) of eukaryotic pathogens

Analysis of genetic polymorphism is a powerful tool for epidemiological surveillance and research. Powerful inference from pathogen genetic variation, however, is often restrained by limited access to representative target DNA, especially in the study of obligate parasitic species for which ex vivo culture is resource-intensive or bias-prone. Modern sequence capture methods enable pathogen genetic variation to be analyzed directly from vector/host material but are often too complex and expensive for resource-poor settings where infectious diseases prevail. This study proposes a simple, cost-effective genome-wide locus sequence typing (GLST) tool based on massive parallel amplification of information hotspots throughout the target pathogen genome. The multiplexed polymerase chain reaction amplifies hundreds of different, user-defined genetic targets in a single reaction tube, and subsequent agarose gel-based clean-up and barcoding completes library preparation at under 4 USD per sample. Approximately 100 libraries can be sequenced together in one Illumina MiSeq run. Our study generates a flexible GLST primer panel design workflow for Trypanosoma cruzi, the parasitic agent of Chagas disease. We successfully apply our 203-target GLST panel to direct, culture-free metagenomic extracts from triatomine vectors containing a minimum of 3.69 pg/l T. cruzi DNA and further elaborate on method performance by sequencing GLST libraries from T. cruzi reference clones representing discrete typing units (DTUs) TcI, TcIII, TcIV, and TcVI. The 780 SNP sites we identify in the sample set repeatably distinguish parasites infecting sympatric vectors and detect correlations between genetic and geographic distances at regional (< 150 km) as well as continental scales. The markers also clearly separate DTUs. We discuss the advantages, limitations and prospects of our method across a spectrum of epidemiological research.

genetics↗

bioRxiv2019

Remarkable genetic diversity of Trypanosoma cruzi and Trypanosoma rangeli in two localities of southern Ecuador identified via deep sequencing of mini-exon gene amplicons

Trypanosoma cruzi, causative agent of Chagas disease, and T. rangeli are kinetoplastid parasites endemic to Latin America. Although closely-related to T. cruzi and capable of infecting humans, T. rangeli is non-pathogenic. Both parasite species are transmitted by triatomine bugs, and the presence of T. rangeli constitutes a confounding factor in the study of Chagas prevalence and transmission dynamics. T. cruzi possesses high molecular heterogeneity: six discrete typing units (DTUs) are currently recognized. In Ecuador, TcI predominates while other DTUs are seldom reported. Here, infection by T. cruzi and/or T. rangeli in triatomine bugs from two communities of southern Ecuador was evaluated via PCR product size polymorphism of kinetoplast-minicircle sequences and the non-transcribed spacer region of the mini-exon gene. Additionally, mini-exon amplicons were deep-sequenced to analyze single nucleotide polymorphisms and mixed infections. As a control, mini-exon products from several monoclonal reference strains were included. T. cruzi genetic diversity was significantly greater in adult vectors than in nymphal stage V vectors. Among infected triatomines, deep sequencing revealed one T. rangeli infection (3%), 9 T. cruzi infections (27.3%) and 23 T. cruzi / T. rangeli mixed infections (69.7%), suggesting that T. rangeli prevalence has been largely underestimated in the region. Furthermore, deep-sequencing detected TcIV sequences in six samples (first TcIV record in southern Ecuador). Our data indicate that amplicon size analysis alone is not reliable for parasite identification/typing in mixed infections containing both T. cruzi and T. rangeli, or when multiple T. cruzi DTUs are present. Additionally, our analysis showed extensive overlap among the parasite populations present in the two studied localities (ca. 28 km apart); suggesting active parasite dispersal over the study area. Our results highlight the value of amplicon sequencing methodologies to clarify the population dynamics of kinetoplastid parasites in endemic regions and inform control campaigns in southern Ecuador.

genetics↗

bioRxiv2018

Parallel sexual and parasexual population genomic structure in Trypanosoma cruzi

Genetic exchange and hybridization in parasitic organisms is fundamental to the exploitation of new hosts and host populations. Variable mating frequency often coincides with strong metapopulation structure, where patchy selection or demography may favor different reproductive modes. Evidence for genetic exchange in Trypanosoma cruzi over the last 30 years has been limited and inconclusive. The reproductive modes of other medically important trypanosomatids are better established, although little is known about their variability on a spatio-temporal scale. Targeting a contemporary focus of T. cruzi transmission in southern Ecuador, we present compelling evidence from 45 sequenced genomes that T. cruzi (discrete typing unit I) maintains sexual populations alongside others that represent clonal bursts of parasexual origin. Strains from one site exhibit genome-wide Hardy-Weinberg equilibrium and intra-chromosomal linkage decay consistent with meiotic reproduction. Strains collected from adjacent areas (>6 km) show excess heterozygosity, near-identical haplo-segments, common mitochondrial sequences and levels of aneuploidy incompatible with Mendelian sex. Certain individuals exhibit trisomy in as many as fifteen chromosomes. Others present fewer, yet shared, aneuploidies reminiscent of mitotic genome erosion and parasexual genetic exchange. Genomic and intra-genomic phylogenetics as well as haplotype co-ancestry analyses indicate a clear break in gene-flow between these distinct populations, despite the fact that they occasionally co-occur in vectors and hosts. We propose biological explanations for the fine-scale disconnectivity we observe and discuss the epidemiological consequences of flexible reproductive modes and their genomic architecture for this medically important parasite.

evolutionary biology↗