Antimicrobial resistance (AMR) is a public health threat where efficient surveillance is needed to prevent outbreaks. Existing methods for detection of gastrointestinal colonization of multidrug-resistant organisms (MDRO) are limited to specific organisms or resistance mechanisms. Metagenomic next-generation sequencing (mNGS) is a more rapid and agnostic diagnostic approach for microbiome and resistome investigations. We determined if mNGS can detect MDRO from rectal swabs in concordance with standard microbiology results. We performed and compared mNGS performance on short-read Illumina MiSeq (N = 10) and long-read Nanopore MinION (N = 5) platforms directly from rectal swabs to detect vancomycin-resistant enterococci (VRE) and carbapenem-resistant Gram-negative organisms (CRO). We detected Enterococcus faecium (N = 8) and Enterococcus faecalis (N = 2) with associated van genes (9/10) in concordance with VRE culture-based results. We studied the microbiome and identified CRO, Pseudomonas aeruginosa (N = 1), Enterobacter cloacae (N = 1), and KPC-producing Klebsiella pneumoniae (N = 1). Nanopore real-time analysis detected the bla_KPC gene in 2.3 min and provided genetic context (bla_KPC harbored on pKPC_Kp46 IncF plasmid). Illumina sequencing provided accurate allelic variant determination (i.e., bla_KPC-2) and strain typing of the K. pneumoniae (ST-15). We demonstrated an agnostic approach for surveillance of MDRO, examining advantages of both short- and long-read mNGS methods for AMR detection.

抗菌素耐药性（AMR）是一种公共卫生威胁，需要进行有效的监测以防止疾病爆发。用于检测多药耐药生物（MDRO）胃肠道定植的现有方法仅限于特定生物或耐药机制。新一代基因组测序（mNGS）是一种用于微生物组和抵抗组研究的更快速，更不可知的诊断方法。我们确定了mNGS是否可以根据标准微生物学结果从直肠拭子中检测出MDRO。我们在短读Illumina MiSeq（N  = 10）和长读Nanopore MinION（N = 5）直接从直肠拭子平台检测耐万古霉素的肠球菌（VRE）和耐碳青霉烯的革兰氏阴性菌（CRO）。我们检测了粪肠球菌（N  = 8）和粪肠球菌（N  = 2）以及相关的van基因（9/10），这与基于VRE培养的结果一致。我们研究了微生物组，并确定了CRO，铜绿假单胞菌（N  = 1），阴沟肠杆菌（N  = 1）和产生KPC的肺炎克雷伯菌（N  = 1）。纳米孔实时分析检测到bla _KPC基因在2.3分钟内提供遗传背景（bla _KPC藏在pKPC_Kp46 IncF质粒上）。Illumina测序提供了准确的等位基因变异测定（即bla _KPC-2）和肺炎克雷伯菌的菌株分型（ST-15）。我们展示了一种MDRO监视的不可知论方法，检查了用于AMR检测的短读和长读mNGS方法的优势。