Distribution of CRISPR and association to antimicrobial in Escherichia coli from animal waste
Antibiotics; CRISPR-Cas; Mobile genetic elements; One Health.
The use of animal bedding as fertilizer in agriculture may introduce pathogens capable of disseminating antimicrobial resistance through mobile genetic elements in soil. Bacteria, however, possess the CRISPR-Cas defense system, which identifies and degrades exogenous DNA. Evidence suggests an inverse correlation between the presence of the CRISPR system and the occurrence of antimicrobial resistance. This study investigated Escherichia coli isolates from three types of animal waste during a composting process: conventional poultry litter (CAC), organic poultry litter (CAO), and horse bedding (CC). The primary objective was to characterize the distribution of type I-E CRISPR arrays and evaluate their possible association with the incidence of antimicrobial resistance. Among the 37 E. coli isolates analyzed, coexistence of CRISPR1 and CRISPR2 systems was predominant, being detected in 23 samples. Isolates susceptible to all antimicrobials tested exhibited, in most cases, both CRISPR arrays and a greater number of spacers. In contrast, multidrug-resistant isolates CAC10 and CC28 lacked the investigated CRISPR arrays. Detection of spacers corresponding to plasmid and bacteriophage sequences indicates that these bacteria possess active defense mechanisms against mobile genetic elements and diverse histories of exposure to these elements. The low detection of integrons and transposons in the studied population suggests that the presence of the CRISPR-Cas system may limit the acquisition of these elements. The study of CRISPR-Cas systems in E. coli from animal waste may provide insights for developing effective measures to contain the acquisition and transmission of antimicrobial resistance in these environments, contributing to management strategies from a One Health perspective.