Genome-wide analysis exploring mechanisms used by Shigella sonnei to survive long-term nutrient starvation

Shigella is a major cause of severe diarrhea, with Shigella flexneri and Shigella sonnei accounting for over 90% of infections. Progressive economic growth worldwide correlates with the replacement of S. flexneri by S. sonnei as the dominant cause of shigellosis. The basis of the epidemiological shift remains unclear, but it highlights the urgent need for further studies on the increasingly prevalent, but less well-studied, S. sonnei. Here, we investigated whether S. sonnei is better equipped to survive nutrient starvation, a crucial condition for persistence both outside the host and within the colonic lumen. S. sonnei exhibited greater survival under long-term nutrient starvation (LTNS) than S. flexneri, rapidly activating survival mechanisms. We interrogated the genome of S. sonnei using transposon-directed insertion-site sequencing (TraDIS), revealing that metabolic pathways (ATP, nucleotide, and amino acid synthesis) and envelope homeostasis systems (e.g., Tol-Pal complex, Bam complex, peptidoglycan recycling, and RpoE stress response) are conditionally essential for LTNS. TraDIS findings were validated by non-competitive and competitive survival of wild-type and deletion mutant strains. We compared the homology of conditionally essential genes between S. sonnei and S. flexneri to identify genes potentially involved in differential LTNS survival between the species. However, S. sonnei strains in which a single gene was replaced with the S. flexneri allele showed wild-type survival phenotypes. This suggests that the divergent survival of these two species may be more complex than a monogenic difference. Together, these data define the molecular adaptations of starvation resistance in S. sonnei and provide insights into its epidemiological dominance in high-income countries.

Understanding why Shigella sonnei has a higher prevalence than Shigella flexneri as a country undergoes economic growth is an important challenge in Shigella research. The investigation of their biological and genetic differences is key to tackling the impact of the disease. We discovered that S. sonnei resists nutrient deprivation better than S. flexneri, suggesting a better adaptation to an extracellular lifestyle and a greater preservation of metabolic capabilities. Using a genome-wide transposon sequencing approach, we uncovered the key pathways behind the survival of S. sonnei facing nutrient starvation, which include ATP, nucleotide, and amino acid synthesis as well as maintenance of cell envelope integrity. Comparative analysis between S. sonnei and S. flexneri did not identify an individual gene responsible for the differing survival and may reflect a multifactorial difference. Our data provide a genome-wide basis for understanding how S. sonnei is adapted to nutrient-deprived settings, which may be advantageous in the gut lumen and for environmental survival, potentially contributing to its dominance in high-income countries.