Evaluation of 16S-Based Metagenomic NGS as Diagnostic Tool in Different Types of Culture-Negative Infections
Abstract
:1. Introduction
2. Materials and Methods
2.1. Standard Culture Methods
2.2. Culture-Negative Samples
2.3. Next Generation Sequencing
3. Results
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Sample Type | Sample Number | |
---|---|---|
Total Samples (n) | 105 | % |
orthopedics | 50 | 0.48 |
calcaneus biopsy | 1 | 0.01 |
joint fluid | 4 | 0.04 |
synovial tissue | 3 | 0.03 |
bone | 40 | 0.38 |
articular capsule | 2 | 0.02 |
CNS | 16 | 0.15 |
cerebrospinal fluid | 5 | 0.05 |
ventriculoperitoneal shunt | 8 | 0.07 |
brain abscess | 1 | 0.01 |
ventricular biopsy | 2 | 0.02 |
heart | 13 | 0.12 |
heart valve | 13 | 0.12 |
general surgery | 11 | 0.10 |
breast implant | 1 | 0.01 |
esophageal biopsy | 1 | 0.01 |
duodenal biopsy | 1 | 0.01 |
abdominal resection | 1 | 0.01 |
wound | 2 | 0.02 |
gluteal abscess | 2 | 0.02 |
lymph node | 3 | 0.02 |
lung | 6 | 0.06 |
lung biopsy | 1 | 0.01 |
pleural fluid | 1 | 0.01 |
bronchial brushing | 3 | 0.03 |
sputum | 1 | 0.01 |
fluids | 4 | 0.04 |
blood culture | 2 | 0.02 |
dialysis fluid | 1 | 0.01 |
ascitic fluid | 1 | 0.01 |
H&N | 3 | 0.03 |
maxillary sinus | 1 | 0.01 |
tracheal tissue | 1 | 0.01 |
auricle bone | 1 | 0.01 |
eye | 2 | 0.02 |
ocular prosthesis | 1 | 0.01 |
vitreous humor | 1 | 0.01 |
culture unidentifiable | 13 |
n | ||
---|---|---|
Samples | 105 | % |
Microorganism | ||
Cutibacterium acnes | 12 | 0.11 |
Staphylococcus epidermidis | 11 | 0.10 |
Staphylococcus aureus | 10 | 0.10 |
Streptococcus gallolyticus | 4 | 0.04 |
Finegoldia magna | 4 | 0.04 |
Fusobacterium nucleatum | 3 | 0.03 |
Abiotrophia defectiva | 3 | 0.03 |
Actinomyces spp. | 4 | 0.04 |
Bacteroides vulgatus | 2 | 0.02 |
Corynebacterium spp. | 2 | 0.02 |
Prevotella spp. | 4 | 0.04 |
Staphylococcus intermedius | 2 | 0.02 |
Streptococcus pneumoniae | 3 | 0.03 |
Alloprevotella spp. | 1 | 0.01 |
Berthella aurantiaca | 1 | 0.01 |
Bacteroides fragilis | 1 | 0.01 |
Bacillus cereus sushi | 1 | 0.01 |
Bacteroides spp. | 1 | 0.01 |
Burkholderia spp. | 1 | 0.01 |
Enterobacter cloacae | 1 | 0.01 |
Enterobacter spp. | 1 | 0.01 |
Granulicatella spp. | 1 | 0.01 |
Haemophilus parainfluenzae | 1 | 0.01 |
Klebsiella pneumoniae | 1 | 0.01 |
Leifsonia aquatica | 1 | 0.01 |
Parvimonas micra | 1 | 0.01 |
Paenibacillus spp. | 1 | 0.01 |
Proteus spp. | 1 | 0.01 |
Pseudomonas spp. | 1 | 0.01 |
M. catarrhalis | 1 | 0.01 |
Veillonella spp. | 1 | 0.01 |
Biological Specimen | NGS Result | n | ||
---|---|---|---|---|
orthopedics—total | 50 | % | ||
orthopedics | calcaneus biopsy | |||
negative | 1 | 0.02 | ||
joint fluid | ||||
C. acnes | 1 | 0.02 | ||
negative | 3 | 0.06 | ||
synovial tissue | ||||
K. pneumoniae | 1 | 0.02 | ||
C. acnes | 1 | 0.02 | ||
negative | 1 | 0.02 | ||
articular capsule | ||||
negative | 2 | 0.04 | ||
bone | ||||
F. nucleatum | 2 | 0.04 | ||
Actinomyces spp. | 1 | 0.02 | ||
B. vulgatus | 2 | 0.04 | ||
Proteus spp. | 1 | 0.02 | ||
S. aureus | 6 | 0.12 | ||
C. acnes | 6 | 0.12 | ||
Prevotella spp. | 1 | 0.02 | ||
Corynebacterium spp. | 1 | 0.02 | ||
E. cloacae | 1 | 0.02 | ||
F. magna | 3 | 0.06 | ||
S. epidermidis | 10 | 0.20 | ||
P. micra | 1 | 0.02 | ||
B. smithii | 1 | 0.02 | ||
A. defectiva | 1 | 0.02 | ||
negative | 3 | 0.06 | ||
CNS—total | 16 | % | ||
CNS | cerebrospinal fluid | |||
S. intermedius | 1 | 0.06 | ||
Paenibacillus spp. | 1 | 0.06 | ||
H. parainfluenzae | 1 | 0.06 | ||
