18Bordetella pertussis (B. pertussis) is the causative agent of pertussis (whooping cough). 19 Since the 1990s, pertussis has re-emerged in the United States despite an estimated 20 95% vaccine coverage. Our goal was to characterize neutrophil responses and gene 21 expression profiles of murine lungs in the context of vaccination and B. pertussis 22 challenge. We utilized a bioluminescent neutrophil mouse model (NECre luc) to track 23 neutrophil recruitment. NECre luc mice were immunized with whole cell vaccine (WCV), 24 acellular vaccine (ACV), or a truncated adenylate cyclase toxoid (RTX) vaccine. 25 Neutrophil recruitment was measured in live mice across time and corroborated by flow 26 cytometry and other data. WCV immunized mice showed signs of neutrophilia in response 27 to B. pertussis challenge. Mice immunized with either ACV or WCV cleared the challenge 28 infection; however immunization with RTX alone was not protective. RNA sequencing 29 revealed distinctive gene expression profiles for each immunization group. We observed 30 an increase in expression of genes associated with responses to infection, and changes 31 in expression of distinct genes in each vaccine group, providing a complex view of the 32 immune response to B. pertussis infection in mice. This study suggests that combination 33 of immunological analysis with transcriptomic profiling can facilitate discovery of pre-34 clinical correlates of protection for vaccine development.35 36 37 38 39 41Pertussis is a human disease primarily caused by a respiratory infection of the Gram-42 negative pathogen Bordetella pertussis (B. pertussis). The hallmark of pertussis is a distinctive 43 whooping cough. What is surprising about pertussis is that the cause of the cough has never been 44 elucidated, which highlights the fact that there are many under-researched aspects of this 45 disease. Aerosolized B. pertussis bacterium are inhaled and adhere to airway respiratory 46 epithelial cells through bacterial adhesins such as filamentous hemagglutinin (FHA), fimbriae and 47 pertactin 1 . After colonization B. pertussis express multiple toxins including pertussis toxin (PT) 48 and adenylate cyclase toxin (ACT). B. pertussis releases PT, which dysregulates the immune 49 response through ADP-ribosylation of the G-protein α-subunit of cytokine receptors present on a 50 range of leukocytes 2-5 . The secretion of PT has long range effects, ACT is thought to act locally 51 on host cells by converting ATP into supraphysiological levels of cAMP, further dysregulating the 52 host immune response 6 . 53In the 1940s, an effective whole cell vaccine (WCV) was developed and as a result, basic research 54 efforts on B. pertussis decreased. The WCVs were highly reactogenic and caused prolonged and 55 unusual crying after administration, hyporesponsivness, and febrile convulsions 7-9 . These issues 56 led to the development of acellular vaccines (ACV), known today as DTaP/Tdap (hereafter 57 referred to as ACV). The ACVs utilize an alum adjuvant and induce a Th2 response ...