Microbial communities of biofilms developed in a chlorinated drinking water distribution system: A field study of antibiotic resistance and biodiversity

Exploring the potential of machine learning to understand the occurrence and health risks of haloacetic acids in a drinking water distribution system

Determining the occurrence of disinfection byproducts (DBPs) in drinking water distribution system (DWDS) remains challenging. Predicting DBPs using readily available water quality parameters can help to understand DBPs associated risks and capture the complex interrelationships between water quality and DBP occurrence. In this study, we collected drinking water samples from a distribution network throughout a year and measured the related water quality parameters (WQPs) and haloacetic acids (HAAs). 12 machine learning (ML) algorithms were evaluated. Random Forest (RF) achieved the best performance (i.e., R2 of 0.78 and RMSE of 7.74) for predicting HAAs concentration. Instead of using cytotoxicity or genotoxicity separately as the surrogate for evaluating toxicity associated with HAAs, we created a health risk index (HRI) that was calculated as the sum of cytotoxicity and genotoxicity of HAAs following the widely used Tic-Tox approach. Similarly, ML models were developed to predict the HRI, and RF model was found to perform the best, obtaining R2 of 0.69 and RMSE of 0.38. To further explore advanced ML approaches, we developed 3 models using uncertainty-based active learning. Our findings revealed that Categorical Boosting Regression (CAT) model developed through active learning substantially outperformed other models, achieving R2 of 0.87 and 0.82 for predicting concentration and the HRI, respectively. Feature importance analysis with the CAT model revealed that temperature, ions (e.g., chloride and nitrate), and DOC concentration in the distribution network had a significant impact on the occurrence of HAAs. Meanwhile, chloride ion, pH, ORP, and free chlorine were found as the most important features for HRI prediction. This study demonstrates that ML has the potential in the prediction of HAA occurrence and toxicity. By identifying key WQPs impacting HAA occurrence and toxicity, this research offers valuable insights for targeted DBP mitigation strategies.

Antibiotic resistant bacteria and antibiotic resistance genes as contaminants of emerging concern: Occurrences, impacts, mitigations and future guidelines

Antibiotic resistance, driven by the proliferation of antibiotic resistance genes (ARGs) and antibiotic resistance bacteria (ARBs), has emerged as a pressing global health concern. Antimicrobial resistance is exacerbated by the widespread use of antibiotics in agriculture, aquaculture, and human medicine, leading to their accumulation in various environmental compartments such as soil, water, and sediments. The presence of ARGs in the environment, particularly in municipal water, animal husbandry, and hospital environments, poses significant risks to human health, as they can be transferred to potential human pathogens. Current remediation strategies, including the use of pyroligneous acid, coagulants, advanced oxidation, and bioelectrochemical systems, have shown promising results in reducing ARGs and ARBs from soil and water. However, these methods come with their own set of challenges, such as the need for elevated base levels in UV-activated persulfate and the long residence period required for photocatalysts. The future of combating antibiotic resistance lies in the development of standardized monitoring techniques, global collaboration, and the exploration of innovative remediation methods. Emphasis on combination therapies, advanced oxidation processes, and monitoring horizontal gene transfer can pave the way for a comprehensive approach to mitigate the spread of antibiotic resistance in the environment.

Antibiotic resistance pattern of waterborne causative agents of healthcare-associated infections: A call for biofilm control in hospital water systems

BACKGROUND

In recent years, the global spread of antimicrobial resistance has become a concerning issue, often referred to as a "silent pandemic". Healthcare-associated infections (HAIs) caused by antibiotic-resistant bacteria (ARB) are a recurring problem, with some originating from waterborne route. The study aimed to investigate the presence of clinically relevant opportunistic bacteria and antibiotic resistance genes (ARGs) in hospital water distribution systems (WDSs).

