A comparison of AFLP and ERIC-PCR analyses for discriminating Escherichia coli from cattle, pig and human sources

• Published in: FEMS microbiology ecology 2004-01, Vol.47 (1), p.111-119
• Main Authors: Leung, Kam Tin, Mackereth, Rob, Tien, Yuan-Ching, Topp, Edward
• Format: Article
• Language: English
• Subjects: Action of physical and chemical agents on bacteria; Amplified fragment length polymorphism; Amplified Fragment Length Polymorphism Analysis - methods; Animal, plant and microbial ecology; Animals; Bacteriology; Biological and medical sciences; Cattle - microbiology; DNA Fingerprinting - methods; DNA, Bacterial - analysis; DNA, Bacterial - isolation & purification; Enterobacterial repetitive intergenic consensus polymerase chain reaction; Enterotoxigenic Escherichia coli; Escherichia coli; Escherichia coli - classification; Escherichia coli - genetics; Escherichia coli - isolation & purification; Escherichia coli - pathogenicity; Escherichia coli Infections - microbiology; Fundamental and applied biological sciences. Psychology; Humans; Microbial ecology; Microbial source tracking; Microbiology; Normal microflora of man and animals. Rumen; Polymerase Chain Reaction - methods; Repetitive Sequences, Nucleic Acid - genetics; Source typing; Species Specificity; Stepwise discriminant function analysis; Swine - microbiology; Verocytotoxigenic Escherichia coli; Virulence
• ISSN: 0168-6496; 1574-6941
• DOI: 10.1016/S0168-6496(03)00254-X

Amplified fragment length polymorphism (AFLP) and enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) genomic fingerprinting assays were compared for their ability to differentiate Escherichia coli isolates obtained from various host sources, and with respect to their pathogenicity. One hundred and ten verotoxigenic, enterotoxigenic and non-pathogenic E. coli isolates obtained from cattle, humans and pigs were used in this study. The AFLP assay was shown to be highly effective in predicting both the host source and pathogenicity of the E. coli isolates. A stepwise discriminant function analysis showed that 91.4, 90.6 and 97.7% of the human, bovine and pig isolates were classified into the correct host types, respectively. The analysis also distinguished the non-pathogenic E. coli from the verocytotoxigenic and enterotoxigenic virulence phenotypes at 100, 100 and 90.9% accuracy, respectively. Sixty-two E. coli strains from the collection were subjected to the ERIC-PCR fingerprinting analysis. Using this method, only 28.6, 0 and 75.0% of the human, bovine and pig isolates were classified into the correct host types, respectively. Overall, the AFLP method was able to ascribe host source with a high level of confidence and readily discriminate pathogenic from non-clinical isolates of E. coli.