High Throughput Sequencing in Antimicrobial Resistance-the State of the Art / 中国生物化学与分子生物学报

ABSTRACT

Antimicrobial resistance (AMR) is one of the greatest concerns for human health globally. Developing rapid and accurate methods to identify and characterize AMR is critical to improve patient outcome and limit the spread of antibiotic resistance. High throughput sequencing allows for high-throughput massively sequencing of thousands to billions of DNA fragments independently and simultaneously being used to identify AMR. The 3 main applications of high throughput sequencing in AMR include whole genome sequencing (WGS), targeted NGS (tNGS) and metagenomics NGS (mNGS). The sequencing platforms include the second sequencing platforms (Illumina, Ion Torrent, BGIseq) and the third sequencing platforms (Pacific Biosciences, Oxford Nonopore). The computational prediction of AMR depends largely on the maturation of well-curated gene databases of antimicrobial resistance. Generalized, specialized and hidden Markov model-based databases have been developed and updated continuously. We highlighted the high throughput sequencing technologies, computational methods, platforms and AMR databases used in antimicrobial resistance studies.