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1. Cast iron drinking water pipe biofilms support diverse microbial communities containing antibiotic resistance genes, metal resistance genes, and class 1 integrons

   https://doi.org/10.1039/D0EW01059F  

   Kimbell, Lee K.; LaMartina, Emily Lou; Kappell, Anthony D.; Huo, Jingwan; Wang, Yin; Newton, Ryan J.; McNamara, Patrick J. (March 2021, Environmental Science: Water Research & Technology)

   null (Ed.)

   Antimicrobial resistance is a well-documented public health concern. The role that drinking water distribution pipes have as sources of antibiotic resistance genes (ARGs) is not well known. Metals are a known stressor for antibiotic resistance development, implying that aging metal-pipe infrastructure could be a source of ARGs. The objective of this study was to determine if ARGs, metal resistance genes (MRGs), and intI 1 were pervasive across various pipe biofilm sample types (biomass surfaces, pipe surfaces, corrosion tubercles, and under corrosion tubercles) and if the resistance genes associated with particular microbial taxa. Eight sample types in triplicate ( n = 24) were taken from inside a >100 year-old, six ft. section of a full-scale chloraminated cast iron drinking water main. Droplet digital PCR (ddPCR) was employed as a novel approach to quantify ARGs in pipes from full-scale drinking water distribution systems (DWDS) because it yielded higher detection frequencies than quantitative PCR (qPCR). Illumina sequencing was employed to characterize the microbial community based on 16S rRNA genes. ARGs and MRGs were detected in all 24 pipe samples. Every sample contained targeted genes. Interestingly, the mean absolute abundances of ARGs and MRGs only varied by approximately one log value across sample types, but the mean relative abundances (copy numbers normalized to 16S rRNA genes) varied by over two log values. The ARG and MRGs concentrations were not significantly different between sample types, despite significant changes in dominant microbial taxa. The most abundant genera observed in the biofilm communities were Mycobacterium (0.2–70%), and β-lactam resistance genes bla TEM , bla SHV , and the integrase gene of class 1 integrons ( intI 1) were positively correlated with Mycobacterium . The detection of ARGs, MRGs, and class 1 integrons across all sample types within the pipe indicates that pipes themselves can serve as sources for ARGs in DWDS. Consequently, future work should investigate the role of pipe materials as well as corrosion inhibitors to determine how engineering decisions can mitigate ARGs in drinking water that stem from pipe materials. 

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2. Contaminated drinking water facilitates Escherichia coli strain-sharing within households in urban informal settlements

   https://doi.org/10.1038/s41564-025-01986-w  

   Kim, Daehyun D; Swarthout, Jenna M; Worby, Colin J; Chieng, Benard; Mboya, John; Earl, Ashlee M; Njenga, Sammy M; Pickering, Amy J (May 2025, Nature Microbiology)

   Abstract Identifying bacterial transmission pathways is crucial to inform strategies that limit the spread of pathogenic and antibiotic-resistant bacteria. Here we assessedEscherichia colistrain-sharing and overlap of antibiotic resistance genes (ARGs) across humans, poultry, canines, soil, and drinking water within and between households in urban informal settlements in Nairobi, Kenya. We collected 321 samples from 50 households with half having access to chlorinated water. We performed Pooling Isolated Colonies-seq, which sequences pools of up to fiveE. colicolonies per sample to capture strain diversity. Pooling Isolated Colonies-seq captured 1,516 colonies and identified 154 strain-sharing events, overcoming limitations of single-isolate sequencing and metagenomics. Within households, strain-sharing rates and resistome similarities across sample types were strongly correlated, suggesting clonal transmission of ARGs.E. coliisolated from the environment carried clinically relevant ARGs. Strain-sharing was rare between animals and humans but frequent between humans and drinking water.E. coli-contaminated stored drinking water was associated with higher human–human strain-sharing within households. These results suggest that contaminated drinking water facilitates human to human strain-sharing, and water treatment can disrupt transmission. 

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3. Occurrence and Mitigation of Bacterial Regrowth in Stored Household Water in Eastern Coastal Madagascar

   https://doi.org/10.3390/w16111592  

   Judah, Lauren A; Andriambololonirina, Cathy; Rakotoarisoa, Lova; Barrett, Luke_John Paul; Khaliq, Mahmooda; Mihelcic, James R; Cunningham, Jeffrey A (June 2024, Water)

