Antimicrobial Resistance Gene Profiles in Integron-Positive and Integron-Negative Third-Generation Cephalosporin-Resistant E. coli from Human and Animal Sources

Background/Objectives: Integrons are genetic platforms that allow bacteria to acquire antimicrobial resistance (AMR) genes, making them a focal point for many AMR studies and surveillance programs. This study investigated how the prevalence of integrons (intI and attI genes) in third-generation cephalosporin-resistant E. coli (3GCR-Ec) varied across three different sources (i.e., healthy children, domestic animals and urinary tract infections). The study aimed to determine how different classes of AMR genes vary among 3GCR-Ec with integrons present versus those where integrons are absent. Methods: We analyzed 3GCR-Ec isolates collected from semirural parishes of Eastern Quito, Ecuador, that included: (1) 3GCR-Ec from healthy children (n = 946), (2) 3GCR-Ec from domestic animal species (n = 673), and 3GCR-Ec from patients with urinary tract infections (UTIs) (n = 138). Genomic analyses were performed for all 1757 sequences to determine how the presence and absence of integrons was associated with AMR gene carriage. Results: Among the total sequences of 3GCR-Ec evaluated across all datasets, nearly one-third (31%) were integron-negative. 3GCR-Ec from UTI patients, however, had a higher percentage containing integrons (79%). Across all sets of 3GCR-EC, integron-positive isolates carried an average of 10.3 (±3.0 SD) AMR genes versus 4.8 (±2.5 SD) AMR genes in integron-negative isolates. This study found that between 21% to 33% of 3GCR-Ec across the three different sources lacked integrons but maintained the ability to carry diverse classes of AMR genes, including beta-lactams, aminoglycosides, tetracyclines, and multidrug resistance mechanisms (e.g., general-purpose efflux pumps). Conclusions: While integrons were associated with greater AMR genes on average, the study highlights that solely relying on integrons for tracking drug-resistant bacteria misses a substantive portion of AMR that is present in integron-negative strains.