Microbial genomics and antimicrobial susceptibility testing

ABSTRACTIntroduction: Antimicrobial susceptibility testing is key in modern clinical microbiology. With pandemic emergence of (multi-)antibiotic resistance, methods to detect and quantify resistance of clinically important bacterial species are imperative. Historically, antimicrobial susceptibility testing (AST) was mostly performed using methods relying on bacterial growth. Such methods may be time-consuming and more rapid alternatives have been actively sought for.Areas covered: Among the new AST methods there are many that focus on detection of causal resistance genes and/or gene mutations. The approaches most used are based on nucleic acid amplification and, more recently, high-throughput (next generation) sequencing of amplified targets and complete microbial genomes. The authors provide a review of PCR-mediated and genomic AST methods used for human and veterinary pathogens and show where these approaches work well or may become difficult to interpret.Expert commentary: Microbial genome sequencing w...