Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland.
Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland.
Nat Commun. 2024 Aug 28;15(1):7450. doi: 10.1038/s41467-024-51929-y.
The increasing prevalence of gut colonization with CTX-M extended-spectrum β-lactamase- and/or DHA plasmid-mediated AmpC-producing Escherichia coli is a concern. Here, we evaluate Nanopore-shotgun metagenomic sequencing (Nanopore-SMS) latest V14 chemistry to detect bla and bla genes from healthy stools. We test 25 paired samples characterized with culture-based methods (native and pre-enriched). Antimicrobial resistant genes (ARGs) are detected from reads and meta-assembled genomes (MAGs) to determine their associated genetic environments (AGEs). Sensitivity and specificity of native Nanopore-SMS are 61.1% and 100%, compared to 81.5% and 75% for pre-enriched Nanopore-SMS, respectively. Native Nanopore-SMS identifies only one sample with an AGE, whereas pre-enriched Nanopore-SMS recognizes 9/18 plasmids and 5/9 E. coli chromosomes. Pre-enriched Nanopore-SMS identifies more ARGs than native Nanopore-SMS (p < 0.001). Notably, bla and bla AGEs (plasmid and chromosomes) are identified within 1 hour of sequencing. Furthermore, microbiota analyses show that pre-enriched Nanopore-SMS results in more E. coli classified reads (47% vs. 3.1%), higher differential abundance (5.69 log fold) and lower Shannon diversity index (p < 0.0001). Nanopore-SMS has the potential to be used for intestinal colonization screening. However, sample pre-enrichment is necessary to increase sensitivity. Further computational improvements are needed to reduce the turnaround time for clinical applications.
CTX-M 型扩展谱β-内酰胺酶和/或 DHA 质粒介导的 AmpC 型大肠埃希菌在肠道中的定植率不断上升，令人担忧。在此，我们评估了最新的 V14 化学纳米孔 shotgun 宏基因组测序（Nanopore-SMS）技术，以检测健康粪便中的 bla 和 bla 基因。我们测试了 25 对用基于培养的方法（天然和预富集）进行特征描述的配对样本。从读数和宏基因组（MAG）中检测到抗生素耐药基因（ARGs），以确定其相关的遗传环境（AGEs）。与预富集 Nanopore-SMS 的 81.5%和 75%相比，天然 Nanopore-SMS 的敏感性和特异性分别为 61.1%和 100%。与预富集 Nanopore-SMS 相比，天然 Nanopore-SMS 仅识别出一个具有 AGE 的样本，而预富集 Nanopore-SMS 则识别出 9/18 个质粒和 5/9 个大肠埃希菌染色体。预富集 Nanopore-SMS 鉴定出的 ARGs 多于天然 Nanopore-SMS（p<0.001）。值得注意的是，bla 和 bla AGEs（质粒和染色体）在测序 1 小时内即可识别。此外，微生物组分析表明，预富集 Nanopore-SMS 导致更多的大肠埃希菌分类读数（47%比 3.1%）、更高的差异丰度（5.69 对数倍）和更低的香农多样性指数（p<0.0001）。Nanopore-SMS 具有用于肠道定植筛选的潜力。然而，需要进行样品预富集以提高敏感性。需要进一步的计算改进来减少临床应用的周转时间。
