High-throughput identification of clinically important bacterial pathogens using DNA microarray.
Rapid and accurate detection of pathogenic bacteria is important for the treatment of patients with suitable antibiotics. Here we report the development of a diagnostic DNA microarray for the high-throughput identification of 39 pathogenic bacteria selected based on their high prevalence rate and/or difficulty of cultivation. The 23S ribosomal DNA and 16S-23S rDNA intergenic spacer region were used as target DNAs for pathogen detection. Universal- and species-specific probes were designed based on the unique and common sites within the target DNA sequences. New target DNA sequences were determined for the detection of 19 bacterial pathogens. The usefulness of the designed probes was validated using 39 reference bacteria and also with 515 clinical isolates from various clinical samples including blood, stool, pus, sputum, urine and cerebrospinal fluid. The DNA microarray developed in this study allowed efficient detection of bacterial pathogens with the specificities of 100%. The sensitivities were 100% as well except for the two pathogens, Enterobacter cloacae (75%) and Enterococcus faecium (85%). These results suggest that the DNA microarray-based assay developed in this study outperforms current diagnostic systems with respect to sensitivity, specificity, and high-throughput detection, and thus should be useful in pathogen diagnosis in the clinical setting.
Yoo
Seung Min
SM
Department of Chemical & Biomolecular Engineering (BK21 Program), KAIST, Daejeon 305-701, Republic of Korea.
Lee
Sang Yup
SY
Chang
Kyung Hee
KH
Yoo
So Young
SY
Yoo
Nae Choon
NC
Keum
Ki Chang
KC
Yoo
Won Min
WM
Kim
June Myung
JM
Choi
Jun Yong
JY
D001419:Bacteria / Q000235:genetics* / Q000302:isolation & purification* / Q000472:pathogenicity; D001424:Bacterial Infections / Q000175:diagnosis* / Q000382:microbiology*; D003141:Communicable Diseases / Q000382:microbiology; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D016972:Enterobacter cloacae / Q000235:genetics / Q000302:isolation & purification / Q000472:pathogenicity; D016984:Enterococcus faecium / Q000235:genetics / Q000302:isolation & purification / Q000472:pathogenicity; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity
D021903:DNA, Ribosomal Spacer