Abundance of the nasopharyngeal microbiome effects pertussis diagnosis and explains the sensitivity difference between bacterial culture and real-time PCR

Abstract Quantitative real time PCR (qPCR)is used for pertussis diagnosis. The positive rate of qPCR is generally much higher than that of bacterial culture, which may cause confusion. The current study utilized the 16S ribosomal RNA (16S rRNA) sequencing to assess the correlation between conventional culture and qPCR and to explore the value of 16S rRNA in diagnosing pertussis. Nasopharyngeal swabs, collected from 102 children meeting clinical diagnostic criteria for pertussis, were subjected toBordetella pertussis culture and qPCR. Bioinformatic microbiota analysis was based on 16S rRNA V3-V4 gene sequencing. Among 102 samples, 14 (13.7%) were culture-positive forBordetella pertussis, while 61 (59.8%) were qPCR positive. GenusBordetella was identified in 68 (66.7%) samples via 16S rRNA sequencing. When the relative abundance ofBordetella genus exceeded 0.70%, both qPCR and culture results were positive. Samples with a relative abundance of less than 0.20% exhibited positive qPCR and negative culture results. Samples with a lowBordetella abundance are the key factors underlying poor correlation between culture and qPCR  results in laboratory tests.
Source: European Journal of Clinical Microbiology and Infectious Diseases - Category: Microbiology Source Type: research