Viehweger Adrian, Marquet Mike, Hölzer Martin, Dietze Nadine, Pletz Mathias W, Brandt Christian
Institute of Medical Microbiology and Virology, University Hospital Leipzig, Leipzig, Germany.
Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany.
GigaByte. 2023 Jan 25;2023:gigabyte75. doi: 10.46471/gigabyte.75. eCollection 2023.
Rapid screening of hospital admissions to detect asymptomatic carriers of resistant bacteria can prevent pathogen outbreaks. However, the resulting isolates rarely have their genome sequenced due to cost constraints and long turn-around times to get and process the data, limiting their usefulness to the practitioner. Here we used real-time, on-device target enrichment ("adaptive") sequencing as a highly multiplexed assay covering 1,147 antimicrobial resistance genes. We compared its utility against standard and metagenomic sequencing, focusing on an isolate of harbouring three carbapenemases (, , ). Based on this experimental data, we then modelled the influence of several variables on the enrichment results and predicted the large effect of nucleotide identity (higher is better) and read length (shorter is better). Lastly, we showed how all relevant resistance genes are detected using adaptive sequencing on a miniature ("Flongle") flow cell, motivating its use in a clinical setting to monitor similar cases and their surroundings.
快速筛查住院患者以检测耐药菌的无症状携带者可预防病原体爆发。然而，由于成本限制以及获取和处理数据的周转时间长，所得到的分离株很少进行全基因组测序，这限制了它们对从业者的有用性。在此，我们使用实时、设备上的目标富集（“自适应”）测序作为一种高度多重的检测方法，涵盖1147个抗菌药物耐药基因。我们将其效用与标准测序和宏基因组测序进行了比较，重点关注一株携带三种碳青霉烯酶（、、）的分离株。基于这些实验数据，我们随后模拟了几个变量对富集结果的影响，并预测了核苷酸同一性（越高越好）和读长（越短越好）的巨大影响。最后，我们展示了如何在微型（“Flongle”）流动槽上使用自适应测序检测所有相关的耐药基因，这促使其在临床环境中用于监测类似病例及其周围环境。
