Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA.
Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA.
Sci Total Environ. 2024 Dec 10;955:176834. doi: 10.1016/j.scitotenv.2024.176834. Epub 2024 Oct 11.
Most existing wastewater surveillance studies that focus on viruses have identified a large fraction of bacteriophages. Identifying bacteria by considering bacteriophage-host interactions is a novel method for detecting bacterial pathogens circulating in a community, using wastewater surveillance. This study aims to identify human-related bacterial pathogens in municipal wastewater collected in metro Detroit, using high-throughput sequencing and bioinformatics. Untreated municipal wastewater samples were collected on August 11, 2020, and bacteriophages were concentrated using the VIRus ADsorption-ELution (VIRADEL) method. Bacteriophage-related contigs in samples ranged from 15.53 % to 18.91 %, with 2477 classified and 8853 unclassified contigs. Most identified bacteriophages were from Caudoviricetes and Malgrandaviricetes classes belonging to 19 families. Hosts of bacteriophages were predicted with the PhaBOX (CHERRY) tool. The results indicated that out of the 2477 classified phages, 2373 were associated with known bacterial hosts. Also, out of 8853 unclassified bacteriophages, 8421 were associated with known bacterial hosts, and the remaining 432 were with unknown bacterial hosts. Among all bacteriophage-associated hosts, 399 were identified as pathogenic bacteria at the species level. Approximately, 85 % of the identified pathogenic bacteria are reported to be associated with human diseases. Genome quality assessments showed that 15 bacteriophages had nearly complete genomes, which were further analyzed to understand bacteriophage-bacteria interactions in wastewater. Identified hosts of these complete-genome phages included human pathogens such as Salmonella enterica, Bacillus cereus, Achromobacter xylosoxidans, and Escherichia coli. The S. enterica bacteriophage (k141_1005294) genomic map was annotated, and responsible open reading frames (ORFs) were characterized to illustrate bacteriophage behavior during infection of pathogenic bacteria in untreated wastewater. To the best of our knowledge, this is the first attempt to characterize human bacterial pathogens in wastewater through bacteriophage-pathogen interactions. Novel bioinformatic approaches enhance pathogen detection and improve the understanding of community wastewater microbiomes.
大多数现有的专注于病毒的废水监测研究已经鉴定出大量噬菌体。通过考虑噬菌体-宿主相互作用来鉴定细菌是一种通过废水监测检测社区中循环的细菌病原体的新方法。本研究旨在使用高通量测序和生物信息学方法鉴定在底特律都会区收集的市政废水中与人类相关的细菌病原体。2020 年 8 月 11 日采集未经处理的市政废水样本，并使用 VIRus ADsorption-ELution (VIRADEL) 方法浓缩噬菌体。样本中噬菌体相关序列的范围为 15.53%至 18.91%，其中 2477 个为分类序列，8853 个为未分类序列。大多数鉴定的噬菌体来自长尾病毒科和马尔格兰病毒科，属于 19 个科。使用 PhaBOX (CHERRY) 工具预测噬菌体的宿主。结果表明，在 2477 个分类噬菌体中，有 2373 个与已知细菌宿主相关。此外，在 8853 个未分类噬菌体中，有 8421 个与已知细菌宿主相关，其余 432 个与未知细菌宿主相关。在所有与噬菌体相关的宿主中，有 399 个在种水平上被鉴定为致病菌。大约 85%的鉴定致病菌与人类疾病有关。基因组质量评估表明，有 15 个噬菌体具有近乎完整的基因组，进一步分析这些基因组以了解废水中噬菌体-细菌的相互作用。这些完整基因组噬菌体的鉴定宿主包括沙门氏菌、蜡样芽孢杆菌、木糖氧化无色杆菌和大肠杆菌等人类病原体。对 S. enterica 噬菌体 (k141_1005294) 基因组图谱进行了注释，并对其负责的开放阅读框 (ORF) 进行了特征描述，以说明噬菌体在未经处理的废水中感染致病菌时的行为。据我们所知，这是首次通过噬菌体-病原体相互作用来描述废水中的人类细菌病原体。新颖的生物信息学方法增强了病原体的检测，并提高了对社区废水微生物组的理解。
