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

Abstract

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 simultaneously detect and identify the presence of  Salmonella typhimurium  in a sample, 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  Salmonella typhimurium , 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  Salmonella typhimurium , 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  Salmonella typhimurium  and said second and third target bacterial species in said sample.