Positivity analysis of Bordetella spp. and SARS-CoV-2 coinfections in clinical samples from Colombia, 2021-2022.

Pertussis and COVID-19 are respiratory diseases with similar clinical manifestations, complicating diagnosis. In Colombia, pertussis surveillance is based on probable cases confirmed through laboratory detection of Bordetella pertussis. During the COVID-19 pandemic, pertussis incidence declined sharply. Given limited data on coinfections with COVID-19 and pertussis, this study aimed to estimate the positivity of Bordetella spp. in SARS-CoV-2-positive samples collected in Colombia during 2021-2022. A retrospective analysis was conducted on samples collected between January 2021 and December 2022 through simple random sampling from specimens stored at the National Reference Laboratory (NRL). Demographic data, symptoms, complications, and race were obtained from the National Surveillance System (SIVIGILA), and PCR results were used to identify Bordetella spp. coinfections. National and departmental positivity rates were estimated with Clopper-Pearson confidence intervals. PCR testing for Bordetella spp. was positive in 0.54% (6/1,102) of samples, with four cases involving B. pertussis and two involving B. parapertussis; no B. holmesii coinfections were detected. The national positivity rate of SARS-CoV-2 and Bordetella spp. coinfections was 1.92% in 2021, decreasing to 1.25% in 2022. Although coinfections with viral agents and B. pertussis are common, this study found low positivity of SARS-CoV-2 and Bordetella spp. coinfections in Colombia during 2021-2022, likely due to non-pharmacological interventions, the cyclical pattern of B. pertussis, and possible underestimation related to the geographic and demographic scope of the sample. This is the first report of such coinfections in Colombia, offering a reference for future studies in Latin America.IMPORTANCEThis is the first report of SARS-CoV-2 and Bordetella spp. coinfections in Colombia, providing key evidence of their low occurrence during 2021-2022. Given that both diseases share clinical features and may complicate differential diagnosis, these findings underscore the importance of integrated surveillance for respiratory pathogens. The observed decrease in positivity may be linked to non-pharmaceutical interventions and the cyclical nature of pertussis, while also highlighting potential limitations in the geographic and demographic representativeness of the sample. This study offers a valuable baseline for future research in Latin America and reinforces the need to strengthen diagnostic capacity to detect coinfections, particularly in epidemic or pandemic contexts.