Metagenomic assembly provides a deep insight into the antibiotic resistome alteration induced by drinking water chlorination and its correlations with bacterial host changes

Jia, Shuyu; Wu, Jialu; Ye, Lin; Zhao, Fugeng; Li, Tong; Zhang, Xuxiang

doi:10.1016/j.jhazmat.2019.120841

Cited by 88 publications

(24 citation statements)

References 63 publications

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“…At the MAN location, it was detected in the initial and final timepoint and at higher abundance at the final timepoint. Pseudomonas alcaligenes carries multiple antibiotic resistance genes, are considered opportunistic human pathogens and have been identified in previous literature characterizing drinking water systems, particularly in chlorinated systems ( Jia et al., 2019 ; Ma et al., 2019 ).…”

Section: Resultsmentioning

confidence: 99%

Spatial-temporal targeted and non-targeted surveys to assess microbiological composition of drinking water in Puerto Rico following Hurricane Maria

et al. 2021

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Highlights Post hurricane tap water quality was assessed at nine sites in six sampling events. Total bacterial concentrations decreased between early and late timepoints. Genome resolved metagenomics showed similar community membership to other systems. A small number of metagenome assembled genomes showed similarity to known pathogens. Disruptions did not result in sustained impact on drinking water microbial community.

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Section: Resultsmentioning

confidence: 99%

Spatial-temporal targeted and non-targeted surveys to assess microbiological composition of drinking water in Puerto Rico following Hurricane Maria

et al. 2021

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“…Within the Proteobacteria phylum, the Sphingomonas was the main compositions of the genus. It was reported that the genome of Sphingomonas contains multiple efflux pumps ( Jia et al, 2019 ), suggesting that Sphingomonas might better exist in the sediments of aquatic environments. A previous study implied that the physiochemical properties of the environment may influence the bacterial community by affecting the nutrient availability or physiological activity ( Li et al, 2019 ).…”

Section: Discussionmentioning

confidence: 99%

Analysis of Antibiotic Resistance Genes, Environmental Factors, and Microbial Community From Aquaculture Farms in Five Provinces, China

Cheng

Song

et al. 2021

Front. Microbiol.

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The excessive use of antibiotics speeds up the dissemination and aggregation of antibiotic resistance genes (ARGs) in the environment. The ARGs have been regarded as a contaminant of serious environmental threats on a global scale. The constant increase in aquaculture production has led to extensive use of antibiotics as a means to prevent and treat bacterial infections; there is a universal concern about the environmental risk of ARGs in the aquaculture environment. In this study, a survey was conducted to evaluate the abundance and distributions of 10 ARGs, bacterial community, and environmental factors in sediment samples from aquatic farms distributed in Anhui (AP1, AP2, and AP3), Fujian (FP1, FP2, and FP3), Guangxi (GP1, GP2, and GP3), Hainan (HP1, HP2, and HP3), and Shaanxi (SP1, SP2, and SP3) Province in China. The results showed that the relative abundance of total ARGs was higher in AP1, AP2, AP3, FP3, GP3, HP1, HP2, and HP3 than that in FP1, FP2, GP1, GP2, SP1, SP2, and SP3. The sul1 and tetW genes of all sediment samples had the highest abundance. The class 1 integron (intl1) was detected in all samples, and the result of Pearson correlation analysis showed that the intl1 has a positive correlation with the sul1, sul2, sul3, blaOXA, qnrS, tetM, tetQ, and tetW genes. Correlation analysis of the bacterial community diversity and environmental factors showed that the Ca2+ concentration has a negative correlation with richness and diversity of the bacterial community in these samples. Of the identified bacterial community, Proteobacteria, Firmicutes, Chloroflexi, and Bacteroidota were the predominant phyla in these samples. Redundancy analysis showed that environmental factors (TN, TP, Cl–, and Ca2+) have a positive correlation with the bacterial community (AP1, GP1, GP2, GP3, SP1, SP2, and SP3), and the abundance of ARGs (sul1, tetW, qnrS, and intl1) has a positive correlation with the bacterial community (AP2, AP3, HP1, HP2, and HP3). Based on the network analysis, the ARGs (sul1, sul2, blaCMY, blaOXA, qnrS, tetW, tetQ, tetM, and intl1) were found to co-occur with bacterial taxa from the phyla Chloroflexi, Euryarchaeota, Firmicutes, Halobacterota, and Proteobacteria. In conclusion, this study provides an important reference for understanding the environmental risk associated with aquaculture activities in China.

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“…Mapping of sequencing reads against theses catalogues allows taxonomic resolution of gene entries, together with linking of genes to MAGs and reconstructed full-length 16S rRNA genes [137]. For example, the pipeline MGS-Fast uses the reference catalogue of the human gut microbiome [138]. Although still incomplete, these existing catalogues continue to grow to become a detailed classification of the composition of each microbial ecosystem.…”

Section: Wgs Metagenomicsmentioning

confidence: 99%

Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses

2020

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Metagenomics and marker gene approaches, coupled with high-throughput sequencing technologies, have revolutionized the field of microbial ecology. Metagenomics is a culture-independent method that allows the identification and characterization of organisms from all kinds of samples. Whole-genome shotgun sequencing analyses the total DNA of a chosen sample to determine the presence of micro-organisms from all domains of life and their genomic content. Importantly, the whole-genome shotgun sequencing approach reveals the genomic diversity present, but can also give insights into the functional potential of the micro-organisms identified. The marker gene approach is based on the sequencing of a specific gene region. It allows one to describe the microbial composition based on the taxonomic groups present in the sample. It is frequently used to analyse the biodiversity of microbial ecosystems. Despite its importance, the analysis of metagenomic sequencing and marker gene data is quite a challenge. Here we review the primary workflows and software used for both approaches and discuss the current challenges in the field.

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Metagenomic assembly provides a deep insight into the antibiotic resistome alteration induced by drinking water chlorination and its correlations with bacterial host changes

Cited by 88 publications

References 63 publications

Spatial-temporal targeted and non-targeted surveys to assess microbiological composition of drinking water in Puerto Rico following Hurricane Maria

Spatial-temporal targeted and non-targeted surveys to assess microbiological composition of drinking water in Puerto Rico following Hurricane Maria

Analysis of Antibiotic Resistance Genes, Environmental Factors, and Microbial Community From Aquaculture Farms in Five Provinces, China

Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses

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