Table 3.

Description of 19 clinical specimens which were positive by broad-range bacterial PCR assay and negative by culture as well as clinical data regarding the results of blood cultures, administration of antimicrobial therapy, and the final clinical diagnosis for the patient

Specimen no.SpecimenPCR resultSequencing resulta% HomologybSequence length (bp)bCulture resultGram staining result
1Bone biopsy+ Staphylococcus sp., probably also other species94.7216
2Bone biopsy+ Staphylococcussp.100284NDe
3Bone biopsy+Enterobacterial sp.f 96.3g 297
4Lung biopsy+Enterobacterial sp.f 92.9g 266
5g Lung biopsy+Several speciesND
6Muscle biopsy+ Bacteroidessp.98.5262ND
7Heart valve+ Abiotrophia defectiva 100495
8Heart valve+ Bartonella (B. quintana)99.81,406
9CSFh + Streptococcus(S. pneumoniae)100360GPC+i
10CSF+ Neisseria(N. meningitidis)100230
11CSF+ Neisseria(N. meningitidis)100237ND
12Ascitic fluid+ Bacteroides fragilis 99.6239
13Pleural fluid+ Prevotella (P. oris)100310
14Amniotic fluid+ Ureaplasma urealyticum 100300ND
15Amniotic fluid+ U. urealyticum, probably also other species88.1208ND
16Puncture from Douglas' pouch+ U. urealyticum 100468
17Brain abscess+ Staphylococcussp.100300
18Pus from empyema+ Streptococcussp.100343ND
19Pus from soft tissue+ Bartonellasp.96.7g 271
Blood culture resultcAntimicrobial therapydFinal diagnosis
S. aureus (15 days)Yes (15 days)Sepsis, spondylitis and spinal abscess
NDYes (10 days)Osteomyelitis
Klebsiella pneumoniae (30 days)Yes (30 days)Spondylitis and paravertebral abscess
NDYes (>30 days)Aspergillosis, probable PCR contamination
Lactobacillus sp., coagulase-negativeStaphylococcus YesHospital-acquired pneumonia in a compromised host
NDYes (>30 days)Intramuscular abscess
Abiotrophia defectiva (28 days)Yes (28 days)Infective endocarditis
Yes (5 days)Infective endocarditis
S. pneumoniae (2 days)Yes (2 days)Bacterial meningitis
Yes (7 hours)Bacterial meningitis
N. meningitidis B (2 hours)Yes (2 hours)Bacterial meningitis
Yes (17 days)Spontaneous peritonitis
NDYes (11 days)Lung abscess and pleural empyema in a compromised host
NDYesIntra-amniotic infection
NDYesIntra-amniotic infection
YesMesenterial thrombosis and intra-abdominal infection
Yes (5 days)Postoperative brain abscess
S. pneumoniae (30 days)Yes (30 days)Pneumonia and pleural empyema
NDYes (7 days)Cat-scratch disease
  • a The sequencing result is reported according to the principles described in the text.

  • b The percent homology and the length of the overlapping sequence for the best match are presented.

  • c The times of a positive blood culture result before the specimen for the PCR assay and culture was taken are given in parentheses. The blood samples that were negative by culture were taken on the same day (±2 days.)

  • d The durations of antimicrobial therapy usually effective against the microbe recognized by sequencing are given in parentheses. Patient 5 received ceftazidime, and patients 14 to 16 received ineffective therapy.

  • e ND, the test was not done.

  • f A species belonging to the familyEnterobacteriaceae.

  • g Recognition was based on the 23S rDNA sequence. Preferably, the 16S rDNA sequence was used. Data for patient 5 were excluded from the final analysis of sensitivity and specificity.

  • h CSF, cerebrospinal fluid.

  • i GPC+, few cells of gram-positive cocci.