Application of Bacterial Genotyping Techniques in Molecular Epidemiology of Foodborne Diseases

Application of Bacterial Genotyping Techniques in Molecular Epidemiology of Foodborne Diseases

Genotyping of bacterial isolates has been performed as a routine measure in most public health laboratories for disease surveillance and disease outbreak investigation. Among bacterial genotyping methods, pulsed-field gel electrophoresis (PFGE) and multilocus variable number tandem repeat analysis (MLVA) are the most frequently used methods for their high discriminatory power in most bacterial pathogens. When using genotyping data to elucidate a disease outbreak investigation, three hypothetical modes should be considered: H1, a disease outbreak is caused by one genotype of a pathogen (by one strain); H2, a disease outbreak is caused by multiple genotypes of a pathogen (multiple strains) or by multiple pathogens; H3, various disease outbreaks are caused by one genotype of a pathogen. With the advance of next generation sequencing (NGS) techniques, whole genome sequencing (WGS) of bacterial isolates has become practical in public health laboratories. WGS can provide genetic data for retrieving useful information including serotypes, virulence gene profiles, antimicrobial resistance genes, and genetic fingerprints to represent short-term and long-term evolutionary relationships among bacterial strains. WGS will replace PFGE and MLVA within a few years to be the determining subtyping tool for bacteria in public health laboratories. Taiwan Centers for Disease Control has to establish the laboratory capability and capacity in WGS and data analysis as soon as possible.