The emergence of multidrug-resistant (MDR) typhoid is a major global health threat affecting many countries where the disease is endemic. Here whole-genome sequence analysis of 1,832 Salmonella enterica serovar Typhi (S. Typhi) identifies a single dominant MDR lineage, H58, that has emerged and spread throughout Asia and Africa over the last 30 years. Our analysis identifies numerous transmissions of H58, including multiple transfers from Asia to Africa and an ongoing, unrecognized MDR epidemic within Africa itself. Notably, our analysis indicates that H58 lineages are displacing antibiotic-sensitive isolates, transforming the global population structure of this pathogen. H58 isolates can harbor a complex MDR element residing either on transmissible IncHI1 plasmids or within multiple chromosomal integration sites. We also identify new mutations that define the H58 lineage. This phylogeographical analysis provides a framework to facilitate global management of MDR typhoid and is applicable to similar MDR lineages emerging in other bacterial species.

Typhoid (enteric fever) remains a major cause of morbidity and mortality worldwide, causing over 21 million new infections annually, with the majority of deaths occurring in young children. As typhoid fever-causing Salmonella have no known environmental reservoir, the chronic, asymptomatic carrier state is thought to be a key feature of continued maintenance of the bacterium within human populations. In spite of the importance of this disease to public health, our understanding of the molecular mechanisms that catalyze carriage, as well as our ability to reliably identify and treat the Salmonella carrier state, have only recently begun to advance.

BackgroundSalmonella Typhi is a major cause of fever in children in low- and middle-income countries. The recently WHO prequalified typhoid conjugate vaccine (TCV) was shown to be efficacious in a human challenge model but no efficacy trials in endemic populations have been completed.MethodsIn this phase III participant- and observer-blinded randomized controlled trial in Lalitpur, Nepal, children aged 9 months to <16 years of age, were randomized 1:1 to receive either TCV or a capsular group A meningococcal conjugate vaccine (Men A) as control. The primary endpoint was blood culture-confirmed typhoid fever. Study follow-up continues for 2 years; here we present the interim analysis after 12 months of follow-up, for safety, immunogenicity and efficacy.Results10,005 participants received TCV and 10,014 received Men A. Blood culture-confirmed typhoid fever occurred in 7 participants who received TCV and 38 receiving Men A; vaccine efficacy: 81.6% (95% CI, 58.8%, 91.8%, P<0.001). 132 SAEs occurred in the first 6 months with one (pyrexia) identified as vaccine-related. The participant remains blinded. Seroconversion (≥ four-fold rise in Vi-IgG 28 days after vaccination) was 99% in the TCV group (N=677/683) and 2% in the control group (N=8/380).ConclusionA single dose of TCV is safe, immunogenic, and effective, and the deployment of the vaccine will reduce the burden of typhoid in high-risk populations. This new evidence of efficacy is especially timely with the recent spread of extensively drug resistant typhoid fever which threatens child health in affected regions.Trial registration numberISRCTN43385161