Spatial behavior and source tracking of extracellular antibiotic resistance genes in a chlorinated drinking water distribution system

Comparative analysis of chlorine-resistant bacteria after chlorination and chloramination in drinking water treatment plants

Chlorine-resistant bacteria (CRB) in drinking water treatment plants (DWTPs) jeopardize water quality and pose a potential risk to human health. However, the specific response of CRB to chlorination and chloramination remains uncharacterized. Therefore, we analyzed 16 S rRNA sequencing data from water samples before and after chlorination and chloramination taken between January and December 2020. Proteobacteria and Firmicutes dominated all finished water samples. After chloramination, Acinetobacter, Pseudomonas, Methylobacterium, Ralstonia, and Sphingomonas were the dominant CRB, whereas Ralstonia, Bacillus, Acinetobacter, Pseudomonas, and Enterococcus were prevalent after chlorination. Over 75% of the CRB e.g. Acinetobacter, Pseudomonas, Bacillus, and Enterococcus were shared between the chlorination and chloramination, involving potentially pathogens, such as Acinetobacter baumannii and Pseudomonas aeruginosa. Notably, certain genera such as Faecalibacterium, Geobacter, and Megasphaera were enriched as strong CRB after chloramination, whereas Vogesella, Flavobacterium, Thalassolituus, Pseudoalteromonas, and others were enriched after chlorination according to LEfSe analysis. The shared CRB correlated with temperature, pH, and turbidity, displaying a seasonal pattern with varying sensitivity to chlorination and chloramination in cold and warm seasons. These findings enhance our knowledge of the drinking water microbiome and microbial health risks, thus enabling better infectious disease control through enhanced disinfection strategies in DWTPs.

Antibiotic resistance genes alterations in murine guts microbiome are associated with different types of drinking water

Antibiotic resistance genes (ARGs) are emerging contaminants threatening public health and commonly found in drinking water. However, the effect of different types of drinking water on ARG alterations in the gut microbiome is unclear. This study examines this issue in murine models in three phases (phase I: acclimation using ddH2O; phase II: treatment using different types of water, i.e. river water (RW), tap water (TW) and commercial bottled water (CBW); and phase III: recovery using ddH2O) using high-throughput qPCR and 16S rRNA amplicon sequencing. Results reveal that exposure to different types of drinking water could lead to significant changes in the gut microbiome, mobile genetic elements (MGEs), and ARGs. In phase II, treatment of RW and TW significantly increased the abundance of aminoglycoside and tetracycline resistance genes in mice guts (P < 0.01). In the recovery phase, consuming distilled water was found to restore ARG profiles to a certain extent in mice guts. Procrustes, network, redundancy and variation partitioning analysis indicated that ARG alterations in mice guts might relate to MGEs and bacterial communities. Our work suggests that the type of drinking water consumed may play a crucial role in shaping ARGs in gut microbiomes, emphasizing the urgent need for access to clean drinking water to mitigate the growing threat of antimicrobial resistance.

Solar/periodate inhibits ARGs transformation by degradation of DNA without damaging cell membrane

Antibiotic-resistant bacterial infections are a growing global threat to public health. Chlorine-based water disinfection and some advanced oxidation processes significantly increase the risk of ARGs release and transmission in the aquatic environment. Therefore, it is critical to develop or optimize disinfection methods to reduce the conversion and transmission of ARGs in natural water. This study investigated whether the solar/periodate (PI) system inhibited the natural transmission of ARGs and its mechanism. The results showed that solar/PI systems could effectively inhibit the propagation of ARGs in two simulated natural transformation systems, up to more than 100 times. By characterizing the cellular process of bacteria treated by the solar/PI system, we found that the solar/PI system could directly cause damage to DNA bases and its dual effect with almost no damage to the bacterial cell membrane, which was the main reason why this technology could inhibit natural transformation processes. Specifically, the inhibition effect of solar/PI on bacteria did not result in enhanced membrane permeability under appropriate PI dosage (<200 μM), which greatly reduced the risk of secondary contamination of eARGs released by traditional disinfection. Our findings could help improve existing disinfection strategies to ensure that antibiotic resistance is not spread in the natural water environment.

