The present invention relates to
DNA-based methods for universal bacterial detection, for
specific detection of the common bacterial pathogens
Escherichia coli,
Klebsiella pneumoniae,
Pseudomonas aeruginosa,
Proteus mirabilis,
Streptococcus pneumoniae,
Staphylococcus aureus,
Staphylococcus epidermidis,
Enterococcus faecalis,
Staphylococcus saprophyticus,
Streptococcus pyogenes,
Haemophilus influenzae and
Moraxella catarrhalis as well as for
specific detection of commonly encountered and clinically relevant bacterial
antibiotic resistance genes directly from clinical specimens or, alternatively, from a
bacterial colony. The above bacterial species can account for as much as 80% of bacterial pathogens isolated in routine
microbiology laboratories. The core of this invention consists primarily of the
DNA sequences from all species-specific
genomic DNA fragments selected by hybridization from genomic libraries or, alternatively, selected from data banks as well as any
oligonucleotide sequences derived from these sequences which can be used as probes or amplification primers for PCR or any other
nucleic acid amplification methods. This invention also includes
DNA sequences from the selected clinically relevant
antibiotic resistance genes. With these methods,
bacteria can be detected (universal primers and / or probes) and identified (species-
specific primers and / or probes) directly from the clinical specimens or from an isolated
bacterial colony.
Bacteria are further evaluated for their putative susceptibility to
antibiotics by resistance
gene detection (
antibiotic resistance gene specific primers and / or probes). Diagnostic kits for the detection of the presence, for the bacterial identification of the above-mentioned bacterial species and for the detection of
antibiotic resistance genes are also claimed. These kits for the rapid (one hour or less) and accurate diagnosis of bacterial infections and antibiotic resistance will gradually replace conventional methods currently used in clinical
microbiology laboratories for routine diagnosis. They should provide tools to clinicians to help prescribe promptly optimal treatments when necessary. Consequently, these tests should contribute to saving human lives, rationalizing treatment, reducing the development of antibiotic resistance and avoid unnecessary hospitalizations.