Biology subjects

Roche, B.

Publications and source records attributed to Roche, B..

At least 19 recordsLinked to original sources

bioRxiv2025

Host competence-abundance relationships drive the dilution effect across multiple small mammal-borne pathogens

The "dilution effect" hypothesis suggests that high host diversity can reduce the prevalence of certain zoonotic pathogens. Despite growing interest, its generality and practical relevance remain debated. In particular most previous studies have focused on large scale analyses or meta-analyses, limiting their potential use for zoonotic outbreak prevention. Here, we present an extensive field-based study of small mammals and their multiple pathogens to assess diversity-disease relationships at a local scale, revealing pathogen-specific patterns. While no significant association was detected between the prevalence of some pathogens and host diversity, others such as Orthopoxvirus and a strain of Mycoplasma haemomuris exhibited dilution effect patterns, whereas another Mycoplasma haemomuris strain and Mycoplasma coccoides displayed amplification effects. Crucially, we demonstrate that these contrasting outcomes are consistently explained by the host competence-abundance relationship. Our findings underscore the importance of host community composition and highlight the need to consider multiple pathogens when evaluating the ecological mechanisms underpinning the diversity-disease relationships.

ecology↗

bioRxiv2025

Experimental evolution of Plasmodium yoelii in single and helminth-coinfected mice

Coinfection has the potential to affect key traits describing the infection dynamics, the severity of the disease and in fine parasite fitness. However, despite its pervasiveness, experimental work investigating how parasites adapt to the conditions provided by a coinfected host is mostly missing. Here, we adopted an experimental evolution approach to investigate if coinfection with the nematode Heligmosomoides polygyrus (Hp) affected the infection dynamics and virulence of the murine malaria parasite Plasmodium yoelii (Py). To this purpose, lines of Py were passaged either in single infected hosts (SI-lines) or in hosts that had been previously infected with Hp (COI-lines). After five and seven passages, the infection dynamics and virulence of evolved lines were compared to the ancestral Py population during single infection trials. As expected, we found that serial passages increased parasitemia and Py virulence, due to the competitive advantage of genotypes with the fastest replication rate, but SI-lines and COI-lines had similar replication rate and virulence. Hosts infected with evolved lines of Py were also less tolerant (steeper slope between red blood cell counts and parasitemia) but again there was no difference between SI-lines and COI-lines. In a second experiment, COI-lines were also used to infect hosts during coinfection trials, allowing us to compare within-host Py replication when the environment during the evaluation trials matched the environment experienced during the passages and when they were mismatched. The results showed that COI-lines used during single infection trials (mismatched environment) had a slower replication rate compared to both SI-lines and COI-lines used during matched-environment trials. Overall, although we did not find any difference in the virulence of SI-lines and COI-lines after seven passages, Py rapidly adapted to the environmental conditions provided by single infected or coinfected hosts, as shown by the slower replication rate found in mismatched-environment trials. Author SummaryCoinfection can alter infection dynamics, disease severity, and parasite fitness, yet experimental evidence on parasite adaptation to coinfected hosts is scarce. Here we used experimental evolution to assess whether coinfection with the nematode Heligmosomoides polygyrus influences the infection dynamics and virulence of the murine malaria parasite Plasmodium yoelii. Parasite lines were serially passaged in either single infected hosts or hosts previously infected with Heligmosomoides polygyrus. After multiple passages, evolved lines exhibited increased parasitemia and virulence compared to the ancestral strain, but no significant differences were found between lines evolved in single or coinfected hosts. Notably, parasite replication was reduced when lines evolved in coinfected hosts were tested in single infection environments, indicating rapid adaptation to host infection context. This suggests that while coinfection shapes within-host conditions, Plasmodium adapts rapidly to these conditions. These results have possible implications for understanding parasite evolution in fluctuating host environments, and the microevolutionary consequences for malaria of the deworming campaigns that are implemented to control helminthiases.

