Fig. 6

Characterization of AR phenotypes and genotypes for the isolates in the culture collection, with special emphasis on Enterococcus spp. strains. A Proportion of samples where antibiotic resistant isolates or ARGs were detected on FPE surfaces (n = 229). Color indicates detection of, at least, one phenotypically antibiotic-resistant isolate on selective agar plates (dark pink), or a positive PCR for one of the ARGs (light pink). Samples were grouped according to sampling time (n = 57 for T1, n = 70 for T2, and n = 102 for T3), processing room (n = 48 for Pre-cutting, n = 48 for Cutting_Iberian_pork, n = 40 for Cutting_white_pork and n = 93 for Post_cutting) and surface type (n = 67 for Drain, n = 35 for Equipment, n = 67 for Floor, n = 7 for Knife, n = 20 for Meat, n = 19 for Table, and n = 14 for Tray). Only significant differences (p < 0.05) obtained from the two-proportion Z test are represented. B Antibiotic resistance profile obtained for Enterococcus isolates from Sensititre panels. ECOFF values from EUCAST (see Additional file 2: Table S3) served as threshold to classify Enterococcus isolates (n = 58) as antibiotic resistant or susceptible. Isolates resistant to antibiotics of three different families were considered multidrug resistant. * E. faecalis is intrinsically resistant to quinupristin.dalfopristin. C Proportion of Enterococcus isolates (n = 14 for T1, n = 14 for T2, and n = 30 for T3) showing phenotypic resistance, with statistically significant changes along time as determined through the Fisher’s exact test. D Correlogram of phenotypic antibiotic resistance levels in Enterococcus isolates. Pearson correlation coefficients between the MIC values of those antibiotics included in the Sensititre panels (n = 12) were calculated. Only significant coefficients (p < 0.05) are represented in blue color (positive correlation) or red color (negative correlation). Antibiotics names are colored according to the ARG classes as on Fig. 5A. E. fecalis isolates (n = 2 for T1, n = 13 for T2, and n = 17 for T3) were removed from quinupristin.dalfopristin on (C) and (D) sections, due to their intrinsic resistance