Biology subjects

Borges, V.

Publications and source records attributed to Borges, V..

13 recordsLinked to original sources

bioRxiv2025

cgDist: An Enhanced Algorithm for Efficient Calculation of pairwise SNP and InDel differences from Core Genome Multilocus Sequence Typing

Bacterial genomic surveillance requires balancing computational efficiency with genetic resolution for effective outbreak investigation. Traditional cgMLST distance calculations treat all allelic differences as equivalent units, potentially obscuring nucleotide-level variation critical for source attribution. While SNP-based methods provide enhanced resolution, their computational requirements limit routine deployment in surveillance laboratories. We present cgDist, an algorithm that bridges this resolution gap by calculating nucleotide-level distances directly from cgMLST allelic profiles. The unified cache architecture stores comprehensive alignment statistics, enabling multiple distance calculation modes without redundant computation and supporting both dataset-specific and schema-complete cache generation. This design transforms genomic surveillance from batch processing to continuous streaming analysis, with cumulative performance benefits as laboratories accumulate alignment data. cgDist functions optimally as a precision "zoom lens" for the detailed investigation of clusters identified through initial cgMLST screening. Rather than restructuring entire population relationships, this targeted approach maximizes epidemiological insight precisely where enhanced resolution is most valuable. The algorithm ensures that cgDist distances are always greater than or equal to corresponding cgMLST distances, preserving epidemiological interpretability while adding critical genetic discrimination. The system includes integrated recombination detection capabilities that leverage cached alignment statistics to identify potential horizontal gene transfer events through mutation density analysis. This multi-scale analytical framework--from population screening through cluster zoom analysis to recombination detection--provides comprehensive surveillance capabilities within the computational constraints of routine public health practice.

bioinformatics↗

bioRxiv2024

Hypothermia protects against ventilator-induced lung injury by limiting IL-1beta release and NETs formation

Although mechanical ventilation is a critical intervention for acute respiratory distress syndrome (ARDS), it can trigger an IL-1{beta}-associated complication known as ventilator-induced lung injury. In mice, we found that LPS and high-volume ventilation, LPS-HVV, leads to hypoxemia with neutrophil extracellular traps (NETs) formation in the alveoli. Furthermore, Il1r1-/- LPS-HVV mice did not develop hypoxemia and had reduced NETs, indicating that IL-1R1 signaling is important for NETs formation and hypoxemia. Therapeutic hypothermia (TH) is known to reduce the release of inflammatory mediators. In LPS-HVV mice, TH (32 {degrees}C body temperature) prevented hypoxemia development, reducing albumin leakage, IL-1{beta}, gasdermin D (GSDMD) and NETs formation. We also observed that LPS-primed macrophages, when stimulated at 32{degrees}C with ATP or nigericin, release less IL-1{beta} associated with reduced GSDMD cleavage. Thus, hypothermia is an important modulating factor in the NLRP3 inflammasome activation, IL-1{beta} release and NETs formation, preventing LPS-HVV-induced acute respiratory failure.

immunology↗

bioRxiv2024

The Switchmaze: an open-design device for measuring motivation and drive switching in mice

Animals need to switch between motivated behaviours, like drinking, feeding or social interaction, to meet environmental availability, internal needs and more complex ethological needs such as hiding future actions from competitors. Inflexible, repetitive behaviours are a hallmark of many neuropsychiatric disorders. However, how the brain orchestrates switching between the neural mechanisms controlling motivated behaviours, or drives, is unknown. This is partly due to a lack of appropriate measurement systems. We designed an automated extended home-cage, the Switchmaze, using open-source hardware and software. In this study, we use it to establish a behavioural assay of motivational switching in mice. Individual animals access the Switchmaze from the home-cage and choose between entering one of two chambers containing different goal objects or returning to the home-cage. Motivational switching is measured as a ratio of switching between chambers and continuous exploitation of one chamber. Behavioural transition analysis is used to further dissect altered motivational switching. As proof-of-concept, we show environmental manipulation, and targeted brain manipulation experiments which altered motivational switching without effect on traditional behavioural parameters. Chemogenetic inhibition of the prefrontal-hypothalamic axis increased the rate of motivation switching, highlighting the involvement of this pathway in drive switching. This work demonstrates the utility of open-design in understanding animal behaviour and its neural correlates.

neuroscience↗

bioRxiv2023

Putative APOBEC3 deaminase editing in MPXV as evidence for sustained human transmission since at least 2016.

