Biology subjects

Marti-Carreras, J.

Publications and source records attributed to Marti-Carreras, J..

8 recordsLinked to original sources

bioRxiv2026

Direct quantitative PCR detects genetic biomarkers of antileishmanial drug resistance in clinical samples from dogs with leishmaniosis

BackgroundTreatment response in canine leishmaniosis is driven by the dog host, the Leishmania parasite, and pharmacological factors, with drug resistance increasingly undermining the effectiveness of therapy. A direct quantitative PCR test (LeishGenR) was applied to 104 clinical samples from 95 dogs in the Mediterranean area diagnosed with leishmaniosis in veterinary clinical settings and testing positive for Leishmania infantum by PCR. The assay enabled rapid detection of genetic drug-resistance biomarkers for allopurinol (metk), meglumine antimoniate (mrpa), and miltefosine (LdMT), providing a clinically relevant, timely alternative to culture-based approaches by directly analyzing circulating Leishmania infantum amastigotes. ResultsThe assay (LeishGenR) showed high specificity (100%) and sensitivity (>87.5%) for genetic drug-resistance profile assignment and a strong correlation with whole-genome sequencing for gene copy number assessment (metk: r = 0.878; mrpa: r = 0.943 and LdMT = 0.691). Genetic drug-resistance biomarkers were detected in 24.3% of L. infantum DNA from clinical samples analyzed (20/82; 95% CI 16.3-34.6)), most commonly for allopurinol (13.4%; 95% CI 7.6-22.4), then meglumine antimoniate (9.4%; 95% CI 4.6-18.2), and for miltefosine (5.4%; 95% CI 1.8-14.8). Prevalence was higher in dogs previously treated for leishmaniosis. ConclusionThis study demonstrates the ability to detect genetic biomarkers of drug resistance in L. infantum directly from clinical samples of dogs with leishmaniosis. This method enables rapid, precise detection of genomic biomarkers, circumventing delays associated with culture-based methods and supporting more effective clinical management and surveillance. Among dogs with high parasitemia referred to clinics in Mediterranean regions sampled in this study, the findings reveal a significant prevalence of circulating L. infantum strains carrying genomic drug resistance biomarkers to standard treatments for canine leishmaniosis.

genetics↗

bioRxiv2025

Leishmania tarentolae and Leishmania infantum in geckos from Mallorca Island, Spain

Leishmania tarentolae and Leishmania infantum are two sympatric parasites of significant ecological and epidemiological interest in the Mediterranean basin. This study investigated the prevalence of L. tarentolae and L. infantum in two gecko species (Tarentola mauritanica and Hemidactylus turcicus) present on Mallorca Island, Spain, using duplex quantitative PCR. A total of 59 geckos were sampled across the island, including 53 T. mauritanica and six H. turcicus. Tissue and blood samples were screened for both parasites, and generalized linear models were used to assess organ-specific infection patterns. The results revealed the prevalence of Leishmania infection in adult T. mauritanica, with 10/49 (20.41%) testing positive for L. tarentolae and with 1/49 (2.04%) for L. infantum. Coinfection with both parasites was detected in 3/49 geckos (6.12%). No positives were identified in H. turcicus, probably due to small sample size. Regarding positivity by tissues, coleomic organs were more likely to be positive for L. tarentolae in adult T. mauritanica than blood, with a slighter positivity in the liver, spleen and lung. Interestingly, L. infantum was detected more frequently coinfecting with L. tarentolae than as a single parasite. These prevalence rates and the existence of coinfections highlight potential ecological interactions between the two parasites and reptiles. This study provides valuable data on the potential role of geckos in endemic areas like Mallorca. Author SummaryLeishmaniosis is a zoonotic disease caused by parasites that can infect both animals and humans. In Europe, Leishmania infantum is the main species responsible for the disease, with dogs acting as its primary host. However, recent research suggests that other animals, including reptiles, might also play a role in their spread. In this study, centered in wild geckos from Mallorca Island (Spain), we investigated the prevalence of L. tarentolae and L. infantum in two gecko species (Tarentola mauritanica and Hemidactylus turcicus). Using quantitative PCR, it was found that 14/49 (28.57%) of adult Tarentola mauritanica were positive for Leishmania parasites, 13/49 (26.53%) for L. tarentolae and 74/49 (8.16%) for L. infantum. Additionally, coinfection of both parasites was detected in three geckos (3/49, 6.12%). The second gecko species studied, Hemidactylus turcicus, was not positive for Leishmania, possible due to a small sample size. These results reinforce previous studies suggesting that geckos may carry both parasites. Since L. tarentolae has also been detected in dogs, and both Leishmania species are sympatric, it raises questions about the role of reptiles in leishmaniosis cycle and transmission, as well as the reliability of current diagnostic tests in coinfections of closely related parasite species.

