AMR - Antimicrobial Resistance

About the Project

Coordinator

Prof. Dra. Vania Aparecida Vicente

Federal University of Paraná (UFPR)

Thematic Line

VI. Research Networks for identification, monitoring and genetic sequencing of resistant strains throughout the national territory

Description

This project establishes a network for monitoring and detecting antimicrobial resistance (AMR) patterns in causative agents of infectious-parasitic diseases, preserved in reference collection repositories and in environmental samples from various Brazilian biomes. It uses metagenomic approach and NGS sequencing, aiming at the development of a widely accessible panel, with application of notification of the circulation of AMR genes and species in Brazilian macroregions.

Objectives

General Objective

Establish a network for monitoring and detecting antimicrobial resistance (AMR) patterns in causative agents of infectious-parasitic diseases, preserved in reference collection repositories and in environmental samples from various Brazilian biomes, through metagenomic approach and NGS sequencing, aiming at the development of a widely accessible panel, with application of notification of the circulation of AMR genes and species in Brazilian macroregions.

Specific Objectives

Elucidate through phenotypic and molecular markers the resistance profile of clinical and environmental strains deposited in different repositories of reference and working collections of public institutions and hospitals and private laboratories, located in different Brazilian macroregions.
Sequence the complete genome of strains with resistance profile of fungi, bacteria and protozoa, aiming at the creation of databases of resistant species and genes.
Build fosmid libraries and perform functional screening for elucidation of new targets in resistant strains.
Establish a temporal line of AMR in fungi, bacteria and parasites based on the history of repository deposits.
Perform metagenome analyses and bioprospecting of environmental samples, hemodialysis water and biological waste from hospital disposal, aiming at environmental tracking of AMR species and genes through target-specific and total metagenomic approaches.

Compare metagenomic data (target-specific, total library and fosmid library) from conserved environments (biomes Amazon, Cerrado, Atlantic Forest, Pantanal) and anthropized (agricultural regions and deforested areas) and from evaluated repositories and build new barcodes.
Perform in silico search of resistant species and genes in metagenomic banks of cultivated and uncultivated soils and diversified ecosystems, including human gut microbiome banks previously developed by project collaborating members.
Correlate AMR data from different approaches aiming to track cross-AMR occurrence in clinical and environmental settings.
Select possible AMR genes as candidates for new markers through emerging artificial intelligence techniques in bioinformatics.
Create a real-time data recording panel based on AMR strain prospecting and resistance genes aiming to feed and expand existing notification systems.

Executing Team

Managers - National Focal Groups

Prof. V. A. Vicente

UFPR-CMRP/Taxonline UFPR/PR

Prof. Terezinha I. E. Svidzinski

CMRP/Taxonline-UEM/PR

Prof. Juliana V. M. Bittencourt

CMRP/Taxonline-UTFPR/PR

Prof. A.B. J. Matsuura

Fiocruz Amazônia AM

Prof. Marcia S. C. Melhem

UFMS - MS

Prof. Emanuel M. de Souza

UFPR - PR

Prof. Cristina M. S. Motta

URM-UFPE - PE

Prof. Conceição M. P. S. de Azevedo

UFMA - MA

Prof. Líbera M. Dalla Costa

IPP-PR

Prof. Arnaldo L. Colombo

UNIFESP - SP

Dra. M. Glória S. Stafocker

MT-USP/SP

Prof. Flávio Queiroz-Telles

CHC-UFPR - PR

Prof. Rafaella C. B. Santos

UNILA - PR

Prof. Keite Nogueira

CHC-UFPR - PR

Prof. Vanete Thomaz-Soccol

UFPR / PR - Parasitological Collection

International Partnership

Prof. Sybren de Hoog

Radboud University Netherlands

Prof. Eelco Meijer

CWZ/RadboudUMC Netherlands

Prof. Amir Seyedmousavi

NIH USA

Prof. Nina Gunde-Cimerman

Ljubljana University Slovenia

Prof. Laura Selbmann

Tuscia University Italy

Prof. Yinggai Song

Peking University China

Results Summary

Monitoring in Brazilian Biomes

Analysis of environmental samples from different biomes: Amazon, Transition Zone, Caatinga, Atlantic Forest, Pantanal and Cerrado.

Caves
Mangroves
Soils from preserved, agricultural and urban areas
River water and hemodialysis
Hospital biological waste

Evaluated Strains

Fungi

Candida
Aspergillus
Fusarium
Dermatophytes
Black and Rare Yeasts
Sporothrix
Cryptococcus

Bacteria

ESKAPEE
Enterococcus
Staphylococcus
Klebsiella
Acinetobacter
Pseudomonas
Enterobacter
Mycobacterium

Applied Methodologies

NGS Sequencing: Complete genomic analysis of resistant strains
Metagenomics: Environmental prospecting of AMR species and genes
Artificial Intelligence: Identification of new markers and biological patterns
Fosmid Libraries: Functional screening for elucidation of new targets
EUCAST Analysis: Evaluation of antimicrobial susceptibility