Development of a novel crAss-like phage detection method with a broad spectrum for microbial source tracking

IF 11.4 1区环境科学与生态学 Q1 ENGINEERING, ENVIRONMENTAL

Water Research Pub Date : 2024-08-24 DOI:10.1016/j.watres.2024.122330

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Abstract

CrAssphage has been recognized as the most abundant and human-specific bacteriophage in the human gut. Consequently, crAssphage has been used as a microbial source tracking (MST) marker to monitor human fecal contamination. Many crAss-like phages (CLPs) have been recently discovered, expanding the classification into the new order Crassvirales. This study aims to assess CLP prevalence in South Korea and develop a detection system for MST applications. Thirteen CLPs were identified in six human fecal samples and categorized into seven genera via metagenomic analysis. The major head protein (MHP) displayed increased sequence similarity within each genus. Eight PCR primer candidates, designed from MHP sequences, were evaluated in animal and human feces. CLPs were absent in animal feces except for those from raccoons, which hosted genera VI, VIIa, and VIIb. CLPs were detected in 91.52% (54/59) of humans, with genus VI (38 out of 59) showing the highest prevalence, nearly double that of p-crAssphage in genus I (22 out of 59). This study highlights genus VI as a potent MST marker, broadening the detection range for CLPs. Human-specific and selectively targeted MST markers can significantly impact hygiene regulations, lowering public health costs through their application in screening liver, sewage, wastewater, and various environmental samples.

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开发用于微生物源追踪的广谱新型 crAss-like 噬菌体检测方法

CrAssphage 被认为是人类肠道中最丰富、最具人类特异性的噬菌体。因此，crAssphage 被用作微生物源追踪（MST）标记来监测人类粪便污染。最近发现了许多类似于 crAss 的噬菌体（CLPs），并将其分类扩展为新的 Crassvirales 目。本研究旨在评估 CLP 在韩国的流行情况，并开发一种用于 MST 应用的检测系统。通过元基因组分析，在六份人类粪便样本中鉴定出 13 种 CLP，并将其分为七个属。主要头部蛋白（MHP）在每个属中的序列相似性都有所增加。根据 MHP 序列设计的八种 PCR 引物候选物在动物和人类粪便中进行了评估。动物粪便中不存在 CLPs，但浣熊粪便除外，因为浣熊粪便中含有 VI、VIIa 和 VIIb 属。在 91.52%（54/59）的人类粪便中检测到了 CLPs，其中 VI 属（59 个中有 38 个）的感染率最高，几乎是 I 属中 p-crAssphage 感染率（59 个中有 22 个）的两倍。这项研究强调了 VI 属是一种有效的 MST 标记，扩大了 CLP 的检测范围。人类特异性和选择性靶向 MST 标记可显著影响卫生法规，通过应用于肝脏、污水、废水和各种环境样本的筛查，降低公共卫生成本。

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来源期刊

Water Research 环境科学-工程：环境

CiteScore

20.80

自引率

9.40%

发文量

1307

审稿时长

38 days

期刊介绍： Water Research, along with its open access companion journal Water Research X, serves as a platform for publishing original research papers covering various aspects of the science and technology related to the anthropogenic water cycle, water quality, and its management worldwide. The audience targeted by the journal comprises biologists, chemical engineers, chemists, civil engineers, environmental engineers, limnologists, and microbiologists. The scope of the journal include: •Treatment processes for water and wastewaters (municipal, agricultural, industrial, and on-site treatment), including resource recovery and residuals management; •Urban hydrology including sewer systems, stormwater management, and green infrastructure; •Drinking water treatment and distribution; •Potable and non-potable water reuse; •Sanitation, public health, and risk assessment; •Anaerobic digestion, solid and hazardous waste management, including source characterization and the effects and control of leachates and gaseous emissions; •Contaminants (chemical, microbial, anthropogenic particles such as nanoparticles or microplastics) and related water quality sensing, monitoring, fate, and assessment; •Anthropogenic impacts on inland, tidal, coastal and urban waters, focusing on surface and ground waters, and point and non-point sources of pollution; •Environmental restoration, linked to surface water, groundwater and groundwater remediation; •Analysis of the interfaces between sediments and water, and between water and atmosphere, focusing specifically on anthropogenic impacts; •Mathematical modelling, systems analysis, machine learning, and beneficial use of big data related to the anthropogenic water cycle; •Socio-economic, policy, and regulations studies.