Plattner Michel, Catelani Maurizio, Gmür Sarah-Lisa, Hartmann Maximilian, Kiliç Fatmanur, Haldimann Klara, Crich David, Hobbie Sven N
Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland.
Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602, USA.
Antibiotics (Basel). 2024 Dec 8;13(12):1196. doi: 10.3390/antibiotics13121196.
Whole genome sequencing of clinical bacterial isolates holds promise in predicting their susceptibility to antibiotic therapy, based on a detailed understanding of the phenotypic manifestation of genotypic variation. The ' aminoglycoside acetyltransferase gene family is the most abundant aminoglycoside resistance determinant encountered in clinical practice. A variety of AAC(6') isozymes have been described, suggesting a phenotypic distinction between subtype I, conferring resistance to amikacin (AMK), and subtype II, conferring resistance to gentamicin (GEN) instead. However, the epidemiology and thus clinical relevance of the various and diverse isozymes and their phenotypic distinction demand systematic and contemporary re-assessment to reliably predict bacterial susceptibility to aminoglycoside antibiotics.
We analyzed the resistance gene annotations of 657,603 clinical bacterial isolates to assess the prevalence and diversity of ' genes. Seventeen unique ' amino acid sequences were cloned and expressed under defined promoter control in otherwise isogenic cells for phenotypic analysis with twenty distinct aminoglycoside antibiotics. A panel of clinical isolates was analyzed for the genotype-phenotype correlation of '.
An ' resistance gene annotation was found in 139,236 (21.2%) of the clinical isolates analyzed. AMK resistance-conferring ' genes dominated in (28.5%). In and , a gene conferring the ' phenotype but annotated as ' was the most prevalent. None of the ' genes were annotated as subtype III, but gene ' identified in Gram-positive isolates displayed a subtype III phenotype. Genes that were annotated as ' in conferred resistance to both AMK and GEN, which we propose constitutes a novel subtype IV when applying established nomenclature. A phenotypic assessment facilitated structural re-assessment of the substrate promiscuity of AAC(6') enzymes.
Our study provides the most comprehensive analysis of clinically relevant ' gene sequence variations to date, providing new insights into a differentiated substrate promiscuity across the genotypic spectrum of this gene family, thus translating into a critical contribution towards the development of amino acid sequence-based in silico antimicrobial susceptibility testing (AST).
基于对基因型变异表型表现的详细了解，临床分离细菌的全基因组测序在预测其对抗生素治疗的敏感性方面具有前景。“氨基糖苷乙酰转移酶基因家族是临床实践中最常见的氨基糖苷类耐药决定因素。已描述了多种AAC(6')同工酶，这表明I型亚型（赋予对阿米卡星（AMK）的耐药性）和II型亚型（赋予对庆大霉素（GEN）的耐药性）之间存在表型差异。然而，各种同工酶的流行病学及其临床相关性以及它们的表型差异需要进行系统和当代的重新评估，以可靠地预测细菌对氨基糖苷类抗生素的敏感性。
我们分析了657,603株临床分离细菌的耐药基因注释，以评估“基因的流行情况和多样性。克隆了17个独特的“氨基酸序列，并在确定的启动子控制下在其他方面为同基因的细胞中表达，以便用20种不同的氨基糖苷类抗生素进行表型分析。分析了一组临床分离株的“基因型-表型相关性。
在所分析的临床分离株中，139,236株（21.2%）发现了“耐药基因注释。赋予AMK耐药性的“基因在（28.5%）中占主导地位。在和中，赋予“表型但注释为“的基因最为普遍。没有“基因被注释为III型亚型，但在革兰氏阳性分离株中鉴定出的基因“显示出III型亚型表型。在中被注释为“的基因赋予对AMK和GEN的耐药性，当应用既定命名法时，我们提议将其构成一种新的IV型亚型。表型评估有助于对AAC(6')酶的底物混杂性进行结构重新评估。
我们的研究提供了迄今为止对临床相关“基因序列变异最全面的分析，为该基因家族基因型谱中不同的底物混杂性提供了新的见解，从而为基于氨基酸序列的计算机抗菌药敏试验（AST）的发展做出了关键贡献。