   In communities where people lack on-demand, safely managed drinking water, stored household water often becomes contaminated by fecal bacteria, regardless of the source-water quality. The objectives of this paper are to assess and control bacterial contamination in stored household water in Toamasina, a rapidly urbanizing city in eastern coastal Madagascar. We collected samples of source water and stored household water from 10 representative households that use different water sources and different storage strategies, and we analyzed the samples for several fecal indicator bacteria. We also tested three methods that residents of Toamasina could realistically employ for cleaning their household water storage vessels, assessing the effect of the cleaning methods on measured bacterial levels in the water. Consistent with the previous literature, we found that concentrations of total coliforms in stored household water were significantly higher than in the corresponding source water (p < 0.05). In 100% of households that stored their water in 20 L polyethylene jerrycans (n = 4), biofilms on the walls of the jerrycan harbored total coliforms and Enterococcus. The use of a closed storage container was, on its own, not found to provide a meaningful protective effect against bacterial regrowth; to be protective, closed storage containers must be combined with high-quality source water and/or with adequate cleaning to prevent biofilm formation. A dilute solution of sodium hypochlorite, known locally as Sûr’Eau or Manadio Rano, was both the most effective and the least expensive method for cleaning household water storage containers. We conclude that regular and effective cleaning of storage containers is an essential component of safe water storage. Because household storage of collected water is common in many low- and middle-income countries, these results are important towards the worldwide achievement of the United Nations’ Sustainable Development Goal 6. 

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4. New Drinking Water Genome Catalog Identifies a Globally Distributed Bacterial Genus Adapted to Disinfected Drinking Water Systems

   https://doi.org/10.1021/acs.est.4c05086  

   Sudarshan, Ashwin S; Dai, Zihan; Gabrielli, Marco; Oosthuizen-Vosloo, Solize; Konstantinidis, Konstantinos T; Pinto, Ameet J (September 2024, Environmental Science & Technology)

   Genome-resolved insights into the structure and function of the drinking water microbiome can advance the effective management of drinking water quality. To enable this, we constructed and curated thousands of metagenome-assembled and isolate genomes from drinking water distribution systems globally to develop a Drinking Water Genome Catalog (DWGC). The current DWGC disproportionately represents disinfected drinking water systems due to a paucity of metagenomes from nondisinfected systems. Using the DWGC, we identify core genera of the drinking water microbiome including a genus (UBA4765) within the order Rhizobiales that is frequently detected and highly abundant in disinfected drinking water systems. We demonstrate that this genus has been widely detected but incorrectly classified in previous amplicon sequencing-based investigations of the drinking water microbiome. Further, we show that a single genome variant (genomovar) within this genus is detected in 75% of drinking water systems included in this study. We propose a name for this uncultured bacterium as “Raskinella chloraquaticus” and describe the genus as “Raskinella” (endorsed by SeqCode). Metabolic annotation and modeling-based predictions indicate that this bacterium is capable of necrotrophic growth, is able to metabolize halogenated compounds, proliferates in a biofilm-based environment, and shows clear indications of disinfection-mediated selection. 

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5. Patterns of sediment-associated fecal indicator bacteria in an urban estuary: Benthic-pelagic coupling and implications for shoreline water quality.

   O'Mullan, G.; Juhl, A.; Reichert, R.; Schneider, E.; and Martinez, N. (January 2019, Science of the total environment)

   Estuarine and coastal waterways are commonly monitored for fecal and sewage contamination to protect recreator health and ecosystem functions. Such monitoring programs commonly rely on cultivation-based counts of fecal indicator bacteria (FIB) in water column samples. Recent studies demonstrate that sediments and beach sands can be heavily colonized by FIB, and that settling and resuspension of colonized particles may significantly influence the distribution of FIB in the water column. However, measurements of sediment FIB are rarely incorporated into monitoring programs, and geographic surveys of sediment FIB are uncommon. In this study, the distribution of FIB and the extent of benthic-pelagic FIB coupling were examined in the urbanized, lower Hudson River Estuary. Using cultivation-based enumeration, two commonly-measured FIB, enterococci and Escherichia coli, were widely distributed in both sediment and water, and were positively correlated with each other. The taxonomic identity of FIB isolates from water and sediment was confirmed by DNA sequencing. The geometric mean of FIB concentration in sediment was correlated with both the geometric mean of FIB in water samples from the same locations and with sediment organic carbon. These two positive associations likely reflect water as the FIB source for underlying sediments, and longer FIB persistence in the sediments compared to the water, respectively. The relative representation of other fecal associated bacterial genera in sediment, determined by 16S rRNA gene sequencing, increased with the sequence representation of the two FIB, supporting the value of these FIB for assessing sediment contamination. Experimental resuspension of sediment increased shoreline water column FIB concentrations, which may explain why shoreline water samples had higher average FIB concentrations than samples collected nearby but further from shore. In combination, these results demonstrate extensive benthic-pelagic coupling of FIB in an urbanized estuary and highlight the importance of sediment FIB distribution and ecology when interpreting water quality monitoring data. 

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