Landscape of antibiotic resistance genes and bacterial communities in groundwater on the Tibetan Plateau, and distinguishing their difference with low-altitude counterparts

Groundwater is a vital source of drinking water for Tibetans. Antibiotic resistance genes (ARGs) and bacterial communities in groundwater on the Tibetan Plateau remain unclear. Furthermore, the characterization of their differences between high-altitude and low-altitude groundwater is still unrevealed. Herein, 32 groundwater samples were collected on the plateau, and intra- and extracellular ARGs (iARGs and eARGs), and bacterial communities were characterised through qPCR assays to 19 ARGs and 16S rRNA sequencing. It showed top four abundant intra- and extracellular last-resort ARGs (LARGs) were blaOXA-48, mcr-1, vanA, and vanB, whereas dominant common ARGs (CARGs) were tetA and ermB, respectively. CARGs had higher abundances than LARGs, and iARGs were more frequently detected than eARGs. Proteobacteria, an invasive resident phylum, and Firmicutes dominated eDNA release. Network analysis revealed all observed LARGs co-occurred with pathogenic and non-pathogenic bacteria. Community diversity was significantly associated with longitude and elevation, while nitrate correlated with ARGs. Comparative analysis demonstrated eARG frequencies and abundances were higher at high altitudes than at low altitudes. Additionally, Acinetobacter and Pseudomonas specifically dominated at high altitudes. This study reveals the widespread prevalence of ARGs, particularly LARGs, in groundwater on the less-disturbed Tibetan Plateau and underlines the potential risks associated with the LARG-carrying bacteria. ENVIRONMENTAL IMPLICATION: Antibiotic resistance genes (ARGs), which are defined as emerging environmental contaminants, are becoming a global concern due to their ability to confer antibiotic resistance to pathogens. Our findings highlight the prevalence of ARGs, particularly LARGs, in groundwater on the Tibetan Plateau, and the possibility that naturally-occurring pathogenic and non-pathogenic bacteria carry multiple LARGs. In addition, we further reveal differences in the distribution of ARGs and bacterial community between high-altitude and low-altitude groundwater. Collectively, our findings offer an important insight into the potential public risks related to groundwater on the Tibetan Plateau.

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.

Extended chloramination significantly enriched intracellular antibiotic resistance genes in drinking water treatment plants

Chloramination and chlorination are both strong barriers that prevent the transmission of potential pathogens to humans through drinking water. However, the comparative effects of chloramination and chlorination on the occurrence of antibiotic resistance genes (ARGs) in drinking water treatment plants (DWTPs) remain unknown. Herein, the antibiotic resistome in water before and after chloramination or chlorination was analyzed through metagenomic sequencing and then verified through quantitative real-time polymerase chain reaction (qPCR). After the treatment of 90 min, chloramination led to higher enrichment of the total relative abundance of intracellular ARGs (iARGs) in water than chlorination, whereas chlorination facilitated the release of more extracellular ARGs (eARGs) than chloramination. According to redundancy and Pearson's analyses, the total concentration of the observed iARGs in the finished water exhibited a strong positive correlation with ammonium nitrogen (NH₄⁺-N) concentration, presenting a linear upward trend with an increase in the NH₄⁺-N concentration. This indicated that NH₄⁺-N is a crucial driving factor for iARG accumulation during chloramination. iARG enrichment ceases if the duration of chloramination is shortened to 40 min, suggesting that shortening the duration would be a better strategy for controlling iARG enrichment in drinking water. These findings emphasized the potential risk of antibiotic resistance after extended chloramination, shedding light on the control of transmission of antibiotic-resistant bacteria through water by optimizing disinfection procedures in DWTPs.

Metagenomics analysis of antibiotic resistance genes, the bacterial community and virulence factor genes of fouled filters and effluents from household water purifiers in drinking water

The aim of this study was to explore the influence and removal of household water purifiers (HWPs) on emerging contaminants in drinking water, and their distribution characteristics. The antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), virulence factor genes (VFGs) and bacterial communities were profiled in the fouled filters, influents, and effluents from HWPs with five steps of filtration after 150 days operation, using metagenomics. The results showed that the diversity of dominant species in Poly Propylene 1 μm (PP1) and nanofiltration membrane (NM) was significantly higher than that in other filters. Post-activated carbon (AC) was used to detect low species richness or diversity, and the highest proportion of dominant species, which contributes to the greater microbial risk of HWPs effluents in drinking water. The number of dominant bacterial genera in the filters disinfected with chloramine was higher than that in the same group disinfected with chlorine. The bacterial species richness or diversity in water was reduced by the purification of HWPs because the filter elements effectively trapped a variety of microorganisms. The relative abundance of Antibiotic efflux in the effluents of chlorinated and chloraminated HWPs was 5.58 × 10-3 and 4.60 × 10-3, respectively, which was the main resistance mechanism. High abundance of VFGs was found in HWPs effluents and the relative abundance of aggressive VFGs was significantly higher than those of defensive VFGs. Based on the co-occurrence results, 243 subtypes of ARGs co-occurred with VFGs, and a variety of bacteria were thought to be possible ARGs hosts, which indicated that the host bacteria of VFGs in HWP effluents had a stronger attack ability. The effluent of HWPs with only filtration processes is exposed to the risk of ARGs and VFGs. This study helps to understand the actual purification effect of HWPs and provides a theoretical reference for the management and control of ARGs pollution in domestic drinking water.

