BioProject

Background: Nontyphoidal Salmonellae (NTS) mainly S. Typhimurium and S. Enteritidis are among the commonest causes of bacteraemia in sub-Saharan Africa, particularly in children under 2. In Malawian children case fatality rates of NTS bacteraemia ranges from 20-25%, even when appropriate antibiotics are administered. Asymptomatic gastrointestinal exposure to Salmonella is also common in young children (up to 47% of children <18 months are exposed to Salmonella at least once in 1 year period). Most children have attained protective immunity by the age of 3 years, however the relationship between Salmonella colonization within the gastro intestinal tract and protection against NTS bacteraemia in Malawian children is not known. NTS strains in SSA have developed resistance to commonly used antibiotics, and MLW is already documenting emergence of resistance to the next in line agents, Ciprofloxacin and Ceftriaxone among gram negative organisms. The need to develop a NTS vaccine for human use is a crucial and urgent matter. Development of an effective Salmonella vaccine will require knowledge on what provides naturally acquired protective immunity. We know that serum immunity to NTS in children develops by 24 months of age, as demonstrated by the cohort of Malawian children aged 6 to 18 months that will form the basis of this PhD. However the role of gut microbiota mediated resistance to Salmonella has not been explored in Malawian children. Whether Salmonella exposure within the gut lumen is associated with the development of protective immunity, and with changes in gut microbiota is an important question that has not been investigated in Malawian children. The gut microbiota mediated resistance is thought to be important in preventing enteric pathogens dissemination into the blood stream and also shedding. Changes in gut microbiota may be influence by age, antibiotic intake and nutritional status. Methods: To study whether changes in gut microbiota facilitates Salmonella colonization, we propose to conduct a laboratory based study, using a comprehensive sample set already collected in a longitudinal prospective study. A total of 600 stool DNA samples and clinical records, and 300 serum samples collected before (from August 2013 to December 2014) in a cohort of Malawian children aged 6 to 18 months will be used. RT- PCR (already validated during the candidates Masters project) will be used to quantify the frequency of Salmonella colonization in longitudinal stool DNA samples from healthy children, and serum bactericidal assays (SBA) used to quantify the development of Salmonella specific antibody immunity. We will employ 16S ribosomal RNA (rRNA) sequencing technology to quantify changes in gut microbiota in stool DNA samples, and multiplex pathogen TAC cards to assess the frequency of co-infections with other GI pathogens which might affect microbiota and immunity. Expected outcome: This project will help to understand the relationship between asymptomatic colonisation with Salmonella, the development of protective serum immunity, and alterations in gut microbiota. This will help immediately by providing diagnostic markers of exposure to Salmonella which are longitudinally evaluated in healthy children, and in the development and evaluation of iNTS vaccines against known and exploratory antigens, and in the further future, in potential gut mucosal health and nutritional and feeding interventions. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/