evolutionary biology↗

bioRxiv2025

RiboCop surveils pre-rRNA processing by Dicer in cellular quiescence

In nature, most cells exist in a quiescent G0 state in which cellular homeostasis must be rigorously maintained in the absence of cell division. Non-coding RNAs are prevalent in G0 and are important regulators of development and differentiation, but their function in quiescence is unclear. Here, we identify pre-rRNA as a direct target of the RNase III enzyme Dicer specifically in quiescence. Dicer is physically present at the rDNA, and improper rRNA processing in mutants results in a nucleolar stress response involving a novel trans-acting non-coding RNA (RiboCop) in complex with the highly conserved proteins Enp2/NOL10 and RNase H1. RiboCop is complementary to unprocessed pre-rRNA and triggers rDNA repeat silencing via Sir2, RENT, and histone H3-lysine-9 (H3K9) methylation. Thus RiboCop silences rDNA specifically during dormancy, when silencing of non-functional rRNA becomes essential.

genetics↗

bioRxiv2025

Coinfection with malaria alters the dynamics and fitness of an intestinal nematode

Infections with soil transmitted helminths (STHs) are highly prevalent in humans living in the intertropical region. While, in most cases, STHs can establish chronic infections, the dynamics of the infection can be altered when other parasites exploit the same host. These changes can have consequences in terms of the health of the host, the epidemiology of the disease (e.g., the duration of the infection and the inter-host transmission success) and the fitness of the parasite. Here, we investigated if the coinfection with Plasmodium yoelii alters the dynamics and the fitness of the murine nematode Heligmosomoides polygyrus. We found that, compared to single infected mice, coinfection produced an increase in the number of excreted eggs, while the biomass of adult worms in the intestine did not differ between single infected and coinfected mice. Moreover, the increase in egg excretion was also observed when Plasmodium infected hosts that had been harboring the nematode during the past four weeks (i.e., when the population size of adult worms can only decrease due to mortality). Therefore, the enhanced shedding of eggs reflects a plastic adjustment of worm fecundity to the environment provided by a coinfected host. This plastic response was modulated by the host Th2 immunity, as coinfection inhibited IL-4 and IL-13 gene expression, plasma levels of IL-5 and IL-13, and the expansion of GATA-3+ CD4+ T cells in the spleen. In agreement with this, experimentally inhibiting IL-13 with neutralizing antibodies reproduced the results observed in coinfected mice (an increase in egg excretion), while the administration of recombinant IL-13 reduced egg shedding. Interestingly, coinfection had a net positive effect on parasite fitness as shown by a longer persistence within the host and higher cumulative number of eggs excreted up to 99 days post-infection. Although the gene expression of Th2 cytokines was lower at day 99 p.i., coinfected mice still had a downregulated expression compared to single infected hosts. These results show that coinfection with Plasmodium has the potential to affect the epidemiology of STHs by increasing the number of eggs excreted over the whole infectious period and maintaining a larger environmental reservoir of transmissible stages. Author SummaryCoinfection between soil-transmitted helminths and malaria is common in several countries of the intertropical region, especially among the most vulnerable populations. Coinfection has the potential to worsen the symptoms caused by malaria, therefore it is important to understand what are the epidemiological and ecological factors that promote the occurrence of coinfection. Transmission of soil-transmitted helminths usually requires human contact with transmissible stages (parasitic eggs or larvae) in the environment; therefore, high egg excretion in the feces of infected people is a key factor contributing to maintain a reservoir of infective stages from which humans can get infected. In this study, we experimentally investigated whether coinfection with malaria alters the dynamics (egg excretion, infection persistence) of a murine intestinal nematode. We found that hosts infected with malaria and subsequently infected with the nematode, excreted more nematode eggs for a longer period, compared to single infected hosts. These changes were mediated by an impaired Th2 immune response in coinfected hosts. These results suggest that malaria coinfection produces positive feedback on key epidemiological traits of the nematode that can further enhance the risk of malaria/helminths cooccurrence.