Mpox is often described as being endemic in West and Central Africa as a zoonotic disease that transmits through contact with the reservoir rodent host, likely a species of African squirrel. In May 2022, human cases of Mpox were detected spreading internationally beyond countries with known endemic reservoirs. At time of writing, 84,700 confirmed cases have been reported in 110 countries. When the first cases from 2022 were sequenced, it was seen that they shared 42 single nucleotide differences from the closest mpox virus (MPXV) genome sampled in 2018. This number of changes within 3-4 years is unexpectedly large and points to a much greater evolutionary rate than expected for a poxvirus. Strikingly, most nucleotide changes are of a specific type - a dinucleotide change from TC->TT or its reverse complement GA->AA. This mutation type is characteristic of the action of APOBEC3 deaminases; host-enzymes with reported antiviral function. Analysis of MPXV genomes sampled from 2017 to 2022 showed further evidence of TC->TT mutation pattern enrichment, with 93% of transmitted single nucleotide mutations since 2017 consistent with APOBEC3 editing. Assuming APOBEC-editing is characteristic of MPXV infection in human hosts, we propose an APOBEC clock that - at a rate of ~6 APOBEC3 mutations per year - estimates MPXV has been circulating in humans since 2016. This evolutionary pattern of host-enzyme editing has implications for the longer-term fitness of the virus in this epidemic as such mechanisms are primarily antiviral in function, but in the context of a poxvirus also provide a source of variation that may conceivably facilitate adaptation.

evolutionary biology↗

bioRxiv2023

Genetics of Latin American Diversity (GLAD) Project: insights into population genetics and association studies in recently admixed groups in the Americas

Latin America is underrepresented in genetic studies, which can exacerbate disparities in personalized genomic medicine. However, genetic data of thousands of Latin Americans are already publicly available, but require a bureaucratic maze to navigate all the data access and consenting issues. We present the Genetics of Latin American Diversity (GLAD) Project, a platform that compiles genome-wide information of 54,077 Latin Americans from 39 studies representing 45 geographical regions. Through GLAD, we identified heterogeneous ancestry composition and recent gene-flow across the Americas. Also, we developed a simulated-annealing-based algorithm to match the genetic background of external samples to our database and share summary statistics without transferring individual-level data. Finally, we demonstrate the potential of GLAD as a critical resource for evaluating statistical genetic softwares in the presence of admixture. By making this resource available, we promote genomic research in Latin Americans and contribute to the promises of personalized medicine to more people.

genetics↗

bioRxiv2021

Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution

Background and objectivesTo understand how organisms evolve, it is fundamental to study how mutations emerge and establish. Here, we estimated the rate of mutation accumulation of SARS-CoV-2 in vitro and investigated the repeatability of its evolution when facing a new cell type but no immune or drug pressures. MethodologyWe performed experimental evolution with two strains of SARS-CoV-2, one carrying the originally described spike protein (CoV-2-D) and another carrying the D614G mutation that has spread worldwide (CoV-2-G). After 15 passages in Vero cells and whole genome sequencing, we characterized the spectrum and rate of the emerging mutations and looked for evidences of selection across the genomes of both strains. ResultsFrom the mutations accumulated, and excluding the genes with signals of selection, we estimate a spontaneous mutation rate of 1.25x10-6 nt-1 per infection cycle for both lineages of SARS-CoV-2. We further show that mutation accumulation is heterogeneous along the genome, with the spike gene accumulating mutations at rate five-fold higher than the genomic average. We also observe the emergence of mutators in the CoV-2-G background, likely linked to mutations in the RNA-dependent RNA polymerase and/or in the error-correcting exonuclease protein. Conclusions and implicationsThese results provide valuable information on how spontaneous mutations emerge in SARS-CoV-2 and on how selection can shape its genome towards adaptation to new environments. Lay summaryMutation is the ultimate source of variation. We estimated how the SARS-COV-2 virus--cause of the COVID-19 pandemic--mutates. Upon infecting cells, its genome can change at a rate of 0.04 per replication. We also find that this rate can change and that its spike protein can adapt, even within few replications.

