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Epidemiology is the study of the distribution and determinants of health-related states or events in populations, with the aim of controlling health problems. Epidemiologists investigate patterns of disease occurrence and transmission to inform public health interventions and policies. The development of molecular typing methods has revolutionized the field of epidemiology by providing powerful tools for tracking and characterizing infectious disease outbreaks.

Historically, epidemiology has played a crucial role in disease reduction through the identification of risk factors, implementation of preventative measures, and control of infectious diseases. Early investigations, such as John Snow's 19th-century cholera outbreak in London, demonstrated the importance of mapping disease occurrences to identify sources of infection and implement intervention measures.

Epidemiologists utilize tools such as morbidity and mortality rates or demographic information to monitor and control disease outbreaks. Organizations such as WHO or CDC provide centralized data collection, analysis, and dissemination of epidemiological information to guide global health policies.

WHO included COVID-19 in their Disease Outbreak News. The pandemic was caused by SARS-CoV-2, a member of the Coronaviridae family, which spreads through close contact or respiratory droplets. Many variants, such as Alpha, Beta, Gamma, or Delta, emerged at its peak.

Biological typing methods include serotyping, which involves the identification of specific surface antigens or antibodies on microbial surfaces. Biochemical testing assesses the metabolic capabilities of microorganisms, such as the detection of enzyme activities like catalase. Antibiotic susceptibility testing evaluates the sensitivity of microbial strains to antimicrobial agents, for example, using the disk diffusion method.

These methods are simpler, faster, and less expensive, making them suitable for routine laboratory testing. However, they may lack discriminatory power to differentiate between closely related strains.

Molecular typing methods include plasmid analysis, which examines the presence, size, and composition of plasmids found in bacteria, useful for studying dissemination. Ribotyping analyzes variations in ribosomal RNA genes of microorganisms. Pulse-field gel electrophoresis separates large DNA fragments onto agarose gel, providing high-resolution patterns that offer genomic fingerprints for microbial strains. Restriction fragment length polymorphism involves digesting genomic DNA with restriction enzymes and separating the resulting fragments on gel electrophoresis. Multilocus sequencing typing involves sequencing multiple housekeeping genes and microbial genomes, comparing the allelic profiles of different isolates. These methods offer high resolution and specificity, allowing for precise strain characterization and epidemiological analysis, however, they are high cost and techically complex.

NGS represents a major advancement in molecular typing, offering unprecedented resolution and discriminatory power for pathogen characterization. It allows for rapid and cost-effective sequencing of entire microbial genomes, providing detailed genetic information that can be used to identify outbreaks, strains, track transmission dynamics, and elucidate the mechanism of pathogen evolution. Studies such as the 2011 E. coli O104:H4 outbreak in Germany have utilized NGS, leading to the rapid identification of the contaminated sprout as the source and the implementation of control measures. NGS overcomes the limitations of molecular typing by providing comprehensive genomic data with high accuracy and scalability. Compared to traditional methods, NGS offers great discriminatory power and resolution, allowing for the identification of closely related strains and subtle genetic variations that would be missed with other techniques.

For healthcare-associated infections acquired in a healthcare setting, such as the MRSA outbreak in hospitals, PFGE or WGS can be employed to analyze MRSA isolates collected from infected patients. By comparing genetic fingerprints from isolates, epidemiologists can determine related strains and identify the source of transmission. For foodborne infections, such as a salmonella outbreak from consuming contaminated food, WGS can be used to analyze salmonella isolates from clinical samples or food products. By comparing the genetic profiles of isolates, investigators can identify the genetic profile of isolates and the unique signature of outbreak strains, tracking it back to contaminated produce.