Biology subjects

Salvador, L. C. M.

Publications and source records attributed to Salvador, L. C. M..

6 recordsLinked to original sources

bioRxiv2026

Scale- and genotype-dependent spatial concordance of Mycobacterium bovis in cattle and badgers

Mycobacterium bovis causes tuberculosis (TB) in cattle, badgers (Meles meles), other wildlife, and humans, posing major animal and public health challenges in Britain and Ireland. Shared genotypes between cattle and badgers have been reported at regional scales, but whether this concordance holds at finer spatial scales, where control interventions operate, and whether it varies by genotype combination, remains unknown. Resolving this is critical for interpreting cross-species transmission risk and designing targeted control measures. We analyzed 1,248 M. bovis isolates from cattle and badgers (Northern Ireland, 1986-2018), including samples from a small, densely sampled intervention research area, using Multi-Locus Variable Number of Tandem Repeats Analysis (MLVA) and kernel discriminant analysis (KDA) across multiple spatial scales (25-95% density contours). We identified 36 MLVA types with four shared between species and one (MLV06) endemic to the area. Spatial concordance varied by type combination and scale: MLVA004-MLVA297 showed strong, bidirectional, scale-robust concordance; MLVA006-MLVA297 was concordant only at fine spatial scales; MLVA004-MLVA006 showed weak, asymmetric concordance; and no concordance was detected when all three types were analysed together. Our findings reveal spatial concordance between shared M. bovis genotypes varied by genotype combination and scale, indicating genotype-specific dynamics within this multi-host system.

ecology↗

bioRxiv2026

Neglecting movement-disease feedback biases wildlife epidemic forecasts

In wildlife populations, movement drives host contact networks and disease spread. Growing evidence from veterinary science and experimental biology shows that infection commonly modifies host movement itself, a widespread feature of host biology. Yet conventional wildlife disease models treat movement as independent of infection, a mechanistic omission that could bias epidemic forecasts and management decisions. Here, we introduce a general framework in which recent infection temporarily alters a hosts home-ranging behavior and where pathogens are shed, integrating movement and disease ecology through spatially explicit, individual-based simulations. We show that infection-modified movement (IMM) responses, including anorexia, disorientation, and hypokinesia, can enhance or suppress epidemics, and most responses reverse direction depending on environmental conditions, grouping structure, and social behavior. We further show that models without IMM alternately underestimate and overestimate epidemic size as ecological context changes. Because our model parameters map onto quantities routinely estimated from tracking and surveillance data, our framework enables movement-disease feedback to be measured and incorporated into wildlife disease models.

ecology↗

bioRxiv2023

Leptospira transcriptome sequencing using long-read technology reveals unannotated transcripts and potential polyadenylation of mRNA molecules

Leptospirosis caused by the spirochete bacteria Leptospira is an emerging zoonosis that causes life-threatening disease in humans and animals. However, a detailed understanding of Leptospiras RNA profiles is limited. In this study, we sequenced and analyzed the transcriptome of multiple Leptospira serovars using Oxford Nanopore Technologies direct cDNA and direct RNA sequencing methods. We identified several operon transcriptional units, novel RNA coding regions, and evidence of potential posttranscriptional polyadenylation in the Leptospira transcriptome. Some coding regions of multiple RNA molecules that have not been previously annotated could be potential sRNA or ncRNA molecules that support gene expression regulation purposes in Leptospira. Many of the relative positions of these unannotated RNA coding regions were consistent in their neighboring coding regions across the reference genomes of two pathogenic Leptospira analyzed in this study. Besides, the majority of the unannotated coding regions and operon transcriptional units were not detected in the nonpathogenic Leptospira, suggesting potential virulence-related functions for these RNA molecules coding regions. Overall, our study confirms the utility of ONTs sequencing in studying prokaryotic transcriptome profiles and offers a tool to improve our understanding of the structural composition of RNA molecules and prokaryotic polyadenylation. However, the findings from our study also warrant that the presence of homopolymers of adenine bases in the transcripts may interfere with the interpretation of bacterial transcriptome profiles. Carefully designed experiments are needed to unravel the role of the features described in this study in Leptospira virulence and pathogenesis. Author SummaryLeptospirosis caused by the spirochete bacteria, Leptospira, is recognized as one of the most widespread zoonotic diseases. Leptospirosis is a neglected disease and has been estimated to cause over one million annual human clinical cases and over 60,000 deaths. Leptospira are maintained in the renal tubules of asymptomatic animal reservoirs, and in contaminated environments, such as soil and water. Studying gene expression profiles is an important component of bacterial pathogenesis studies, and a number of methods are available to do it. Our study compared various transcriptome sequencing methods using one of the latest next generation sequencing tools (Oxford Nanopore Technologies) and evaluated the compositions of RNA in different Leptospiras transcriptomes. We identified many previously undescribed and potentially significant features within the Leptospira transcriptome that may contribute to the virulence and pathogenesis of Leptospira sp. Our findings lead to new opportunities for researchers to sequence prokaryotic RNA molecules and to unravel many regulatory mechanisms.

microbiology↗

bioRxiv2022

Leptospira enrichment culture followed by ONT Nanopore sequencing allows better detection of Leptospira presence and diversity in water and soil samples.

