Genomic epidemiology of from pharyngeal and skin swabs in Gabon.

Unlabelled: The disease burden of is particularly high in low- and middle-income countries. However, data on the molecular epidemiology of in such regions, especially sub-Saharan Africa, are scarce. To address this, whole-genome sequencing (WGS) of from Gabon was performed to identify transmission clusters and provide valuable genomic data for public repositories. A total of 76 . isolates from 73 patients, collected between September 2012 and January 2013, were characterized by short-read whole-genome sequencing. The predominant emm types were 58.0, 81.2 and 223.0 with 9.2% (7 of 76), 7.9% (6 of 76), and 6.6% (5 of 76), respectively. Single-nucleotide polymorphism analysis revealed 16 putative transmission clusters. Four of these were household transmissions. Four antimicrobial genes (, , , and ) were found in the isolates from this study. All strains carried . Of the 76 isolates, 64 (84.2%) carried at least one tetracycline resistance gene ( or ). Comparisons with other publicly available African genomic data revealed a significant correlation between geographical location and genetic diversity of , with Gabonese strains showing similarities to those from Kenya and certain Oceanian regions. Our study showed that transmission of can occur at the community/household level and that high-resolution molecular typing is needed to monitor changes in circulating clones and to detect community outbreaks. Advocacy for the adoption of WGS for comprehensive molecular characterization of and data sharing through public repositories should be encouraged to understand the molecular epidemiology and evolutionary trajectory of in sub-Saharan Africa.

Importance: The study conducted in Gabon underscores the critical importance of addressing the limited knowledge of the molecular epidemiology of in low- and middle-income countries, particularly sub-Saharan Africa. Our molecular analysis identified predominant types and unveiled 16 putative transmission clusters, four involving household transmissions. Furthermore, the study revealed a correlation between geographical location and genetic diversity, emphasizing the necessity for a comprehensive understanding of the molecular epidemiology and evolutionary trajectory of in various regions. The call for advocacy in adopting whole-genome sequencing for molecular characterization and data sharing through public repositories is crucial for advancing our knowledge and implementing effective strategies to combat the spread of in sub-Saharan Africa.