FORINGEN

RESEARCH NETWORK FOR INFECTOGENOMICS

DT-1 Improvement of a DNA array for diagnostics of clinically relevant enterobacteria

Enterobacteria comprise a variety of non-pathogenic, commensal variants, which belong to the normal gut flora of humans and many animals. Additionally, several pathogenic variants have been identified which cause various types of intestinal or extraintestinal infections in men and animals thus resulting in considerable economic losses. The most prevalent type of community-acquired extraintestinal infections caused by enterobacteria is urinary tract infection (UTI). Furthermore, UTI caused by E. coli also represents one of the most frequent nosocomial infections. Diarrhea caused by enterobacteria poses a severe health problem with the serious risk of morbidity and mortality, especially for the elderly and young children. Furthermore, there are indications that E. coli variants may be associated with chronic inflammatory diseases of the gut (Crohn’s disease). Accordingly, there is a need for improved and facilitated enterobacterial diagnostics and risk assessment in human and veterinary medicine. The number of completely sequenced bacterial genome sequences is constantly increasing and has already been used to develop conventional DNA arrays based on individual or a few complete bacterial genomes. An “intelligent” DNA array based on comparative genomic analyses of complete enterobacterial genome sequences that facilitates detection of species and/or pathotype-specific combinations of virulence- and antibiotic resistance-associated genes of clinically relevant enterobacteria is currently not available. For this purpose, the publicly available enterobacterial genome sequences will be compared and used for the development of a DNA array, which allows a facilitated risk assessment as well as the rapid and exact typing of pathogenic enterobacterial isolates in human-, veterinary-, environmental medicine as well as in food and microbiological diagnostics. We plan to develop and optimize a new DNA array format with a reduced number of probes to facilitate the DNA array handling and which will be adapted to a broader spectrum of users, especially in clinical laboratories.