negative | 2 | 0.13 | ||
ventriculoperitoneal shunt | ||||
Pseudomonas spp. | 1 | 0.06 | ||
Corynebacterium spp. | 1 | 0.06 | ||
C. acnes | 1 | 0.06 | ||
K. pneumoniae | 1 | 0.06 | ||
negative | 4 | 0.25 | ||
brain abscess | ||||
S. aureus | 1 | 0.06 | ||
ventricular biopsy | ||||
Prevotella spp.—C. acnes | 2 | 0.13 | ||
heart | heart—total | 13 | % | |
heart valve | ||||
S. gallolyticus | 2 | 0.14 | ||
A. defectiva | 1 | 0.08 | ||
S. pneumoiae | 1 | 0.08 | ||
B. fragilis | 1 | 0.08 | ||
B. aurantica | 1 | 0.08 | ||
Granulicatella | 1 | 0.08 | ||
S. gallolyticus | 1 | 0.08 | ||
S. intermedius | 1 | 0.08 | ||
negative | 4 | 0.30 | ||
general surgery—total | 11 | % | ||
general surgery | breast implant | |||
Bacteroides spp. | 1 | 0.09 | ||
esophageal biopsy | ||||
F. nucleatum | 1 | 0.09 | ||
duodenal biopsy | ||||
negative | 1 | 0.09 | ||
abdominal resection | ||||
negative | 1 | 0.09 | ||
wound | ||||
Enterobacter spp. | 1 | 0.09 | ||
negative | 1 | 0.09 | ||
gluteal abscess | ||||
S. aureus | 2 | 0.18 | ||
lymph node | ||||
S. aureus—A. defectiva | 1 | 0.09 | ||
Prevotella spp. | 1 | 0.09 | ||
negative | 1 | 0.09 | ||
lung—total | 6 | % | ||
lung | lung biopsy | |||
F. magna—Actinomyces spp. | 1 | 0.17 | ||
pleural fluid | ||||
Alloprevotella spp. | 1 | 0.17 | ||
bronchial brushing | ||||
Burkholderia spp. | 1 | 0.17 | ||
Veillonella spp. | 1 | 0.17 | ||
Actinomyces spp. | 1 | 0.17 | ||
sputum | ||||
S. pneumoniae—M. catarrhalis | 1 | 0.17 | ||
fluid | fluid—total | 4 | % | |
blood culture | ||||
negative | 2 | 0.50 | ||
dialysis fluid | ||||
L. aquatica | 1 | 0.25 | ||
ascitic fluid | ||||
negative | 1 | 0.25 | ||
H&N | H&N—total | 3 | % | |
maxillary sinus | ||||
Prevotella spp.—Actinomyces spp. | 1 | 0.33 | ||
auricle bone | ||||
C. acnes | 1 | 0.33 | ||
tracheal tissue | ||||
C. acnes | 1 | 0.33 | ||
eye | eye—total | 2 | % | |
ocular prosthesis | ||||
S. epidermidis | 1 | 0.50 | ||
vitreous humor | ||||
S. gallolyticus | 1 | 0.50 |
NGS Result | n | ||
---|---|---|---|
Culture Unidentifiable | 13 | % | |
Acinetobacter lwoffii | 2 | 0.15 | |
Peptostreptococcus spp. | 2 | 0.15 | |
Actinomyces spp. | 1 | 0.08 | |
Bacillus vietnamensis | 1 | 0.08 | |
Enterobacter spp. | 1 | 0.08 | |
Facklamia languida | 1 | 0.08 | |
Pantoea cypripedii | 1 | 0.08 | |
Pseudomonas spp. | 1 | 0.08 | |
Terribacillus spp. | 1 | 0.08 | |
negative | 2 | 0.15 |
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Rimoldi, S.G.; Tamoni, A.; Rizzo, A.; Longobardi, C.; Pagani, C.; Salari, F.; Matinato, C.; Vismara, C.; Gagliardi, G.; Cutrera, M.; et al. Evaluation of 16S-Based Metagenomic NGS as Diagnostic Tool in Different Types of Culture-Negative Infections. Pathogens 2024, 13, 743. https://doi.org/10.3390/pathogens13090743
Rimoldi SG, Tamoni A, Rizzo A, Longobardi C, Pagani C, Salari F, Matinato C, Vismara C, Gagliardi G, Cutrera M, et al. Evaluation of 16S-Based Metagenomic NGS as Diagnostic Tool in Different Types of Culture-Negative Infections. Pathogens. 2024; 13(9):743. https://doi.org/10.3390/pathogens13090743
Chicago/Turabian StyleRimoldi, Sara Giordana, Alessandro Tamoni, Alberto Rizzo, Concetta Longobardi, Cristina Pagani, Federica Salari, Caterina Matinato, Chiara Vismara, Gloria Gagliardi, Miriam Cutrera, and et al. 2024. "Evaluation of 16S-Based Metagenomic NGS as Diagnostic Tool in Different Types of Culture-Negative Infections" Pathogens 13, no. 9: 743. https://doi.org/10.3390/pathogens13090743