Spread of macrolide-resistant Bordetella pertussis and co-transmission with Bordetella holmesii during a pertussis outbreak from January to July 2025 in Kobe City, Japan

Background and Aims The emergence and spread of macrolide-resistant Bordetella pertussis (MRBP) and Bordetella holmesii have become global public health concerns. Methods 4Plex RT-PCR and bacterial culture were performed in 182 patients clinically diagnosed with pertussis. The A2047G mutation in the 23S rRNA gene was examined in 165 IS481-positive and recA-negative samples. A hIS1001-targeted qPCR assay to detect B. holmesii was conducted for all samples. The genomic sequence of KBH0001, isolated in this study, was compared with human-derived B. holmesii genomes. Results We report the spread of MRBP during a pertussis outbreak in Kobe City, Japan, from January to July 2025, along with two cases of co-infection with B. holmesii. Among 165 specimens, 81 (49.1%) harboured the A2047G mutation associated with macrolide resistance. Of the 91 culture-positive specimens, 29 macrolide-sensitive B. pertussis (MSBP) strains, 61 MRBP strains, and one B. holmesii strain (KBH0001) were isolated. The hIS1001-targeted qPCR assay, which is more sensitive for detecting B. holmesii than the recA gene-based 4Plex RT-PCR currently used for laboratory-based surveillance in Japan, identified two cases of MRBP and B. holmesii co-infection. Whole-genome sequencing revealed that the Japanese B. holmesii strain KBH0001 belongs to a lineage that has existed since at least the 2010s. Conclusion The concurrent circulation of MRBP and vaccine-insensitive B. holmesii complicates treatment and prevention efforts, highlighting the need for strengthened and sustained surveillance systems.