Design and validation of Dolosigranulum pigrum specific PCR primers using the bacterial core genome

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 x 10(4)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.

Automated summary

This study developed and validated a PCR assay for detecting D. pigrum with high sensitivity and specificity. The assay targeted the murJ gene, a single-copy core species gene identified through whole genome sequence analysis. It achieved 100% sensitivity and specificity against D. pigrum and diverse bacterial isolates, and 91.1% sensitivity using nasal swabs. This assay provides a valuable tool for investigating the role of generalist and specialist bacteria in the nasal environment.