BackgroundLeptospirosis, a life-threatening disease in humans and animals, is one of the most widespread global zoonosis. Contaminated soil and water are the major transmission sources in humans and animals. Clusters of disease outbreaks are common during rainy seasons. Methodology/Principal FindingsIn this study, to detect the presence of Leptospira, we applied PCR, direct metagenomic sequencing, and enrichment culture followed by metagenomic sequencing on water and soil samples. Direct sequencing and enrichment cultures followed by PCR or sequencing effectively detected pathogenic and nonpathogenic Leptospira compared to direct PCR and 16S amplification-based metagenomic sequencing in soil or water samples. Among multiple culture media evaluated, Ellinghausen-McCullough-Johnson-Harris (EMJH) media containing antimicrobial agents was superior in recovering and detecting Leptospira from the environmental samples. Our results show that enrichment culture followed by PCR can be used to confirm the presence of pathogenic Leptospira in environmental samples. Metagenomic sequencing on enrichment cultures effectively detects the abundance and diversity of Leptospira spp from environmental samples. Conclusions/SignificanceThe selection of methodology is critical when testing environmental samples for the presence of Leptospira. Selective enrichment culture improves Leptospira detection efficacy by PCR or metagenomic sequencing and can be used successfully to understand the presence and diversity of pathogenic Leptospira during environmental surveillance. Author SummaryLeptospirosis, a life-threatening disease in humans and animals, is one of the most widespread global zoonosis. Contaminated soil and water are major sources of transmission in humans and animals. For this reason, clusters of disease outbreaks are common during the rainy season. In this study, Leptospira enrichment cultures followed by PCR and sequencing detected pathogenic and nonpathogenic Leptospira in soil and water samples. The pathogenic and intermediate groups of Leptospira were more prevalent in soil samples tested. Metagenomic sequencing on enrichment culture is effective in detecting the abundance and diversity of various Leptospira spp. in environmental samples. Soil samples in proximity to water may be an ideal niche for Leptospira growth and survival and may be an appropriate sample of choice for testing.

microbiology↗

bioRxiv2021

Phylogenomics Sheds Light on the population structure of Mycobacterium bovis from a Multi-Host Tuberculosis System

Molecular analyses of Mycobacterium bovis based on spoligotyping and Variable Number Tandem Repeat (MIRU-VNTR) brought insights into the epidemiology of animal tuberculosis (TB) in Portugal, showing high genotypic diversity of circulating strains that mostly cluster within the European 2 clonal complex. The genetic relatedness of M. bovis isolates from cattle and wildlife have also suggested sustained transmission within this multi-host system. However, while previous surveillance highlighted prevalent genotypes in areas where livestock and wild ungulates are sympatric and provided valuable information on the prevalence and spatial occurrence of TB, links at the wildlife-livestock interfaces were established mainly via genotype associations. Therefore, evidence at a local fine scale of transmission events linking wildlife hosts and cattle remains lacking. Here, we explore the advantages of whole genome sequencing (WGS) applied to cattle, red deer and wild boar isolates to reconstruct the evolutionary dynamics of M. bovis and to identify putative pathogen transmission events. Whole genome sequences of 44 representative M. bovis isolates, obtained between 2003 and 2015 from three TB hotspots, were compared through single nucleotide polymorphism (SNP) variant calling analyses. Consistent with previous results combining classical genotyping with Bayesian population admixture modelling, SNP-based phylogenies support the branching of this M. bovis population into five genetic clades, three with geographic specificities, as well as the establishment of a SNPs catalogue specific to each clade, which may be explored in the future as phylogenetic markers. The core genome alignment of SNPs was integrated within a spatiotemporal metadata framework to reconstruct transmission networks, which together with inferred secondary cases, further structured this M. bovis population by host species and geographic location. WGS of M. bovis isolates from Portugal is reported for the first time, refining the spatiotemporal context of transmission events and providing further support to the key role of red deer and wild boar on the persistence of animal TB in this Iberian multi-host system.

genomics↗

bioRxiv2021

Genomic epidemiology of Mycobacterium bovis infection in sympatric badger and cattle populations in Northern Ireland.

BackgroundBovine tuberculosis (bTB) is a costly, epidemiologically complex, multi-host, endemic disease. Pathogen whole genome sequencing can improve the resolution of epidemiological tracing. We genome sequenced an exceptional data set of 619 Mycobacterium bovis isolates from badgers and cattle in a 100km2 bTB hotspot. Historical molecular subtyping data permitted the targeting of an endemic pathogen lineage, whose long-term persistence provided an opportunity to study genome epidemiology in detail. To assess whether badger population genetic structure was associated with the spatial distribution of pathogen genetic diversity, we microsatellite genotyped hair samples from 769 badgers trapped in this area. ResultsEight lineages of M. bovis were circulating in the study area, seven of which were likely non-endemic, and imported by animal movement. The endemic lineage exhibited low genetic diversity with an average inter-isolate genetic distance of 7.6 SNPs (s.d. {+/-} 4.0), consistent with contemporary transmission. Bayesian phylogenetic methods determined an evolutionary rate of 0.30 substitutions per genome per year for this lineage, estimating its emergence 40-50 years before present, while Bayesian Skyline analysis identified significant population expansion of the endemic lineage in the 1990s and again in 2011-2012. The phylogeny revealed distinct sub-lineages, all of which contained isolates from both cattle and badger hosts, indicative of the sharing of closely related strains and inter-species transmission. However, the presence of significant badger population genetic structure was not associated with the spatial distribution of M. bovis genetic diversity. ConclusionsOur data provided unparalleled detail on the evolutionary history of an endemic M. bovis lineage. Findings are consistent with ongoing interspecies transmission in the study area but suggest that badger intra-species transmission may not be a major driver of persistence in this area. In addition, the data collected permitted the tracking of incursions of novel pathogen lineages into the study area and means to determine if they were involved in disease transmission.

evolutionary biology↗