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Bacterial pathogens in peritoneal dialysis peritonitis: Insights from next-generation sequencing
Wesley G van Hougenhouck-Tulleken1,2, Pedro H Lebre3, Mohamed Said4,5
1Department of Nephrology, Steve Biko Academic Hospital, Pretoria, South Africa.
Background:
Peritoneal dialysis (PD) peritonitis is a feared complication of PD, with significant sequelae for the patient. The cause of PD peritonitis is largely due to a single organism (≥75% of cases) and rarely due to multiple organisms.
Methods:
In this pilot study, we investigated 25 cases of PD peritonitis with 16S ribosomal RNA (rRNA) next-generation sequencing (NGS) techniques.
Results:
Total concordance between culture and NGS was noted. In addition, the NGS technique was highly sensitive, identifying 33 different bacteria (including a nonculturable bacterium), compared to 13 bacterial species using culture-based techniques. This was counterbalanced by a lack of specificity with NGS, largely due to the small size of the 16S rRNA gene segment sequenced.
Conclusions:
For the clinician, our results suggest that PD peritonitis may often be a polymicrobial disease and that treating a dominant organism may not totally eradicate all bacterial contamination within the peritoneum. For the clinical scientist, additional use of a larger 16S rRNA segment (V5 or V6) is likely to outperform the use of the V4 segment only.
Insights
Next-generation sequencing (NGS) reveals more bacteria in peritoneal dialysis (PD) peritonitis than traditional cultures. This suggests PD peritonitis may be polymicrobial, requiring broader treatment strategies.
Area of Science:
- Microbiology
- Nephrology
- Genomics
Background:
- Peritoneal dialysis (PD) peritonitis is a serious complication of PD.
- It is traditionally believed to be caused by a single organism in most cases.
Purpose of the Study:
- To investigate the microbial etiology of PD peritonitis using 16S ribosomal RNA (rRNA) next-generation sequencing (NGS).
- To compare the diagnostic performance of NGS with conventional culture-based methods.
Main Methods:
- Pilot study involving 25 cases of PD peritonitis.
- Utilized 16S rRNA gene sequencing (V4 region) for microbial identification.
Main Results:
- NGS identified 33 bacterial species, significantly more than the 13 identified by culture.
- High sensitivity of NGS was observed, detecting a nonculturable bacterium.
- Concordance between NGS and culture was noted, but NGS showed lower specificity due to the limited gene segment.
Conclusions:
- PD peritonitis may frequently be a polymicrobial infection, challenging the single-organism paradigm.
- Targeting only the dominant organism might not eliminate all bacterial contamination.
- Using larger 16S rRNA gene segments (e.g., V5 or V6) could improve NGS specificity and performance.
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