Evidence for the clustering of antibacterial resistance phenotypes of enterococci within integrated poultry companies.

From July to December 2006, a panel of 401 enterococci was isolated from carcass rinse samples collected in five poultry processing plants in New Zealand. Agar diffusion assays for nine antibacterial drugs were used to obtain a resistance phenotype for each isolate. Hierarchical clustering techniques and diversity indices showed a high diversity of resistance phenotypes within each plant, with populations of Enterococcus faecalis showing greater heterogeneity than Enterococcus faecium. Bayesian modelling identified three clusters of phenotype patterns within the panel: the E. faecium isolates showed a high probability of containing two distinct clusters, whilst the E. faecalis isolates all grouped together to form the third cluster. The validity of these three clusters was examined using pairwise fixation indices and analysis of variance. Comparing the three clusters to the structure of the participating companies showed that resistance phenotypes for E. faecium isolated from processing plants that were geographically separated but were operated by the same integrated poultry company were more similar than E. faecium isolated from unconnected companies. Company-level management factors, such as the routine use of antibacterial drugs and the genetic line of birds reared, mirrored the structure of these clusters, thus indicating that company-level factors were the dominant selective pressures upon resistance phenotypes across all operating units within these integrated poultry companies.