METHODS

Water and biofilm samples (n = 192) were collected from nine hospitals in Isfahan and Kashan, located in central Iran, between May 2022 and June 2023. The samples were analyzed to determine the presence and quantities of opportunistic bacteria and ARGs using cultural and molecular methods.

RESULTS

Staphylococcus spp. were highly detected in WDS samples (90 isolates), with 33 % of them harboring mecA gene. However, the occurrences of E. coli (1 isolate), Acinetobacter baumannii (3 isolates), and Pseudomonas aeruginosa (14 isolates) were low. Moreover, several Gram-negative bacteria containing ARGs were identified in the samples, mainly belonging to Stenotrophomonas, Sphingomonas and Brevundimonas genera. Various ARGs, as well as intI1, were found in hospital WDSs (ranging from 14 % to 60 %), with higher occurrences in the biofilm samples.

CONCLUSION

Our results underscore the importance of biofilms in water taps as hotspots for the dissemination of opportunistic bacteria and ARG within hospital environments. The identification of multiple opportunistic bacteria and ARGs raises concerns about the potential exposure and acquisition of HAIs, emphasizing the need for proactive measures, particularly in controlling biofilms, to mitigate infection risks in healthcare settings.

Influence of drinking water biofilm microbiome on water quality: Insights from a real-scale distribution system

Biofilms, constituting over 95 % of the biomass in drinking water distribution systems, form an ecosystem impacting both the aesthetic and microbiological quality of water. This study investigates the microbiome of biofilms within a real-scale drinking water distribution system in eastern Spain, utilizing amplicon-based metagenomics. Forty-one biofilm samples underwent processing and sequencing to analyze both bacterial and eukaryotic microbiomes, with an assessment of active biomass. Genus-level analysis revealed considerable heterogeneity, with Desulfovibrio, Ralstonia, Bradyrhizobium, Methylocystis, and Bacillus identified as predominant genera. Notably, bacteria associated with corrosion processes, including Desulfovibrio, Sulfuricella, Hyphomicrobium, and Methylobacterium, were prevalent. Potentially pathogenic bacteria such as Helicobacter, Pseudomonas, and Legionella were also detected. Among protozoa, Opisthokonta and Archaeplastida were the most abundant groups in biofilm samples, with potential pathogenic eukaryotes (Acanthamoeba, Naegleria, Blastocystis) identified. Interestingly, no direct correlation between microbiota composition and pipe materials was observed. The study suggests that the usual concentration of free chlorine in bulk water proved insufficient to prevent the presence of undesirable bacteria and protozoa in biofilms, which exhibited a high concentration of active biomass.

Seasonal variations of biofilm C, N and S cycling genes in a pilot-scale chlorinated drinking water distribution system

Biofilms in drinking water distribution systems (DWDS) host diverse microorganisms. However, the functional attributes of DWDS biofilms and their associations with seasonality remain unclear. This study aims to characterize variations in the microbial metabolic traits of DWDS biofilms collected during different seasons, using a pilot-scale DWDS in dark under plug-flow conditions during one-year operation period. Network analysis was used to predict the functional gene hosts. The overall functional attributes determined by shotgun metagenomics exhibited significant differences among seasons. Genes associated with aromatic metabolism, fatty acid biosynthesis and degradation, and capsular extracellular polymeric substance (EPS) were significantly upregulated in summer owing to the higher temperatures and chlorine in the influent of the DWDS. Moreover, the pathways associated with nitrogen, sulfur, glycolysis, and tricarboxylic acid (TCA) cycling, as well as carbon fixation were reconstructed and displayed according to the sampling season. Nitrogen reduction pathways [dissimilatory nitrate reduction to ammonium (DNRA) 73 %, assimilatory nitrate reduction to ammonium (ANRA) 21 %] were identified in DWDS biofilms, but nitrogen oxidation pathways were not. Sulfur cycling were involved in diverse pathways and genes. Glycolysis and TCA cycling offered electron donors and energy sources for nitrogen and sulfur reduction in biofilms. Carbon fixation was observed in DWDS biofilms, with the predominant pathway for fixing carbon dioxide being the reductive citrate cycle (38 %). Constructed functional gene networks composed of carbon, nitrogen, and sulfur cycling-related genes demonstrated synergistic effects (Positive proportion: 63.52-71.09 %). In addition, from spring to autumn, the network complexity decreased and network modularity increased. The assembly mechanism of carbon, nitrogen and sulfur cycling-related genes was driven by stochastic processes for all samples. These results highlight the diverse functional genes in DWDS biofilms, their synergetic interrelationships, and the seasonality effect on functional attributes.

