The swine waste resistome: Spreading and transfer of antibiotic resistance genes in Escherichia coli strains and the associated microbial communities
Alice Checcucci, Enrico Buscaroli, Monica Modesto, Diana Luise, Sonia Blasioli, Donatella Scarafile, Maura Di Vito, Francesca Bugli, Paolo Trevisi, Ilaria Braschi, Paola Mattarelli
Abstract
The overuse of antimicrobials in livestock farming has led to the development of resistant bacteria and the spread of antibiotic-resistant genes (ARGs) among animals. When manure containing these antibiotics is applied to agricultural fields, it creates a selective pressure that promotes the acquisition of ARGs by bacteria, primarily through horizontal gene transfer. Most research on ARGs focuses on their role in clinical antibiotic resistance and their transfer from environmental sources to bacteria associated with humans, such as Escherichia coli . The study investigates the spread of antibiotic-resistant genes (ARGs) through class 1 integrons in 27 Escherichia coli strains from pig manure. It focuses on six common ARGs ( erm B, cml A, flo R, qnr S, tet A, and TEM) and the class 1 integron gene, assessing their prevalence in manure samples from three pig farms. The study found correlations and anticorrelations among these genes, indicating a predisposition of the integron in spreading certain ARGs. Specifically, cml A and tet A genes were positively correlated with each other and negatively with int1, suggesting they are not transferred via Int 1. Farm B had the highest int1 counts and a higher abundance of the TEM gene, but lower levels of cml A and tet A genes. The results underscore the complexity of predicting ARG spread in agricultural environments and the associated health risks to humans through the food chain. The study's results offer valuable insights into the antibiotic-resistant genes (ARGs) profile in swine livestock, potentially aiding in the development of methods to trace ARGs in the environment. • Overuse of antibiotics in livestock farming increases ARGs spread in the environment. • Genetic analysis at different stages of manure management, from production to final collection. • ARGs and int1 genes are present in both E. coli sentinel strains and farm manure samples. • Not all ARGs correlate with int1 , suggesting other MGE systems are involved. • Predicting ARGs’ spread in livestock environments is challenging.