evolutionary biology↗

bioRxiv2020

Emergence and global spread of Listeria monocytogenes main clinical clonal complex

Retracing microbial emergence and spread is essential to understanding the evolution and dynamics of pathogens. The bacterial foodborne pathogen Listeria monocytogenes clonal complex 1 (Lm-CC1) is the most prevalent clonal group associated with listeriosis, and is strongly associated with cattle and dairy products. Here we analysed 2,021 Lm-CC1 isolates collected from 40 countries, since the first Lm isolation to the present day, to define its evolutionary history and population dynamics. Our results suggest that Lm-CC1 spread worldwide from North America following the Industrial Revolution through two waves of expansion, coinciding with the transatlantic livestock trade in the second half of the 19th century and the rapid growth of cattle farming in the 20th century. Lm-CC1 then firmly established at a local level, with limited inter-country spread. This study provides an unprecedented insight into Lm-CC1 phylogeography and dynamics and can contribute to effective disease surveillance to reduce the burden of listeriosis.

genomics↗

bioRxiv2020

Genomic insights on DNase production in Streptococcus agalactiae ST17 and ST19 strains

Streptococcus agalactiae evasion from the human defense mechanisms has been linked to the production of DNases. These were proposed to contribute to the hypervirulence of S. agalactiae ST17/capsular-type III strains, mostly associated with neonatal meningitis. We performed a comparative genomic analysis between ST17 and ST19 human strains with different cell tropism and distinct DNase production phenotypes. All S. agalactiae ST17 strains, with the exception of 2211-04, were found to display DNase activity, while the opposite scenario was observed for ST19, where 1203-05 was the only DNase(+) strain. The analysis of the genetic variability of the seven genes putatively encoding secreted DNases in S. agalactiae revealed an exclusive amino acid change in the predicted signal peptide of GBS0661 (NucA) of the ST17 DNase(-), and an exclusive amino acid change alteration in GBS0609 of the ST19 DNase(+) strain. Further core-genome analysis identified some specificities (SNVs or indels) differentiating the DNase(-) ST17 2211-04 and the DNase(+) ST19 1203-05 from the remaining strains of each ST. The pan-genomic analysis evidenced an intact phage without homology in S. agalactiae and a transposon homologous to TnGBS2.3 in ST17 DNase(-) 2211-04; the transposon was also found in one ST17 DNase(+) strain, yet with a different site of insertion. A group of nine accessory genes were identified among all ST17 DNase(+) strains, including the Eco47II family restriction endonuclease and the C-5 cytosine-specific DNA methylase. None of these loci was found in any DNase(-) strain, which may suggest that these proteins might contribute to the lack of DNase activity. In summary, we provide novel insights on the genetic diversity between DNase(+) and DNase(-) strains, and identified genetic traits, namely specific mutations affecting predicted DNases (NucA and GBS0609) and differences in the accessory genome, that need further investigation as they may justify distinct DNase-related virulence phenotypes in S. agalactiae.

genomics↗

bioRxiv2020

Global gene expression analysis of Streptococcus agalactiae at exponential growth phase

Streptococcus agalactiae is a leading cause of neonatal infections and an increasing cause of infections in adults with underlying diseases. One of the first S. agalactiae isolates to be subjected to whole genome sequencing was NEM316, a strain responsible for a fatal case of septicemia that has been widely used as reference strain for in vitro assays. Whole transcriptome analyses may provide an essential contribute to the understanding of the molecular mechanisms responsible for bacteria adaptation and pathogenicity, still, so far, very few studies were dedicated to the analysis of global gene expression of S. agalactiae. Here, we applied RNA-sequencing to perform a comparative overview of the global gene expression levels of the S. agalactiae reference strain NEM316 at the exponential growth phase. Genes were ranked by expression level and grouped by functional category and 46% of the top-100 expressed genes encode proteins involved in "Translation, ribosomal structure and biogenesis". Among the group of highly expressed genes were also represented genes with no assigned functional category. Although this result warrants further investigation, most of them might be implicated in stress response. As very little is known about the molecular mechanisms behind the release of DNases in vitro and in vivo, we also performed preliminary assays to understand whether direct DNA exposure affects the gene expression of strain NEM316 at the exponential growth phase. No differentially expressed genes were detected, which indicates that follow-up studies are needed to disclose the complex molecular pathways (and stimuli) triggering the release of DNases. In general, we provide data on the global expression levels of NEM316 at exponential growth phase that may contribute to better understand S. agalactiae adaptation and virulence.

