Deadly Salmonella ST313 Evolves Faster, Outsmarting Antibiotics in Africa
A new study has uncovered how one of the deadliest forms of invasive salmonellosis is evolving. Published in Nature Communications in 2026, the research tracks the rapid spread and genetic changes of Salmonella Typhimurium ST313 strains. These findings could help shape future strategies to combat the disease, which has devastated parts of sub-Saharan Africa.
The team, led by researchers Jia, C., Zhou, H., Cao, Q., and colleagues, identified key shifts in the bacterium's genome. Their work reveals how ST313 has adapted to human hosts, becoming both more virulent and harder to treat.
ST313 was first detected in Kenya and Uganda between 2006 and 2007. Since then, it has spread across Malawi, South Africa, Mozambique, and the Democratic Republic of the Congo. Cases outside Africa remain rare, with only isolated imports reported in Europe and the US.
The study highlights several factors driving its expansion. Overcrowded urban slums, such as Kibera in Nairobi, have enabled rapid human-to-human transmission. Poor sanitation and limited antibiotic monitoring have worsened the problem, while multidrug resistance—against ampillicin, chloramphenicol, and trimethoprim—has made infections harder to control. Existing vaccines, like TY21a, have also proven less effective against these strains.
Genomic analysis shows ST313 has undergone significant changes. Researchers observed widespread pseudogenization, where key metabolic pathways broke down, suggesting a shift toward an intracellular lifestyle. The strains also developed discrete genomic rearrangements, loss-of-function mutations, and acquired mobile genetic elements that boost virulence and host adaptation.
Convergent evolution was another key finding. Even in geographically separated strains, similar genetic adaptations emerged, pointing to shared pressures in human hosts. The study also noted the recent rise of new ST313 sublineages, closely linked to urbanisation and increased antibiotic use in affected regions.
Virulence factors have diversified too. The bacterium's type III secretion system effectors—proteins that help it infect cells—have expanded. At the same time, plasmids carrying antibiotic resistance genes have grown, creating a dual threat of heightened aggression and treatment resistance.
The research provides a detailed map of ST313's evolution, offering critical insights for public health responses. With high mortality rates among immunocompromised populations in sub-Saharan Africa, the findings underscore the need for targeted interventions. Improved sanitation, stricter antibiotic stewardship, and updated vaccines could help curb the bacterium's spread and impact.
