The dynamics of circulation of antibiotic resistant microorganisms between animal farming and medical hospital assistance
Federal University of Santa Catarina (UFSC)
n Dept. of Microbiology, Immunology and Parasitology
Carlos Rodrigo Zárate-Bladés
Carlos Rodrigo Zárate-Bladés
English; Spanish; Portuguese
4 weeks
Cities/Months Jan Feb Mar Apr May Jun Jul Augt Sep Oct Nov Dec
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Type of Research Project
- Basic science
What is the background of the project?
Antimicrobial resistant microorganisms (ARM) are responsible for the increase of deaths worldwide and therefore constitute a global problem of public health. Up to 75% of hospitalized patients are estimated to receive antimicrobials and 50% of prescriptions are considered inappropriate. In addition, antimicrobials are used extensively in swine and poultry farms to avoid infections and as growth promoters. The state of Santa Catarina is the largest swine producer and the second largest poultry producer in Brazil, generating annual revenues of more than 2 billion dollars. However, understanding the risks of the use of antimicrobials in the state is scarce. Thus, the project aims to study the circulation dynamics of ARM, characterizing microbial communities from key sources: hospitalized patients, animal husbandry and environment. Therefore, samples will be obtained from swine and poultry farms, patients that live in the regions were the farms are localized (west of the state) and that look for attention at the University Hospital in Florianopolis (east of the state) and from the environment. The project is funded by the Bill and Melinda Gates Foundation.
What is the aim of the project?
To understand the circulation of AMR between animal husbandry and hospital environment using metagenomic analysis.
What techniques and methods are used?
Samples will be used to: 1)DNA isolation 2)Bio-repository composition 3)Microbiological analysis (culture, sub-culture, microbial identification, etc). 4)DNA sequencing for metagenomic analysis 5)Bioinformatics for resistome, microbiome and metagenomic analysis 6)Data modeling for AMR circulation Methodology overview: Samples from animal farming, environment and hospital are being collected since August 2019. The samples are used to perform classical microbiological analysis to identify certain types of bacteria and their antibiotic resistance profile. In parallel, samples are used for DNA extraction and to perform a metagenomic sequencing. Data analysis are being performed using various softwares in order to define the composition of the metagenome of each type of sample as well as to detect all types of antibiotic resistance genes.
What is the role of the student?
- The student will observe the practical experiments but will be highly involved in the analysis of the results
- If the project includes “lab work”
- the student will take active part in the practical aspect of the project
- The tasks will be done under supervision
What are the tasks expected to be accomplished by the student?
Expected to follow other students of the laboratory in their routines and interact with new methodologies while learning about metagenomic studies. The activities will include: to follow the identification process of potential patients to be invited to participate in the study, to follow sample collection, to participate in organizing data; to follow microbiological cultures; to be trained to how to perform DNA extraction and DNA sequencing; to be trained to learn and use the basic bioinformatics tools for metagenomic analysis. It is also expected the fellow participatation of the laboratory meetings.
Will there be any theoretical teaching provided (preliminary readings, lectures, courses, seminars etc)
The student will be encouraged to read some literature to be able to maximize his/her learning during the visit of our lab. The fellow could contact the Principal Investigator of the lab at any time after the end of the selection process.
What is expected from the student at the end of the research exchange? What will be the general outcome of the student?
- The student will prepare a scientific report
What skills are required of the student? Is there any special knowledge or a certain level of studies needed?
To be curious and proactive. To be interested in microbiology, bioinformatics, metagenomics, immunology and have the skills for interacting with several people o different professional and technical backgorunds.
Are there any legal limitations in the student’s involvement
Type of students accepted
This project accepts:
- Medical students
- Graduated students (less than 6 months)
- Pre-Medical students from the American-British system
- Students in biomedical fields
- Llor C; Bjerrum L. Antimicrobial resistance: risk associated with antibiotic overuse and initiatives to reduce the problem. Ther Adv Drug Saf. 2014;5(6):229-41.
- Andersson DI; Hughes D. Microbiological effects of sublethal levels of antibiotics. Nat Rev Microbiol. 2014;12(7):465-78.Collignon PJ; McEwen SA. One Health-Its Importance in Helping to Better Control Antimicrobial Resistance. Trop Med Infect Dis. 2019;4(1).