Genomic Analysis of Antimicrobial Resistance Genotype-to-Phenotype Agreement in .

Antimicrobial resistance (AMR) in is increasing and can result in treatment failure and inappropriate antibiotic usage. This study used whole genome sequencing (WGS) to comprehensively analyze the resistome and phylogeny in order to characterize Israeli . Israeli isolates ( = 48) underwent antimicrobial susceptibility testing (AST) against five antimicrobials and WGS analysis. Literature review identified 111 mutations reported to correlate with phenotypic resistance to these antimicrobials. Analysis was conducted via our bioinformatics pipeline targeting point mutations in the relevant genes (, 23S , , and ) in order to assess genotype-to-phenotype correlation. Resistance rates of study isolates were as follows: clarithromycin 54%, metronidazole 31%, amoxicillin 10%, rifampicin 4%, and levofloxacin 2%. Genotype-to-phenotype correlation was inconsistent; for every analyzed gene at least one phenotypically susceptible isolate was found to have a mutation previously associated with resistance. This was also observed regarding mutations commonly used in commercial kits to diagnose AMR in cases. Furthermore, 11 novel point mutations associated with a resistant phenotype were detected. Analysis of a unique set of isolates demonstrates that inferring resistance phenotypes from WGS in remains challenging and should be optimized further.