Banca de DEFESA: JÚLIA FIRME FREITAS

Uma banca de DEFESA de DOUTORADO foi cadastrada pelo programa.
STUDENT : JÚLIA FIRME FREITAS
DATE: 30/09/2024
TIME: 09:00
LOCAL: Link do Google Meet: https://meet.google.com/ugt-munq-nio
TITLE:

Virosphere and bacteriosphere of wastewater from the city of Natal - RN

KEY WORDS:

Pathogens; SARS-CoV-2; wastewater; metagenomics; genomic surveillance;antimicrobial resistance genes; virulence factors; metavirome.

PAGES: 185
BIG AREA: Ciências Biológicas
AREA: Genética
SUMMARY:

The COVID-19 pandemic has highlighted the need to develop pathogen surveillance systems for the early detection and management of zoonotic diseases and pandemic threats. In the context of genomic surveillance, some studies have shown that wastewater treatment plants are critical points for the dissemination of genes, such as antimicrobial resistance genes (ARG), due to the high density and diversity of microbial communities and the presence of mobile genetic elements that facilitate horizontal gene transfer. Thus, sewage can reflect the population's health, and understanding the microbiota present in this waste can provide essential information for public health authorities. In this context, the present study aimed to evaluate the virosphere and bacteriosphere of wastewater from the city of Natal to identify the main pathogens present, antimicrobial resistance genes, and virulence factors and their correlations to obtain biomarkers for monitoring and provide subsidies for public policies. For this purpose, the study was conducted longitudinally, with weekly collections over a year (June 2021 to May 2022) at three of Natal's main water treatment plants. A flocculation protocol was used to concentrate viral particles, and viral DNA and RNA extraction was performed using commercial kits to obtain the virosphere. The water samples were also subjected to total DNA extraction to evaluate the microbial community. The weekly samples were combined by month and sequenced via the NextSeq 1000 platform. Several bioinformatics tools were used to access the taxonomic profile, assemble contigs and genomes, and identify resistance and virulence genes. Co-occurrence networks were obtained via Bray-Curtis dissimilarity analysis. The virosphere was stable throughout the year, mainly in viruses infecting microorganisms or plants. An alternation in the representation of viruses that infect animals was observed. Bacteriophages associated with genera Escherichia, Pseudomonas, and Caulobacter bacteria were among the most abundant. The Odontoglossum ringspot virus was identified as a potential biomarker of RNA viruses of agricultural importance. Among the DNA viruses that infect animals, members of the Poxviridae family were observed in the samples. Co-occurrence network analysis identified potential biomarkers such as the Volepox virus, Anatid herpesvirus 1, and Caviid herpesvirus 2. Among RNA viruses that affect animals, the genera Mamastrovirus, Rotavirus, and Norovirus were the most abundant pathogens. Additionally, members of the Coronaviridae family, including SARS-CoV-2, exhibited high centrality in the co-occurrence network, connecting even with unclassified viruses. Furthermore, we confirmed the presence of SARS-CoV-2 by qPCR. We observed an association between Coronaviridae sequences, rainfall, and the number of reported COVID-19 cases. The rarefaction curve showed that all samples reached species stability regarding the metagenome. Phylogenetic diversity analysis did not reveal significant differences in the richness and evenness of communities over the months, suggesting a similar taxonomic composition throughout the year. However, differences in the proportion of some taxa were observed between samples. The genus Aliarcobacter was the most predominant in all samples. Non-metric multidimensional scaling (NMDS) analysis revealed four distinct groups indicating seasonality. Canonical correlation analysis (CCA) allowed the evaluation of the relationship between the taxonomic profile and variations in rainfall and temperature, indicating the same groupings. However, these environmental variables individually did not have a statistically significant impact on microbial composition. Among the viral communities identified in the metagenome, the genus Paundivirus predominated in most samples. Between January and March, crAssphage was the predominant virus. 221 antimicrobial resistance genes (ARG) classified into 16 categories were identified, with multidrug resistance genes being the most abundant. The genes msrE, mphE, sulI, and tetC were more abundant, with significant enrichment in January, July, and December. Virulence factors genes (VFG) analysis revealed 213 genes, classified into 14 categories, with the most prevalent adhesion factors. The genes tapT and mrkC were the most abundant, with significant enrichment in January and April. Co-occurrence networks revealed that ARG showed significant co-occurrence with viruses, while few ARG co-occurred with VFG. CrAssphage was the only virus that co-occurred with VFG. NMDS analyses confirmed the direct proportional relationship between ARG and viruses and the inversely proportional relationship between ARG and VFG. A total of 95 MAG (metagenome-assembled genomes) were obtained, among which 69 resistance genes, mainly related to multidrug resistance, were identified. Additionally, 33 MAG are those with the highest number of ARG. The most recurrent gene was the adeF gene (associated with tetracycline and fluoroquinolone resistance). Of the 33 MAG obtained, the genera Tolumonas and Rivicola were the most represented. In conclusion, this study's findings highlight the microbial community's complexity and stability in wastewater environments and the presence and dynamics of antimicrobial resistance genes and virulence factors over time. These advances will significantly contribute to our preparedness and response to future threats. Additionally, our study contributes to the knowledge of microbial dynamics, offering insights that can contribute to the direction of future public health policies and interventions and identifying potential monitoring biomarkers.

COMMITTEE MEMBERS:
Externo à Instituição - PABLO IVAN RAMOS - FIOCRUZ
Interno - 1880243 - DANIEL CARLOS FERREIRA LANZA
Externo à Instituição - JÔNATAS SANTOS ABRAHÃO
Presidente - 1149647 - LUCYMARA FASSARELLA AGNEZ LIMA
Externo ao Programa - 1507794 - RODRIGO JULIANI SIQUEIRA DALMOLIN - null