Diagnosis of external ventricular drainage related infections with real-time 16S PCR and third-generation 16S sequencing
(2024) In Infectious Diseases- Abstract
Objective: Investigate the performance of real-time 16S PCR and third-generation 16S sequencing in the diagnosis of external ventricular drain related infections (EVDRI). Methods: Subjects with suspected EVDRI were prospectively included at Uppsala University Hospital. Subjects were included into three groups: subjects with negative CSF culture with and without antibiotic treatment and subjects with positive CSF culture, respectively. CSF was analysed with real-time 16S PCR and third-generation 16S sequencing. Real-time 16S PCR positivity/negativity and number of 16S sequence reads were compared between groups. For culture positive subjects, species identification in third-generation sequencing and routine culture was compared. Results:... (More)
Objective: Investigate the performance of real-time 16S PCR and third-generation 16S sequencing in the diagnosis of external ventricular drain related infections (EVDRI). Methods: Subjects with suspected EVDRI were prospectively included at Uppsala University Hospital. Subjects were included into three groups: subjects with negative CSF culture with and without antibiotic treatment and subjects with positive CSF culture, respectively. CSF was analysed with real-time 16S PCR and third-generation 16S sequencing. Real-time 16S PCR positivity/negativity and number of 16S sequence reads were compared between groups. For culture positive subjects, species identification in third-generation sequencing and routine culture was compared. Results: 84 subjects were included. There were 18, 44 and 22 subjects in the three groups. Real-time PCR was positive in 17 of 22 subjects in the culture positive group and negative in 61 of the 62 subjects in the two culture negative groups. The sensitivity and specificity for real-time 16S PCR compared to culture was estimated to 77% and 98%, respectively. Species identification in 16S sequencing and culture was concordant in 20 of 22 subjects. The number of 16S sequence reads were significantly higher in the culture positive group than in both culture negative groups (p < 0.001). There was no significant difference in number of 16S sequences between the two culture negative groups. Conclusions: Real-time 16S PCR predict culture results with sufficient reliability. Third-generation 16S sequencing could enhance sensitivity and species identification in diagnostics of EVD-related infections. False negative culture results appear to be uncommon in patients with suspected EVDRI.
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- author
- Widén, Johan LU ; Morén, Jakob ; Mölling, Paula ; Fagerström, Anna ; Enblad, Per ; Eriksson, Britt Marie ; Ronne-Engström, Elisabeth ; Sundqvist, Martin and Westman, Gabriel
- organization
- publishing date
- 2024
- type
- Contribution to journal
- publication status
- epub
- subject
- keywords
- 16s PCR, cerebrospinal fluid, External ventricular drain, nanopore, NGS, ventriculostomy related infection
- in
- Infectious Diseases
- publisher
- Informa Healthcare
- external identifiers
-
- scopus:85189567110
- pmid:38530119
- ISSN
- 2374-4235
- DOI
- 10.1080/23744235.2024.2331260
- language
- English
- LU publication?
- yes
- id
- eddb48d8-be9b-411b-8d2e-b1b31b34cf0b
- date added to LUP
- 2024-04-22 12:06:47
- date last changed
- 2024-06-17 17:03:12
@article{eddb48d8-be9b-411b-8d2e-b1b31b34cf0b, abstract = {{<p>Objective: Investigate the performance of real-time 16S PCR and third-generation 16S sequencing in the diagnosis of external ventricular drain related infections (EVDRI). Methods: Subjects with suspected EVDRI were prospectively included at Uppsala University Hospital. Subjects were included into three groups: subjects with negative CSF culture with and without antibiotic treatment and subjects with positive CSF culture, respectively. CSF was analysed with real-time 16S PCR and third-generation 16S sequencing. Real-time 16S PCR positivity/negativity and number of 16S sequence reads were compared between groups. For culture positive subjects, species identification in third-generation sequencing and routine culture was compared. Results: 84 subjects were included. There were 18, 44 and 22 subjects in the three groups. Real-time PCR was positive in 17 of 22 subjects in the culture positive group and negative in 61 of the 62 subjects in the two culture negative groups. The sensitivity and specificity for real-time 16S PCR compared to culture was estimated to 77% and 98%, respectively. Species identification in 16S sequencing and culture was concordant in 20 of 22 subjects. The number of 16S sequence reads were significantly higher in the culture positive group than in both culture negative groups (p < 0.001). There was no significant difference in number of 16S sequences between the two culture negative groups. Conclusions: Real-time 16S PCR predict culture results with sufficient reliability. Third-generation 16S sequencing could enhance sensitivity and species identification in diagnostics of EVD-related infections. False negative culture results appear to be uncommon in patients with suspected EVDRI.</p>}}, author = {{Widén, Johan and Morén, Jakob and Mölling, Paula and Fagerström, Anna and Enblad, Per and Eriksson, Britt Marie and Ronne-Engström, Elisabeth and Sundqvist, Martin and Westman, Gabriel}}, issn = {{2374-4235}}, keywords = {{16s PCR; cerebrospinal fluid; External ventricular drain; nanopore; NGS; ventriculostomy related infection}}, language = {{eng}}, publisher = {{Informa Healthcare}}, series = {{Infectious Diseases}}, title = {{Diagnosis of external ventricular drainage related infections with real-time 16S PCR and third-generation 16S sequencing}}, url = {{http://dx.doi.org/10.1080/23744235.2024.2331260}}, doi = {{10.1080/23744235.2024.2331260}}, year = {{2024}}, }