Introduction
Materials and methods
Ethics statement
Sample collection and study design
Routine bacterial culture
Micelle PCR and NGS
Bioinformatics pipeline
Quantitative PCR methods
Results
Development of an easy-to-use bioinformatics pipeline
Validation of the MYcrobiota process
Comparing MYcrobiota results to routine bacterial culture
Bacterial taxa | Number of positive samples | Sensitivity (%) | Specificity (%) | |
---|---|---|---|---|
Routine bacterial culture | MYcrobiota | |||
Acinetobacter
| 1 | 4 | 100 | 98 |
Enterobacteriaceae*
| 7 | 8 | 100 | 98 |
Pasteurella
| 1 | 1 | 100 | 100 |
Proteus
| 2 | 2 | 100 | 100 |
Pseudomonas
| 2 | 2 | 67 | 100 |
Staphylococcus
| 14 | 20 | 93 | 100 |
Stenotrophomonas
| 1 | 2 | 100 | 100 |
Streptococcus
| 10 | 16 | 100 | 97 |
Anaerobic bacteria | 3 | 21 | 100 | 71 |
Total | 41 | 76 | 95 | 95 |