A5031983257- Genomics and Phylogenetic Studies
- SARS-CoV-2 and COVID-19 Research
- Plant Pathogenic Bacteria Studies
- Salmonella and Campylobacter epidemiology
- SARS-CoV-2 detection and testing
- Gut microbiota and health
- Plant Virus Research Studies
- Microbial Community Ecology and Physiology
- Leptospirosis research and findings
- Virology and Viral Diseases
- Data Analysis with R
- COVID-19 Clinical Research Studies
- Viral gastroenteritis research and epidemiology
- Streptococcal Infections and Treatments
- Microbial infections and disease research
- Plant Diversity and Evolution
- COVID-19 epidemiological studies
- Helicobacter pylori-related gastroenterology studies
- Mosquito-borne diseases and control
- Cancer Research and Treatments
- Genetic diversity and population structure
- Turtle Biology and Conservation
- Bacterial biofilms and quorum sensing
- Microbial Fuel Cells and Bioremediation
- COVID-19 diagnosis using AI
Institut Pasteur de Montevideo
2017-2023
University of Colombo
2021
Netherlands Food and Consumer Product Safety Authority
2021
National Institute for Public Health and the Environment
2021
Utrecht University
2021
Wageningen University & Research
2021
General Sir John Kotelawala Defence University
2021
Despite recent advances in our understanding of the genomics members genus Leptospira , little is known on how virulence has emerged this heterogeneous bacterial as well lifestyle pathogenic outside animal hosts. Here, we isolated 12 novel species from tropical soils, significantly increasing number to 35 and finding evidence highly unexplored biodiversity genus. Extended comparative phylogenomics pan-genome analyses at level by incorporating 26 genomes, revealed that, traditional...
Three strains, CLM-U50T, CLM-R50 and IVIC-Bov1, belonging to the genus Leptospira, were isolated in Venezuela from a patient with leptospirosis, domestic rat (Rattus norvegicus) cow (Bos taurus), respectively. The initial characterisation of these strains based on rrs gene (16S rRNA) suggested their designation as novel species within 'intermediates' group Leptospira. Further phylogenomic single copy core genes was consistent separation into species. average nucleotide identity between three...
Plasmids are mobile genetic elements important for bacterial adaptation. The study of plasmids from sequencing data is challenging because short reads produce fragmented assemblies, requiring subsequent discrimination between chromosome and plasmid sequences. Although circularized assemblies now possible using long-read data, there still a need to differentiate other circular elements. Here, we present plaSquid, dockerized tool developed in Nextflow that expands detection improves replicon...
Pangenome analysis is fundamental to explore molecular evolution occurring in bacterial populations. Here, we introduce Pagoo, an R framework that enables straightforward handling of pangenome data. The encapsulated nature Pagoo allows the storage complex and phenotypic information using object-oriented approach. This facilitates go back forward data a single programming environment saving any stage (including raw data) file, making it sharable reproducible. provides tools query, subset,...
ABSTRACT Background South America has become the new epicenter of COVID-19 pandemic with more than 1.1M reported cases and >50,000 deaths (June 2020). Conversely, Uruguay stands out as an outlier managing this health crisis remarkable success. Methods We developed a molecular diagnostic test to detect SARS-CoV-2. This methodology was transferred research institutes, public hospitals academic laboratories all around country, creating “ lab network ”. also implemented active epidemiological...
Uruguay is one of the few countries in Americas that successfully contained coronavirus disease 19 (COVID-19) epidemic during first half 2020. Nevertheless, intensive human mobility across dry border with Brazil a major challenge for public health authorities. We aimed to investigate origin severe acute respiratory syndrome 2 (SARS-CoV-2) strains detected Uruguayan localities bordering as well measure viral flux this ∼1,100 km uninterrupted frontier. Using complete SARS-CoV-2 genomes from...
Multilocus sequence typing (MLST) is a standard tool in population genetics and bacterial epidemiology that assesses the genetic variation present reduced number of housekeeping genes (typically seven) along genome. This methodology assigns arbitrary integer identifiers to variations at these loci which allows us efficiently compare isolates using allele-based methods. Now, increasing availability whole-genome sequences for hundreds thousands strains from same species has allowed apply...
We developed a genomic surveillance program for real-time monitoring of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants concern (VOCs) in Uruguay. report on PCR method SARS-CoV-2 VOCs, the workflow, and multiple independent introductions community transmission P.1 VOC
Abstract Campylobacter hyointestinalis is an emerging pathogen currently divided in two subspecies: C. subsp. lawsonii which predominantly recovered from pigs, and can be found a much wider range of mammalian hosts. Despite being reported as pathogen, its evolutionary host-associated diversification patterns are still vastly unexplored. For this reason, we generated whole-genome sequences 13 strains performed comprehensive comparative analysis including publicly available genomes, to gain...
Multiple downstream analyses are necessary to interpret the output of bacterial pangenome reconstruction software. This requires integrating diverse kinds genetic and phenotypic data, which date left each user's criterion. To fill this gap, we created Pagoo, a post-processing tool that leverages standardized but flexible extensible framework for data integration, analysis, storage. Here, provide protocol running Pagoo performing from simple more complex comparative on data. For complete...
