[Rapid diagnosis of common pathogenic bacteria infection in newborn infants by 16SrDNA oligonucleotide array]

The rapid identification of pathogenic bacteria is important for earlier effective patient management and antimicrobial therapy, especially for the infant patient, whose immunological system is not fully developed. However conventional microbiogical techniques of bacterial identification, culture and isolation of pathogenic bacteria, identification by biochemistry and serological assay, are time-consuming and require intensive labor. On the basis of special gene sequence, PCR provides simple and rapid way to identify bacteria. But it is difficult to identify all of bacteria species which are suspicious of pathogenic agents. Oligonucleotide arrays provide a powerful tool for parallel detection of target genes. The objective of this study was to test a reverse oligonucleotide assay, which hybridize with the PCR product of 16SrDNA using a pair of universal primers, to rapidly identify common infant pathogenic bacteria.

By comparison and analysis of the 16SrDNA sequences of common pathogenic bacteria, a region, which has numerous sequence variations and flanked by highly conserved sequences, was found. A pair of universal primers was designed according to its flanking conservative sequence, and a set of probes specially targeting to eight species of infant pathogenic bacteria, including staphylococcus aureus, Pseudomonas aeruginosa, Klebsiella pneumoniae, Streptococcus faecalis, Hemophilus influenzae, Enterobacter cloacae, Escherichia coli, and Acinetobacter baumannii,according to the variable sequences. The probes were fixed on the nylon membrane with positive electricity, and hybridized them with the products of PCR using the universal primers.

The universal primers could amplify the target sequence from bacteria including the eight common infant pathogenic bacteria and Staphylococcus epidermidis, Enterobacter aerogenes, Streptococcus pneumoniae,beta-hemolytic streptococcus, Neisseria meningitides, Citrobacter freundii, Bacillus subtilis, and Salmonella infantis,but could not amplify rotavirus and human DNA as control. The results showed that the oligonucleotide array could specially hybridize with the eight bacteria to be examined and could not hybridize with other bacteria. The lowest concentration of DNA (product of PCR) for oligonucleotide array was about 25 ng/ml. The results proved that the probes are highly selective and the oligonucleotide arrays could parallelly detect the eight common infant pathogenic bacteria. The results suggested that the oligonucleotide array system was able to identify the eight common infant pathogenic bacteria from clinical specimens and the results were the same as identified by automated bacterial detection machine. From the further experiments, the oligonucleotide array system could directly diagnose the common infant pathogenic bacteria from the broths of samples culture.

Despite limited number of identifiable bacteria and lack of information on antibiotic susceptibility of bacteria, the reverse oligonucleotide assay system, which contains amplification of the segment of 16rDNA from samples using the universal primers and parallel detection of PCR products using specific probes, is an effective method to rapidly identify the eight common infant pathogenic bacteria.