Application of high-throughput sequencing technologies and analytical tools for pathogen detection in urban water systems: Progress and future perspectives

Zhao，Yanmei1; Huang，Fang2; Wang，Wenxiu3; Gao，Rui2; Fan，Lu3,4; Wang，Aijie1,2; Gao，Shu Hong1

2023-11-20

10.1016/j.scitotenv.2023.165867

Science of the Total Environment   Impact Factor & Quartile

0048-9697

1879-1026

The ubiquitous presence of pathogenic microorganisms, such as viruses, bacteria, fungi, and protozoa, in urban water systems poses a significant risk to public health. The emergence of infectious waterborne diseases mediated by urban water systems has become one of the leading global causes of mortality. However, the detection and monitoring of these pathogenic microorganisms have been limited by the complexity and diversity in the environmental samples. Conventional methods were restricted by long assay time, high benchmarks of identification, and narrow application sceneries. Novel technologies, such as high-throughput sequencing technologies, enable potentially full-spectrum detection of trace pathogenic microorganisms in complex environmental matrices. This review discusses the current state of high-throughput sequencing technologies for identifying pathogenic microorganisms in urban water systems with a concise summary. Furthermore, future perspectives in pathogen research emphasize the need for detection methods with high accuracy and sensitivity, the establishment of precise detection standards and procedures, and the significance of bioinformatics software and platforms. We have compiled a list of pathogens analysis software/platforms/databases that boast robust engines and high accuracy for preference. We highlight the significance of analyses by combining targeted and non-targeted sequencing technologies, short and long reads technologies, sequencing technologies, and bioinformatic tools in pursuing upgraded biosafety in urban water systems.

Bioinformatics analytical tools Environmental application High-throughput sequencing Pathogen detection Urban water system

SCI

English

Corresponding

National Natural Science Foundation of China[52230004];National Natural Science Foundation of China[52293441];National Natural Science Foundation of China[52293443];

Environmental Sciences & Ecology

Environmental Sciences

WOS:001051052100001

ELSEVIER

ENVIRONMENT/ECOLOGY

2-s2.0-85166261559

Scopus

1.State Key Laboratory of Urban Water Resource and Environment,School of Civil & Environmental Engineering,Harbin Institute of Technology Shenzhen,Shenzhen,518055,China
2.State Key Laboratory of Urban Water Resource and Environment,School of Environment,Harbin Institute of Technology,Harbin,150090,China
3.Department of Ocean Science and Engineering,Southern University of Science and Technology (SUSTech),Shenzhen,China
4.Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou),Guangzhou,China

Zhao，Yanmei,Huang，Fang,Wang，Wenxiu,et al. Application of high-throughput sequencing technologies and analytical tools for pathogen detection in urban water systems: Progress and future perspectives[J]. Science of the Total Environment,2023,900.

Zhao，Yanmei.,Huang，Fang.,Wang，Wenxiu.,Gao，Rui.,Fan，Lu.,...&Gao，Shu Hong.(2023).Application of high-throughput sequencing technologies and analytical tools for pathogen detection in urban water systems: Progress and future perspectives.Science of the Total Environment,900.

Zhao，Yanmei,et al."Application of high-throughput sequencing technologies and analytical tools for pathogen detection in urban water systems: Progress and future perspectives".Science of the Total Environment 900(2023).