Table 2.

Description of 33 clinical specimens which were positive by broad-range bacterial PCR assay and bacterial culture and 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 resultc
1Lung biopsy+ Staphylococcussp.100300 Staphylococcus epidermidis(++)
2CSFh + Streptococcus(S. pneumoniae)97.8269 S. pneumoniae(+++)
3CSF+ Streptococcus (S. pneumoniae)100230 S. pneumoniae(+++)
4CSF+ Neisseria (N. meningitidis)99.1228 N. meningitidis B (+++)
5CSF+ Neisseria (N. meningitidis)98.7i 287 N. meningitidis B (+)
6CSF+ Neisseria (N. meningitidis)99.7i 287 N. meningitidis B (+++)
7CSF+ Neisseria (N. meningitidis)100230 N. meningitidis C (+++)
8CSF+ Neisseria (N. meningitidis)98.3i 287 N. meningitidis B (++)
9CSF+ E. coli 99.0i 300 E. coli(++)
10CSF+Enterobacterial sp.l 90.2i 246 E. coli
11Ascites+ Enterococcussp.99.0471 Enterococcus faecium (++)
12Pleural fluid+ Streptococcus sp.99.7319 S. pyogenes(+)
13Pleural fluid+ Pseudomonas (P. aeruginosa)98.6217 P. aeruginosa(++)
14Amniotic fluid+ Streptococcus (S. sanguis)100260 Streptococcus, viridans group (+++)
15Synovial fluid+ Staphylococcussp.100279 S. aureus (+++)
16Synovial fluid+ Staphylococcus sp.99.7285 S. aureus(+)
17Synovial fluid+ Neisseriasp.98.1422 N. meningitidis B (++)
18Synovial fluid+ Salmonella (S. enteritidis)100i 292 S. enteritidis (++)
19Brain abscess+ Streptococcussp.95.8484 Streptococcus equinus (+++)
20Brain abscess+ Streptococcussp.96.5i 285 Streptococcus, viridans group (+)
21Brain abscess+ Streptococcus(S. milleri group)99.6458 Streptococcus, viridans group (+++)
22Brain abscess+ Peptostreptococcussp.95.7243Anaerobic gram-positive cocci (+++)
23Brain abscess+ Propionibacterium acnes 99.7299 P. acnes (+++)
24Brain abscess+Several species Bacteroides gracilis (+), Peptostreptococcus sp. (+), S. intermedius (++)
25Gall bladder abscess+ P. aeruginosa 100240 P. aeruginosa(+++)
26Paravertebral abscess+Several species S. epidermidis (+); Streptococcus, group C (+); Streptococcus, nonhemolytic (+)
27Pus from periost+ Staphylococcus sp.99.6239 S. aureus (+++)
28Pus from soft tissue+ Staphylococcus sp.100513 S. aureus(++)
29Pus from soft tissue+ Staphylococcussp.99.6260 S. aureus (+++)
30Amniotic fluidi + Capniocytophaga (C. sputigena)99.7319 Capnocytophaga sputigena (+++),Fusobacterium sp. (++)
31Pus from spinal abscessj + Staphylococcus sp., probably also other species86.3164 S. aureus(++)
32Pleural fluidk + Haemophilussp.93.0199 Bacillus sp.; S. epidermidis;Streptococcus, beta-hemolytic, non-A
33Amniotic fluidk + Bacteroides ureolyticus 98.9273 Fusobacterium sp. (+++)
Gram stain resultdBlood culture resulteAntimicrobial therapyfFinal diagnosis
NDg YesPneumonia in a compromised host
GPC (+++) S. pneumoniae NoBacterial meningitis
GPC (+) S. pneumoniae NoBacterial meningitis
GNC (+)NoBacterial meningitis
NoBacterial meningitis
GNC (+) N. meningitidisBNoBacterial meningitis
GNC (+)NoBacterial meningitis
GNC (+)NoBacterial meningitis
GPC (+) E. coli NoBacterial meningitis
ND E. coli NoBacterial meningitis
YesMesenterial thrombosis and intra-abdominal infection
GPC (+++)NoPneumonia and pleuritis
NDYesHospital-acquired pneumonia
ND S. mitis Yes (2 h)Intra-amniotic infection
GPC (+++)NoSeptic arthritis
S. aureus Yes (4 days)Septic arthritis
NDNoSeptic coxitis
Salmonellasp.NoSeptic arthritis
GPC (++)Yes (14 h)Brain abscess
NoBrain abscess
GPC (+++)NoBrain abscess
GPC (+++)NDYes (12 h)Brain abscess
NoPostoperative brain abscess
GPC (+++)NoBrain abscess
NDYesRecurrent cholecystitis
NDNDYesPostoperative spondylitis
GPC (+++)NDYes (5 days)Osteomyelitis
GPC (++) S. aureus (−3 days)Yes (3 days)Septicemia
NDNDNoSubcutaneous abscess
NDNDNoIntra-amniotic infection
ND S. aureus (−8 days)Yes (8 days)Sepsis, spondylitis, and spinal abscess
NDNDYes (1 day)Pneumonia and empyema
NDNDNoIntra-amniotic infection
  • a The sequencing result is reported according to the principles reported in the text.

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

  • c Symbols in parentheses are relative number of colonies on the primary culture plate: +, few; ++, moderate; +++, many.

  • d GPC, gram-positive cocci; GNC, gram-negative cocci. Symbols in parentheses are relative number of cells seen in the stain: +, few; ++, moderate; +++, many; −, negative result.

  • e Unless otherwise indicated, the blood for culture was taken on the same day (±2 days) that the specimen for the PCR assay and culture was taken. −, negative result.

  • f The durations of antimicrobial therapy effective against the microbe(s) recognized in the specimen are given in parentheses. Patients 1, 11, 13, 25, and 26 received ineffective therapy.

  • g ND, the test was not done.

  • h CSF, cerebrospinal fluid.

  • i Recognition was based on the 23S rDNA sequence. Preferably, the 16S rDNA sequence was used.

  • j Specimens had partly concordant results.

  • k Specimens had discordant results.

  • l A species belonging to the familyEnterobacteriaceae.