Integrative Analysis of Whole Genome Sequencing and Phenotypic Resistance Toward Prediction of Trimethoprim-Sulfamethoxazole Resistance in Staphylococcus aureus.

摘要: As whole genome sequencing is becoming more accessible and affordable for clinical microbiological diagnostics, the reliability of genotypic antimicrobial resistance (AMR) prediction from data an important issue to address. Computational AMR can be performed at multiple levels. first-level approach, such as simple search relies heavily on quality information fed into database. However, due mutations are often undetected, since this not included in database or poorly documented. Using co-trimoxazole (trimethoprim-sulfamethoxazole) Staphylococcus aureus, we compared single-level multi-level analysis investigate strengths weaknesses both approaches. The results revealed that a single mutation gene nucleotide level may produce false positive results, which could have been detected if protein sequence would performed. For predictions based chromosomal mutations, folP S. natural genetic variations should taken account differentiate between variants linked lineage (MLST) over-estimate potential resistant variants. Our study showed careful additional criterion lineage-independent useful identification leading phenotypic resistance. Furthermore, creation reliable point needed fully automatized prediction.