The rising prevalence of antibiotic resistance in foodborne Staphylococcus aureus underscores the critical importance of accurate and rapid antimicrobial susceptibility testing in guiding effective clinical therapy.

A comparative evaluation of the diagnostic accuracy of E-test and whole-genome sequencing (WGS) was performed for the detection of clinically significant antimicrobial resistance in foodborne Staphylococcus aureus.

Seventy-two foodborne Staphylococcus aureus were collected from the foodborne disease surveillance programs conducted by the Beijing Chaoyang District Center for Disease Prevention and Control and Xinjiang Uygur Autonomous Region Center for Disease Prevention and Control between March and November 2025, then tested in parallel against eight key antimicrobial agents (oxacillin, vancomycin, daptomycin, linezolid, rifampicin, ciprofloxacin, levofloxacin, and moxifloxacin) using both the E-test and WGS. The broth microdilution method (BMD), performed according to CLSI guideline M07, served as the reference standard for evaluating the diagnostic performance of both methods.

When evaluated against the BMD reference method, high sensitivity (80.0%-100.0%), specificity (94.4%-100.0%), and inter-method agreement (Kappa=0.86-1.00) were observed for the E-test in detecting resistance to oxacillin, linezolid, rifampicin, levofloxacin, and moxifloxacin. Specificity was absolute (100.0%) for both daptomycin and vancomycin. A notable exception was ciprofloxacin, for which the E-test exhibited low sensitivity (57.1%) alongside 100.0% specificity and substantial agreement (Kappa=0.70). Genotypic analysis by WGS accurately identified major resistance determinants (mecA, 23S rRNA G2576T, rpoB H481N), which correlated highly with the phenotypic resistance profile. The predictive performance of WGS was excellent for ciprofloxacin (sensitivity: 100.0%; specificity: 96.9%; Kappa=0.85). However, for levofloxacin and moxifloxacin, predicted phenotypic resistance, while perfectly sensitive (100.0%), showed only moderate specificity (88.4%) and fair agreement (Kappa=0.38) with the BMD reference.

Notwithstanding its reliable performance against the BMD standard for key antibiotics, the E-test is compromised by specific shortcomings, namely: a tendency to overestimate the minimal inhibitory concentration (MIC) of daptomycin, potential failure to detect intermediate resistance to vancomycin, and inadequate sensitivity for identifying low-level ciprofloxacin resistance mediated by the parC S80F mutation. While the performance of WGS is highly concordant for predicting resistance to oxacillin, linezolid, rifampicin, daptomycin and vancomycin via accurate genotyping, it is imperative to integrate and interpret mutations from multiple loci to achieve reliable phenotypic prediction for fluoroquinolones (ciprofloxacin, levofloxacin, moxifloxacin).

食源性金黄色葡萄球菌对抗菌药物的耐药性日益严重，获取准确快速的药敏结果对临床治疗至关重要。

比较分析E-test法与全基因组测序（WGS）检测食源性金黄色葡萄球菌对临床重要抗菌药物耐药性的性能评价。

于2025年3—11月收集北京市朝阳区疾病预防控制中心与新疆维吾尔自治区疾病预防控制中心开展的食源性疾病监测项目中的72株食源性金黄色葡萄球菌，以微量肉汤稀释法（BMD）为金标准，平行检测菌株对苯唑西林、万古霉素、达托霉素、利奈唑胺、利福平、环丙沙星、左氧氟沙星和莫西沙星共8种药物的耐药性，系统评估E-test法与WGS的诊断性能。

E-test法检测苯唑西林、利奈唑胺、利福平、左氧氟沙星及莫西沙星的灵敏度为80.0%~100.0%，特异度为94.4%~100.0%，Kappa值为0.86~1.00；对达托霉素和万古霉素的特异度均为100.0%；对环丙沙星的灵敏度、特异度和Kappa值分别为57.1%、100.0%和0.70。WGS分析显示，对mecA基因、利奈唑胺耐药相关23S rRNA G2576T突变及利福平耐药相关rpoB H481N突变等主要机制的识别与表型结果高度一致；对环丙沙星的灵敏度、特异度和Kappa值分别为100.0%、96.9%和0.85；对左氧氟沙星和莫西沙星则均分别为100.0%、88.4%和0.38。

E-test法在检测苯唑西林、利奈唑胺、利福平、左氧氟沙星和莫西沙星方面与金标准BMD法高度一致，适用于常规筛查；但存在高估达托霉素最低抑菌浓度（MIC）、漏检万古霉素中介耐药及对环丙沙星低水平耐药parC S80F突变灵敏度不足的局限。WGS在检测苯唑西林、利奈唑胺、利福平、达托霉素及万古霉素耐药方面表现可靠，可精准识别关键突变；但在预测喹诺酮类药物（环丙沙星、左氧氟沙星、莫西沙星）表型时需综合多位点突变分析。