Supplemental Digital Content 3. Diagnostic results: Comparison of histopathology, conventional testing, when broad-range PCR was positive
Patient (age)
Clinical scenario
Immuno- compromise
d
Antibiotics Pre- Treatment
Specimen Histopathology
& stain results
Microbiology results
PCR result Action based on PCR result Bacterial
1 (15 years)
Meningitis, multiple ring
enhancing lesions
No -- CSF Path: review of
slide was negative
CSF culture x5 (-)
S. intermedius Narrowed Abx
2 (13 month)
Meningitis s/p tethered cord
release
No + CSF Path review of
slide was negative
CSF culture (-) S. agalactiae No changes in Abx due to complicated post-operative course 3
(23 month)
Recurrent neck and retropharyngea
l abscess
No + Right neck
mass tissue
Path: Non- specific inflammation Stain: AFB, GMS, GS, Giemsa, W-S
Tissue culture (-)
S. agalactiae Narrowed Abx
4 (17 years)
Vegetation on mitral valve
No + Tissue:
mitral valve
Path:
GS + rare small weakly staining GPC
Blood cx x5 (-) Tissue cx (-) Intraop bacterial swab cx (-)
S. pneumoniae or S.
pseudopneumoniae
Narrowed Abx
5 (27 years)
Fever, known tricuspid valve
anomaly
No + Tissue: Heart
valve
Infective endocarditis, GPC present
Blood cx + 1 of 11 + for S.
epidermidis Tissue cx x2 (-)
Staphylococcus (Staph.) epidermidis
Narrowed Abx
6 (4 years)
Knee effusion No -- Synovial
fluid
ND Synovial fluid
cx (-)
Kingella kingae Narrowed Abx
7 (11 years)
Swollen finger No -- Tissue: Bone
aspirate
ND ND S. aureus Abx class added
8 (17 years)
Persistent fevers, wound following ankle fracture, CT
findings suggestive of
osteo
No + Tissue: Bone
fragment
Path: Chronic inflammation c/w
osteomyelitis Stain: GS, PAS, AFB, W-S
Blood cx (-) Tissue cx (-)
Ureaplasma urealyticum or Ureaplasma parvum
Abx class added
9 (18 months
CT with lung abscess and
pleural
Yes:
DiGeorge’s syndrome
+ Aspirate, lung abscess
ND Blood cx (-)
Tissue cx (-)
S. mitis No changes in Abx due to critical illness
) effusions 9
(18 months
)
Yes:
DiGeorge’s syndrome
+ Tissue: Lung ND Blood cx (-)
Tissue cx (-)
S. pneumoniae or S.
pseudopneumoniae
No change in Abx due to critical illness 10
(18 years)
Pleural effusion No + Pleural
effusion
ND Pleural fluid cx
(-)
GNR of
bacteroidales DNA
Narrowed Abx
11 (26 years)
Peritonitis with recurrent abdominal fluid
collections
Yes:
Small bowel transplant
+ Abdominal
abscess fluid
ND Blood cx x2 (-)
Abdominal fluid cx x2 (-)
Mycoplasma hominis
Antibiotic class added
Bacterial and Fungal 12
(16 years)
CT with liver abscess
No -- Aspirate,
liver lesion
ND Body fluid cx
x4 (-) though GPC present
S. intermedius, Cryptococcus uzbekistanensis
Narrowed Abx.
Cryptococcus result prompted more fungal work up Fungal
13 (11 years)
Periorbital swelling, neutropenia
Yes:
AML
+ Tissue:
ethmoid sinus biopsy
Path: non- specific inflammation Stain: GMS (-)
Blood cx (-) Tissue cx (-)
Lichtheimia species Abx narrowed, fungal tx continued.
Aggressive surgical intervention pursued 14
(18 years)
Neutropenia, fever, CT with pansinusitis
Yes:
AML s/p HCT
+ Tissue: sinus Path: non- specific inflammation Stain: No comment about stains
Tissue cx x2 (-) Aspergillus fumigatus
Antifungal narrowed
15 (18 years)
CT with lung nodules in lung,
unable to tolerate empiric voriconazole
Yes:
AML
+ Tissue: lung Path: Branching hyphae not entirely typical of aspergillus Stain: GMS (-)
Tissue cx (-) Aspergillus fumigatus
Antifungal narrowed
16 (6 years)
Recurrent fevers, CT with
hilar lymphadenopat
hy
Yes:
CGD
+ Tissue: lung Path: non- specific inflammation Stain: PAS negative
blood cx (-) Tissue cx (-)
Cladosporium species
Antibiotics initially discontinued and antiinflammatory medication started for presumed hypersensitivity pneumonitis 17 CT with lung Yes: + Tissue: lung Path: GMS stain Tissue cx x2 (-) Aspergillus Additional
There are 23 results for BR-PCR from 22 unique samples obtained 21 different patients. Patient #9 had results from 2 unique samples and Patient #12 had results from both a bacterial and fungal BR-PCR from one sample, but the fungal result was considered a false positive. +, pre- treatment with antibiotics; --, no prior antibiotics; (-), negative result; AML, acute myelogenous leukemia; CGD, chronic granulomatous disease;
CT, computed tomography; cx, culture; GMS, Gomori methenamine silver stain; GPC, Gram-positive cocci; HCT, hematopoietic cell transplantation; neg, negative; ND, not done; PAS, Periodic acid-Schiff stain; W-S, Warthin-Starry stain
Histopathology results that are bolded were supportive of the BR-PCR result.
(11 years)
nodules AML with necrotizing
granuloma with fungal hyphae
fumigatus antifungal added
Positive BRPCR considered falsely positive by treating team 18
(5 months
)
Abdominal fluid collection
No + Peritoneal
fluid
ND Body fluid,
fungal, AFB cx (-)
Mycobacterium gordonae
Deemed environmental contaminant 19
(10 years)
FUO, liver mass
No -- Liver tissue ND Tissue,
anaerobic, fungal, AFB cx (-)
Propionibacterium acnes
Deemed skin contaminant
20 (36 years)
Post- transplant surveillance
Yes: Lung transplant
+ Lung tissue No acute rejection, no small airway inflammation
Tissue, fungal, AFB cx (-)
Malassezia restricta
Not treated
21 (18 years)
Fevers, lung nodules on
CT
Yes:
T-cell ALL
+ BAL Predominance
of macrophages
Resp, fungal, AFB cx (-)
C. albicans Not treated
12 (16 years)
CT with liver abscess
No -- Liver abscess
aspirate
ND Body fluid cx
x4 (-) though GPC present
Cryptococcus uzbekistanensis
Prompted fungal work up, no antifungal medications added