An Overview of the Impact of Pharmaceuticals on Aquatic Microbial Communities

Pharmaceuticals are present as pollutants in several ecosystems worldwide. Despite the reduced concentrations at which they are detected, their negative impact on natural biota constitutes a global concern. The consequences of pharmaceuticals' presence in water sources and food have been evaluated with a higher detail for human health. However, although most of the pharmaceuticals detected in the environment had not been designed to act against microorganisms, it is of utmost importance to understand their impact on the environmental native microbiota. Microbial communities can suffer serious consequences from the presence of pharmaceuticals as pollutants in the environment, which may directly impact public health and ecosystem equilibrium. Among this class of pollutants, the ones that have been studied in more detail are antibiotics. This work aims to provide an overview of the impacts of different pharmaceuticals on environmental biofilms, more specifically in biofilms from aquatic ecosystems and engineered water systems. The alterations caused in the biofilm function and characteristics, as well as bacteria antimicrobial tolerance and consequently the associated risks for public health, are also reviewed. Despite the information already available on this topic, the need for additional data urges the assessment of emerging pollutants on microbial communities and the potential public health impacts.

Microbiota and metabolites alterations in proximal and distal gastric cancer patients

Background

Globally, gastric cancer is the third most common cancer and the third leading cause of cancer death. Proximal and distal gastric cancers have distinct clinical and biological behaviors. The microbial composition and metabolic differences in proximal and distal gastric cancers have not been fully studied and discussed.

Methods

In this study, the gastric microbiome of 13 proximal gastric cancer tissues, 16 distal gastric cancer tissues, and their matched non-tumor tissues were characterized using 16S rRNA amplicon sequencing. Additionally, 10 proximal gastric cancer tissues, 11 distal gastric cancer tissues, and their matched non-tumor tissues were assessed by untargeted metabolomics.

Results

There was no significant difference in microbial diversity and richness between the proximal and distal gastric cancer tissues. At the genus level, the abundance of Rikenellaceae_RC9_gut_group, Porphyromonas, Catonella, Proteus, Oribacterium, and Moraxella were significantly increased in Proximal T, whereas that of Methylobacterium_Methylorubrum was significantly increased in Distal T. The untargeted metabolomics analysis revealed 30 discriminative metabolites between Distal T and Distal N. In contrast, there were only 4 discriminative metabolites between Proximal T and Proximal N. In distal gastric cancer, different metabolites were scattered through multiple pathway, including the sphingolipid signaling pathway, arginine biosynthesis, protein digestion and absorption, alanine, aspartate and, glutamate metabolism, etc.In proximal gastric cancer, differential microbial metabolites were mainly related to hormone metabolism.

Conclusion

Methylobacterium-Methylorubrum was significantly increased in Distal T, positively correlated with cancer-promoting metabolites, and negatively correlated with cancer-inhibiting metabolites. Rikenellaceae_RC_gut_group was significantly increased in Proximal T and positively correlated with cancer-promoting metabolites. Further studies regarding the functions of the above-mentioned microorganisms and metabolites were warranted as the results may reveal the different mechanisms underlying the occurrence and development of proximal and distal gastric cancers and provide a basis for future treatments.

Importance

First, the differences in microbial composition and metabolites between the proximal and distal gastric cancers were described; then, the correlation between microbiota and metabolites was preliminarily discussed. These microbes and metabolites deserve further investigations as they may reveal the different mechanisms involved in the occurrence and development of proximal and distal gastric cancers and provide a basis for future treatments.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12967-022-03650-x.

