Pertussis upsurge, age shift and vaccine escape post-COVID-19 caused by ptxP3 macrolide-resistant Bordetella pertussis MT28 clone in China: a genomic epidemiology study

Background: The upsurge of pertussis post-COVID-19 and expansion of macrolide-resistant Bordetella pertussis (MRBP) pose significant public health challenges worldwide. China has experienced notable pertussis upsurge post-COVID-19, alongside an age shift to older children, vaccine escape and a notable rise in MRBP prevalence. We describe the genomic epidemiological investigation of these events. Method: We did a retrospective, population-based study using culture-positive B. pertussis from Children's Hospital of Fudan University (CHFU), the exclusive referral hospital for childhood notifiable infectious diseases, in Shanghai, China between June 2016 and March 2024. We analysed strain and pertussis epidemiology dynamics by integrating whole-genome sequencing of 723 strains with antimicrobial susceptibility, transcriptomic proflie, and clinical data. We compared the genome sequences of Shanghai strains with 6450 Chinese and global strains. Findings: Coincident with national situtation, pertussis cases upsurged post-COVID-19 in Shanghai. At CHFU, the number of confirmed cases (n=349) in the first three months of 2024 exceeded the total case of previously years (n≤177). Post-COVID-19, patients shifted from predominantly infants (90%, 397/442) to widespread infection among older children (infant: 16%, 132/844), with vaccinated individuals surging from 31% (107/340) to 88% (664/756); MRBP prevalence increased from 60% (267/447) to 98% (830/845). The emergence and expansion of a ptxP3-linage, macrolide-resistant novel clone with MLVA type 28, MR-MT28, uniquely capable of causing substantial infections among older children and vaccinated individuals, temporally strongly associated with the pertussis upsurge and epidemiological transition. MR-MT28 exhibited increased expression of antigen genes including pertussis toxin genes, along with high incidence of abnormal C-reactive protein, but associated with siginicantly milder clinical symtoms (e.g. wheezing, facial blushing, p<0.01), higher proportion of normal chest computed tomography (p<0.05) and lower hospitalization rate (p<0.01). Phylogenomic clustering analysis revealed a higher proportion of MR-MT28 strains grouping into clusters representing putative transmission. We reconstructed the evolutionary history of MR-MT28, and showed that it most likely originated in China around 2016 (95% highest probability density: 2013-2017) after acquring several mutations, including a novel antigen allele prn150 and 23S rRNA A2047G mutation. Approximately one quarter (26%, 50/195) of MR-MT28 has evolved into predicted PRN-deficient strains. MR-MT28 has been identified in four regions (Anhui, Shanghai, Beijing and Guangdong) of China and continuously detected in Shanghai and Beijing, suggesting domestic spread and colonization. Interpretation: We identified a ptxP3-linage, macrolide-resistant novel clone, MR-MT28, and provide evidence that pathogen evolution is more likely the primary factor driving pertussis upsurge, age shift and vaccine escape. MR-MT28 potentially poses a high global spread risk and warrants global surveillance. Macrolides may no longer be suitable as first-line drugs for pertussis treatment in China. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement National Key Research and Development Program of China (2021YFC2701800 and 2022YFC2304700), National Natural Science Foundation of China (82202567 and 32270003), Youth Innovation Promotion Association, Chinese Academy of Sciences (2022278), Shanghai Rising-Star Program (23QA1410500), and Shanghai municipal three-year action plan for strengthening the construction of the public health system (2023-2025) GWVI-2.1.2. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The study protocol was approved by the Ethics Committee of the CHFU (No. 2022-66). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors