Nonrepresentative PCR amplification of variable gene sequences in clinical specimens containing dilute, complex mixtures of microorganisms.
PCR amplification and DNA sequencing of the expression locus from Neisseria gonorrhoeae contained in urine sediments collected from experimentally infected human subjects produced two observations. First, different pilin sequences were obtained when separate aliquots of the same sample were amplified and sequenced. In contrast, the same pilin sequence was obtained when repeated amplifications were performed on individual colonies grown from the clinical samples. Second, mixed sequences (i.e., more than one nucleotide at variable positions in the pilin gene sequence) were observed in both the direct clinical isolates and individual cultures grown from the isolates. These results suggest that when clinical samples are directly examined by PCR amplification and sequencing, multiple amplifications may be required to detect sequence variants in the sample and minority variant sequences will not always be detected.
Wright
C J
CJ
Department of Microbiology-Immunology, Northwestern University Medical School, Chicago, Illinois 60611.
Jerse
A E
AE
Cohen
M S
MS
Cannon
J G
JG
Seifert
H S
HS
D000293:Adolescent; D000328:Adult; D001426:Bacterial Proteins / Q000235:genetics; D001483:Base Sequence; D004269:DNA, Bacterial / Q000235:genetics; D036781:Fimbriae Proteins; D010861:Fimbriae, Bacterial; D005798:Genes, Bacterial; D014644:Genetic Variation; D006069:Gonorrhea / Q000175:diagnosis / Q000382:microbiology; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D009344:Neisseria gonorrhoeae / Q000235:genetics* / Q000302:isolation & purification; D016133:Polymerase Chain Reaction
D001426:Bacterial Proteins; D004269:DNA, Bacterial; C074063:pilE protein, Neisseria gonorrhoeae; D036781:Fimbriae Proteins