evolutionary biology↗

bioRxiv2025

Parasite virulence in coinfected hosts: the importance of infection order

When hosts are simultaneously infected by different pathogens, the severity of the disease might be altered compared to hosts harboring single infections. The reasons underlying these changes in parasite virulence are manifold. Here, we investigated the importance of order and timing of infection. We used a model of rodent coinfection between two parasites that do not compete for common resources, an intestinal nematode (Heligmosomoides polygyrus, Hp) and an apicomplexan protozoan (Plasmodium yoelii, Py). During single infections, Hp induced only mild disease symptoms. Plasmodium produced a substantial reduction in the number of red blood cells but all mice recovered from the infection. A different picture emerged in coinfected hosts. Hp maintained a profile of mostly asymptomatic infection when infecting hosts that had been previously infected with Py. On the contrary, Py incurred substantially higher costs in hosts that had been previously infected with Hp. We then investigated the possible reasons underlying the increase of Py virulence in hosts that had been previously infected with Hp. We found that coinfected hosts were less able to control Py multiplication and to recover from infection-induced anemia. Coinfected hosts had similar levels of erythropoietin and similar renewal of lost red blood cells compared to single Py infected hosts, resulting in decreased tolerance to Py infection. Experimental administration of erythropoietin in coinfected (Hp infecting first) hosts, partially decreased the severity of disease symptoms and improved tolerance. The detoxification of free heme released during the lysis of red blood cells, and the expression of Th1 and anti-inflammatory cytokine genes were also similar between coinfected and single infected hosts. However, coinfected mice had higher proportions of regulatory T cells expressing the CTLA-4 immune checkpoint, suggesting an enhanced immunosuppressive activity of Tregs. Py infection also induced the exhaustion of CD8+ T cells, as coinfected mice had higher proportions of both PD-1+ and LAG-3+ CD8+ T cells, and an increase in the CD4+/CD8+ ratio. Overall, these results stress the importance of the order of infection as a major determinant of malaria severity in hosts harboring a gastrointestinal nematode infection. We discuss the possible epidemiological and evolutionary consequences of these results.

evolutionary biology↗

bioRxiv2024

Drivers of host-pathogen community assemblies in European forests and urban green spaces

Major advances in the understanding of infectious diseases have been achieved in the last decades. However, the persistence and re-emergence of pathogens continue to raise public and veterinary health concerns, of which the recent COVID-19 pandemic may be one of the most dramatic examples. Understanding the impact of habitat alterations and concomitant biodiversity loss on pathogen transmission and emergence from wildlife remains challenging. Here, we aim to elucidate the interlinkages between biodiversity and rodent-borne diseases at local and European scales. We present recently collected host-pathogen data from 21 temperate forest sites and eight urban green spaces throughout five European countries, environments where rodents are abundant and human/domestic animals - wildlife interactions are likely to occur. 3766 specimens were analyzed during the period from 2020 to 2022 comprising 15 different small mammal species. Different organ tissues of each specimen were screened for bacteria by either 16S rRNA amplicon sequencing or specific PCR. The presence of antibodies to different families of viruses was screened using immunofluorescent assays. A multitude of pathogens of zoonotic potential from several genera including Bartonella, Borrelia, Mycoplasma, Anaplasma, Neoehrlichia, Leptospira, Orthohantavirus and Orthopoxvirus were detected at non-negligible prevalence in 11 different terrestrial mammal species. A shift in host community composition was observed along the anthropization gradient with more urban adapters in more anthropized sites. Pathogen richness increased with an increase in host species diversity, following the "host-diversity begets parasite-diversity" hypothesis. The absence of some vector-transmitted parasites in urban areas suggests a shift in pathogen community along the anthropization gradient. Host species and host intrinsic factors were dominant explanatory variables for endoparasitic Mycoplasma species and Sarcocystidae, while extrinsic environmental and climatic factors where influential in explaining variations in occurrences of several vector-transmitted pathogens. Apodemus sylvaticus and Clethrionomys glareolus were important connector host species in respectively urban green spaces and temperate forests. Increased host diversity, but not anthropization, correlated with a richer pathogen community. These results ultimately lead to an increased understanding of the complex host-pathogen system at the local landscape that can aid future management decisions and support the public health sector.

