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Design and validation of Dolosigranulum pigrum specific PCR primers using the bacterial core genome
oleh: Maliha Aziz, Amber Palmer, Søren Iversen, Juan E. Salazar, Tony Pham, Kelsey Roach, Karsten Becker, Ursula Kaspar, Lance B. Price, Sharmin Baig, Marc Stegger, Paal Skytt Andersen, Cindy M. Liu
| Format: | Article |
|---|---|
| Diterbitkan: | Nature Portfolio 2023-04-01 |
Deskripsi
Abstract Dolosigranulum pigrum—a lactic acid bacterium that is increasingly recognized as an important member of the nasal microbiome. Currently, there are limited rapid and low-cost options for confirming D. pigrum isolates and detecting D. pigrum in clinical specimens. Here we describe the design and validation of a novel PCR assay targeting D. pigrum that is both sensitive and specific. We designed a PCR assay targeting murJ, a single-copy core species gene identified through the analysis of 21 D. pigrum whole genome sequences. The assay achieved 100% sensitivity and 100% specificity against D. pigrum and diverse bacterial isolates and an overall 91.1% sensitivity and 100% specificity using nasal swabs, detecting D. pigrum at a threshold of 1.0 × 104 D. pigrum 16S rRNA gene copies per swab. This assay adds a reliable and rapid D. pigrum detection tool to the microbiome researcher toolkit investigating the role of generalist and specialist bacteria in the nasal environment.