Incidence of co-resistance to antibiotics and chlorine in bacterial biofilm of hospital water systems: Insights into the risk of nosocomial infections

The presence of biofilms in drinking water distribution systems (DWDS) in healthcare settings poses a considerable risk to the biological security of water, particularly when the biofilm bacteria demonstrate antimicrobial resistance characteristics. This study aimed to investigate the occurrence of antibiotic-resistant bacteria (ARB) in biofilms within DWDS of hospitals. The chlorine resistance of the isolated ARB was analyzed, and then chlorine-resistant bacteria (CRB) were identified using molecular methods. Additionally, the presence of several antibiotic resistance genes (ARGs) was monitored in the isolated ARB. Out of the 41 biofilm samples collected from hospitals, ARB were detected in 32 (78%) of the samples. A total of 109 colonies of ARB were isolated from DWDS of hospitals, with β-lactam resistant bacteria, including ceftazidime-resistant and ampicillin-resistant bacteria, being the most frequently isolated ARB. Analyzing of ARGs revealed the highest detection of aac6, followed by sul1 gene. However, the β-lactamase genes blaCTX-M and blaTEM were not identified in the ARB, suggesting the presence of other β-lactamase genes not included in the tested panel. Exposure of ARB to free chlorine at a concentration of 0.5 mg/l showed that 64% of the isolates were CRB. However, increasing the chlorine concentration to 4 mg/l decreased the high fraction of ARB (91%). The domi‌‌nant CRB identified were Sphingomonas, Brevundimonas, Stenotrophomonas, Bacillus and Staphylococcus with Bacillus exhibiting the highest frequency. The results highlight the potential risk of biofilm formation in the DWDS of hospitals, leading to the dissemination of ARB in hospital environments, which is a great concern for the health of hospitalized patients, especially vulnerable individuals. Surveillance of antimicrobial resistance in DWDS of hospitals can provide valuable insights for shaping antimicrobial use policies and practices that ensure their efficacy.

The bacterial biofilm resistome in drinking water distribution systems: A systematic review

Antibiotic resistance in drinking water systems poses human health risks. Earlier studies, including reviews on antibiotic resistance in drinking water systems are limited to the occurrence, behaviour and fate in bulk raw water and drinking water treatment systems. By comparison, reviews on the bacterial biofilm resistome in drinking water distribution systems are still limited. Therefore, the present systematic review investigates the occurrence, behaviour and fate and, detection methods of bacterial biofilm resistome in the drinking water distribution systems. A total of 12 original articles drawn from 10 countries were retrieved and analyzed. Antibiotic resistant bacteria and antibiotic resistance genes detected in biofilms include those for sulfonamides, tetracycline, and beta-lactamase. The genera detected in biofilms include Staphylococcus, Enterococcus, Pseudomonas, Ralstonia, Mycobacteria, as well as Enterobacteriaceae family and other gram-negative bacteria. The presence of Enterococcus faecium, Staphylococcusaureus, Klebsiella pneumoniae, Acinetobacterbaumannii, Pseudomonas aeruginosa, and Enterobacter species (ESKAPE bacteria) among the detected bacteria points to potential human exposure and health risks especially for susceptible individuals via the consumption of drinking water. Besides, the effects of water quality parameter and residual chlorine, the physico-chemical factors controlling the emergence, persistence and fate of the biofilm resistome are still poorly understood. Culture-based methods, and molecular methods, and their advantages and limitations are discussed. The limited data on the bacterial biofilm resistome in drinking water distribution system points to the need for further research. To this end, future research directions are discussed including understanding the formation, behaviour, and fate of the resistome and the controlling factors.

