Evaluation of qPCR for Quantifying Escherichia coli and Tetracycline Resistance Genes in Pig Caecal and Pork Skin Samples: A Comparison with Culture-Based Method

Background/Objectives: Rapid surveillance tools are needed to monitor antimicrobial-resistant bacteria in the food chain. This study evaluated whether qPCR-based quantification of tetracycline resistance genes could replace culture-based quantification of tetracycline-resistant Escherichia coli in pig caecal content and carcass skin swabs. Methods: Caecal content (n = 89) and skin swab samples (n = 68) were collected across four Danish abattoirs and analysed by both qPCR and Petrifilm cultivation. Method comparisons were restricted to samples within the quantifiable range of Petrifilm. E. coli concentrations (uidA gene) and tetA/tetB gene concentrations were compared with Petrifilm counts of E. coli and culturable tetracycline-resistant E. coli. Method agreement was evaluated using paired t-tests, Bland–Altman analysis, and Spearman correlation. Results: In caecal samples (n = 84), no significant difference in mean log E. coli concentration was observed between uidA qPCR and Petrifilm counts (p = 0.33). However, Bland–Altman analysis showed poor agreement at the individual-sample level, with limits of agreement ranging from −1.09 to 1.21 log10 CFU/g. In skin swab samples (n = 43), qPCR systematically overestimated E. coli counts compared with cultivation, with a significant bias of 0.75 log10 CFU/1400 cm2 (p < 0.001). No significant correlation was observed between tetA/tetB and culturable tetracycline-resistant E. coli in caecal (rs = 0.091, p = 0.44) or skin swab samples (rs = 0.13, p = 0.48). Conclusions: qPCR may be useful for population-level surveillance of tetracycline resistance genes in pig caecal samples but cannot replace culture-based methods for accurate quantification of tetracycline-resistant E. coli in individual samples.