{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T15:49:07Z","timestamp":1753890547910,"version":"3.41.2"},"reference-count":68,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,6,11]],"date-time":"2025-06-11T00:00:00Z","timestamp":1749600000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"<jats:sec><jats:title>Introduction<\/jats:title><jats:p>Various strains emerged in <jats:italic>B. pertussis<\/jats:italic> re-emergence, the pathogenic characteristics and mechanisms remain elusive. We aimed to explore the relationship between the <jats:italic>in vivo<\/jats:italic> transcriptome and colonization advantage of various pertussis clinical strains during the <jats:italic>B. pertussis<\/jats:italic> re-emergence.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Four pertussis strains were isolated from clinically suspected cases by active surveillance. The phylogenetic relationships of clinical strains and global isolates were compared by a genome-wide SNP-based phylogenetic tree and allele genotyping. LC-MS\/MS analysis and binding affinity detection allowed the identification of expression and antigenicity of pertactin. The characteristics of infection and immunity of clinical strains were compared in a BALB\/c mouse aerosol challenge model. <jats:italic>In vivo<\/jats:italic> RNA-seq analysis was performed in NSG mouse model to describe the transcriptome during infection, and verified by detecting biofilm formation and paraquat tolerance.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The partial pertactin-deficient strain BP-L2 was first reported. It showed significantly enhanced tracheal colonization compared to both CS and BP-L1 strains in naive mice (<jats:italic>P<\/jats:italic> &amp;lt; 0.0001 <jats:italic>vs<\/jats:italic>. CS) and exhibited superior fitness over BP-L1 in immunized mice (<jats:italic>P<\/jats:italic> &amp;lt; 0.001). BP-L1 showed superior lung colonization (<jats:italic>P<\/jats:italic> &amp;lt; 0.0001) and tissue-resident memory T cell induction versus BP-L2 and CS (<jats:italic>P<\/jats:italic> &amp;lt; 0.001). Colonization dominance of BP-L1 in lungs and BP-L2 in trachea aligned with the pathological injury (<jats:italic>P<\/jats:italic> &amp;lt; 0.05) and the inflammatory cytokine enhancement (IL-6 in lungs of BP-L1 group, <jats:italic>P<\/jats:italic> &amp;lt; 0.01). <jats:italic>In vivo<\/jats:italic> RNA-seq results revealed that BP-L2 significantly upregulated <jats:italic>relA<\/jats:italic> (log2FC = 2.1, <jats:italic>FDR P-value<\/jats:italic> = 0.019) and <jats:italic>sodA<\/jats:italic> (log2FC =2.4, <jats:italic>FDR P-value<\/jats:italic> = 8.61E-06) compared to BP-L1, functionally linked to enhanced stringent response and oxidative stress defense. BP-L1 exhibited significant <jats:italic>in vivo bipA<\/jats:italic> upregulation over BP-L2 (log2FC = 1.8, <jats:italic>FDR P-value<\/jats:italic> = 0.027) without concurrent biofilm enhancement (<jats:italic>P<\/jats:italic> = 0.51 <jats:italic>vs<\/jats:italic>. BP-L2). Furthermore, the BP-L2 and BP-L3 strains of the same <jats:italic>ptxP1-ptxA1-fhaB3<\/jats:italic> lineage showed significantly higher paraquat tolerance than other strains (<jats:italic>P<\/jats:italic> &amp;lt; 0.001), showing extremely high SODs activity.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>The emerging pertussis strains exhibit different colonization advantages in the trachea or lungs, which will influence the transmission patterns of the clinical strains. The tracheal colonization advantage of the partial pertactin-deficient strain may be associated with the overexpression of the <jats:italic>relA<\/jats:italic> and <jats:italic>sodA in vivo<\/jats:italic> infection.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fcimb.2025.1547751","type":"journal-article","created":{"date-parts":[[2025,6,11]],"date-time":"2025-06-11T05:14:29Z","timestamp":1749618869000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["In vivo RNA-seq and infection model reveal the different infection and immune characteristics of B. pertussis strains in China"],"prefix":"10.3389","volume":"15","author":[{"given":"Weilun","family":"Zuo","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chen","family":"Wei","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Meiyan","family":"He","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mengyao","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiangli","family":"Liang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiao","family":"Ma","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Na","family":"Gao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qin","family":"Gu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yan","family":"Ma","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jingyan","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuyuan","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yan","family":"Huang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mingbo","family":"Sun","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Li","family":"Shi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2025,6,11]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.3390\/pathogens11070794","article-title":"Characterization of Bordetella pertussis strains isolated from India","volume":"11","author":"Alai","year":"2022","journal-title":"Pathogens"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-11-627","article-title":"Comparative genomics of prevaccination and modern Bordetella pertussis strains","volume":"11","author":"Bart","year":"2010","journal-title":"BMC Genomics"},{"key":"B3","doi-asserted-by":"publisher","first-page":"e01301","DOI":"10.1128\/genomeA.01301-14","article-title":"Complete genome sequences of Bordetella pertussis isolates B1917 and B1920, representing two predominant global lineages","volume":"2","author":"Bart","year":"2014","journal-title":"Genome Announc"},{"key":"B4","doi-asserted-by":"publisher","first-page":"2608","DOI":"10.1080\/21505594.2021.1980987","article-title":"Pathogenicity and virulence of Bordetella pertussis and its adaptation to its strictly human host","volume":"12","author":"Belcher","year":"2021","journal-title":"Virulence"},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.1093\/femspd\/ftv064","article-title":"Bordetella pertussis evolution in the (functional) genomics era","volume":"73","author":"Belcher","year":"2015","journal-title":"Pathog. 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