Introduction
16S rRNA and ITS1
Next generation sequencing based species identification using 16S rRNA
Credence rapid infection detection™ (credence RID™)
Material and methods
Ethics statement
Specimen collection
DNA extraction
Library preparation
Semi-conductor sequencing
Data processing and bioinformatics
Phylogenetic output & relative abundance
Analysis of culture negative specimens
Results
Assessment criteria
Overview of results comparison
Total Specimens | 103 | |||
NGS processed specimens | 97 | |||
Total Specimens | Bacterial PCR Results | |||
Negative | Positive | |||
Culture results | No Bacterial Growth | 36 | 19 | 17 |
Culture Positive | 61 | 1 | 60 |
Culture Negatives (%) | Culture Positives (%) | Total Specimens | |
---|---|---|---|
Matches with metagenomic results | 19 (52.8%) | 56 (91.9%) | 75 (77.3%) |
Conflicts with metagenomic results | 17 (47.2%) | 5 (8.1%) | 22 (22.7%) |
Total | 36 (100%) | 61 (100%) | 97 (100%) |
Analysis of culture positive results
Specimen Type | Culture Results | Metagenomic Results (no. of species within the genus) |
---|---|---|
Sputum (P25)c a
| Coliforms |
Porphyromonas pasteri
b
Streptococcus species. (9)
Prevotella species (10) |
Throat Swab (P29)a
|
Moraxella spp
|
Prevotella species (9)
Prevotella melaninogenica
b
|
Pus Swab (P70) | Coagulase negative Staphylococcus species |
Streptococcus
b
Filifactor alocis
Prevotella intermedia
|
Pus Swab (P75) |
Acinetobacter spp
|
Prevotella bivia
b
Peptoniphilus indolicus
Finegoldia magna
Dialister micraerophilus
Veillonella montpellierensis
Streptococcus anginosus
Ureaplasma parvum
|
Pus Swab (P97) | Coliform Organisms | (−) |
Analysis of culture negative results
SRN | Specimen Type | NGS results |
---|---|---|
P1c
| Urine |
Enterococcus faecalis*, Enterococcus phoeniculicola
|
P5c
| Urine |
Methylobacterium longum*, Paracoccus sphaerophysae, Burkholderiale, Paracoccus sphaerophysae, Aquabacterium parvum, Bacillus amyloliquefaciens, Kytococcus aerolatus
|
P14d
| Urine |
Morganella morganii*, Stenotrophomonas maltophilia
|
P23d
| CSF |
Ralstonia
a
|
P24d
| Pleural Fluid |
Tessaracoccus * |
P30d
| Pus Swab |
Finegoldia magna*, Pseudomonas aeruginosa (low abudance), Staphylococcus aureus (low abundance) |
P34d
| Urine |
Prevotella bivia*, Streptococcus infantis
|
P37b, d
| Endo tracheal secretion |
Streptococcus
a, Streptococcus parasanguinis, Streptococcus mitis, Raoultella planticola, Porphyromonas gingivalis
|
P40d
| Pus Swab |
Rhizobiales
a, Corynebacterium, Prevotella bivia, Corynebacterium tuberculostearicum
|
P51d
| Pus Swab |
Corynebacterium*, Jonquetella anthropi, Staphylococcus (low abundance) |
P53d
| Cyst fluid |
Micrococcus luteus
a, Streptococcus spp., Staphylococcus spp. |
P54d
| CSF |
Mycoplasma hominis, Comamonas denitrificans
|
P57d
| Wound Swab |
Phyllobacteriaceae
a, Sphingopyxis fribergensis, Staphylococcus spp. (9), Corynebacterium (6) |
P59d
| Pleural Fluid |
Staphylococcus aureus
a, Sphingopyxis fribergensis
|
P60d
| Sputum |
Comamonas denitrificans
a, Acinetobacter baumannii, Streptococcus spp. (5), Staphylococcus spp. (5) |
P67d
| Pus Swab |
Staphylococcus aureus
a, Burkholderia multivorans
|
P81b, d
| Seminal Fluid |
Prevotella bivia*, Staphylococcus intermedius, Staphylococcus petrasii, Lactobacillus fermentum
|
Fungal results
Specimen type (number of specimens with identified species) | Fungal NGS Species |
---|---|
Throat Swab (1), Sputum (1), Seminal fluid (1), |
Candida albicans
a
|
Sputum (1), Bronchial wash (1) |
Candida tropicalis
a
|
Throat Swab (1) |
Lomatium nevadense
a
|
Endotracheal secretion (1) |
Saccharomyces cerevisiae
a
|
Pus Swab (1) |
Uwebraunia
a
|
Pus Swab (1) |
Candida orthopsilosis
a
|