It is estimated that more than three quarters of the Earth’s biosphere in perennially cold environments. Despitethe extreme environmental conditions desiccation and freezing, microbes can colonize these habitats through adaptationof metabolic functions synthesis structurally adapted enzymes. Enzymes within psychrophilic exhibit highspecific activity at low moderate temperature, with thermostability. In this study we used a classic microbiologicalapproach to isolate Antarctic bacteria...
Abstract Background Helicobacter valdiviensis is a recently described enterohepatic species isolated from wild bird's fecal samples. Currently, its pathogenic potential and clinical significance are unknown mainly due to the lack of whole‐genome sequences compare with other helicobacters absence specific screenings determine prevalence in humans. Materials Methods The type strain ( WBE 14 T ) was whole‐genome‐sequenced, comparative analyses were carried out including genomes exact...
Background After its emergence in China December 2019, the new coronavirus disease (COVID-19) caused by SARS-CoV-2, has rapidly spread infecting more than 3 million people worldwide. South America is among last regions hit COVID-19 pandemic. In Uruguay, first cases were detected on March 13 th 2020 presumably imported travelers returning from Europe. Methods We performed whole-genome sequencing of 10 SARS-CoV-2 patients diagnosed during week (March 16 to 19 ) outbreak Uruguay. Then, we...
Summary Background Uruguay is one of the few countries in Americas that successfully contained COVID-19 epidemic during first half 2020. Nevertheless, intensive human mobility across dry border with Brazil a major challenge for public health authorities. We aimed to investigate origin SARS-CoV-2 strains detected Uruguayan localities bordering as well measure viral flux this ∼1,100 km uninterrupted frontier. Methods Using complete genomes from Uruguayan-Brazilian region and phylogeographic...
Uruguay controlled the viral dissemination during first nine months of SARS-CoV-2 pandemic. Unfortunately, towards end 2020, number daily new cases exponentially increased. Herein, we analyzed country-wide genetic diversity between November 2020 and April 2021. We identified that most prevalent variant epidemic wave in (December 2020-February 2021) was a B.1.1.28 sublineage carrying Spike mutations Q675H + Q677H, now designated as P.6, followed by lineages P.2 P.7. P.6 probably arose around...
The pangenome concept describes genetic variability as the union of genes shared in a set genomes and constitutes current paradigm for comparative analysis bacterial populations. However, there is lack tools to simulate structure using defined evolutionary models.We developed simurg, an R package that allows pangenomes different combinations constraints such gene gain, loss mutation rates. Our tool straightforward reproducible simulation real sequence data, providing valuable benchmarking...
High-throughput sequencing is dramatically increasing the amount of genetic data available from all domains life, but particularly bacteria.The smaller size bacterial genomes allows to sequence large collections strains, mainly species that deserve interest for their importance as human or farm animal pathogens.Phylogenetic analysis has become a standard tool understand evolutionary history, epidemiology and virulence these bacteria, availability genomic information allowed move single-gene...
Most biologically relevant and diagnostic mutations in the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genome have been identified S gene through global genomic surveillance efforts. However, large-scale whole-genome sequencing (WGS) is still challenging developing countries due to higher costs, reagent delays limited infrastructure. Consequently, only a small fraction of SARS-CoV-2 samples are characterized WGS these regions. Here, we present complete workflow consisting...
Abstract We developed a genomic surveillance program for real-time monitoring of SARS-CoV-2 variants concern in Uruguay. Here, we present the first results, including proposed qPCR-VOC method, general workflow and report introduction community transmission VOC P.1 Uruguay multiple independent events.
A metagenomic fosmid library of approximately 52 000 clones was constructed to identify functional genes encodingcold-adapted enzymes. Metagenomic DNA extracted from a sample glacial meltwater, collected on the Antarctic Peninsuladuring ANTARKOS XXIX Expedition during austral summer 2012-2013. Each clone contained an insert about35-40 kb, so represented almost 2 Gb genetic information DNA. Activity-driven screening wasused detect cold-adapted functions expressed by library. Fifty...
Abstract Campylobacter hyointestinalis is an emerging pathogen currently divided in two subspecies: C. subsp. lawsonii which restricted to pigs, and can be found a much wider range of mammalian hosts. Despite has been reported as pathogen, its evolutionary host-associated diversification patterns are still vastly unexplored. For this reason, we whole-genome sequenced 13 strains performed comprehensive comparative analysis including publicly available genomes gain insight into the genomic...
Pathogenic Leptospira species represent a major concern for livestock but also human health, as they cause zoonotic infections. Forty strains representing L. interrogans , borgpetersenii and noguchii were isolated from naturally infected cattle in Uruguay. Here, we report the whole-genome sequences these strains.
Pangenome analysis is fundamental to explore evolutionary processes occurring in bacterial populations. However, the lack of standardized methods for handling diverse pangenomic datasets and complex metadata hinders more straightforward reproducible downstream analyses. To fill this gap, we introduce Pagoo, a new framework that integrates pangenome data, analytical visualization tools single object can be easily stored, shared responsively queried improved biological interpretation evolution.
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