Sascha Braun

DNA-based Microarrays for GenoSeroTyping and GenoTyping of Escherichia coli - an Overview

Sascha D. Braun^1,2, Stefan Monecke^1,2, Lutz Geue³ and Ralf Ehricht^1,2

Two rapid, economic, and automated DNA-based microarrays for both, GenoSeroTyping of Escherichia coli and GenoTyping of Shiga toxins are discussed. The GenoSeroTyping microarray based assay allows one to determine within a few hours and a single experiment, 94 of the over 180 yet described O-antigen groups as well as 47 of the 53 different H-antigens. The microarray was initially validated with a set of defined strains that had previously been serotyped by conventional agglutination in various reference centers. For further validation, 180 clinical E. coli isolates of human origin (from urine samples, blood cultures, bronchial secretions, and wound swabs) and 53 E. coli isolates from cattle, pigs, and poultry were used. A high degree of concordance between the results of classical antibody‐based serotyping and DNA‐based GenoSeroTyping was demonstrated during validation of the 94 O-antigen groups (100%) as well as for the field strains of human and animal origin.

The microarray for Stx identification harbors oligonucleotide probes specifically designed to distinguish between all Stx subtypes according to the previously established new nomenclature (Scheutz et al. 2012). The assay facilitates the identification of single and multiple subtypes within a single isolate within one experiment. Specific software was developed to automatically analyze the microarray data. The assay was validated with 21 Shiga toxin-producing E. coli (STEC) reference strains that were previously tested by the complete set of conventional subtyping PCRs. The microarray results showed 100% concordance with the PCR results. For further validation of the microarray the Stx subtypes or combinations thereof in 446 STEC field isolates of human and animal origin were identified.

The described tools are user‐friendly, more efficient than classical serotyping and provide advantages over the standard PCR-based Stx subtyping. Furthermore, both tests can be performed with the same device in almost every routine lab and can easily be expanded, standardized and combined with any other assay.

¹Alere Technologies GmbH, Jena, Germany

²InfectoGnostics Research Campus, Jena, Germany

³Friedrich-Loeffler-Institute, Jena, Germany