• Korean Journal of Microbiology
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• v.54 no.3
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• pp.188-199
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• 2018

Genomic epidemiology exploits various basic microbial research areas. High-throughput sequencing technologies dramatically have been expanding the number of microbial genome sequences available. Abundant genomic data provide an opportunity to perform strain typing more effectively, helping identify microbial species and strains at a higher resolution than ever before. Genomic epidemiology needs to find antimicrobial resistance genes in addition to standard genome annotations. Strain typing and antimicrobial resistance gene finding are static aspects of genomic epidemiology. Finding which hosts infected which other hosts requires the inference of transient transmission routes among infected hosts. The strain typing, antimicrobial resistance gene finding, and transmission tree inference would allow for better surveillance of microbial infectious diseases, which is one of the ultimate goals of genomic epidemiology. Among several high-throughput sequencing technologies, genomic epidemiology will benefit from the more portability and shorter sequencing time of the Oxford Nanopore Technologies's MinION, the third-generation sequencing technology. Here, this study reviewed computational methods for quantifying antimicrobial resistance genes and inferring disease transmission trees. In addition, the MinION's applications to genomic epidemiology were discussed.