text: Definition of pathogens
  It remains difficult to determine whether the organisms detected by the DNA Detection Kit are true pathogens. This also applies, although to a much lesser degree, to conventional blood culture analysis. However, detected organisms were considered to be pathogens if the results of culture tests from samples of the suspected infectious sites coincided with the results of DNA Detection Kit or blood culture analysis. The culture data of sputum, urine, pus and drainage fluid were used to define the pathogens.
  A decision as to whether an identified organism was a pathogen was taken based on the decision tree shown in Figure 1. Thus, when the same organism was detected by both DNA Detection Kit and blood culture analysis, the detected organism was considered an infectious pathogen. If there was a discrepancy between the organism that was detected by SeptiFast analysis and that detected by blood culture analysis, or if an organism was only detected in one of these tests, then other samples taken from the infection site were analyzed. If this second culture test of the suspected infectious site revealed the presence of the same organism, this organism was considered to be a pathogen. If the microbial strain was only detected once for a sample, we then checked the second culture results in the suspected infectious sites. If this result identified the same strain as that identified by SeptiFast analysis then it was decided that this strain was a pathogen. However, if the strain was still only detected in some of the assays, we next determined if the patient involved suffered from sepsis. Sepsis is defined as SIRS caused by infection. The definition of sepsis that we used was based on the International Sepsis Forum Definition of Infection at the ICU Consensus Conference [7]. However, if the underlying disease is acute lymphoma leukemia (ALL), malignant lymphoma (ML), or acute myelogenous leukemia (AML), the definition of infection is defined as the ability to detect infectious organisms by blood culture analysis. If the patient was not defined as having sepsis when whole blood was administered to the patient, we decided that the strain detected by subsequent DNA Detection Kit or blood culture analysis was not a pathogen.
  Figure 1
  Flowchart for pathogen decision.
  Samples were defined as negative for pathogens if a pathogen could not be detected by any method of analysis within seven days, and if another type of culture test did not detect this pathogen but could detect other organisms.
  CoNS bacteria, which are represented by the Staphylococcus epidermidis (S. epidermidis) and Streptococcus spp. are indigenous bacteria and often cause contamination in assays of pathogens. Therefore, when CoNS or Streptococcus spp. were detected by blood culture and SeptiFast analysis, the following criteria were applied to define whether these strains represented a pathogenic infection: (1) Tests were performed at least twice within 48 hours before and after CoNS were detected by blood culture or SeptiFast analysis; (2) CoNS or Streptococcus spp. were detected in two different blood culture tests that were separately performed twice within 48 hours; and, (3) CoNS or Streptococcus spp. were detected twice or more in tests that were performed three times [11-15]. If a sample's results met any of these three criteria, then the sample was evaluated as a pathogen.
  The distinction between pathogen and contamination was also determined for CoNS or Streptococcus spp. from the crossing point (Cp) obtained using the LightCycler analysis software v4.05. The Cp represents the point in the amplification cycle where the amplification curve crosses the detection threshold. When CoNS or Streptococcus spp. were detected using the LightCycler analysis software v4.05, a Cp of less than 20 was defined as indicating a pathogen and a Cp of over 20 was defined as contamination by checking the amplification curve.
  
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entities.text: ['blood']
entities.type: Organism_substance
entities.entity_id: PMC-2945143-sec-13_T2
entities.text: ['sputum']
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entities.text: ['urine']
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entities.text: ['pus']
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entities.text: ['fluid']
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entities.text: ['blood']
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entities.text: ['blood']
entities.type: Organism_substance
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entities.text: ['malignant lymphoma']
entities.type: Pathological_formation
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entities.text: ['ML']
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entities.text: ['whole blood']
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entities.text: ['blood']
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entities.text: ['blood']
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entities.text: ['blood']
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entities.text: ['blood']
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entities.text: ['sample']
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