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Volume 8, Number 2—February 2002

Research

Broad-Range Bacterial Detection and the Analysis of Unexplained Death and Critical Illness

Simo Nikkari*†, Fred A. Lopez*†, Paul W. Lepp*, Paul R. Cieslak‡, Stephen Ladd-Wilson‡, Douglas Passaro§, Richard Danila¶, and David A. Relman*Comments to Author 
Author affiliations: *Stanford University School of Medicine, Stanford, California, USA; †VA Palo Alto Health Care System, Palo Alto, California, USA; ‡Oregon Health Division, Department of Human Services, Portland, Oregon, USA; §California Emerging Infections Program, Berkeley, California, USA; and ¶Minnesota Department of Health, Minneapolis, Minnesota, USA;

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Table 2

Variability in the amplified Streptococcus pneumoniae 16S rDNA sequencesa

Pleural fluid Cerebrospinal fluid
XEB44b XMN22 XCA73c Bacterial isolates Ref.
straind
Specimen 1-
PCR analysis 1 Specimen 1-PCR
analysis 2 Specimen 1-PCR
analysis Specimen 1-PCR analysis 1 Specimen 2-PCR
analysis 1
Corresponding
E. coli 16S
rDNA position Original PCR
product Clones from
PCR products Clones from PCR products Clones from
PCR products Original
PCR
product Clones from
PCR products Original
PCR
product Clones
from PCR
products
A B C D E F G H I J K SF10014 SF10175 SF10314
120 A/G G G A A A A A A A A A A A A A A A
260 A/G G A G G A G G G G G G G G G G G G
273 A A A A A A G A A A A A A A A A A A
279 A A A A G A A A A A A A A A A A A A
442 T T T T C T T T T T T T T T T T T T

aNucleotides in bold type differ with the reference strain sequence at the indicated rDNA position.
bOne pleural fluid sample was analyzed with PCR on two occasions.
cTwo cerebrospinal fluid specimens were taken 5 days apart from the same patient.
dPCR = polymerase chain reaction; E. coli = Escherichia coli.
eStreptococcus pneumoniae NCTC 7465T (GenBank accession no. AJ001246).

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