Association Between Isolation Source, Clonal Composition, and Antibiotic Resistance Genes in Escherichia coli Samples Collected in Washington State

The growing prevalence of antimicrobial resistance (AMR) represents a significant global health problem. AMR is caused by the overuse of antibiotics in humans, animals, and the environment, making it necessary to apply a One Health approach to address the problem. Methods: We used whole genome sequencing (WGS) data from 1,449 Escherichia coli (E. coli) isolates from Washington State to evaluate the relationship between isolation source (either humans, animals, food, or the environment) and the presence of antibiotic resistance genes (ARGs). We performed sequence typing using PubMLST and used ResFinder to identify ARGs. We categorized isolates as being pan-susceptible, resistant, or multidrug resistant (MDR). We used chi-square tests to assess differences between isolation sources in the frequency of antibiotic resistance genes and sequence types (STs). Results: The 1,449 isolates were distributed among 341 unique STs. When comparing the distribution of isolates in the six most common STs overall (ST131, ST73, Unidentified ST, ST95, ST12, and ST69), there was evidence of a difference in the frequency of STs between humans, animals, food, and environmental isolates (p < 0.001). In total, 60% of isolates were pan-susceptible, while 18% were resistant, and 22% were MDR. The resistance pattern varied significantly between the four isolation sources (p < 0.001). The most resistance was detected in isolates from humans, followed by animals, and environmental isolates showed the least antimicrobial resistance. Discussion: Our study demonstrates that there is a relationship between isolation source and the presence of ARGs in E. coli samples from Washington State and highlights the need to further characterize transmission of antibiotic resistance genes and antibiotic resistant bacteria between humans, animals, and the environment using from a One Health perspective, both in Washington State and elsewhere.