Pathogen emergence & spread

Pathogen emergence and spread – prevention and mitigation of risks

CREID investigators use the evolutionary analysis of whole genome sequencing of selected pathogens as a common framework for the “genomic risk assessment” of pathogen emergence and spread. Identifying high-risk lineages and “clones” will more accurately inform public health responses to new outbreaks. A novel genomic risk assessment involves evolutionary analysis of microbial whole genome sequences to identify markers of potential emergence and spread. 

Exemplar pathogens represent different routes of transmission: 
• Vector-borne (arboviruses such as Dengue virus, Chikungunya viruses, and Zika virus)
• Enteric/foodborne (Salmonella)
• Respiratory (influenza viruses, enteroviruses, Streptococcus pneumoniae)
• Health care-associated (methicillin-resistant Staphylococcus aureus; multi-resistant Klebsiella pneumonia)

Pathogen evolution is driven by different selection and distribution pressures:
• Travel/trade (arboviruses; Salmonella)
• Population immunity (influenza viruses, S. pneumoniae, enteroviruses); 
• Antimicrobial use/abuse (healthcare associated pathogens; S. pneumoniae, Salmonella). 

All pathogens under investigation are affected by environmental and socioeconomic factors, such as overcrowding (including in healthcare settings), environmental hygiene and infection control measures and climate.