Research Sandra Van Puyvelde

Abstract

People are frequently exposed to bacteria in the urban environment. Kitchen sinks within the urban environment harbour a wide variety of bacteria, potentially leading to increased risks of food contamination. Studies on the microbial community in domestic and institutional kitchen sinks, including characterization of antimicrobial resistance and biofilms, is often limited by low sample numbers or sequencing depth upon metagenomics analysis. Given the increasing population density in Flanders and the need to provide safe food, extensive characterisation of the sink microbiome is necessary. In this FWO SB-Beurs titled POEMBAKterie, I will use a Citizen Science approach to investigate the kitchen sink (or in Antwerp dialect "Poembak") microbiome on a large scale in Antwerp. Participants from households and various institutions (e.g. schools, retirement homes) will respond to a survey, swab their own kitchen sink and return the samples to our lab. I will use a combination of state-of-the-art metagenomic approaches and wet-lab microbiological analyses to investigate the taxonomy, presence of pathogens, antimicrobial resistance and biofilm formation in the presence of detergents and on different materials. Results will shed light on the bacteria living in sinks within the urban environment, and the implications for food safety, cleaning practices and sink design.

Researcher(s)

• Promoter: Van Puyvelde Sandra
• Co-promoter: de Bruijn Gert-Jan
• Fellow: Arconada Nuin Enya

Research team(s)

• Laboratory of Medical Microbiology (LMM)

Project type(s)

• Research Project

Abstract

Horizontal gene transfer (HGT) plays a role in bacterial evolution, facilitating the acquisition of beneficial traits like antibiotic resistance and virulence factors, enabling adaptation to changing environments. However, the extent and impact of HGT in the evolution of Salmonella, particularly in the context of increasing invasiveness, remains poorly understood. This project aims to elucidate the prevalence and role of HGT in the evolution of invasive Salmonella (S.) enterica serovar Typhimurium, a major cause of invasive non-typhoidal Salmonella (iNTS) disease in sub-Saharan Africa. By integrating bioinformatics with classical bacterial wet-lab technologies, the project seeks to characterize HGT events and assess recombination rates in invasive clinical isolates, using whole-genome sequencing data, phylogenetic analyses, and bacterial recombination techniques. Furthermore, this project aims to develop a novel technology for the reverse evolutionary reconstruction of extinct ancestor strains using the principles of recombination, which will contribute to our understanding of bacterial evolution and pathogenesis. Overall, this research project will provide insights into the mechanisms involved in the evolution towards invasiveness of S. Typhimurium, with potential implications for public health, and the application of recombination to reconstruct ancestor strains will be groundbreaking from a synthetic biology perspective.

Researcher(s)

• Promoter: Van Puyvelde Sandra
• Fellow: Hoeben Ine

Research team(s)

• Laboratory of Medical Microbiology (LMM)

Project type(s)

• Research Project

Abstract

Bacterial genomics is a flourishing research field, in which relatedness is assessed by genetic variation between bacterial strains. Single nucleotide polymorphisms (SNPs) are typically used as the sole source of genetic variation. However, there is likely much variation between bacteria that is currently overlooked. In this project, the role of DNA satellites during bacterial evolution will be studied. Hereto, DNA satellites will be systematically identified in Salmonella Typhimurium and across the bacterial kingdom. Thereafter, the dynamics of DNA satellites and SNPs during evolution will be assessed. Finally, the effect on the cellular transcriptome response will be measured and compared between DNA satellites and SNPs. Together, this study will provide a comprehensive view on the role of DNA satellites during bacterial evolution and shed a novel perspective on bacterial genetics.

Researcher(s)

• Promoter: Van Puyvelde Sandra
• Fellow: Arconada Nuin Enya

Research team(s)

• Laboratory of Medical Microbiology (LMM)

Project type(s)

• Research Project

Abstract

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.

Researcher(s)

• Promoter: Van Puyvelde Sandra

Research team(s)

• Laboratory of Medical Microbiology (LMM)

Project type(s)

• Research Project