Tracking the establishment of local endemic populations of an emergent enteric pathogen

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Abstract
Shigella sonnei is a human-adapted pathogen that is emerging globally as the dominant agent of bacterial dysentery. To investigate local establishment, we sequenced the genomes of 263 Vietnamese S. sonnei isolated over 15 y. Our data show that S. sonnei was introduced into Vietnam in the 1980s and has undergone localized clonal expansion, punctuated by genomic fixation events through periodic selective sweeps. We uncover geographical spread, spatially restricted frontier populations, and convergent evolution through local gene pool sampling. This work provides a unique, high-resolution insight into the microevolution of a pioneering human pathogen during its establishment in a new host population. Significance Shigella sonnei is a globally emerging agent of bacterial dysentery. Here, we use genomics to examine the microevolution of S. sonnei in Vietnam. We show that S. sonnei was introduced into Vietnam in the early 1980s, where it continued to evolve, spreading geographically to establish localized founder populations. The population in Ho Chi Minh City has undergone several localized clonal replacement events, during which a small number of microevolutionary changes have risen to dominance. These changes, induced by horizontal gene transfer and substitution mutations, confer high-level antimicrobial resistance and the ability to kill other gut bacteria. This work provides a unique, high-resolution insight into the microevolution of a pioneering human pathogen during its establishment in a new host population.