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Microbiol."},{"key":"10.1016\/j.drup.2026.101494_bib70","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1080\/22221751.2019.1587315","article-title":"Genomic epidemiology of erythromycin-resistant Bordetella pertussis in China.","volume":"8","author":"Xu","year":"2019","journal-title":"Emerg. 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