Next generation sequencing approaches to evaluate water and wastewater quality

Garner, Emily; Davis, Benjamin C.; Milligan, Erin; Blair, Matthew Forrest; Keenum, Ishi; Maile-Moskowitz, Ayella; Pan, Jin; Gnegy, M. E.; Liguori, Krista; Gupta, Suraj; Prussin, Aaron J.; Marr, Linsey C.; Heath, Lenwood S.; Vikesland, Peter J.; Zhang, Liqing; Pruden, Amy

doi:10.1016/j.watres.2021.116907

Cited by 67 publications

(40 citation statements)

References 379 publications

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“…The official Peruvian environmental quality standards for surface water evaluate only two microorganisms, Escherichia coli and Vibrio choleare [60]. Our results are aligned with previous work [61,62] that corroborate that next-generation sequencing is capable to identify potential bacterial pathogens in the water samples. Thus, we believe that a future national water surveillance system shall include evidence from amplicon sequencing and metagenomics.…”

Section: Discussionsupporting

confidence: 89%

From the Andes to the desert: 16S rRNA metabarcoding characterization of aquatic bacterial communities in the Rimac river, the main source of water for Lima, Peru

et al. 2021

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The Rimac river is the main source of water for Lima, Peru’s capital megacity. The river is constantly affected by different types of contamination including mine tailings in the Andes and urban sewage in the metropolitan area. In this work, we aim to produce the first characterization of aquatic bacterial communities in the Rimac river using a 16S rRNA metabarcoding approach which would be useful to identify bacterial diversity and potential understudied pathogens. We report a lower diversity in bacterial communities from the Lower Rimac (Metropolitan zone) in comparison to other sub-basins. Samples were generally grouped according to their geographical location. Bacterial classes Alphaproteobacteria, Bacteroidia, Campylobacteria, Fusobacteriia, and Gammaproteobacteria were the most frequent along the river. Arcobacter cryaerophilus (Campylobacteria) was the most frequent species in the Lower Rimac while Flavobacterium succinicans (Bacteroidia) and Hypnocyclicus (Fusobacteriia) were the most predominant in the Upper Rimac. Predicted metabolic functions in the microbiota include bacterial motility and quorum sensing. Additional metabolomic analyses showed the presence of some insecticides and herbicides in the Parac-Upper Rimac and Santa Eulalia-Parac sub-basins. The dominance in the Metropolitan area of Arcobacter cryaerophilus, an emergent pathogen associated with fecal contamination and antibiotic multiresistance, that is not usually reported in traditional microbiological quality assessments, highlights the necessity to apply next-generation sequencing tools to improve pathogen surveillance. We believe that our study will encourage the integration of omics sciences in Peru and its application on current environmental and public health issues.

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Section: Discussionsupporting

confidence: 89%

From the Andes to the desert: 16S rRNA metabarcoding characterization of aquatic bacterial communities in the Rimac river, the main source of water for Lima, Peru

et al. 2021

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“…This provides a new dimension for the analysis of pathogenic bacteria in wastewater. The application methodology of NGS technologies in wastewater study can be divided into four subcategories: whole genome sequencing (WGS), metagenomic sequencing, metatranscriptomic sequencing, and sequencing of an amplified targeted gene (e.g., 16S rRNA and 18S rRNA genes) [198]. WGS is a powerful approach for microorganism identification in wastewater, while it relies on bacteria isolation and culture, extraction of long DNA, and the development of long read sequencing platforms.…”

Section: Profiling Potential Pathogensmentioning

confidence: 99%

“…In addition, the excess of ribosomal RNA (rRNA) in transcriptomes also interferes with the identification of mRNA in environmental samples. All these challenges limit its application in wastewater systems [198]. Comparison studies have also been conducted to access the performance of various methods to identify pathogens and associated virulence genes.…”

Section: Profiling Potential Pathogensmentioning

confidence: 99%

Molecular Methods for Pathogenic Bacteria Detection and Recent Advances in Wastewater Analysis

Zhang

et al. 2021

Water

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With increasing concerns about public health and the development of molecular techniques, new detection tools and the combination of existing approaches have increased the abilities of pathogenic bacteria monitoring by exploring new biomarkers, increasing the sensitivity and accuracy of detection, quantification, and analyzing various genes such as functional genes and antimicrobial resistance genes (ARG). Molecular methods are gradually emerging as the most popular detection approach for pathogens, in addition to the conventional culture-based plate enumeration methods. The analysis of pathogens in wastewater and the back-estimation of infections in the community, also known as wastewater-based epidemiology (WBE), is an emerging methodology and has a great potential to supplement current surveillance systems for the monitoring of infectious diseases and the early warning of outbreaks. However, as a complex matrix, wastewater largely challenges the analytical performance of molecular methods. This review synthesized the literature of typical pathogenic bacteria in wastewater, types of biomarkers, molecular methods for bacterial analysis, and their recent advances in wastewater analysis. The advantages and limitation of these molecular methods were evaluated, and their prospects in WBE were discussed to provide insight for future development.

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“…With Next-Generation genome Sequencing (NGS) technologies become widespread in recent years, they are commonly used in AMR surveillance studies either in clinical settings [12,13], or in the agriculture and food industry [14][15][16][17] and the environment [12,18,19]. In line with the importance of genomic surveillance of AMR, several annotation tools and databases has been developed for the analysis of ARG content of bacterial genomes or NGS metagenomic samples [20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35].…”

Section: Introductionmentioning

confidence: 99%

Review and Comparison of Antimicrobial Resistance Gene Databases

Papp¹,

Solymosi²

2022

Preprint

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As the prevalence of antimicrobial resistance genes is increasing in microbes, we are facing the return of the preantibiotic era. Consecutively, the number of studies concerning antibiotic resistance and its spread in the environment is rapidly growing. Next generation sequencing technologies are widespread used in many areas of biological research and antibiotic resistance is no exception. For the rapid annotation of whole genome sequencing and metagenomic results considering antibiotic resistance, several tools and data resources were developed. These databases, however can differ fundamentally in the number and type of genes and resistance determinants they comprise. Furthermore, the annotation structure and metadata stored in these resources can also contribute to their differences. Several previous reviews were published on the tools and databases of resistance gene annotation, however, to our knowledge, no previous review focused solely and in depth on the differences in the databases. In this review, we compare the most well-known and widely used antibiotic resistance gene databases based on their structure and content. We believe that this knowledge is fundamental for selecting the most appropriate database for a research question and for the development of new tools and resources of resistance gene annotation.

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Next generation sequencing approaches to evaluate water and wastewater quality

Cited by 67 publications

References 379 publications

From the Andes to the desert: 16S rRNA metabarcoding characterization of aquatic bacterial communities in the Rimac river, the main source of water for Lima, Peru

From the Andes to the desert: 16S rRNA metabarcoding characterization of aquatic bacterial communities in the Rimac river, the main source of water for Lima, Peru

Molecular Methods for Pathogenic Bacteria Detection and Recent Advances in Wastewater Analysis

Review and Comparison of Antimicrobial Resistance Gene Databases

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