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Comparison of five real-time PCR assays for detecting virulence genes in isolates of Escherichia coli from septicaemic neonatal foals

¹ Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, 1 Shields Avenue, Davis, CA 95616, USA
² Lucy Whittier Molecular and Diagnostic Core Facility, School of Veterinary Medicine, University of California, 1 Shields Avenue, Davis, CA 95616, USA

Correspondence: Correspondence to Dr Pusterla

Fifty-five isolates of Escherichia coli from septicaemic neonatal foals were used to validate five real-time PCR assays targeting different known virulence factor genes: curli fibre (csgD), ferric hydroxamate uptake (fhuA), type 1A pilin (fimA), aerobactin (lutA) and yersiniabactin (fyuA). A PCR assay targeting a universal sequence of the bacterial 16S rRNA gene served as quality control. The PCR assays showed good analytical specificity and sensitivity on the basis of sequencing the PCR products, their lack of cross-reactivity with non-E coli organisms, high amplification efficiency and a limit of detection as low as 25 E coli colony-forming units. There were differences between the detection rates and amplification efficiencies for the five virulence genes. The PCR assays targeting genes csgD, fhuA and fyuA were able to detect all 55 E coli isolates, with gene csgD having the best amplification efficiency. The lowest detection rate and amplification efficiency of the E coli isolates was found for the lutA gene.