genomics↗

bioRxiv2020

Mitogenome diversity of Aedes (Stegomyia) albopictus: Detection of multiple introduction events in Portugal and potential within-country dispersal

Aedes albopictus, along with Ae. aegypti, are key arbovirus vectors that have been expanding their geographic range over the last decades. In 2017, Ae. albopictus was detected for the first time at two distinct locations in Portugal. In order to understand how the Ae. albopictus populations recently introduced in Portugal are genetically related and which is their likely route of invasion, we performed an integrative cytochrome C oxidase I gene (COI)- and mitogenome-based phylogeographic analysis of mosquitoes samples collected in Portugal in 2017 and 2018 in the context of the global Ae. albopictus diversity. COI-based analysis (31 partial sequences obtained from 83 mosquitoes) revealed five haplotypes (1 to 5), with haplotype 1 (which is widely distributed in temperate areas worldwide) being detected in both locations. Haplotypes 2 and 3 were exclusively found in Southern region (Algarve), while haplotype 4 and 5 were only detected in the North of Portugal (Penafiel, Oporto region). Subsequent high discriminatory analyses based on Ae. albopictus mitogenome (17 novel sequences) not only confirmed a high degree of genetic variability within and between populations at both geographic locations (compatible with the Ae. albopictus mosquito populations circulating in Europe), but also revealed two mitogenome mutational signatures not previously reported at worldwide level. While our results generally sustain the occurrence of multiple introduction events, fine mitogenome sequence inspection further indicates a possible Ae. albopictus migration within the country, from the Northern introduction locality to the Southern region. In summary, the observed scenario of high Ae. albopictus genetic diversity in Portugal, together with the detection of mosquitoes in successive years since 2017 in Algarve and Penafiel, points that both Ae. albopictus populations seem to be already locally establish, as its presence has been reported for three consecutive years, raising the public health awareness for future mosquito-borne diseases outbreaks. Author SummaryIn 2017, Aedes albopictus was reported for the first time in Portugal at two distinct locations, in the premises of a tyre company in Penafiel, in the North, and nearby a golf course in Algarve, a tourism destination in the southernmost country region. The geographical spread of this species is boosted by larvae and desiccation-resistant eggs transport in aquatic trade goods, as tires and aquatic plants, and adult anthropophilic behavior that favors passive land transportation. In Portugal, especially in the Southern region, temperate climate conditions are adequate for adult mosquitoes survival most of the year. In a way to understand the genetic variability of Ae. albopictus populations introduced in Portugal, we analyzed 31 cytochrome C oxidase I gene (COI) partial sequences and 17 mitogenome sequences, integrating them in the context of the global Ae. albopictus phylogeographic diversity (i.e., 183 COI and 26 mitogenome sequences previously reported at worldwide level). Although COI haplotype 1 predominated, four additional haplotypes (2 to 5) were detected in Portugal. Subsequent in-depth mitogenome analysis revealed considerable genetic diversity, including not only sequences relating to mitogenomes reported mainly from Italy, Japan and China, but also two novel mitogenome mutational signatures. Our study indicate that Ae. albopictus is locally established in Portugal and intra-country dispersal may have already happened, highlighting the challenges for vector surveillance and control programs aiming at restraining arbovirus disease burden in the future.

genomics↗

bioRxiv2019

Virulence and antibiotic resistance plasticity of Arcobacter butzleri: insights on the genomic diversity of an emerging human pathogen