ecology↗

bioRxiv2024

De novo evolution of transmissible tumors in Hydra

While most cancers are not transmissible, there are rare cases where cancer cells have acquired the ability to spread vertically or horizontally to other individuals, and sometimes species, causing epidemics in their hosts. However, as these transmissible cancers are usually detected once they are relatively well disseminated in host populations, the conditions associated with their origin remain poorly understood. Using the freshwater cnidarian Hydra oligactis, which exhibits spontaneous tumor development that in some strains became vertically transmitted, this study presents the first experimental observation of the evolution of a transmissible tumor. Specifically, we assessed the initial vertical transmission rate of spontaneous tumors and explored the potential for optimizing this rate through artificial selection. One of the hydra strains, which evolved transmissible tumors over five generations, was characterized by analysis of cell type and microbiome, as well as assessment of life-history traits. Our findings indicate that tumor transmission can be immediate for some strains and can be enhanced by selection. The resulting tumors are characterized by overproliferation of large interstitial stem cells and, in contrast with other transmissible tumors on Hydra, are not associated with a specific microbiome. Furthermore, although tumor transmission has only been established over 5 generations, it was sufficient to alter life-history traits in the host, suggesting a compensatory response. This work, therefore, makes the first contribution to understanding the conditions of transmissible cancer emergence and their short-term consequences for the host.

evolutionary biology↗

bioRxiv2023

SPATEs promote the survival of Shigella to the plasma complement system upon hemorrhage and bacteremia

Shigella spp. are the causative agents of shigellosis, which remains a leading cause of death in children under the age of five. Shigellosis is characterized by fever and results in hemorrhagic diarrhea; in more severe cases, Shigella bacteremia has been reported. These clinical features strongly suggest that Shigella survive exposure to plasma, although this has not yet been studied at the molecular level. In this report, we confirmed in a guinea pig model of shigellosis that local hemorrhages were induced by S. flexneri 5a and S. sonnei, and we demonstrated that Shigella reached mucosal CD31+/CD34+ blood vessels during the late stages of infection and further disseminated in the bloodstream. These results confirmed the exposure of Shigella to plasma components within the hemorrhagic colonic mucosa and in the bloodstream. We demonstrated that all the tested Shigella strains survived plasma exposure in vitro, and we showed that Serine Protease Autotransporters of Enterobacteriaceae (SPATEs) are essential for Shigella dissemination within the colonic mucosa. We have confirmed that SPATEs are expressed and secreted in poorly oxygenated environments encountered by Shigella from hypoxic foci of infection to the bloodstream. We further demonstrated that SPATEs promoted Shigella survival in plasma, by cleaving complement component 3 (C3), thereby impairing complement system activation. We have shown here that the ability of Shigella to survive plasma exposure is a key factor in its virulence, both within primary foci and systemically. Significance StatementIn this study we aimed to better understand the significance of the ability of Shigella to survive plasma exposure, as we observed that non-pathogenic E. coli rapidly lysed upon exposure. Indeed, we reported that Shigella was already exposed to plasma components within the colonic mucosa, as we reported in a guinea pig model of shigellosis that hemorrhages were induced, that were associated with local diffusion of plasma components in the infected colonic mucosa. Shigella was obviously exposed to plasma during bacteremia. The ability of Shigella to survive in plasma has not been previously reported. Here we have shown, first, that Shigella was able to divide and grow in the presence of human plasma, and second, we found that SPATEs played a central role in this process by impairing with the activation of the complement system.

microbiology↗

bioRxiv2023

Heterogeneous dual-metal control of Salmonella infection

Iron controls bacterial infections through diverse pathogen and host mechanisms that remain challenging to disentangle. Here, we determined how individual Salmonella cells access iron in infected mice. Our results showed that the iron transporter SLC11A1 restricted iron availability. However, many Salmonella bypassed this restriction by targeting macrophage endosomes that contained remnants of iron-rich red blood cells. These iron-replete bacteria dominated overall Salmonella growth and masked the relieve of iron-starved bacteria under iron overload. These data, combined with our previous discovery of magnesium deprivation as a primary mechanism for controlling Salmonella, reveal a heterogeneous dual-metal mechanism of nutritional immunity, and highlight the power of single-cell analyses under physiological in-vivo conditions to unravel complex anti-bacterial host mechanisms. One sentence summaryIron and magnesium limitations control distinct Salmonella subsets during infection.

