Table 2.
Main advantages and disadvantages of classic techniques and 16S rRNA gene-targeted NGS for the microbiological diagnosis of infected endocarditis.
| Technique | Advantages | Disadvantages |
|---|---|---|
| Blood culture | Cornerstone of diagnosis Bacterial identification and susceptibility testing Simple collection procedure Faster if associated with MALDI-TOF Available for clinical microbiology labs |
Limited sensitivity, especially after antibiotic therapy or for fastidious microorganisms Delayed diagnosis if negative Processing time: several days |
| PCR | More sensitive and faster than culture Applicable for blood and valve tissue (variable collection procedure) Can be broad range or specifically targeted (high specificity) Especially useful for BCNE Processing time: several hours (<1 day) |
Variable sensitivity (blood vs. valve; 16S rRNA gene vs. specific targets) Requires careful clinical correlation (detection of viable and non-viable organisms, risk of contamination) Not available for all clinical microbiology labs |
| Valve culture | Definitive diagnosis Bacterial identification and susceptibility testing Available for clinical microbiology labs |
Low specificity (tedious handling of sample) Limited sensitivity, especially after antibiotic therapy or for fastidious microorganisms Difficulty for sample acquisition (surgery) Delayed diagnosis Processing time: several days |
| Serology | Particularly useful in BCNE caused by Coxiella burnetii, Bartonella spp., and other fastidious microorganisms Simple collection procedure Processing time: two hours |
Low sensitivity and specificity High seroprevalence in certain collectives for C. burnetii and Bartonella spp. High titers can persist and require careful clinical correlation |
| 16S rRNA gene-targeted NGS | High-throughput sequencing Detection of all bacteria present in a sample Culture independent Promising diagnostic tool |
Variable sensitivity (targeted region, bioinformatics pipeline, equipment, etc.) Lack of consensus for processing and data analysis Bioinformatics skills and computational resources are needed Requires careful clinical correlation (detection of viable and non-viable organisms, risk of contamination) Processing is time-consuming |
MALDI-TOF, matrix-assisted laser desorption/ionization-time-of-flight; PCR, polymerase chain reaction; BCNE, blood culture-negative endocarditis; NGS, next-generation sequencing.