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.
How was the experiment
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.
Why is it innovative
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.
Implications for the brazilian health system
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".
- Human pandemic K27-ST392 CTX-M-15 extended-spectrum β-lactamase-positive Klebsiella pneumoniae: A one health clone threatening companion animals - 12/2022
- World Health Organization critical priority Escherichia coli clone ST648 in magnificent frigatebird (Fregata magnificens) of an uninhabited insular environment - 08/2022
- Genomic Analysis of a Highly Virulent NDM-1-Producing Escherichia coli ST162 Infecting a Pygmy Sperm Whale (Kogia breviceps) in South America - 06/2022
- Genomic insights of high-risk clones of ESBL-producing Escherichia coli isolated from community infections and commercial meat in southern Brazil - 06/2022
- Genomic features of a multidrug-resistant and mercury-tolerant environmental Escherichia coli recovered after a mining dam disaster in South America - 06/2022
- Phylogenomic analysis of CTX-M-15–producing Enterobacter hormaechei belonging to the high-risk ST78 from animal infection: another successful One Health clone? - 06/2022
- Convergence of virulence and resistance in international clones of WHO critical priority enterobacterales isolated from Marine Bivalves - 04/2022
- Phylogeographical Landscape of Citrobacter portucalensis Carrying Clinically Relevant Resistomes - 03/2022
- Multidrug-resistant Klebsiella pneumoniae: a retrospective study in Manaus, Brazil - 03/2022
- WHO Critical Priority Escherichia coli as One Health Challenge for a Post-Pandemic Scenario: Genomic Surveillance and Analysis of Current Trends in Brazil - 03/2022
- Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli survey in wild seabirds at a pristine atoll in the southern Atlantic Ocean, Brazil: First report of the O25b-ST131 clone harboring blaCTX-M-8 - 02/2022
- Genomic analysis of a Kpi (pilus system)-positive and CTX-M-15-producing Klebsiella pneumoniae belonging to the high-risk clone ST15 isolated from an impacted river in Brazil - 01/2022
- Small IncQ1 Plasmid Encoding KPC-2 Expands to Invasive Nontyphoidal Salmonella - 10/2021
- Genomic analysis of carbapenem-resistant Pseudomonas aeruginosa isolated from urban Rivers confirms spread of clone sequence type 277 carrying broad resistome and virulome beyond the hospital - 09/2021
- Genomic data reveals the emergence of an IncQ1 small plasmid carrying blaKPC-2 in Escherichia coli of the pandemic sequence type 648 - 06/2021
- Endophytic Lifestyle of Global Clones of Extended-Spectrum β-Lactamase-Producing Priority Pathogens in Fresh Vegetables: a Trojan Horse Strategy Favoring Human Colonization? - 02/2021
- Detection of IncN-pST15 one-health plasmid harbouring blaKPC-2 in a hypermucoviscous Klebsiella pneumoniae CG258 isolated from an infected dog, Brazil - 01/2021
- Colistin-resistant Enterobacter kobei carrying mcr-9.1 and blaCTX-M-15 infecting a critically endangered franciscana dolphin (Pontoporia blainvillei), Brazil - 01/2021
- Genomic insights of Klebsiella pneumoniae isolated from a native Amazonian fish reveal wide resistome against heavy metals, disinfectants, and clinically relevant antibiotics - 11/2020
- Genomic analysis of multidrug-resistant CTX-M-15-positive Klebsiella pneumoniae belonging to the highly successful ST15 clone isolated from a dog with chronic otitis - 09/2020
- Genomic characterization of multidrug-resistant ESBL-producing Escherichia coli ST58 causing fatal colibacillosis in critically endangered Brazilian merganser (Mergus octosetaceus) - 06/2020
- International clones of extended-spectrum β-lactamase (CTX-M)-producing Escherichia coli in peri-urban wild animals, Brazil - 04/2020
- Emergence of CTX-M-27-producing Escherichia coli of ST131 and clade C1-M27 in an impacted ecosystem with international maritime traffic in South America - 03/2020
- Genome Sequences of Clinical Isolates of NDM-1-Producing Klebsiella quasipneumoniae subsp. similipneumoniae and KPC-2-Producing Klebsiella quasipneumoniae subsp. quasipneumoniae from Brazil - 03/2020