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KMID : 0364820180540030188
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Korean Journal of Microbiology
2018 Volume.54 No. 3 p.188 ~ p.199
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Genomic epidemiology for microbial evolutionary studies and the use of Oxford Nanopore sequencing technology
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Choi Sang-Chul
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Abstract
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Genomic epidemiology exploits various basic microbial researchareas. High-throughput sequencing technologies dramaticallyhave been expanding the number of microbial genome sequencesavailable. Abundant genomic data provide an opportunity toperform strain typing more effectively, helping identify microbialspecies and strains at a higher resolution than ever before.
Genomic epidemiology needs to find antimicrobial resistancegenes in addition to standard genome annotations. Strain typingand antimicrobial resistance gene finding are static aspects ofgenomic epidemiology. Finding which hosts infected whichother hosts requires the inference of transient transmissionroutes among infected hosts. The strain typing, antimicrobialresistance gene finding, and transmission tree inference wouldallow for better surveillance of microbial infectious diseases,which is one of the ultimate goals of genomic epidemiology.
Among several high-throughput sequencing technologies, genomicepidemiology will benefit from the more portability and shortersequencing time of the Oxford Nanopore Technologies’s MinION,the third-generation sequencing technology. Here, this studyreviewed computational methods for quantifying antimicrobialresistance genes and inferring disease transmission trees. Inaddition, the MinION’s applications to genomic epidemiologywere discussed.
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KEYWORD
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antimicrobial resistance, infectious disease outbreaks, public health, surveillance, transmission tree inference
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