SAL-O5_Asses the variation in lipopolysaccharide structure in circulating African invasive Salmonella Typhimurium isolates to predict vaccine coverage

Summary

In sub-Saharan Africa, invasive non-typhoidal Salmonella (iNTS) is the major cause of bacterial bloodstream infections among young children and disease management is jeopardised by increasing antimicrobial resistance (AMR). The O-antigen portion of Salmonella lipopolysaccharide (LPS) is recognised as key target antigen for protective immunity and O-antigen-based vaccines covering the main serovars Salmonella Typhimurium and Enteritidis are in development. Some of the vaccine candidates are about to enter phase 1 clinical trials; however, efficacy in Africa will not be tested for several years. 

O-antigen structural variability can have an impact on the protective immunity of corresponding vaccines. Serotyping and genomic investigation of recent iNTS isolates from the Democratic Republic of the Congo (DRC) have shown increasing rates of iNTS isolates with variation in O-antigen structure. In particular, more than 45 % of the recent Salmonella Typhimurium isolates do not present O:5 specificity, associated to O-antigen O-acetylation. 

In this project, we will analyse the genomic variation of O-antigen of Salmonella Typhimurium DRC isolates within the African context. The genomic basis of differences in O-antigenic structure will be proven by mutagenesis experiments. We will determine the O-antigen structure from a panel of Salmonella Typhimurium isolates recently collected in DRC, ascertaining the nature of the O-antigen genomic variations. The coverage of current O-antigen based vaccines against iNTS is likely to be impacted by the O-antigen structural variability, and this project will yield key insights on how to improve the current vaccines. 

Project outcomes

In sub-Saharan Africa, infections by nontyphoidal Salmonella bacteria are one of the most important causes of childhood mortality. Whereas Salmonella is a well-known cause of gastro-intestinal diseases across the world, these bacteria can also cause severe infections of the otherwise sterile bloodstream. This disease predominantly affects malnourished children, or people with malaria and/or HIV-coinfections and is seen a lot among young children under five in sub-Saharan Africa. For up to 20 % of these children the infection is fatal.

Nontyphoidal Salmonella bloodstream infections can be treated with antibiotics, but we see increasing rates of antimicrobial resistance which might jeopardise effective treatment in the near future. For example, recently, an outbreak of extensively drug resistant nontyphoidal Salmonella was seen in DR Congo, which could only be treated with one remaining available antibiotic.

Therefore, preventive measures are highly needed, and a vaccine protecting against nontyphoidal Salmonella bloodstream infections would be most promising. No vaccine is available yet, but different vaccines are currently under development. The bacteria’s O-antigen compound, which is part of the bacterial envelope, is a key target to design these vaccines against.

In the DR Congo, bloodstream surveillance is ongoing since 2007 confirming the importance and high burden of nontyphoidal Salmonella infections in the region. Intriguingly however, an increasing number of Salmonella isolates show variation in their O-antigen structure. A novel, so called, O5 negative variant is increasing in numbers in favor of O5 positive variants. O5 negativity implies lack of acetylation of one particular abequose sugar compound in the O-antigen. Changes in the chemical structure of the O-antigen might impact coverage by a vaccine directed towards the O-antigen. Therefore, in our project, we aimed to understand this variation better.

In this BactiVac Catalyst Project SAL-O5, we used an interdisciplinary approach to study the variation of the O-antigen in the nontyphoidal Salmonella population. Our team included experts in (i) bacterial surveillance in DR Congo, (ii) the chemical structure of the O-antigen, (iii) genomics and population structure of nontyphoidal Salmonella and (iiii) immunologists using state-of-the-art methodologies in these fields.

We observed that the O5 negative variants appeared multiple times in the nontyphoidal Salmonella population, suggesting parallel evolution in the same direction. The chemical analyses confirmed the structural difference between O5 positive and negative isolates, but also showed that there is even further chemical variability of the O-antigen in these DR Congo isolates. It was found that acetylation on different sugar compounds could be variable, and that the O-antigen as a whole could be lost as well. All these chemical variants could be explained by changes observed in the genetic make-up of the Salmonella bacteria.

In summary, we observed substantial levels of O-antigen variation among the invasive Salmonella from bloodstream DR Congo. In our work, we could explain the genetic origin of this chemical variation. As the O-antigen compound is the key target for vaccines, this variation might have implications for coverage of future vaccines.