Current and Novel Methods in Clinical Microbiology: Advantages and Pitfalls when Facing the Menace of Antimicrobial Resistance

Microbiological clinical methods were the object of this review. According to WHO antimicrobial resistance is a real and global threat. Researchers aim to develop rapid methods for identification and antimicrobial susceptibility (AST). Actually, most automated solutions available in clinical laboratories are based upon the study of the microbial ability to grow so, take a long time to give results despite its advantages. Molecular tests only detect target genes but are especially useful regarding identification of difficult or slow growing microorganisms. MALDI-TOF started a real revolution in microbial identification since it is growth independent and highly sensitive and specific. Regarding susceptibility evaluation, due to its inherent complexity, molecular or proteomic tests provides answers to known and molecular characterized mechanisms, requiring its prior knowledge. Flow cytometry is an excellent tool that, coupled with specific fluorescent antibodies can be used to identify microorganisms. Moreover, it can help to unveil susceptibility profile. AST phenotype is provided following incubation of the cells for short period (60 minutes) with antimicrobial drugs and fluorescent probes, with excellent correlation with classic AST methods. Furthermore, it can elucidate about the most relevant mechanism of resistance in a functional assay. Novel methods are under study namely sophisticated methods for growth detection like, weighing bacteria by vibrating cantilevers, isothermal microcalorimetry method, simple spectroscopic biomarkers and plasmonic imaging and tracking are discussed. We are close to a change of the paradigm in the clinical laboratory work flow microbiology considering especially MALDI-TOF for identification and flow cytometry for AST/assessment of mechanisms of resistance.