The dynamics of circulation of antibiotic-resistant microorganisms between livestock operations and hospitals

Given the importance of antimicrobials in the livestock industry and the growth of antimicrobial resistance (AMR) in human populations, this project intended to study the dynamics of circulation and transmission of microbial communities, analyzing samples from the main sources of exposure to antimicrobials (hospitals and farms). The project aimed to understand the AMR circulation ecosystem using metagenomic and genetic analysis related to antimicrobial resistance (resistome).

The strategy was based on 5 key elements: 1) an extensive multidisciplinary team involving researchers from basic biological sciences, health professionals, researchers in the environmental sciences, state and federal agricultural research agents, and regulatory bodies (EMBRAPA, MAPA, CIDASC), besides five swine farms and 10 poultry farms in western Santa Catarina state (representing more than 20,000 swine and 400,000 poultry); 2) Identification of AMR in conventional and unconventional sources, from strategic locations of acquisition and transmission of AMR, namely hospitals and farms. The hospital samples included patients, close relatives, and buses provided by the city government to transport patients and relatives from the countryside to the University Hospital. In parallel, samples from the farms included farmers in direct contact with swine and poultry, the livestock bedding, and the farms´ main sanitary drainage system. 3) Characterization of the samples´ resistome using nanopore sequencing (MinION). 4) Integration of current surveillance activities with data provided by this study, taking advantage of the work routine by the hospital and farms in the surveillance of microbial contamination to identify AMR in patients and farmers. 5) Finally, the proposal of modeling the dynamics of AMR circulation from the community to the hospital and vice versa.

Samples from 53 patients, 18 poultry farms, 28 swine, and 5 livestock handlers were collected. In total, 23,571,405 sequences obtained from these samples were generated and analyzed. The sequences were analyzed for the microbiome composition (22,350,429 sequences with taxonomic identification) and the resistome (143,243 sequences identified in the resistance databases, corresponding to 612 non-redundant genes, found 3,929 times in the samples). Data were analyzed using the Easy Data and Matchi platforms developed for this project. Resistance genes to all classes of antimicrobials used in the clinic were widely found in all types of samples: patients (137 isolates), livestock transportation vehicles (33), poultry farms (170), and swine and farm technicians (11).

It is worth noting the higher frequency of aminoglycoside resistance genes in all types of samples. Glycopeptide resistance genes were only found in patient samples. Resistance to beta-lactams prevailed in human samples, likely due to the lower use of this class of antibiotics in animals. Patients' length of hospital stay impacts the colonization rate by culturable multidrug-resistant bacteria. Swine farms showed a low prevalence of polymyxin resistance genes compared to the other samples. Animal management seems to affect the number of genes found, which varies greatly even among the same type of samples. Samples from organic swine operations showed significantly fewer resistance genes than conventionally managed farms. Furthermore, treatment of analytes with anaerobic digestion showed a significant decrease in the number and frequency of resistance genes. In the case of poultry farms, this comparison was not possible since most farms use antibiotics. Finally, we observed the same ratio of the number of genes and their frequency in all samples, suggesting widespread distribution and circulation, regardless of sample origin.

Brazil is a leading exporter of swine and poultry, particularly from the state of Santa Catarina. An estimated 75% of hospitalized patients receive antimicrobials, and 50% of prescriptions are considered inappropriate. Meanwhile, antimicrobials are extensively used in swine and poultry farms to promote growth and prevent infections. However, understanding the risks posed by the use of antimicrobials is limited almost exclusively to indirect observations or focused studies on the most relevant forms of AMR in animals and humans. The project's innovation lies in investigating the dynamics of AMR dissemination in a more systemic and integrated way, establishing a connection between the various ecosystems.

Our data can contribute to the goals of the National Action Plan for the Prevention and Control of Antimicrobial Resistance in the Scope of One Health (PAN-BR) by identifying circulating genes in livestock operations and guiding the use and selection of antimicrobials in One Health settings., aimed at minimizing the selection of resistant microorganisms.

The results so far indicate extensive circulation of resistance genes in Santa Catarina state, one of Brazil's leading producers and exporters of swine and poultry. In partnership with EMBRAPA, we will propose monitoring of zoonotic pathogens and resistance determinants as biomarkers of the efficiency of livestock procedures, aiming to meet international food safety standards. Easy Data and Matchi platforms designed to manage and analyze the generated data can be extended to managers interested in the results. In addition, we intend to incorporate our data into the OneBr Platform, developed by Prof. Dr. Nilton Lincopan, once it is adapted for metagenomic data.