cell biology↗

bioRxiv2023

Effects of forest urbanization on the interplay between small mammal communities and their gut microbiota

Urbanization significantly impacts wild populations, favoring urban dweller species over those that are unable to adapt to rapid and abrupt changes. One possible explanation for differential adaptative abilities between these species is that the microbiome may modulate the host phenotype rapidly through a high degree of flexibility. Conversely, under such anthropic perturbations, the microbiota composition of some species could be disrupted, resulting in dysbiosis and negative impacts on host fitness, potentially causing local extirpation. The links between the impact of urbanization on host communities and their gut microbiota have only been scarcely explored. In this study, we tested the hypothesis that the gut microbiota (GM) could play a role in host adaptation to urban environments. We addressed this question by studying several species of small terrestrial mammals sampled in forested areas along a forested gradient of urbanization (from rural forests to urban parks) during 2020 fall. The gut was collected and bacteria were described using a 16S metabarcoding approach. We tested whether urbanization led to changes in small mammal communities and in their GM. We analyzed these changes in terms of the presence and abundance of taxa and their putative functions to decipher the processes underlying these changes. We found that urbanization had marked impacts on small mammal communities and their GM, either directly or indirectly depending on small mammal species categories. The urban dweller species had a lower taxonomic diversity but a higher functional diversity and a different composition compared to urban adapter species. Their GM assembly was mostly governed by stochastic effects, which could indicate dysbiosis in these urban species. Selection processes and an overabundance of functions were detected that could be associated with adaptation to urban environments despite potential dysbiosis. Urbanization could also impact the diversity and taxonomic composition of GM in urban adapter species. However, their functional diversity and composition remained relatively stable. This observation can be explained by functional redundancy, where certain taxa express the same function. This could explain the adaptation of urban adapter species in various environments, including urban settings. We can therefore assume that there are feedback loops between the gut microbiota and the host species within communities, enabling rapid and flexible adaptation.

ecology↗

bioRxiv2023

Teosinte Pollen Drive guides maize domestication and evolution by RNAi

Meiotic drivers subvert Mendelian expectations by manipulating reproductive development to bias their own transmission. Chromosomal drive typically functions in asymmetric female meiosis, while gene drive is normally postmeiotic and typically found in males. Using single molecule and single-pollen genome sequencing, we describe Teosinte Pollen Drive, an instance of gene drive in hybrids between maize (Zea mays ssp. mays) and teosinte mexicana (Zea mays ssp. mexicana), that depends on RNA interference (RNAi). 22nt small RNAs from a non-coding RNA hairpin in mexicana depend on Dicer-Like 2 (Dcl2) and target Teosinte Drive Responder 1 (Tdr1), which encodes a lipase required for pollen viability. Dcl2, Tdr1, and the hairpin are in tight pseudolinkage on chromosome 5, but only when transmitted through the male. Introgression of mexicana into early cultivated maize is thought to have been critical to its geographical dispersal throughout the Americas, and a tightly linked inversion in mexicana spans a major domestication sweep in modern maize. A survey of maize landraces and sympatric populations of teosinte mexicana reveals correlated patterns of admixture among unlinked genes required for RNAi on at least 4 chromosomes that are also subject to gene drive in pollen from synthetic hybrids. Teosinte Pollen Drive likely played a major role in maize domestication and diversification, and offers an explanation for the widespread abundance of "self" small RNAs in the germlines of plants and animals.

plant biology↗

bioRxiv2022

Small scale geographical variation of three-way relationships between gut microbiota, helminth assemblages and bacterial infections in wild rodent populations

