Cipriani Gabriel, Helmersen Karin, Mazzon Ricardo Ruiz, Wagner Glauber, Aamot Hege Vangstein, Ferreira Fabienne Antunes
Bacterial Molecular Genetics Laboratory (GeMBac), Department of Microbiology, Immunology, and Parasitology, Biological Sciences Center, Universidade Federal de Santa Catarina, Campus Universitário Reitor João David Ferreira Lima, Trindade, Postal Code 88040-960, Florianópolis, SC, Brazil.
Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway.
J Med Microbiol. 2025 Mar;74(3). doi: 10.1099/jmm.0.001990.
Antimicrobial resistance (AMR) poses a critical threat to global health, underscoring the need for rapid and accurate diagnostic tools. Methicillin-resistant (MRSA) and extended-spectrum beta-lactamase (ESBL)-producing (ESBL-Kp) are listed among the World Health Organization's priority pathogens. A rapid nanopore-based protocol can accurately and efficiently detect AMR genes, virulence factors (VFs) and mobile genetic elements (MGEs) in MRSA and ESBL-Kp, offering performance comparable to or superior to traditional sequencing methods. Evaluate whole-genome sequencing (WGS) protocols for detecting AMR genes, VFs and MGEs in MRSA and ESBL-Kp, to identify the most accurate and efficient tool for pathogen profiling. Five distinct WGS protocols, including a rapid nanopore-based protocol (ONT20h) and four slower sequencing methods, were evaluated for their effectiveness in detecting genetic markers. The protocols' performances were compared across AMR genes, VFs and MGEs. Additionally, phenotypic antimicrobial susceptibility testing was performed to assess concordance with the genomic findings. Compared to four slower sequencing protocols, the rapid nanopore-based protocol (ONT20h) demonstrated comparable or superior performance in AMR gene detection and equivalent VF identification. Although MGE detection varied among protocols, ONT20h showed a high level of agreement with phenotypic antimicrobial susceptibility testing. The findings highlight the potential of rapid WGS as a valuable tool for clinical microbiology, enabling timely implementation of infection control measures and informed therapeutic decisions. However, further studies are required to optimize the clinical application of this technology, considering costs, availability of bioinformatics tools and quality of reference databases.
抗菌药物耐药性（AMR）对全球健康构成了严重威胁，凸显了对快速准确诊断工具的需求。耐甲氧西林金黄色葡萄球菌（MRSA）和产超广谱β-内酰胺酶（ESBL）的肺炎克雷伯菌（ESBL-Kp）被列入世界卫生组织的重点病原体名单。一种基于纳米孔的快速检测方案能够准确高效地检测MRSA和ESBL-Kp中的AMR基因、毒力因子（VFs）和可移动遗传元件（MGEs），其性能与传统测序方法相当或更优。评估全基因组测序（WGS）方案在检测MRSA和ESBL-Kp中的AMR基因、VFs和MGEs方面的效果，以确定用于病原体分析的最准确高效的工具。评估了五种不同的WGS方案，包括一种基于纳米孔的快速方案（ONT20h）和四种较慢的测序方法，以检测它们在检测遗传标记方面的有效性。比较了这些方案在AMR基因、VFs和MGEs方面的性能。此外，还进行了表型抗菌药物敏感性测试，以评估与基因组结果的一致性。与四种较慢的测序方案相比，基于纳米孔的快速方案（ONT20h）在AMR基因检测方面表现出相当或更优的性能，在VFs鉴定方面表现相当。尽管不同方案在MGE检测方面存在差异，但ONT20h与表型抗菌药物敏感性测试显示出高度一致性。研究结果突出了快速WGS作为临床微生物学宝贵工具的潜力，能够及时实施感染控制措施并做出明智的治疗决策。然而，考虑到成本、生物信息学工具的可用性和参考数据库的质量，还需要进一步研究以优化该技术的临床应用。