Arcobacter butzleri is a food and waterborne bacteria and an emerging human pathogen, frequently displaying a multidrug resistant character. Still, no comprehensive genome-scale comparative analysis has been performed so far, which has limited our knowledge on A. butzleri diversification and pathogenicity. Here, we performed a deep genome analysis of A. butzleri focused on decoding its core- and pan-genome diversity and specific genetic traits underlying its pathogenic potential and diverse ecology. In total, 49 A. butzleri strains (collected from human, animal, food and environmental sources) were screened.\n\nA. butzleri (genome size 2.07-2.58 Mbp) revealed a large open pan-genome with 7474 genes (about 50% being singletons) and a small core-genome with 1165 genes. The core-genome is highly diverse ([≥]55% of the core genes presenting at least 40/49 alleles), being enriched with genes associated with housekeeping functions. In contrast, the accessory genome presented a high proportion of loci with an unknown function, also being particularly overrepresented by genes associated with defence mechanisms. A. butzleri revealed a plastic virulome (including newly identified determinants), marked by the differential presence of multiple adaptation-related virulence factors, such as the urease cluster ureD(AB)CEFG (phenotypically confirmed), the hypervariable hemagglutinin-encoding hecA, a putative type I secretion system (T1SS) harboring another agglutinin potentially related to adherence and a novel VirB/D4 T4SS likely linked to interbacterial competition and cytotoxicity. In addition, A. butzleri harbors a large repertoire of efflux pumps (EPs) (ten \"core\" and nine differentially present) and other antibiotic resistant determinants. We provide the first description of a genetic determinant of macrolides resistance in A. butzleri, by associating the inactivation of a TetR repressor (likely regulating an EP) with erythromycin resistance. Fluoroquinolones resistance correlated with the Thr-85-Ile substitution in GyrA and ampicillin resistance was linked to an OXA-15-like {beta}-lactamase. Remarkably, by decoding the polymorphism pattern of the porin- and adhesin-encoding main antigen PorA, this study strongly supports that this pathogen is able to exchange porA as a whole and/or hypervariable epitope-encoding regions separately, leading to a multitude of chimeric PorA presentations that can impact pathogen-host interaction during infection. Ultimately, our unprecedented screening of short sequence repeats detected potential phase-variable genes related to adaptation and host/environment interaction, such as lipopolysaccharide modification and motility/chemotaxis, suggesting that phase variation likely modulate A. butzleri key adaptive functions.\n\nIn summary, this study constitutes a turning point on A. butzleri comparative genomics revealing that this human gastrointestinal pathogen is equipped with vast virulence and antibiotic resistance arsenals, which, coupled with its remarkable core- and pan-genome diversity, opens a multitude of phenotypic fingerprints for environmental/host adaptation and pathogenicity.\n\nIMPACT STATEMENTDiarrhoeal diseases are the most common cause of human illness caused by foodborne hazards, but the surveillance of diarrhoeal diseases is biased towards the most commonly searched infectious agents (namely Campylobacter jejuni and C. coli). In fact, other less studied pathogens are frequently found as the etiological agent when refined non-selective culture conditions are applied. A hallmark example is the diarrhoeal-causing Arcobacter butzleri which, despite being also associated with extra-intestinal diseases, such as bacteremia in humans and mastitis in animals, and displaying high rates of antibiotic resistance, has not yet been profoundly investigated regarding its epidemiology, diversity and pathogenicity. To overcome the general lack of knowledge on A. butzleri comparative genomics, we provide the first comprehensive genome-scale analysis of A. butzleri focused on exploring the intraspecies virulome content and diversity, resistance determinants, as well as how this pathogen shapes its genome towards ecological adaptation and host invasion. The unveiled scenario of A. butzleri rampant diversity and plasticity reinforces the pathogenic potential of this food and waterborne hazard, while opening multiple research lines that will certainly contribute to the future development of more robust species-oriented diagnostics and molecular surveillance of A. butzleri.\n\nDATA SUMMARYA. butzleri raw sequence reads generated in the present study were deposited in the European Nucleotide Archive (ENA) (BioProject PRJEB34441). The assembled contigs (.fasta and .gbk files), the nucleotide sequences of the predicted transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA) (.ffn files) and the respective amino acid sequences of the translated CDS sequences (.faa files) are available at http://doi.org/10.5281/zenodo.3434222. Detailed ENA accession numbers, as well as the draft genome statistics are described in Table S1.

genomics↗

bioRxiv2019

Chlamydia trachomatis outbreak: when the virulence-associated genome backbone imports a prevalence-associated major antigen signature

