Deciphering Bordetella pertussis epidemiology through culture-independent multiplex amplicon and metagenomic sequencing

作者：Laurence Don Wai Luu, Raisa Rafique, Michael Payne, Sophie Octavia, Jennifer Robson, Vitali Sintchenko, Ruiting Lan · 发表于：Journal of Clinical Microbiology · 年份：2024 · DOI：10.1128/jcm.01178-24 · 被引用次数：5 · 研究领域：Bacterial Infections and Vaccines、Infective Endocarditis Diagnosis and Management、Pneumonia and Respiratory Infections

ABSTRACT Whooping cough (pertussis) has re-emerged despite high vaccine coverage in Australia and many other countries worldwide, partly attributable to genetic adaptation of the causative organism, Bordetella pertussis, to vaccines. Therefore, genomic surveillance has become essential to monitor circulating strains for these genetic changes. However, increasing uptake of PCR for the diagnosis of pertussis has affected the availability of cultured isolates for typing. In this study, we evaluated the use of targeted multiplex PCR (mPCR) amplicon sequencing and shotgun metagenomic sequencing for culture-independent typing of B. pertussis directly from respiratory swabs. We developed a nine-target mPCR amplicon assay that could accurately type major lineages [ ptxP3/ non- ptxpP3 , fim3A/B , fhaB3/ non- fhaB3, and epidemic lineages (ELs) 1–5] circulating in Australia. Validation using DNA from isolates and 178 residual specimens collected in 2010–2012 ( n = 87) and 2019 ( n = 91) showed that mPCR amplicon sequencing was highly sensitive with a limit of detection of 4.6 copies [IS 481 cycle threshold (Ct) 27.3]. Shotgun metagenomic sequencing was successful in genotyping B. pertussis in 84% of clinical specimens with PCR Ct < 24 and was concordant with mPCR typing results. The results revealed an expansion of EL4 strains from 2010 to 2012 to 2019 in Australia and identified unrecognized co-circulating cases of Bordetella holmesii . This study provides valuable insight into the ...