Immunologic profiling of the infant immune response to whole-cell and acellular pertussis vaccines

Abstract

Despite robust antibody responses, immunity induced by acellular pertussis vaccine (DTaP) wanes over time and risk of pertussis seems to be lower in children who receive whole-cell vaccine (DTP) as their first dose. To interrogate the early immunologic response to pertussis vaccine, we enrolled 56 healthy infants who received either DTP or DTaP at 2-, 4-, 6-, and 18-months of age. RNA-sequencing and ribosome profiling of PBMC were performed prior to vaccination (Day 1) and on either Day 2 or Day 8. Pathway enrichment analysis on Days 2 and 8 showed enrichment of TLR-signaling and FcϒR-mediated phagocytosis among DTP recipients. DTP also led to increases in IRAK-4 and IL-1ß. After booster vaccination, a higher frequency of PT-specific B-cells was observed in DTP- vs. DTaP recipients. These data provide insights into the early immunologic responses to pertussis vaccine and may guide next-generation pertussis vaccine development.

Fig. 1. Study design and schema.

Panel A displays the overall study schema and study procedures; Panel B displays the CONSORT-style disposition of participants in the study and vaccines received. Participants for whom RNA-Seq or RP data did not pass quality control or were not available were excluded from the RNA-Seq/RP analysis. Created in BioRender. Creech, B. (2025) https://BioRender.com/n33d820.

Fig. 2. Reactive B-cell frequencies for FHA, PT, FIM 2/3, and Pn.

Percent reactive B-cells one-month following the primary series (Day 150) and booster immunization (Day 510). In orange: DTP; in purple: DTaP. Extreme outliers are removed from display, inclusive of 2 values for DTaP at Day 510 for FHA (3.5 and 5.6 percent reactive B cells), and 1 value for DTP at Day 510 for FHA (2.3 percent reactive B cells). Extreme outliers were identified as having outlying profiles in one or all of the principal component analysis plots, multidimensional scaling plots, and Euclidean distance based clustering dendrograms. Boxplots are presented as the median and the 25–75th percentile (box) and whiskers (5–95th percentile).

Fig. 3. Top 20 KEGG pathways identified across all assays, arms, and days shaded by enrichment score and color−coded by fold change direction.

Enrichment score is defined as −1 ×log₁₀ (FDR-adjusted p-value). Top pathways are defined based on the greatest change in enrichment score across assays, post-vaccination days, and treatment groups. Circle size is determined based on the mean of mean log₂ fold change relative to pre-vaccination for genes included in the pathway. RP Ribosomal Profiling. In red: increased compared to pre-vaccination, in blue: decreased compared to pre-vaccination. For each of the 9 gene sets and differentially transcribed or translated gene sets, p-values were adjusted using the Benjamini–Hochberg procedure to control the FDR. Gene sets with an FDR-adjusted p-value < 0.1 were considered to be significantly enriched.

Fig. 4. Cell deconvolution data.

Radar plot of the median of the fold change relative to Day 1, estimating the proportion of cell types in the PBMC fraction for DTaP and DTP on Days 2 and 8. In orange: DTP; in purple: DTaP; solid lines: Day 2; dashed lines: Day 8. MAIT Mucosal-associated invariant T cells, mDCs Myeloid dendritic cells, C Monocytes classical monocytes, NC Monocytes non-classical monocytes, LD Neutrophils low-density neutrophils, NK natural killer, pDCs plasmacytoid dendritic cells.