使用长读测序技术对抗菌素耐药病原体进行快速全基因组鉴定,以确定潜在的医疗传播。

IF 3 4区 医学 Q2 INFECTIOUS DISEASES
Chin-Ting Wu, William C Shropshire, Micah M Bhatti, Sherry Cantu, Israel K Glover, Selvalakshmi Selvaraj Anand, Xiaojun Liu, Awdhesh Kalia, Todd J Treangen, Roy F Chemaly, Amy Spallone, Samuel Shelburne
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引用次数: 0

摘要

目的:全基因组测序(WGS)可以帮助鉴定引起卫生保健相关感染(HAIs)的病原体传播。然而,目前基于illumina的短读WGS的黄金标准是劳动和时间密集型的。鉴于牛津纳米孔技术(ONT)测序技术最近的进步,我们试图建立一种低资源方法,在允许感染预防和控制(IPC)干预的时间框架内提供准确的wgs -病原体比较。方法:使用ONT MinION测序仪,采用R10.4.1流式细胞和Dorado碱基调用器,前瞻性地对潜在医疗传播风险增加的病原体进行WGS。通过Ridom SeqSphere+对核心基因组多位点序列分型和MINTyper对基于参考的核心基因组单核苷酸多态性进行潜在传播评估,使用先前公布的截止值。我们的ONT管道的准确性是相对于Illumina确定的。结果:在六个月的时间里,一名操作员对来自216名患者的242株细菌进行了测序。与Illumina金标准相比,我们的ONT管线对组装基因组的平均识别分数达到了Q60,即使覆盖率低至40倍。从开始提取DNA到完成分析的平均时间为2天(IQR 2-3.25天)。我们确定了5个潜在的传播群,包括21个分离株(占测序菌株的8.7%)。将ONT与流行病学数据相结合,发现70%(15/21)的假定传播聚集性分离物来自具有潜在医疗传播链接的患者。结论:通过独立的ONT管道,我们快速准确地检测到潜在传播的HAI病原体,与流行病学数据密切一致。我们的低资源方法有可能帮助IPC工作。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Rapid whole genome characterization of antimicrobial-resistant pathogens using long-read sequencing to identify potential healthcare transmission.

Objective: Whole genome sequencing (WGS) can help identify transmission of pathogens causing healthcare-associated infections (HAIs). However, the current gold standard of short-read, Illumina-based WGS is labor and time intensive. Given recent improvements in long-read Oxford Nanopore Technologies (ONT) sequencing, we sought to establish a low resource approach providing accurate WGS-pathogen comparison within a time frame allowing for infection prevention and control (IPC) interventions.

Methods: WGS was prospectively performed on pathogens at increased risk of potential healthcare transmission using the ONT MinION sequencer with R10.4.1 flow cells and Dorado basecaller. Potential transmission was assessed via Ridom SeqSphere+ for core genome multilocus sequence typing and MINTyper for reference-based core genome single nucleotide polymorphisms using previously published cutoff values. The accuracy of our ONT pipeline was determined relative to Illumina.

Results: Over a six-month period, 242 bacterial isolates from 216 patients were sequenced by a single operator. Compared to the Illumina gold standard, our ONT pipeline achieved a mean identity score of Q60 for assembled genomes, even with a coverage rate as low as 40×. The mean time from initiating DNA extraction to complete analysis was 2 days (IQR 2-3.25 days). We identified five potential transmission clusters comprising 21 isolates (8.7% of sequenced strains). Integrating ONT with epidemiological data, >70% (15/21) of putative transmission cluster isolates originated from patients with potential healthcare transmission links.

Conclusions: Via a stand-alone ONT pipeline, we detected potentially transmitted HAI pathogens rapidly and accurately, aligning closely with epidemiological data. Our low-resource method has the potential to assist in IPC efforts.

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来源期刊
CiteScore
6.40
自引率
6.70%
发文量
289
审稿时长
3-8 weeks
期刊介绍: Infection Control and Hospital Epidemiology provides original, peer-reviewed scientific articles for anyone involved with an infection control or epidemiology program in a hospital or healthcare facility. Written by infection control practitioners and epidemiologists and guided by an editorial board composed of the nation''s leaders in the field, ICHE provides a critical forum for this vital information.
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