BackgroundDespite its central role in host fitness, the gut microbiota may differ greatly between individuals. This variability is often mediated by environmental or host factors such as diet, genetics, and infections. Recently, a particular attention has been given to the interactions between gut bacteriota and helminths, as these latter could affect host susceptibility to other infections. Further studies are still required to better understand the three-way interactions between gut bacteriota, helminths and other parasites, especially because previous findings have been very variable, even for comparable host-parasite systems. MethodsIn our study, we used the V4 region of the 16S rRNA gene to assess the variability of gut bacteriota diversity and composition in wild populations of a small mammal, the bank vole Myodes glareolus. Four sites were sampled at a regional geographical scale (100 km) along a North-South transect in Eastern France. We applied analyses of community and microbial ecology to evaluate the interactions between the gut bacteriota, the gastro-intestinal helminths and the pathogenic bacteria detected in the spleen. ResultsWe identified important variations of the gut bacteriota composition and diversity among bank voles. They were mainly explained by sampling localities and reflected the North/South sampling transect. In addition, we detected two main enterotypes, that might correspond to contrasted diets. We found geographic variations of the Firmicutes/Bacteroidetes ratio, that correlated positively with body mass index. We found positive correlations between the specific richness of the gut bacteriota and of the helminth community, as well as between the composition of these two communities, even when accounting for the influence of geographical distance. The helminths Aonchotheca murissylvatici, Heligmosomum mixtum and the bacteria Bartonella sp were the main taxa associated with the whole gut bacteriota composition. Besides, changes in relative abundance of particular gut bacteriota taxa were specifically associated with other helminths (Mastophorus muris, Catenotaenia henttoneni, Paranoplocephala omphalodes and Trichuris arvicolae) or pathogenic bacteria. Especially, infections with Neoehrlichia mikurensis, Orientia sp, Rickettsia sp and P. omphalodes were associated with lower relative abundance of the family Erysipelotrichaceae (Firmicutes), while coinfections with higher number of bacterial infections were associated with lower relative abundance of a Bacteroidales family (Bacteroidetes). ConclusionsThese results emphasize complex interlinkages between gut bacteriota and infections in wild animal populations. They remain difficult to generalize due to the strong impact of environment on these interactions, even at regional geographical scales. Abiotic features, as well as small mammal community composition and within host parasite coinfections, should now be considered to better understand the spatial variations observed in the relationships between gut bacteriota, gastro-intestinal helminths and bacterial infections.

ecology↗

bioRxiv2021

Clr4SUV39H1 and Bdf2BRD4 ubiquitination mediate transcriptional silencing via heterochromatic phase transitions

Transcriptional silencing by RNAi paradoxically relies on transcription, but how the transition from transcription to silencing is achieved has remained unclear. The Cryptic Loci Regulator complex (CLRC) in Schizosaccharomyces pombe is a cullin-ring E3 ligase required for silencing that is recruited by RNAi. We found that the E2 ubiquitin conjugating enzyme Ubc4 interacts with CLRC and mono-ubiquitinates the histone H3K9 methyltransferase Clr4SUV39H1, promoting the transition from co-transcriptional gene silencing (H3K9me2) to transcriptional gene silencing (H3K9me3). Ubiquitination of Clr4 occurs in an intrinsically disordered region (IDR), which undergoes robust liquid-liquid phase separation (LLPS), along with Swi6HP1 the effector of transcriptional gene silencing. Phase separation of Clr4 and Swi6 is exquisitely sensitive to non-coding RNA (ncRNA), which promotes dimerization, chromatin association, and di-, but not tri-methylation instead. Ubc4-CLRC also targets the transcriptional co-activator Bdf2BRD4, down-regulating centromeric transcription and small RNA production. The deubiquitinase Ubp3 counteracts both activities.

molecular biology↗

bioRxiv2021

Dicer promotes genome stability via the bromodomain transcriptional co-activator Brd4.