Chlamydia trachomatis is the most prevalent sexually transmitted bacteria worldwide and the causative agent of blinding trachoma. Strains are classified based on ompA genotypes, which are strongly linked with differential tissue tropism and disease outcomes. A lymphogranuloma venereum (LGV) epidemics, characterized by ulcerative proctitis, has emerged in the last two decades (mainly L2b genotype), raising high concern especially due to its circulation among men who have sex with men (MSM). Here, we report an ongoing outbreak (mostly affecting HIV-positive MSM engaging in high-risk practices) caused by an L2b strain with a rather unique genome makeup that precluded the laboratory notification of this outbreak as LGV due to its non-LGV ompA signature. Homologous recombination mediated the transfer of a ~4.5Kbp fragment enrolling CT681/ompA and neighboring genes (CT677/rrf, CT678/pyrH, CT679/tsf, CT680/rpsB) from a serovar D/Da strain likely possessing the typical T1 clade genome backbone associated with most prevalent genotypes (E and F). The hybrid L2b/D-Da strain presents the adhesin and immunodominant antigen MOMP (coded by ompA) with an epitope repertoire typical of non-invasive genital strains, while keeping the genome-dispersed virulence fingerprint of a classical LGV (L2b) strain. As previously reported for inter-clade ompA exchange among non-LGV clades, this unprecedented C. trachomatis genomic mosaic involving a contemporary epidemiologically and clinically relevant LGV strain may have implications on its transmission, tissue tropism and pathogenic capabilities. The emergence of such variants with epidemic and pathogenic potential highlights the need of more oriented surveillance strategies focused on capturing the C. trachomatis evolution in action.

genomics↗

bioRxiv2018

INSaFLU: an automated open web-based bioinformatics suite “from-reads” for influenza whole-genome-sequencing-based surveillance

A new era of flu surveillance has already started based on the genetic characterization and exploration of influenza virus evolution at whole-genome scale. Although this has been prioritized by national and international health authorities, the demanded technological transition to whole-genome sequencing (WGS)-based flu surveillance has been particularly delayed by the lack of bioinformatics infrastructures and/or expertise to deal with primary next-generation sequencing (NGS) data. Here, we launch INSaFLU (\"INSide the FLU\"), which, to the best of our knowledge, is the first influenza-specific bioinformatics free web-based suite that deals with primary data (reads) towards the automatic generation of the output data that are actually the core first-line \"genetic requests\" for effective and timely influenza laboratory surveillance (e.g., type and sub-type, gene and whole-genome consensus sequences, variants annotation, alignments and phylogenetic trees). By handling NGS data collected from any amplicon-based schema, the implemented pipeline enables any laboratory to perform advanced, multi-step software intensive analyses in a user-friendly manner without previous training in bioinformatics. INSaFLU gives access to user-restricted sample databases and projects management, being a transparent and highly flexible tool specifically designed to automatically update project outputs as more samples are uploaded. Data integration is thus completely cumulative and scalable, fitting the need for a continuous epidemiological surveillance during the flu epidemics. Multiple outputs are provided in nomenclature-stable and standardized formats that can be explored in situ or through multiple compatible downstream applications for fine-tune data analysis. This platform additionally flags samples as \"putative mixed infections\" if the population admixture enrolls influenza viruses with clearly distinct genetic backgrounds, and enriches the traditional \"consensus-based\" influenza genetic characterization with relevant data on influenza sub-population diversification through a depth analysis of intra-patient minor variants. This dual approach is expected to strengthen our ability not only to detect the emergence of antigenic and drug resistance variants, but also to decode alternative pathways of influenza evolution and to unveil intricate routes of transmission. In summary, INSaFLU supplies public health laboratories and influenza researchers with an open \"one size fits all\" framework, potentiating the operationalization of a harmonized multi-country WGS-based surveillance for influenza virus.\n\nINSaFLU can be accessed through https://insaflu.insa.pt (see homepage view in Figure 1).\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC=\"FIGDIR/small/253161_fig1.gif\" ALT=\"Figure 1\">\nView larger version (26K):\norg.highwire.dtl.DTLVardef@1111419org.highwire.dtl.DTLVardef@3e99c2org.highwire.dtl.DTLVardef@1e0a953org.highwire.dtl.DTLVardef@8c9ea6_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO INSaFLU homepage\n\nC_FIG

bioinformatics↗