microbiology↗

bioRxiv2025

Drug-Resistance Biomarkers in Leishmania infantum through Nanopore-Based Detection of Aneuploidy and Gene Copy Number Variations with LeishGenApp

BackgroundDrug-resistant strains of Leishmania infantum challenge the effectiveness of treatments for clinical leishmaniosis and may lead to more frequent relapses. Copy number variation (CNV) at specific genetic loci is associated with drug resistance and virulence, but information about its prevalence in endemic regions is limited. This study examines the drug resistance and virulence status of Leishmania strains in human and canine isolates from the Mediterranean region. MethodsForty-eight Leishmania infantum isolates were whole-genome sequenced with nanopore long reads, followed by de novo assembly. We analyzed chromosomal aneuploidies and gene copy number variation in loci linked to drug resistance and virulence in Leishmania, alongside the genomic structure and rearrangements responsible for these variations. ResultsComplete genomes were de novo assembled for 35 L. infantum isolates (22 from dogs and 13 from humans), revealing significant chromosomal variability. We assessed copy number variation for 22 potential biomarkers: 15 genes related to drug resistance to first-line drugs (METK for allopurinol; LdSMT for amphotericin B; AQP1 and H-locus for antimonials; LdMT, LdRos3, and MSL for miltefosine; PPM for paramomycin) and seven genes related to virulence (lipophosphoglycan and proteophosphoglycan biosynthesis, and the Lack protein). Drug-resistance biomarkers were identified in 80% of the isolates. Canine strains primarily showed resistance to allopurinol and antimonials, while human isolates exhibited a broader resistance spectrum, especially to antimonials and paromomycin. The co-occurrence of resistance biomarkers was common, especially for allopurinol and antimonial resistance. Distinct mechanisms underlie the observed copy number variations. Virulence-associated genes were less variable among isolates. ConclusionsThe prevalence of drug-resistance biomarkers in Leishmania infantum strains from the Mediterranean region, as revealed by this study, underscores the critical need for routine resistance surveillance in managing clinical leishmaniosis. These findings not only inform current clinical practice but also pave the way for more effective management strategies in the future.

genetics↗

bioRxiv2024

Effects of meglumine antimoniate and allopurinol treatment on the fecal microbiome profile in dogs with leishmaniosis

The combination of meglumine antimoniate and allopurinol is considered one of the most effective treatments for canine leishmaniosis caused by Leishmania infantum. This study investigated the effects of this treatment on the gut microbiome of 10 dogs from Spain, Portugal, and Italy via fecal shotgun metagenomic sequencing over six months. Dogs were sampled at baseline (BL) and at one (M1) and six (M6) months post-treatment. The gut microbiome of Leishmania-infected dogs (BL) is dominated by Prevotella, Collinsella, Bacteroides, and Blautia, with individual variability being the primary determinant of microbiome composition. No significant changes in alpha diversity (Shannon index, gene number) or beta diversity (Bray-Curtis dissimilarity, UniFrac distance) were detected between pre- and post-treatment time points, suggesting that treatment with meglumine antimoniate and allopurinol does not disrupt the gut microbiota. Minor trends in taxonomic shifts were noted, with slight increases in Bifidobacterium pseudocantenulatum, Collinsella tanakaei, and Slackia piriformis after treatment, but these changes were not statistically significant after correction for multiple testing. Linear discriminant analysis and multivariable modeling confirmed that the microbial community structure was resilient to treatment effects. Individual-specific microbiome differences in diversity accounted for 52% of the observed variability, underscoring the personalized nature of the gut microbiota in dogs. Importantly, no adverse microbiome disruptions were detected, even with prolonged allopurinol use. This study highlights the robustness of the canine gut microbiome during antileishmanial therapy and highlights the use of meglumine antimoniate and allopurinol without compromising gut microbial diversity or health. Further studies with larger cohorts are recommended to confirm these findings and explore the functional roles of the gut microbiota in modulating immune responses in Leishmania-infected dogs.

molecular biology↗

bioRxiv2021

Genetic diversity and evolution of SARS-CoV-2 in Belgium during the first wave outbreak