RNA interference is essential for transcriptional silencing and genome stability, but conservation of this role in mammals has been difficult to demonstrate. Dicer1-/- mouse embryonic stem cells have microRNA-independent proliferation defects, and we conducted a CRISPR-Cas9 screen to restore viability. We identified suppressor mutations in transcriptional activators, H3K9 methyltransferases, and chromosome segregation factors, strongly resembling Dicer suppressors in fission yeast. Suppressors rescued chromosomal defects, and reversed strand-specific transcription of major satellite repeats in Dicer1-/-. The strongest suppressors were in Brd4, and in the transcriptional elongator/histone acetyltransferase Elp3. Using viable mutants and pharmaceutical inhibitors, we demonstrate that deletion of specific residues in Brd4 rescue genome instability defects of Dicer1-/- in both mammalian cells and fission yeast, implicating Dicer in coordinating transcription and replication of satellite repeats. SummaryReplication and segregation defects in Dicer1-/- stem cells depend on centromeric transcription by Brd4, and are deeply conserved in fission yeast.

genetics↗

bioRxiv2020

Inferring within-flock transmission dynamics of highly pathogenic avian influenza (H5N8) in France, 2020

Following the emergence of highly pathogenic avian influenza (H5N8) in France in early December 2020, we used duck mortality data of the index case to investigate within-flock transmission dynamics. A stochastic epidemic model was adjusted to the daily mortality data and model parameters were estimated using an approximate Bayesian computation sequential Monte Carlo (ABC-SMC) algorithm. Results suggested that the virus was introduced 4 days (95% credible interval: 3 - 5) prior to the day suspicion was reported and that the transmission rate was 3.7 day-1 (95%CI: 2.6 - 5.3). On average, ducks started being infectious 3.1 hours (95%CI: 0.4 - 8.0) after infection and remained infectious for 4.4 days (95%CI: 3.1 - 5.6). Model outputs also suggested that the number of infectious ducks was already 3239 (95%CI: 26 - 3706) the day before suspicion, emphasising the substantial latent threat this virus could pose to other poultry farms and to neighbouring wildlife. These estimations can be applied to upcoming outbreaks and made available to veterinary services within few hours. This study illustrates how mechanistic models can provide rapid relevant insights to contribute to the management of infectious disease outbreaks of farmed animals.

ecology↗

bioRxiv2020

Combining Natural Language Processing and Metabarcoding to Reveal Pathogen-Environment Associations

Cryptococcus neoformans is responsible for life-threatening infections that primarily affect immunocompromised individuals and has an estimated worldwide burden of 220,000 new cases each year--with 180,000 resulting deaths--mostly in sub-Saharan Africa. Surprisingly, little is known about the ecological niches occupied by C. neoformans in nature. To expand our understanding of the distribution and ecological associations of this pathogen we implement a Natural Language Processing approach to better describe the niche of C. neoformans. We use a Latent Dirichlet Allocation model to de novo topic model sets of metagenetic research articles written about varied subjects which either explicitly mention, inadvertently find, or fail to find C. neoformans. These articles are all linked to NCBI Sequence Read Archive datasets of 18S ribosomal RNA and/or Internal Transcribed Spacer gene-regions. The number of topics was determined based on the model coherence score, and articles were assigned to the created topics via a Machine Learning approach with a Random Forest algorithm. Our analysis provides support for a previously suggested linkage between C. neoformans and soils associated with decomposing wood. Our approach, using a search of single-locus metagenetic data, gathering papers connected to the datasets, de novo determination of topics, the number of topics, and assignment of articles to the topics, illustrates how such an analysis pipeline can harness large-scale datasets that are published/available but not necessarily fully analyzed, or whose metadata is not harmonized with other studies. Our approach can be applied to a variety of systems to assert potential evidence of environmental associations. Author SummaryOur finding that C. neoformans is associated with decomposing wood is reinforced by the general literature on C. neoformans and its close congeneric relatives and warrants further investigation. This work demonstrates the potential utility of pairing Natural Language Processing (NLP) with single-locus metagenetic data for the study of Neglected Tropical Diseases. We present a novel method to study the ecological niches of rare pathogens that leverages the immense amount of data available to researchers in the NCBI Sequence Read Archive (SRA)combined with a text-mining analysis based on Natural Language Processing. We demonstrate that text processing, noun identification, and verb identification can play an important role in analyzing a large corpus of documents together with metagenetic data. Forging this connection requires access to all of the available ecological 18S ribosomal RNA and Internal Transcribed Spacer NCBI SRA datasets. These datasets use metabarcoding to query taxonomic diversity in eukaryotic organisms, and in the case of the Internal Transcribed Spacer, they specifically target Fungi. The presence of specific species is inferred when diagnostic 18S or ITS gene region sequences are found in the SRA data. We searched for C. neoformans in all 18S and ITS datasets available and gathered all associated journal articles that either cite the SRA data accessions or are cited in the SRA data accessions. Published metagenetic data often have associated metadata including: latitude and longitude, temperature, and other physical characteristics describing the conditions in which the metagenetic sample was collected. These metadata are not always be presented in consistent formats, so harmonizing study methods may be needed to appropriately compare metagenetic data as commonly required in metanalysis studies. We present an analysis which takes as input articles associated with SRA datasets that were found to contain evidence of C. neoformans. We apply NLP methods to this corpus of articles to describe the niche of C. neoformans. Our results reinforce the current understanding of C. neoformanss niche, indicating the pertinence of employing a NLP analysis to identify the niche of an organism. This approach could further the description of virtually any other organism that routinely appears in metagenetic surveys, especially pathogens, whose ecological niches are unknown or poorly understood. Optional Striking Image O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/280578v1_ufig1.gif" ALT="Figure 1"> View larger version (66K): org.highwire.dtl.DTLVardef@135ce50org.highwire.dtl.DTLVardef@17bf52borg.highwire.dtl.DTLVardef@11cf682org.highwire.dtl.DTLVardef@7be6ea_HPS_FORMAT_FIGEXP M_FIG C_FIG Cryptococcus neoformans cells budding. Image Provided Courtesy of Felipe H. Santiago-Tirado, colored by Kristina Davis, CC-BY 4.0

