Accessory genome dynamics and structural variation of Shigella from persistent infections

Shigellosis is a diarrhoeal disease caused mainly by Shigella flexneri and Shigella sonnei. Infection from Shigella is thought to be largely self-limiting, with short- to medium- term and serotype-specific immunity provided following clearance. However, cases of men who have sex with men (MSM) associated shigellosis have been reported where Shigella of the same serotype were serially sampled from individuals between 1 to 1862 days apart, possibly due to persistent carriage or reinfection with the same serotype. Here, we investigate the accessory genome dynamics of MSM associated S. flexneri and S. sonnei isolates serially sampled from individual patients at various days apart. We find that pairs likely associated with persistent carriage infection and with smaller single nucleotide polymorphism (SNP) distance, demonstrated significantly less variation in accessory genome content than pairs likely associated with reinfection and with greater SNP-distance. We also observed evidence of antimicrobial resistance (AMR) acquisition during persistent Shigella infection, specifically the gain of extended spectrum beta-lactamase genes in two pairs associated with persistent carriage. Finally, we explored chromosomal structural variations and rearrangements in seven (5 chronic and 2 reinfection associated) pairs of S. flexneri 3a isolates from a MSM-associated epidemic sublineage, which revealed variations at several common regions across pairs. These variations were mediated by insertion sequence (IS) elements which facilitated plasticity of genetic material with a distinct predicted functional profile. This study provides insight on the variation of accessory genome dynamics and large structural genomic changes in Shigella during persistent infection.