We PacBio sequenced eight serially-isolated pairs of Shigella flexneri isolates from an epidemic sub-lineage of MSM-associated S. flexneri 3a.

Shigella flexneri is a causative agent to shigellosis, a diarrhoeal disease that can be sexually transmitted in men who have sex with men (MSM) through oral-anal contact. We PacBio sequenced 15 S. flexneri 3a isolates from a globally distributed MSM-associated epidemic sublineage (Pubmed ID 25936611). These isolates were serial sampled at two time points from eight individual patients, with the exception for one patient by which PacBio sequencing was only successful for the earlier isolate. We performed comparative analysis of the genomes to gain a better understanding of the structural variations in Shigella infections over time.