SPECIFIC AND UNIVERSAL PROBES AND AMPLIFICATION PRIMERS TO RAPIDLY DETECT AND IDENTIFY COMMON BACTERIAL PATHOGENS AND ANTIBIOTIC RESISTANCE GENES FROM CLINICAL SPECIMENS FOR ROUTINE DIAGNOSIS IN MICROBIOLOGY LABORATORIES
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.
1 . A method to detect and identify the presence of Haemophilus influenzae and at least a second and a third target bacterial species in a sample by performing an assay, comprising:
simultaneously contacting a sample with a set of amplification primers comprising a plurality of at least a first, second, and third primer pair, wherein said first primer pair hybridizes solely to the nucleic acids of Haemophilus influenzae , and wherein said second and third primer pairs hybridize solely to target DNA of said second and third target bacterial species, respectively, and are ubiquitous to at least 80% to Haemophilus influenzae , and second and third target bacterial species, respectively, wherein the plurality of primer pairs are chosen to allow amplification under a single amplification protocol;
amplifying target nucleic acid from said sample under said single amplification protocol; and
detecting the presence or amount of amplified product(s) as an indication of the presence of Haemophilus influenzae and said second and third target bacterial species in said sample.