NCT04172025

Development of a Swiss Surveillance Database for Molecular Epidemiology of Hypervirulent and Multi-drug Resistant Pathogens

• Status: Recruiting
• Phase: —
• Study type: Observational
• Enrollment: 10,000 (estimated)
• Sponsor: University Hospital, Basel, Switzerland · Academic / Other
• Sex: All
• Age: —
• Healthy volunteers: Not accepted

Summary

Hypervirulent and multidrug-resistant infections are associated with significant health care costs, substantial morbidity and mortality. Therefore, the rapid recognition of outbreaks and transmissions with hypervirulent and multi-drug resistant pathogen is a key priority for infection control and public health.The main goal is to implement a shared database, connecting human and veterinary microbiology laboratories, which would allow near real-time molecular epidemiology with high spatiotemporal resolution of bacterial pathogens such as transmission and outbreak surveillance between different compartments including humans, animals and the environment in Switzerland. Investigator aims to analyze already collected encoded retrospective datasets of various pathogens by combining epidemiological data and whole genome sequences from pathogens.

Detailed description

Hypervirulent and multidrug-resistant infections are associated with significant health care costs, substantial morbidity and mortality. Therefore, the rapid recognition of outbreaks and transmissions with hypervirulent and multi-drug resistant pathogen is a key priority for infection control and public health. For hospital epidemiologist, infectious disease and public health experts, and microbiologists the identification of an outbreak source is a first important step to establish effective counter-measurements. In Switzerland, the burden of pathogen transmission between humans, animals and the environment is substantial. The main goal is to implement a shared database, connecting human and veterinary microbiology laboratories, which would allow near real-time molecular epidemiology with high spatiotemporal resolution of bacterial pathogens such as transmission and outbreak surveillance between different compartments including humans, animals and the environment in Switzerland. Investigator aims to analyze already collected encoded retrospective datasets of various pathogens by combining epidemiological data and whole genome sequences from pathogens.

Conditions

• Multiresistant Bacterial Pathogens
• Virulent Bacterial Pathogens

Interventions

Type	Name	Description
DIAGNOSTIC_TEST	Analysis of Bacterial Genome	genome assembly; prediction of sequence type (MLST); core genome MLST tree to rapidly compare strains within a project; core genome single nucleotide polymorphism (SNP) tree to compare all Swiss Pathogen Surveillance Platform (SPSP) strains belonging to a same species; whole genome SNP tree to compare all SPSP strains within the same species and ST;; prediction of resistance and virulence factors within pathogen submitted genomes; time trees and calculation of transmission rates, including basic reproduction number; analysis of classical epidemiological data with advanced statistical methods including machine learning.

Timeline

• Start date: 2019-09-30
• Primary completion: 2029-12-31
• Completion: 2029-12-31
• First posted: 2019-11-21
• Last updated: 2025-05-14

Locations

5 sites across 1 country: Switzerland