Skip to main content

Advertisement

Table 7 Comparison of the NGS Results in Terms of Percentage of Species-specific Reads of Investigated Entamoeba spp., Entamoeba histolytica, and Entamoeba dispar Per Total Number of Reads in the Sample with the Respective Largest Standard Deviation above the Mean of All Samples in Multiples of the Standard Deviation (SD), Depicted for the Samples from Patients with Invasive Amebiasis. “Positive” = positive Entamoeba histolytica PCR. “Negative” = negative Entamoeba histolytica PCR. “Uncertain” (for “Specific PCR”) = High cycle threshold value > 35 in real-time PCR with associated uncertain interpretation. “Uncertain” (for “Microscopy in neighboring slides”) = Extremely low parasite density with associated uncertain interpretation. “Match” = NGS result matching the diagnosis “invasive amebiasis”. “Partial match” = NGS result matching the diagnosis “invasive mycosis” on genus level only, so it is neither confirmed nor completely rejected, “Mismatch” = NGS results not matching the diagnosis “invasive amebiasis”, “No match” = No evidence of specific sequences above the respective standard deviation (SD). Highest standard deviations (SD) are shown

From: Next-generation sequencing for hypothesis-free genomic detection of invasive tropical infections in poly-microbially contaminated, formalin-fixed, paraffin-embedded tissue samples – a proof-of-principle assessment

Sample Histological diagnosis Specific PCR [7] Microscopy in neighboring slides [7] NGS > 1st SD NGS > 2nd SD NGS > 3rd SD NGS > 4th SD
18 Invasive amebiasis Positive Many amebae No match No match No match No match
19 Invasive amebiasis Negative Negative No match No match No match No match
20 Invasive amebiasis Positive Many amebae No match Mismatcha No match Matchb
21 Invasive amebiasis Uncertain Few amebae Partial matchc No match No match No match
22 Invasive amebiasis Negative Negative No match No match No match No match
23 Invasive amebiasis Negative Uncertain Partial matchd No match No match No match
  1. a0.0004% Entamoeba dispar, b0.009% Entamoeba histolytica and 0.01% Entamoeba spp., c0.0003% Entamoeba spp., d0.0004% Entamoeba spp.