Study on the distribution characteristics and metabolic mechanism of chlorine-resistant bacteria in indoor water supply networks

The presence and attachment of chlorine-resistant bacteria on the surface of water distribution network will deteriorate water quality and threaten human health. Chlorination is critical in drinking water treatment to ensure the biosafety of drinking water. However, how disinfectants affect the structures of dominant flora during biofilm development and whether the changes are consistent with the free flora remain unclear. Therefore, we investigated changes in species diversity and relative abundance of different bacterial communities in planktonic and biofilm samples at different chlorine residual concentrations (blank, 0.3 mg/L, 0.8 mg/L, 2.0 mg/L and 4.0 mg/L), and the main reasons for the development of chlorine resistance in bacteria was also discussed. The results showed that the richness of microbial species in the biofilm was higher than that in planktonic microbial samples. In the planktonic samples, Proteobacteria and Actinobacteria were the dominant groups regardless of the chlorine residual concentration. For biofilm samples, the dominant position of Proteobacteria bacteria was gradually replaced by actinobacteria bacteria with the increase of chlorine residual concentration. In addition, at higher chlorine residual concentration, Gram-positive bacteria were more concentrated to form biofilms. There are three main reasons for the generation of chlorine resistance of bacteria: enhanced function of efflux system, activated bacterial self-repair system, and enhanced nutrient uptake capacity.

Seasonal variations of microbial community and antibiotic resistome in a suburb drinking water distribution system in a northern Chinese city

Antibiotic resistance genes (ARGs) are an emerging issue for drinking water safety. However, the seasonal variation of ARGs in drinking water distribution systems (DWDS) is still unclear. This work revealed the tempo-spatial changes of microbial community, ARGs, mobile genetic elements (MGEs) co-occurring with ARGs, ARG hosts in DWDS bulk water by means of metagenome assembly. The microbial community and antibiotic resistome varied with sampling season and site. Temperature, ammonia, chlorite and total plate count (TPC) drove the variations of microbial community structure. Moreover, environmental parameters (total organic carbon (TOC), chlorite, TPC and hardness) shifted antibiotic resistome. ARGs and MGEs co-occurring with ARGs showed higher relative abundance in summer and autumn, which might be attributed to detached pipe biofilm. In particular, ARG-bacitracin and plasmid were the predominant ARG and MGE, respectively. ARG hosts changed with season and site and were more diverse in summer and autumn. In winter and spring, Limnohabitans and Mycobacterium were the major ARG hosts as well as the dominant genera in microbial community. In addition, in summer and autumn, high relative abundance of Achromobacter and Stenotrophomonas were the hosts harboring many kinds of ARGs and MGEs at site in a residential zone (0.4 km from the water treatment plant). Compared with MGEs, microbial community had a greater contribution to the variation of antibiotic resistome. This work gives new insights into the dynamics of ARGs in full-scale DWDS and the underlying factors.

Community Composition and Antibiotic Resistance of Tap Water Bacteria Retained on Filtration Membranes

