A5084062750- Genomics and Phylogenetic Studies
- Gut microbiota and health
- Salmonella and Campylobacter epidemiology
- Mycobacterium research and diagnosis
- Tuberculosis Research and Epidemiology
- SARS-CoV-2 and COVID-19 Research
- Plant Pathogenic Bacteria Studies
- Leptospirosis research and findings
- Microbial Community Ecology and Physiology
- SARS-CoV-2 detection and testing
- Bacteriophages and microbial interactions
- Antibiotic Resistance in Bacteria
- Trypanosoma species research and implications
- Microbial infections and disease research
- Clostridium difficile and Clostridium perfringens research
- Viral gastroenteritis research and epidemiology
- Animal Virus Infections Studies
- Plant Virus Research Studies
- Bacterial Identification and Susceptibility Testing
- COVID-19 Clinical Research Studies
- Pharmaceutical and Antibiotic Environmental Impacts
- Parvovirus B19 Infection Studies
- Virus-based gene therapy research
- Streptococcal Infections and Treatments
- Yersinia bacterium, plague, ectoparasites research
Universidad Mayor
2018-2023
Wellcome Sanger Institute
2018-2023
Institut Pasteur de Montevideo
2014-2023
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
New York University
2019
We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog urban microbial ecosystem. This provides an annotated, geospatial profile strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, 838,532 CRISPR arrays not found reference databases. identified 4,246 known species microorganisms consistent...
Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report first extensive genomic characterization microbiomes, pathogens antibiotic resistance cassettes in a tertiary-care hospital, from repeated sampling (up 1.5 years apart) 179 sites associated with 45 beds. Deep shotgun metagenomics unveiled distinct ecological niches genes characterized by biofilm-forming human-microbiome-influenced...
Microbial communities present in environmental waters constitute a reservoir for antibiotic-resistant pathogens that impact human health. For this reason, diverse variety of water environments are being analyzed using metagenomics to uncover public health threats. However, the composition these along coastal environment whole city, where sewage and beach mixed, is poorly understood. We shotgun-sequenced 20 areas from city Montevideo (capital Uruguay) including samples characterize bacterial...
Leptospirosis is an important environmental disease and a major threat to human health causing at least 1 million clinical infections annually. There has recently been growing interest in understanding the lifestyle of Leptospira. However, Leptospira isolation from complex samples difficult time-consuming few tools are available identify isolates species level. Here, we propose polyphasic identification scheme, which might prove useful recover select those be submitted whole-genome...
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...
ABSTRACT Functional recovery after peripheral nerve damage is dependent on the reprogramming of differentiated Schwann cells (dSCs) into repair (rSCs), which promotes axonal regeneration and tissue homeostasis. Transition a phenotype requires expression c-Jun Sox2, transcriptionally mediates inhibition dSC program myelination activates non-cell-autonomous program, characterized by secretion neuronal survival regenerative molecules, formation cellular scaffold to guide regenerating axons...
Antimicrobial resistance is one of the biggest challenges facing modern medicine. Because management COVID-19 increasingly becoming dependent on pharmacological interventions, there greater risk for accelerating evolution and spread antimicrobial resistance. A study in a tertiary hospital environment revealed concerning colonisation patterns microbes during extended periods.1 It also highlighted diversity gene reservoirs hospitals that could facilitate emergence transmission new modes antibiotic
Canine parvovirus (CPV), a fast-evolving single-stranded DNA virus, comprises three antigenic variants (2a, 2b, and 2c) with different frequencies genetic variability among countries. The contribution of co-infection recombination to the CPV is far from being fully elucidated. Here we took advantage natural population, recently formed by convergence divergent CPV-2c CPV-2a strains, study recombination. Complete sequences viral coding region strains 40 samples were generated analyzed using...
Abstract Campylobacter fetus is a venereal pathogen of cattle and sheep, an opportunistic human pathogen. It often assumed that C. infection occurs in humans as zoonosis through food chain transmission. Here we show mammalian consists distinct evolutionary lineages, primarily associated with either or bovine hosts. We use whole-genome phylogenetics on 182 strains from 17 countries to provide evidence may have originated around 10,500 years ago “jumped” into during the livestock domestication...
During a screening study to determine the presence of species genus Campylobacter in reptiles, three putative strains (RC7, RC11 and RC20T) were isolated from different individuals western Hermann's tortoise (Testudo hermanni hermanni). Initially, these isolates characterized as representing C ampylobacter fetus subsp. by multiplex PCR partial 16S rRNA gene sequence analysis. Further whole- genome characterization revealed considerable differences compared other species. A polyphasic was...
Abstract Chagas disease was described by Carlos Chagas, who first identified the parasite Trypanosoma cruzi from a 2-year-old girl called Berenice. Many T. sequencing projects based on short reads have demonstrated that genome assembly and downstream comparative analyses are extremely challenging in this species, given half of its is composed repetitive sequences. Here, we report de novo assemblies, annotation, Berenice strain using combination Illumina MinION long reads. Our work...
Infectious bronchitis virus (IBV) is a coronavirus of chickens that causes great economic losses to the global poultry industry. The present study focuses on South American IBVs and their genetic relationships with strains. We obtained full-length sequences S1 coding region N gene IBV field isolates from Uruguay Argentina, performed Phylodynamic analysis characterize strains estimate time most recent common ancestor. identified two major genotypes, which were here denoted America I (SAI)...
Abstract Canine parvovirus (CPV) is a fast-evolving single-stranded DNA virus that causes one of the most significant infectious diseases dogs. Although dispersed over long distances in past, current populations are considered to be spatially confined and with only few instances migration between specific localities. It unclear whether these dynamics occur South America where global studies have not been performed. The aim this study analyze patterns genetic variability American CPV explore...
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...
Abstract We have created a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities across 3 years. This is the first systematic, worldwide study cataloging urban microbial ecosystem. identify taxonomically-defined microorganisms collected three provides an annotated, geospatial profile strains, functional characteristics AMR markers, and novel genetic elements, including 10,928 viral, 1302 bacteria, 2 archaea species. 4,424 species consistent “core” 31 found nearly...
Abstract Background The microbial community composition of urban environments is primarily determined by human activity. use metagenomics to explore how communities are shaped in a city provides novel input that can improve decisions on public health measures, architectural design, and resilience. Of note, the sewage system acts as complex reservoir bacteria, pharmaceuticals, antimicrobial resistant (AMR) genes be an important source epidemiological information. Hospital effluents rich...
Infectious bursal disease virus (IBDV) is one of the most concerning health problems for world poultry production. IBDVs comprise four well-defined evolutionary lineages known as classic (c), attenuated (ca), variant (va) and very virulent (vv) strains. Here, we characterized from South America by genetic analysis both segments viral genome. Viruses belonging to c, ca vv strains were unambiguously classified presence molecular markers phylogenetic hypervariable region vp2 gene. Notably,...
The genus Campylobacter includes some of the most relevant pathogens for human and animal health; continuous effort in their characterization has also revealed new species putatively involved different kind infections. Nowadays, available genomic data comprise a wide variety with pathogenic potential niche preferences. In this work, we contribute to enlarge information presenting first genome sputorum bv. use already sequenced organisms analyze emergence evolution pathogenicity preferences...
The genus Leptospira is composed of pathogenic and saprophytic spirochetes. Pathogenic the etiological agent leptospirosis, a globally spread neglected disease. A key ecological feature some species their ability to survive both within outside host. For most leptospires, persist host associated with biofilm formation, important bacterial strategy face overcome hostile environmental conditions. architecture biochemistry leptospiral biofilms are rather well understood; however, genetic program...