SARS-CoV-2, the causative agent of COVID-19 was first detected in Belgium on 3rd February 2020, albeit the first epidemiological wave started in March and ended in June 2020. One year after the first epidemiological wave hit the country data analyses reveled the temporal and variant distribution of SARS-CoV-2 and its implication with Belgian epidemiological measures. In this study, 766 complete SARS-CoV-2 genomes of samples originating from the first epidemiological were sequenced to characterize the temporal and geographic distribution of the COVID-19 pandemic in Belgium through phylogenetic and variant analysis. Our analysis reveals the presence of the major circulating SARS-CoV-2 clades (G, GH and GR) and lineages circulating in Belgium at that time. Moreover, it contextualizes the density of SARS-CoV-2 cases over time with non-intervention measures taken to prevent the spread of SARS-CoV-2 in Belgium, specific international case imports and the functional implications of the most representative non-synonymous mutations present in Belgium between February to June 2020.

genomics↗

bioRxiv2021

Exploration of the Ixodes ricinus virosphere unveils an extensive virus diversity including novel Coltiviruses and other reoviruses

Recent metagenomics studies have revealed several tick species to host a variety of previously undiscovered RNA viruses. Ixodes ricinus, which is known to be a vector for many viral, bacterial and protozoan pathogens, is the most prevalent tick species in Europe. For this study, we decided to investigate the virosphere of Belgian I. ricinus ticks. High-throughput sequencing of tick pools collected from six different sampling sites revealed the presence of viruses belonging to many different viral orders and families, including Mononegavirales, Bunyavirales, Partitiviridae and Reoviridae. Of particular interest was the detection of several new reoviruses, two of which cluster together with members of the genus Coltivirus. This includes a new strain of Eyach virus, a known causative agent of tick-borne encephalitis. All genome segments of this new strain are highly similar to those of previously published Eyach virus genomes, except for the fourth segment, encoding VP4, which is markedly more dissimilar, potentially indicating the occurrence of a genetic reassortment. Further PCR-based screening of over 230 tick pools for 14 selected viruses showed that most viruses could be found in all six sampling sites, indicating the wide spread of these viruses throughout the Belgian tick population. Taken together, these results illustrate the role of ticks as important virus reservoirs, highlighting the need for adequate tick control measures.

microbiology↗

bioRxiv2020

A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages

Since the start of the COVID-19 pandemic, an unprecedented number of genomic sequences of the causative virus (SARS-CoV-2) have been generated and shared with the scientific community. The unparalleled volume of available genetic data presents a unique opportunity to gain real-time insights into the virus transmission during the pandemic, but also a daunting computational hurdle if analysed with gold-standard phylogeographic approaches. We here describe and apply an analytical pipeline that is a compromise between fast and rigorous analytical steps. As a proof of concept, we focus on the Belgium epidemic, with one of the highest spatial density of available SARS-CoV-2 genomes. At the global scale, our analyses confirm the importance of external introduction events in establishing multiple transmission chains in the country. At the country scale, our spatially-explicit phylogeographic analyses highlight that the national lockdown had a relatively low impact on both the lineage dispersal velocity and the long-distance dispersal events within Belgium. Our pipeline has the potential to be quickly applied to other countries or regions, with key benefits in complementing epidemiological analyses in assessing the impact of intervention measures or their progressive easement.

evolutionary biology↗

bioRxiv2020

STAT2 signaling as double-edged sword restricting viral dissemination but driving severe pneumonia in SARS-CoV-2 infected hamsters

Introductory paragraphSince the emergence of SARS-CoV-2 causing COVID-19, the world is being shaken to its core with numerous hospitalizations and hundreds of thousands of deaths. In search for key targets of effective therapeutics, robust animal models mimicking COVID-19 in humans are urgently needed. Here, we show that productive SARS-CoV-2 infection in the lungs of mice is limited and restricted by early type I interferon responses. In contrast, we show that Syrian hamsters are highly permissive to SARS- CoV-2 and develop bronchopneumonia and a strong inflammatory response in the lungs with neutrophil infiltration and edema. Moreover, we identify an exuberant innate immune response as a key player in pathogenesis, in which STAT2 signaling plays a dual role, driving severe lung injury on the one hand, yet restricting systemic virus dissemination on the other. Finally, we assess SARS-CoV- 2-induced lung pathology in hamsters by micro-CT alike used in clinical practice. Our results reveal the importance of STAT2-dependent interferon responses in the pathogenesis and virus control during SARS-CoV-2 infection and may help rationalizing new strategies for the treatment of COVID-19 patients.

microbiology↗