Comprehensive insights into profiles and bacterial sources of intracellular and extracellular antibiotic resistance genes in groundwater

Antibiotic resistance genes (ARGs), especially last-resort ARGs (LARGs), are receiving extensive attention as emerging environmental contaminants in groundwater. However, their prevalent intracellular and extracellular patterns and bacterial sources in groundwater remain unclear. Herein, groundwater samples were collected in Tianjin, and characterized based on the profiles of intracellular ARGs (iARGs) and extracellular ARGs (eARGs), as well as the resident bacterial communities and extracellular DNA (eDNA)-releasing bacterial communities. The quantitative real-time PCR assays showed that eARGs presented fewer subtypes than iARGs and generally displayed lower detection frequencies than the corresponding iARGs. Similarly, LARGs exhibited lower detection frequencies than common ARGs, but the total abundance showed no significant differences between them. Genes vanA and bla_VIM were the observed dominant LARGs, and aadA was the observed common ARG independent of location inside or outside the bacteria. Furthermore, the top 10 phyla showed much difference between the main eDNA-releasing bacteria and the dominant resident bacteria. Proteobacteria was the predominant resident bacterial phyla while dominating the source of eDNA in groundwater. Despite representing a minor portion of the abundance in the resident bacteria, Actinobacteriota, Acidobacteriota, and Chloroflex surprisingly accounted for a large majority of eDNA release. Co-occurrence patterns among persistent ARGs, the resident bacteria, and eDNA-releasing bacteria revealed that the dominant common iARG aadA and intracellular LARGs bla_VIM and vanA had significant positive correlations with Methylobacterium_Methylorubrum and Shewanella. Meanwhile, the dominant extracellular LARG bla_VIM may be released by bacteria belonging to at least five genera, including Ellin6067, Bifidobacterium, Blautia, Veillonella, and Dechloromonas. Collectively, the findings of this study extend our understanding regarding the distribution of ARGs and their bacterial sources in groundwater, and indicate the serious pollution of LARGs in groundwater, which poses potential risks to public health.

Nitrogen and sulfamethoxazole removal in a partially saturated vertical flow constructed wetland treating synthetic mariculture wastewater

This study investigated the removal of nitrogen and sulfamethoxazole (SMX), and the microbial communities in a partially saturated vertical flow constructed wetland (PS-VFCW) fed with synthetic mariculture wastewater operated at different saturated zone depths (SZDs), i.e. 51, 70, and 60 cm. Removal efficiencies were 99.8%-100.0% for COD, 34.1%-100.0% for NH4+-N, 67.8%-97.3% for total inorganic nitrogen (TIN), and 29.8%-57.2% for SMX. Excellent nitrification performance was achieved at the SZDs of 51 and 60 cm. Denitrification performed well at 70 and 60 cm SZDs. The highest TIN removal efficiency (97.3%) was achieved as the SZD was 60 cm. SMX removal was significantly influenced by SZD and was promoted by higher SZD. The removal of organics, nitrogen, and SMX mainly occurred in the unsaturated zone. Ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, denitrifying bacteria, and SMX-degrading bacteria were detected in the unsaturated and saturated zones, and showed an increasing trend in abundance along the depth.

Antibiotic Resistance in the Drinking Water: Old and New Strategies to Remove Antibiotics, Resistant Bacteria, and Resistance Genes

Bacterial resistance is a naturally occurring process. However, bacterial antibiotic resistance has emerged as a major public health problem in recent years. The accumulation of antibiotics in the environment, including in wastewaters and drinking water, has contributed to the development of antibiotic resistant bacteria and the dissemination of antibiotic resistance genes (ARGs). Such can be justified by the growing consumption of antibiotics and their inadequate elimination. The conventional water treatments are ineffective in promoting the complete elimination of antibiotics and bacteria, mainly in removing ARGs. Therefore, ARGs can be horizontally transferred to other microorganisms within the aquatic environment, thus promoting the dissemination of antibiotic resistance. In this review, we discuss the efficiency of conventional water treatment processes in removing agents that can spread/stimulate the development of antibiotic resistance and the promising strategies for water remediation, mainly those based on nanotechnology and microalgae. Despite the potential of some of these approaches, the elimination of ARGs remains a challenge that requires further research. Moreover, the development of new processes must avoid the release of new contaminants for the environment, such as the chemicals resulting from nanomaterials synthesis, and consider the utilization of green and eco-friendly alternatives such as biogenic nanomaterials and microalgae-based technologies.