Rapid bacterial identification from clinical specimens by using the MinION™ sequencing device: A pilot study
- Author:
Hoang Bach Nguyen
1
;
Thi Thanh Mai Ho
2
;
Rodney Lea
3
Author Information
- Publication Type:Journal Article
- Keywords: 16S ribosomal RNA; bacterial identification; MinION; nanopores
- From:Malaysian Journal of Microbiology 2023;19(no.4):409-414
- CountryMalaysia
- Language:English
-
Abstract:
Aims :DNA sequencing is a powerful tool and less time-consuming for bacterial detection and identification. The aim of this study was to compare the application of the Oxford Nanopore MinION™ sequencing device for direct DNA sequencing from clinical specimens with the routine workup.
Methodology and results :We used conventional bacteriological-based methods to detect and identify bacterial pathogens in 10 clinical specimens. In addition, the 16S metagenomic sequencing was performed by using a MinION™sequencing device with barcoded primers of a 16S Barcoding kit (Code N° SQK-RAB204, Oxford Nanopore Technologies, UK). The DNA was amplified by PCR using specific 16S primers (27F and 1492R) that contain barcodes and 5' tags which facilitate the ligase-free attachment of Rapid Sequencing Adapters of the 16S Barcoding kit. Data wasanalyzed with WIMP and EPI2ME to classify and identify species in real-time. Ten clinical specimens were processed for bacterial isolation. A total of 8 urine samples were subjected to culture-dependent methods, successfully identifying the presence of pathogenic bacteria. Out of the total eight urine samples, both methods successfully identified six bacterial pathogens. Escherichia coli were identified, and the others were detected as Salmonella enterica, Veillonella parvula and Streptococcus anginosus using MinION™ sequencing. Two urine samples had different results. Escherichia coli was detected directly through MinION™ sequencing, bypassing the need for culture results.
Conclusion, significance and impact of study:MinION™ sequencing of 16S rRNA genes could accurately detect diverse bacterial pathogens in clinical specimens. Additionally, the bacterial species classification generated by analyzing 16S rRNA gene sequences can be helpful for rapid identification. The whole procedure takes less than 8 h to complete; same-day diagnosis can be completed. - Full text:20.2023my0044.pdf
