Amplified fragment length polymorphism fingerprinting of Pseudomonas strains from a poultry processing plant

Abstract

Molecular typing has been used previously to identify and trace dissemination of pathogenic and spoilage bacteria associated with food processing. Amplified fragment length polymorphism (AFLP) is a novel DNA fingerprinting technique which is considered highly reproducible and has high discriminatory power. This technique was used to fingerprint 88 Pseudomonas fluorescens and Pseudomonas putida strains that were previously isolated from plate counts of carcasses at six processing stages and various equipment surfaces and environmental sources of a poultry abattoir. Clustering of the AFLP patterns revealed a high level of diversity among the strains. Six clusters (clusters I through VI) were delineated at an arbitrary Dice coefficient level of 0.65; clusters III (31 strains) and IV (28 strains) were the largest clusters. More than one-half (52.3%) of the strains obtained from carcass samples, which may have represented the resident carcass population, grouped together in cluster III. By contrast, 43.2% of the strains from most of the equipment surfaces and environmental sources grouped together in cluster IV. In most cases, the clusters in which carcass strains from processing stages grouped corresponded to the clusters in which strains from the associated equipment surfaces and/or environmental sources were found. This provided evidence that there was cross-contamination between carcasses and the abattoir environment at the DNA level. The AFLP data also showed that strains were being disseminated from the beginning to the end of the poultry processing operation, since many strains associated with carcasses at the packaging stage were members of the same clusters as strains obtained from carcasses after the defeathering stage.

FIG. 1

AFLP patterns of five Pseudomonas strains isolated from carcasses after the immersion chilling processing stage (stage E) (Table 1). Lanes 1, 6, and 9, molecular weight marker X; lane 2, strain 223; lane 3, strain 224; lane 4, strain 226; lane 5, 1-kb Plus ladder; lane 7, strain 227; lane 8, strain 228.

FIG. 2

Dendrogram based on AFLP fingerprints of 88 P. fluorescens and P. putida strains obtained from carcasses (44 strains) and equipment surfaces and environmental sources (44 strains) associated with poultry processing. For a description of strain sources see Table 1. The dendrogram was constructed by using UPGMA. Levels of similarity between AFLP fingerprints were calculated by using S_D. Clusters were delineated at an arbitrary S_D level of 0.65.