Pan-genome analysis identifies a Burkholderia cepacia-specific gene marker for rapid species-level identification
TL;DR
The identification of this conserved core gene provides a promising basis for the rapid and accurate species-level detection of B. cepacia and may help improve contamination monitoring and quality control in the pharmaceutical, cosmetic, and food industries, thereby contributing to public health protection.
Abstract
Inroduction Burkholderia cepacia is a representative member of the Burkholderia cepacia complex (Bcc) and is widely distributed in water and soil environments. It has a propensity to form biofilms in water-based products, making it a significant contaminant in the pharmaceutical, cosmetic, and food industries and posing threats to product quality control and public health. Therefore, rapid and accurate species-level identification of B. cepacia is of great importance. Methods To achieve rapid and accurate species-level identification of B. cepacia, we performed a pan-genome analysis based on 138 high-quality genome sequences covering B. cepacia and its closely related Bcc species with taxonomic positions validated by average nucleotide identity (ANI) analysis. A conserved core gene encoding a glycosyl hydrolase family 18 (GH18) protein was identified as a species-specific molecular marker. A specific primer pair comprising SEQ ID NO.2 and SEQ ID NO.3 was designed based on this marker and validated with both genome sequences and bacterial pure cultures. Results The GH18-encoding gene is highly conserved across 115 B. cepacia strains (sequence identities ranging from 90.3 to 100.0%) and is absent in all other Bcc species examined. The primer pair exhibited high inclusivity and exclusivity for B. cepacia. The established PCR method achieved a detection limit of 5 pg/μL for pure genomic DNA and 103 CFU/mL in artificially contaminated water-based personal care and medical device products. Discussion The identification of this conserved core gene provides a promising basis for the rapid and accurate species-level detection of B. cepacia. Given the widespread occurrence of B. cepacia in water and soil environments and its ability to form biofilms in water-based products, such a species-specific molecular marker may help improve contamination monitoring and quality control in the pharmaceutical, cosmetic, and food industries, thereby contributing to public health protection.