Fahy Sinead, O'Connor James A, Sleator Roy D, Lucey Brigid
Department of Microbiology, Mercy University Hospital, T12 WE28 Cork, Ireland.
Department of Biological Sciences, Munster Technological University, T12 P928 Cork, Ireland.
Antibiotics (Basel). 2024 Jul 17;13(7):661. doi: 10.3390/antibiotics13070661.
Molecular diagnostics has the potential to revolutionise the field of clinical microbiology. Microbial identification and nomenclature have, for too long, been restricted to phenotypic characterisation. However, this species-level view fails to wholly account for genetic heterogeneity, a result of lateral gene transfer, mediated primarily by mobile genetic elements. This genetic promiscuity has helped to drive virulence development, stress adaptation, and antimicrobial resistance in several important bacterial pathogens, complicating their detection and frustrating our ability to control them. We argue that, as clinical microbiologists at the front line, we must embrace the molecular technologies that allow us to focus specifically on the genetic elements that cause disease rather than the bacterial species that express them. This review focuses on the evolution of microbial taxonomy since the introduction of molecular sequencing, the role of mobile genetic elements in antimicrobial resistance, the current and emerging assays in clinical laboratories, and the comparison of phenotypic versus genotypic analyses. In essence, it is time now to refocus from species to genes as part of a new diagnostic paradigm.
分子诊断学有潜力彻底改变临床微生物学领域。长期以来，微生物的鉴定和命名一直局限于表型特征描述。然而，这种物种层面的观点未能完全解释由主要由移动遗传元件介导的横向基因转移所导致的遗传异质性。这种基因的混杂性在几种重要的细菌病原体中推动了毒力发展、应激适应和抗菌药物耐药性，使它们的检测变得复杂，并阻碍了我们控制它们的能力。我们认为，作为一线的临床微生物学家，我们必须采用分子技术，使我们能够特别关注导致疾病的遗传元件，而不是表达这些元件的细菌物种。本综述重点关注自分子测序引入以来微生物分类学的演变、移动遗传元件在抗菌药物耐药性中的作用、临床实验室目前和新兴的检测方法，以及表型分析与基因型分析的比较。本质上，现在是时候将重点从物种转向基因，作为新诊断范式的一部分了。
