Anthropogenic activities in catchments used for drinking water production largely contaminates source waters, and this may impact the quality of the final drinking water product. These contaminants may also affect taxonomic and functional profiles of the bacterial communities in the drinking water. Here, we report an integrated insight into the microbiome and water quality of four water treatment plants (NWC, NWE, WCA and NWG) that supply portable water to communities in South Africa. A new scoring system based on combined significant changes of physicochemical parameters and microbial abundance from raw to treated water was used to evaluate the effectiveness of the treatment plants at water purification. Physicochemical parameters which include total soluble solids, turbidity, pH, nitrites and phosphorus among others, were measured in source, treated, and distributed water. There were general statistically significant (P � 0.05) differences between raw and treated water, demonstrating the effectiveness of the purification process. Illumina sequencing of the 16S rRNA gene was used for taxonomic profiling of the microbial communities and this data was used to infer functional attributes of the communities. Structure and composition of the bacterial communities differed significantly (P < 0.05) among the treatment plants, only NWE and NWG showed no significant differences (P > 0.05), this correlated with the predicted functional profile of the microbial communities obtained from Phylogenetic Investigation of Communities by Reconstruction of Observed States (PICRUSt), as well as the likely pollutants of source water. Bacteroidetes, Chlorobi and Fibrobacteres significantly differed (P < 0.05) between raw and distributed water. PICRUSt inferred a number of pathways involved in the degradation of xenobiotics such as Dichlorodiphenyltrichloroethane, atrazine and polycyclic aromatic hydrocarbons. More worryingly, was the presence of pathways involved in beta-lactam resistance, potential pathogenic Escherichia coli infection, Vibrio cholerae infection, and Shigellosis. Also present in drinking and treated water were OTUs associated with a number of opportunistic pathogens.

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The extent and impact of plasmid-mediated AmpC beta-lactamase genes (pAmpCs) prevalence in aquatic environments is poorly understood. The aim of this study was to detect and quantify pAmpCs from the aquatic environment. The following pAmpCs were analysed with clinical TaqMan assays from isolated plasmids: ACC, ACT/MIR, BIL/LAT/CMY, DHA, FOX and MOX/CMY. Quantification was conducted using qPCR and 3D chip-based digital PCR. The results of qPCR yielded 4,875.27 copies/ng DNA and dPCR, 1,640.58 copies/ng (Mann–Whitney U Test, p= 0.868). Redundancy analysis indicated that land coverage explains 90.49% (ANOVA, p= 0.601) of pAmpC variance. There was a correlation between the frequency and quantities of pAmpCs detected in each river and this could be related to anthropogenic influence. Frequencies of detection for pAmpCs were 25/36 for the Crocodile West River and 13/36 for the Marico River. Quantification resulted in higher copy numbers for the Crocodile West River and high copies in only two sites of the Marico River, thus reflecting degrees of anthropogenic influences on both rivers. The presence of these clinically relevant pAmpCs in aquatic systems are cause for concern, considering their potential impact if these genes are harboured by pathogens and become dispersed to human populations.

Summary Comparing genomic loci of a given bacterial gene across strains and species can provide insights into their evolution, including information on e.g. acquired mobility, the degree of conservation between different taxa, or indications of horizontal gene transfer events. While thousands of bacterial genomes are available to date, there is no software that facilitates comparisons of individual gene loci for a large number of genomes. GEnView is a Python based pipeline for the comparative analysis of gene-loci in a large number of bacterial genomes, providing users with automated, taxon-selective access to the &gt;840.000 genomes and plasmids currently available in the NCBI Assembly and RefSeq databases, and is able to process local genomes that are not deposited at NCBI, enabling searches for genomic sequences and to analyze their genetic environments through the interactive visualization and extensive metadata files created by GEnView. Availability and Implementation GEnView is implemented in Python 3. Instructions for download and usage can be found at https://github.com/EbmeyerSt/GEnView under GLP3. Contact To contact the developers, report a bug at https://github.com/EbmeyerSt/GEnView, or write to stefan.ebmeyer@gu.se or joakim.larsson@fysiologi.gu.se. Supplementary information Supplementary data are available at Bioinformatics online.