OneBR: integrated genomic database for surveillance, diagnosis, management, and treatment of antimicrobial resistance in the human-animal-environment interface

The project aimed to create a database with curated genomic information integrated into diagnosis and antimicrobial resistance results from human, animal, and environmental samples, from a One Health perspective. The data can be accessed by different health professionals, researchers, and managers on a user-friendly web platform. It can also be used as a surveillance tool for antimicrobial resistance. The platform allows tracking the bacteria's origin, phenotypic and genotypic resistance profile, and dynamics and setting of the dissemination routes with early identification of high-risk clones and/or emerging resistance mechanisms.

The platform was structured around data from three clinically important bacterial species: Klebsiella pneumoniae, Escherichia coli, and Salmonella enterica, expanding to Pseudomonas aeruginosa. The human, animal, and environmental samples were cultured in a specific growth medium. Isolates were identified and characterized for antibiotic sensitivity and stored in a freezer at -20 and/or -80 °C. Each isolate was sequenced using the Illumina NextSeq platform, and genomic data were analyzed using bioinformatic tools. All genomes were curated, employing the best quality assessment practices. Genomes were later reanalyzed by the bioinformatics team to ensure the information´s accuracy. Collection and screening of bacterial isolates and associated information such as antibiogram, virulence, and genome analysis were compiled to establish the database in a cloud-structured web interface. The system was developed using Python for the main algorithms and web2py framework and R (Shiny) for graphics and statistical information processing. Epidemiological data and geolocation of isolates were included in an interactive map of Brazil.

Initially, retrospective data on the strains were used to obtain the genomes. In collaboration with more than 20 Brazilian research institutions*, approximately 100 strains of K. pneumoniae, 100 of E. coli, and 80 of S. enterica were sequenced and isolated from human, animal, or environmental cases, covering all regions of Brazil. The platform shows maps with highlights on each strain's identification and phenotypic and genotypic characteristics, including: a) automatically envisaged information, such as MLST and pMLST; b) plasmid incompatibility groups; c) resistance genes and their variants, and; d) virulence factors. Antimicrobial resistance data include resistance genotypes for antibiotics and chemotherapeutics, disinfectants, and heavy metals. The different host types and plasmids carrying clinically significant genes, such as carbapenemase and MCR type circulating in Brazil, are also indicated, as well as the dynamics of dissemination of international clones of multidrug-resistant bacterial pathogens circulating at the human-environment-animal interface in Brazil´s territory. The data are available at http://www.onehealthbr.com/ and can also be accessed by computer, tablet, or mobile phone.

No previous integrated genomics database tracks the AMR problem in Brazil. Meanwhile, interpreting genomic data requires specific knowledge, which is difficult for most local health professionals to access and use. Therefore, the creation and availability of an integrated and easily accessible genomic web database for health professionals from all regions of Brazil will allow a better approach to solving the problem of antibiotic resistance, particularly within a One Health perspective.

In Brazil, genomic data related to antimicrobial-resistant bacteria have been generated increasingly by independent research groups. Therefore, establishing a platform comprising an integrated national genomic database is paramount for the surveillance system since it allows rapid reporting and mapping of outbreaks and monitoring of emerging pathogens and resistance mechanisms. Through easy and free access via computers, tablets, and/or mobile devices, users can conduct research and interpret genomic data to apply in various clinical or educational activities: printing of medical reports, epidemiological monitoring, development of diagnostic tools, and/or treatment of related infections.

After successfully implementing the OneBR platform, the next steps include expanding the number of bacterial species, including data from human and animal microbiomes, and resistance data on clinically relevant fungi. Currently, the project is being funded by the São Paulo Research Foundation (FAPESP) and the National Council for Scientific Research (CNPq) (public call for proposals). The project now focuses on designing sub-platforms for methicillin-resistant Staphylococcus, Acinetobacter baumannii, Enterobacter spp, and vancomycin-resistant Enterococcus. The research group belongs to the "Ibero-American Network to Combat Resistance" as part of the Union of Ibero-American Universities. We also intend to extend monitoring of transmission dynamics of multidrug-resistant pathogens to agroecosystems and exported and imported foods in multilateral trade between Brazil and other Latin American countries. We additionally intend to create a Latin American platform called "OneLA".