Table 3 Discrepant Clinical Specimens Resolved in Favour of Standard Methods (False Positive or Negative by PCR/Sequencing)a
Specimen No. | Specimen typea | Stain results | Standard methodsb | Initial molecular results | Sequence results | Results of clinical review | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | BAL LUL | CW = fungal elements | Negative | ITS/LSU targets POS, β-globin POS | ITS = Oxyporus corticola LSU = Oxyporus corticola Repeat testing using conventional ITS primers showed A. terreus | False positive PCR No pulmonary disease | ||||||
2 | BAL RLL | CW = no fungal elements | C. albicans, A. flavus | ITS/LSU targets NEG, β-globin POS (weak) | N/A | False negative PCR No pulmonary disease. Repeat testing gave same results. Likely sample deficiency | ||||||
3 | BAL LLL | Gram stain − Hvy WBCs; CW = NEG | C. dublinensis, A fumigatus | ITS/LSU targets POS; β-globin POS | Sequencing indeterminate as mixed sequences could not be resolved for accurate identification | Indeterminate PCR Mixed sequences Clinical diagnosis of Aspergillosis | ||||||
4 | BAL LUL | Gram stain − Hvy WBCs; CW = NEG | C. glabrata, A. terreus | ITS/LSU targets POS; β-globin POS | ITS = C. glabrata LSU = C. glabrata | False negative PCR Clinical diagnosis of invasive Aspergillosis with cavitary lung lesion | ||||||
5 | BAL | Gram stain and CW = NEG | C. glabrata | ITS POS (weak)/LSU target NEG, β-globin POS | ITS (short sequence) = Fusarium merismoides, a plant pathogen | False positive PCR Clinical diagnosis of primary lung adenocarcinoma | ||||||
6 | BAL RML | Gram stain = Hvy WBCs; CW = NEG | C. albicans | ITS/LSU targets NEG, β-globin POS | N/A | False negative PCR Clinical diagnosis of aspiration pneumonia. C. albicans consistent with airway colonization | ||||||
7 | CSF | Gram stain = few yeast | Cryptococcus neoformans | ITS NEG LSU NEG β-globin POS (weak) | N/A | False-negative PCR Repeat PCR/Sequencing Negative Likely sample deficiency given weak β-globin band | ||||||
8 | Bone(mandible) | Gram stain = few bacteria; CW = NEG | C. albicans | ITS NEG LSU NEG β-globin POS (weak) | N/A | False negative PCR Repeat PCR/Sequencing Negative Likely sample deficiency given weak β-globin band | ||||||
9 | Peritoneal fluid | Gram stain − Hvy WBCs; CW = NEG | A. flavus | ITS NEG LSU NEG β-globin POS | N/A | False negative PCR Repeat PCR/Sequencing ITS POS/LSU POS with Aspergillus spp. split identification | ||||||
10 | Dialysate fluid | Gram stain = Hvy WBCs; CW not done | C. tropicalis | ITS NEG LSU NEG β-globin POS | N/A | False negative PCR Repeat PCR/Sequencing Negative Fungal culture of other samples grew same organism | ||||||
11 | Lung tissue | Gram stain = Hvy WBCs; CW = NEG | Coccidiodes immitis | ITS NEG LSU NEG β-globin POS | N/A | False negative PCR Clinical diagnosis of pulmonary Coccidioidomycosis | ||||||