Pathogen genomics and phage-based solutions for accurately identifying and controlling Salmonella pathogens

Area of Science:

• Food microbiology and zoonotic disease surveillance.
• Genomic epidemiology of foodborne pathogens.
• Antimicrobial resistance and virulence factor analysis.

Background:

• Salmonella is a significant foodborne pathogen, frequently associated with poultry, causing human gastrointestinal infections.
• Increasing global prevalence of multidrug-resistant (MDR) Salmonella necessitates enhanced control strategies.
• Understanding genomic diversity is crucial for tracking pathogen spread and disease contribution.

Purpose of the Study:

• To characterize antimicrobial resistance genes and virulence factors in UK and Thai poultry Salmonella isolates.
• To explore the genomic links between virulence and resistance using long-read sequencing.
• To determine the sensitivity of isolates to Salmonella bacteriophages for potential biocontrol applications.

Main Methods:

• Genomic characterization of antimicrobial resistance and virulence genes in 143 poultry Salmonella isolates.
• Long-read sequencing of three MDR isolates to investigate virulence-resistance correlations.
• Bacteriophage sensitivity assays against 22 characterized Salmonella phages.

Main Results:

• Salmonella Typhimurium and its monophasic variants were the most common serovars.
• 14-15% of isolates were multidrug-resistant (MDR), with high prevalence of virulence genes in MDR strains.
• Phage STW-77 demonstrated broad lytic activity against key clinical serovars, including Salmonella Enteritidis and Salmonella Typhimurium.

Conclusions:

• Genomic analysis identified global epidemic MDR clones widespread in poultry.
• Phage sensitivity assays revealed STW-77 as a potential biocontrol agent against important Salmonella serovars.
• Combining genomics and phage sensitivity assays offers a promising approach for Salmonella control in poultry and the food chain.