bioinformatics↗

bioRxiv2019

Infection triggers tumor regression through activation of innate immunity in Drosophila

The pioneering work of Dr. William Coley has shown that infections can stimulate the immune system and improve tumor growth control. However, the immune mechanisms responsible for the protective role of infectious agents have still not been identified. Here, we investigated the role of innate immune pathways in tumor regression by performing experimental infections in genetically modified Drosophila that develop invasive neoplastic tumors. After quantifying tumor size, through image processing, and immune gene expression with transcriptomic analyses, we analyzed the link between tumor size and pathogen-induced immune responses thanks to a combination of statistical and mathematical modeling. Drosophila larvae infected with a naturally-occurring bacterium showed a smaller tumor size compared to controls and fungus-infected larvae, thanks to an increase expression of Imd and Toll pathways. Our mathematical model reinforces this idea by showing that repeated acute infection could results in an even higher decrease in tumor size. Thus, our study suggests that infectious agents can induce tumor regression through the alteration of innate immune responses. This phenomenon, currently neglected in oncology, could have major implications for the elaboration of new preventive and immunotherapeutic strategies. One Sentence SummaryBacterial infections can decrease cancer cell accumulation through stimulation of innate immune responses.

immunology↗

bioRxiv2018

Natural Wolbachia infections are common in the major malaria vectors in Central Africa

During the last decade, the endosymbiont bacterium Wolbachia has emerged as a biological tool for vector disease control. However, for long time, it was believed that Wolbachia was absent in natural populations of Anopheles. The recent discovery that species within the Anopheles gambiae complex hosts Wolbachia in natural conditions has opened new opportunities for malaria control research in Africa. Here, we investigated the prevalence and diversity of Wolbachia infection in 25 African Anopheles species in Gabon (Central Africa). Our results revealed the presence of Wolbachia in 16 of these species, including the major malaria vectors in this area. The infection prevalence varied greatly among species, confirming that sample size is a key factor to detect the infection. Moreover, our sequencing and phylogenetic analyses showed the important diversity of Wolbachia strains that infect Anopheles. Co-evolutionary analysis unveiled patterns of Wolbachia transmission within Anopheles species, suggesting that past independent acquisition events were followed by co-cladogenesis. The large diversity of Wolbachia strains that infect natural populations of Anopheles offers a promising opportunity to select suitable phenotypes for suppressing Plasmodium transmission and/or manipulating Anopheles reproduction, which in turn could be used to reduce the malaria burden in Africa.

ecology↗