Temporal shifts in antimicrobial resistance phenotypes in indicator and third-generation cephalosporin-resistant Escherichia coli from Spanish livestock during a period of reduced veterinary antimicrobial sales

Abstract

Abstract Antimicrobial resistance (AMR) in food-producing animals is a major One Health concern. In Europe, surveillance programs monitor resistance in commensal Escherichia coli as an indicator organism. However, single-drug metrics often overlook co-resistance patterns and links between antimicrobial use (AMU) and multidrug resistance (MDR). Here, we analyzed Spanish surveillance data on indicator and third‑generation cephalosporin‑resistant (3GCR) E. coli from caecal samples of broilers, turkeys, pigs and cattle at slaughter (2014–2023). Minimum inhibitory concentrations (MICs) for 14 antimicrobials were classified as wild type (WT) or non-wild type (NWT) and binary WT/NWT profiles were clustered using multivariate Bernoulli mixture models and linked to veterinary antimicrobial sales for 2014–2022 using multinomial logistic regression. Among 7,532 isolates (3,265 indicator, 4,267 3GCR), high NWT proportions were observed for ampicillin, tetracycline, sulfonamides, trimethoprim, chloramphenicol and fluoroquinolones, with low NWT frequencies (< 2%) to colistin, carbapenems and tigecycline. Indicator isolates grouped into five major resistance-profile clusters, four shared with 3GCR isolates. Over the 2014–2023 period, frequency of high-resistance clusters decreased, especially in poultry, while low‑resistance clusters increased. Higher antimicrobial sales were associated with greater odds of membership in MDR and fluoroquinolone‑resistant clusters. These results suggest that reduced veterinary antibiotics sales in Spain are associated with a shift towards less resistant indicator and, to a lesser extent, 3GCR E. coli populations, and that both compartments show partially overlapping resistance-pattern dynamics.