Community composition and antibiotic resistance of tap water bacteria are still not known well enough. This study fills the gaps in knowledge regarding this matter. To provide representativeness of collected samples, tap water bacteria were concentrated from huge amounts of water, using filtration membranes monthly during the continuous, semi-annual study, covering winter and spring seasons. Biomass was investigated both using a culture-based method (for total and antibiotic-resistant culturable bacteria counts) and metagenomic DNA sequencing (for taxonomic identification of bacteria). The results showed that bacteria resistant to ceftazidime were the most prevalent among the studied resistance phenotypes, whereas bacteria resistant to amoxicillin, ciprofloxacin, and tetracycline were scarce. On average, 20,059 and 26,200 CFU/mL per month was counted in the winter and spring season, respectively, whereas in terms of antibiotic-resistant bacteria, average counts were 14,270 and 9435 CFU/mL per month in the winter and spring season, respectively. In terms of bacterial community composition, Cyanobacteria, Proteobacteria and Actinobacteria were the most abundant phyla, reaching up to 77.71%, 74.40% and 21.85%, respectively, which is supported by previous studies conducted on the same water supply network and other drinking water distribution systems across the world. No season-dependent variations were observed for culturable antibiotic-resistant bacteria or bacterial community composition. The prevalence of culturable antibiotic-resistant bacteria was not correlated with any of the identified taxa.

Occurrence of antibiotic-resistant bacteria and resistance genes in the urban water cycle

This study investigates the antibiotic resistance fate in the urban water cycle, evaluating the dynamics of antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) in three different full-scale wastewater treatment plants (WWTPs) and two drinking water treatment plants (DWTPs) located in the same geographical area (North-West of Italy). ARB (tetracycline-, ampicillin-, and sulfonamide-resistant bacteria) were quantified by plate counting and the abundances of selected ARGs (i.e., tetA, bla_TEM, and sulII) and intI1 gene were measured using quantitative real-time PCR (qPCR). Higher concentrations of ARB and ARGs were observed in the WWTPs with respect to the DWTPs identifying the WWTP as hotspot for the spread of antibiotic resistances. Although a significant reduction of ARB and ARGs was observed in WWTPs and DWTPs after the treatment, none of the detected ARB or ARGs was completely removed in drinking water. The stability of the antibiotic-resistant rates between inlet and outlet associated with the reduction of relative ARG abundances underlined that both the treatments (WWTs and DWTs) did not apply any selective pressure. The overall results highlighted the importance to investigate the antibiotic resistance dynamics in aquatic ecosystems involved in urban water cycle integrating the information obtained by culture-dependent method with the culture-independent one and the need to monitor the presence of ARB and ARGs mainly in drinking water that represents a potential route of transmission to human.

Molecular ecological networks reveal the spatial-temporal variation of microbial communities in drinking water distribution systems

Microbial activity and regrowth in drinking water distribution systems is a major concern for water service companies. However, previous studies have focused on the microbial composition and diversity of the drinking water distribution systems (DWDSs), with little discussion on microbial molecular ecological networks (MENs) in different water supply networks. MEN analysis explores the potential microbial interaction and the impact of environmental stress, to explain the characteristics of microbial community structures. In this study, the random matrix theory-based network analysis was employed to investigate the impact of seasonal variation including water source switching on the networks of three DWDSs that used different disinfection methods. The results showed that microbial interaction varied slightly with the seasons but was significantly influenced by different DWDSs. Proteobacteria, identified as key species, play an important role in the network. Combined UV-chlorine disinfection can effectively reduce the size and complexity of the network compared to chlorine disinfection alone, ignoring seasonal variations, which may affect microbial activity or control microbial regrowth in DWDSs. This study provides new insights for analyzing the dynamics of microbial interactions in DWDSs.

Antibiotic resistance genes removals in stormwater bioretention cells with three kinds of environmental conditions

