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

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. [Display omitted] •Ubiquitous pathogens in urban water systems pose a significant global health risk.•High-throughput sequencing enables full-spectrum pathogens detection in water systems.•Fast and accurate detection with multiple technologies are promising.•Robust software and platforms facilitate comprehensive pathogen annotation.•Future research should integrate targeted and untargeted detection to enhance biosafety.