Characterisation of Bordetella pertussis virulence and macrolide resistance in Australia by targeted culture-independent sequencing: a genomic epidemiology study

作者：Winkie Fong, Rebecca J Rockett, Kingsley King-Gee Tam, Trang Nguyen, Eby Sim, Enoch Tay, Carl J E Suster, Jessica E. Agius, Shona Chandra, Anne E Watt, David Speers, Maryza Graham, Thomas Tran, Chuan Kok Lim, Michael C. Wehrhahn, Andrew N. Ginn, Darcy Gray, Jennifer Robson, Indya Gardner, Rodney McDougall, Lito Papanicolas, Annaleise R. Howard‐Jones, Alexander C. Outhred, Karina Kennedy, Louise Cooley, Qinning Wang, Neisha Jeoffreys, Sharon C-A Chen, Kerri Basile, Tanya Golubchik, Jen Kok, Vitali Sintchenko · 发表于：The Lancet Microbe · 年份：2026 · DOI：10.1016/j.lanmic.2025.101286 · 被引用次数：2 · 研究领域：Bacterial Infections and Vaccines、Pneumonia and Respiratory Infections、Herpesvirus Infections and Treatments

BACKGROUND: Bordetella pertussis continues to circulate globally despite widespread vaccination, with a notable epidemic in 2024. Its resurgence is confounded by the emergence of pertactin-deficient, macrolide-resistant B pertussis strains in Asia and Europe, which are under-recognised by conventional diagnostics. We aimed to apply targeted culture-independent next-generation sequencing (tNGS) of respiratory specimens to improve global B pertussis diagnostic capability and genomic surveillance. METHODS: We did a nationwide genomic epidemiology study of B pertussis RT-PCR-positive respiratory specimens that were retrospectively and prospectively collected by diagnostic and public health laboratories in six of seven states and territories of Australia. Specimens underwent tNGS and macrolide-resistant B pertussis-specific PCR, and an opportunistic subset from New South Wales and Queensland were cultured for confirmatory susceptibility testing and whole-genome sequencing. Sequencing data were analysed for genome recovery, virulence profiles, and macrolide resistance mutations, and were compared with international macrolide-resistant B pertussis genomes and ancestral Australian genomes. The performance of the tNGS approach was assessed with logistic regression relative to RT-PCR cycle threshold values, and sensitivity and specificity values were calculated. FINDINGS: 255 respiratory specimens positive for B pertussis were included in the study. 64 (25%) were retrospectively collec...