Vaccine antigen-based genotyping of by direct Sanger sequencing of clinical samples in Peru from 2018 to 2019.

UNLABELLED

Despite widespread vaccination, pertussis (caused by ) persists in many countries, frequently causing outbreaks and severe cases in infants. The resurgence of pertussis may be due to genetic changes in the vaccine antigens of circulating strains. However, current typing methods, which depend on bacterial cultures, hinder our understanding of genotypes, especially in developing countries. This study aimed to analyze vaccine antigen-based genotypic variants (, , , and ) of in Peru from 2018 to 2019 via direct Sanger sequencing of nasopharyngeal swabs ( = 96). PCR-based sequencing was successful for the genes in 86% (83/96), in 100% (96/96), in 75% (72/96), and in 68% (65/96) of the samples. The variant was found in 100% (83/83), in 100% (96/96), in 97.3% (70/72), in 2.7% (2/72), and in 100% (65/65) of the samples. Sixty-three samples yielded a complete allelic profile, with genotype VI () predominating nationwide (96.8%), mainly in Lima (29.5%), Amazonas (13.1%), Callao (11.5%), and La Libertad (11.5%). Genotype VII () was less common (3.2%), found in Lima (50%) and Callao (50%). The predominance and expansion of genotype VI suggested the presence of biological traits linked to infection, possibly due to the allele, such as high respiratory colonization or increased pertussis toxin production, which could potentially increase disease transmission and severity. These findings will facilitate Peru's ability to monitor and control , improving public health responses and reducing the outbreak incidence and severity.

IMPORTANCE

Despite widespread vaccination, pertussis (caused by ) still causes severe outbreaks in infants worldwide. Genetic changes in the vaccine antigens of strains may drive this resurgence. Current culture-based typing methods limit our understanding of these genotypes, particularly in developing countries. This study provides valuable insights into the genotypic variability of in Peru from 2018 to 2019, employing an isolation-free genotyping method allowing the direct Sanger sequencing of vaccine antigen genes from clinical samples. These findings can enhance public health decision-making by improving our understanding of the genetic changes that drive severe pertussis outbreaks, particularly in developing countries that use whole-cell vaccines. This knowledge enables rapid outbreak responses, improved vaccine strategies, and strengthened surveillance, prevention, and control measures.