The potential associations of antimicrobial resistance in clinical Escherichia coli and Staphylococcus aureus across the human-animal interfaces in Chongming Island, Shanghai

Abstract Background： AMR is a significant concern within the One Health framework due to its ongoing spread across humans, animals, and the environment. Phenotypic data remains the primary form of surveillance data for AMR. Yet, there is a noticeable absence of thorough data analysis across various interfaces. Methods: The AMR phenotypic data of clinical and food animal E. coli and S. aureusfrom Chongming Island over the past five years were analyzed to determine the key characteristics of AMR and its association at the human-animal interface. Results: The clinical isolates of E. coli and S. aureus demonstrated a significant level of AMR rates, including penicillins (83.92%), cephems (63.05%), fluoroquinolones (62.21%), tetracyclines (57.77%) for E. coli and penicillinase-labile penicillins (90.89%), macrolides (51.51%), penicillinase-stable penicillins (43.96%), lincosamides (43.55%) for S. aureus.. ESBL-positive E. coli isolates account for 53.26% (1398/2526), with MRSA prevalence at 43.81% (435/993). Notably, there has been an increase in the number of E. coli isolates resistant to 8 to 12 antimicrobial classes, and that of S. aureus isolates resistant to 5 to 9 classes. Furthermore, certain MDR phenotypes were first identified in food animal isolates. No significant association was found in the identical AMR phenotype between food animals and clinical isolates. However, several MDR phenotypes shared by the two interfaces were identified, with 44 in E. coli and 12 in S. aureus. Through further co-occurrence analysis, 16 pairs of phenotypes were found in both clinical and food animal E. coli isolates. Moreover, two unique co-occurrence clusters of MDR were identified: Pen-βLac-Cep in clinical interface and Ami-Tet-Fpa in food animal interface. Meanwhile, three clusters were identified in clinical S. aureus, namely Ami-Mac-Lin, Ami-Mac-Flu-Lin, and PSPen-Ami-Flu-Lin and two clusters were identified in food animal isolates, namely PSPen-Mac and PSPen-Flu-Lin. Conclusion: A heightened MDR prevalence in clinical E. coli and S. aureus have been discovered. Some MDR profiles manifest in food animal interface before clinical settings, highlighting the potential for AMR association and its transmission between humans and food animals. Within the One Health framework, integrating genomic data into AMR monitoring is an essential next step.