Recently, increasing attention has been paid to antibiotic resistance genes (ARGs) in stormwater runoff. However, there is still no available literature about ARGs removals through stormwater bioretention cells. Batch experiments were conducted to investigate target ARGs (bla_TEM, tetR and aphA) removals under three environmental conditions, including substrate (weight ratios of sand to soil), hydraulic loading rate (HLR) and submerged area depth. The target ARGs removals were the largest (more than 5 log in the bottom outlets) in bioretention cells with 8:2 ratio of sand to soil, HLR 0.044 cm³/cm²/min and 150 mm of submerged area depth. The proportion for both iARGs and eARGs had little effect on target ARGs removals (expect extracellular bla_TEM), although distributions of target ARGs were different in substrate layers. Adsorption behavior tests indicated that both kinetics and isotherms of target ARGs adsorption by biofilms were more suitable to explain their best removals for bioretention cells with 8:2 ratio of sand to soil than that by substrate. At phylum and genus levels, there were respectively 6 dominant microflora related significantly to target ARGs levels, and their relationships changed obviously under different environmental conditions, suggesting that regulating the dominant microflora (like Verrucomicrobia and Actinobacteria) could be feasible to change ARGs removals.

Regrowth potential of chlorine-resistant bacteria in drinking water under chloramination

The regrowth of chlorine-resistant bacteria in drinking water can deteriorate water quality. The study evaluated the relationship between organic carbon and the regrowth potential of chlorine-resistant bacteria remaining in chloraminated water samples. The results showed that the community structure of bacteria changed with the increase of chloramine dosage. The order in which organic carbon utilized by bacteria was affected by the composition of bacterial community. The biodegradable dissolved organic carbon (BDOC), assimilable organic carbon (AOC), bacterial regrowth potential (BRP) and total cell concentration (TCC) in cultivated water sample after disinfection with 1.8 mg/L chloramine increased form 0.22 mg/L, 33.68 µg/L, 2.70 × 10⁵ cells/mL and 3.48 × 10⁴ cells/mL before cultivation to 1.20 mg/L, 193.90 µg/L, 4.74 × 10⁵ cells/mL and 1.46 × 10⁵ cells/mL, respectively. The increase of TCC did not result in the decrease of BDOC, AOC and BRP in the cultivated water samples. The results showed that other biodegradable organic carbon in chloraminated water samples assimilated by residual chlorine-resistant bacteria besides AOC, BDOC, and organic carbon assimilated by indigenous bacteria. AOC, BDOC, and BRP indicators used to characterize the biostability of drinking water were not enough to accurately assess the regrowth potential of chlorine-resistant bacteria remaining in drinking water. It is suggested to supplement the index of TCC in cultivated water samples, which might be able to more accurately evaluate the regrowth potential of chlorine-resistant bacteria remaining in drinking water.

Rationale for the Combined Use of Biological Processes and AOPs in Wastewater Treatment Tasks

This paper aims to form a unified concept of the integrated use of different wastewater treatment methods to form a resistant biological treatment stage of technological systems under the influence of such toxic factors as antibiotics and surfactants. The processes of mechanical treatment, ozonation, UV irradiation, and electrolytic anodic oxidation were implemented in an electrotechnological wastewater treatment facility. Wastewater treatment quality was determined by the concentration of nitrogen compounds in aqueous solutions according to the method of Lurie. Biodiagnostics of the investigated activated sludge via surfactant action was carried out at polyethylene oxide concentrations of 10, 30, and 50 mg/dm3. As a result of experiments on wastewater treatment after aquaculture, an improvement in the reduction of pollutants only by the indicator “nitrate concentration” was determined: by 20% after anodic oxidation, and by 15% after photolysis. At almost all surfactant concentrations studied, the activated sludge was not completely recovered, which was expressed in a decrease in its quantity and in the inability to aggregate flakes of activated sludge. The diameter of the growth retardation of the standard disk with antibiotic (amoxiclav) by the accumulative culture of activated sludge was 17.3 ± 2 mm at a concentration of 4 mg/dm3 and 31.3 ± 3 mm at a concentration of 6 mg/dm3. In the process of studying the state of the activated sludge’s biocenosis under the influence of such toxicants, several regularities were revealed. The directions of using combined approaches of water treatment and wastewater treatment were defined. The structural model of treatment facilities using aerobic and anaerobic bioprocesses together with advanced oxidative technologies was substantiated.