Massive lineage replacements and cryptic outbreaks of Salmonella Typhi in eastern and southern Africa

Abstract

A new large-scale study reports the whole-genome sequences of nearly 2,000 Salmonella enterica serovar Typhi (S. Typhi) strains collected from 63 countries. A recent and dominant multidrug-resistant (MDR) lineage originating from South Asia, which is supplanting a bulk of ancestral drug-sensitive strains, is identified; the success of this lineage is likely driven by plasmid acquisitions and the chromosomal integration of resistance-conferring genes.