Deciphering layer formation in Red Heart Qu: A comprehensive study of metabolite profile and microbial community influenced by raw materials and environmental factors

Environmental-origin microbiota significantly influences Red Heart Qu (RH_Qu) stratification, but their microbial migration and metabolic mechanisms remain unclear. Using high-throughput sequencing and metabolomics, we divided the stratification of RH_Qu into three temperature-based stages. Phase I features rising temperatures, causing microbial proliferation and a two-layer division. Phase II, characterized by peak temperatures, sees the establishment of thermotolerant species like Bacillus, Thermoactinomyces, Rhodococcus, and Thermoascus, forming four distinct layers and markedly altering metabolite profiles. The Huo Quan (HQ), developing from the Pi Zhang (PZ), is driven by the tyrosine-melanin pathway and increased MRPs (Maillard reaction products). The Hong Xin evolves from the Rang, associated with the phenylalanine-coumarin pathway and QCs (Quinone Compounds) production. Phase III involves the stabilization of the microbial and metabolic profile as temperatures decline. These findings enhance our understanding of RH_Qu stratification and offer guidance for quality control in its fermentation process.

Antibiotic resistome in landfill leachate and impact on groundwater

Landfill leachate is a hotspot in antibiotic resistance development. However, little is known about antibiotic resistome and host pathogens in leachate and their effects on surrounding groundwater. Here, metagenomic sequencing was used to explore profiles, host bacteria, environmental risks and influencing factors of antibiotic resistome in raw and treated leachate and surrounding groundwater of three landfills. Results showed detection of a total of 324 antibiotic resistance genes (ARGs). The ARGs conferring resistance to multidrug (8.8 %-25.7 %), aminoglycoside (13.1 %-39.2 %), sulfonamide (10.0 %-20.9 %), tetracycline (5.7 %-34.4 %) and macrolide-lincosamide-streptogramin (MLS, 5.3 %-29.5 %) were dominant in raw leachate, while multidrug resistance genes were the major ARGs in treated leachate (64.1 %-83.0 %) and groundwater (28.7 %-76.6 %). Source tracking analysis suggests non-negligible influence of leachate on the ARGs in groundwater. The pathogens including Acinetobacter pittii, Pseudomonas stutzeri and P. alcaligenes were the major ARG-carrying hosts. Variance partitioning analysis indicates that the microbial community, abiotic variables and their interaction contributed most to the antibiotic resistance development. Our results shed light on the dissemination and driving mechanisms of ARGs from leachate to the groundwater, indicating that a comprehensive risk assessment and efficient treatment approaches are needed to deal with ARGs in landfill leachate and nearby groundwater. ENVIRONMENTAL IMPLICATIONS: Antibiotic resistance genes are found abundant in the landfill sites, and these genes could be disseminated into groundwater via leaching of wastewater and infiltration of leachate. This results in deterioration of groundwater quality and human health risks posed by these ARGs and related pathogens. Thus measures should be taken to minimize potential negative impacts of landfills on the surrounding environment.

Dissemination of antibiotic resistance genes from aboveground sources to groundwater in livestock farms

Antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are prevalent in various environments on livestock farms, including livestock waste, soil, and groundwater. Contamination of groundwater by ARB and ARGs in livestock farms is a growing concern as it may have potentially huge risks to human health. However, the source of groundwater-borne ARB and ARGs in animal farms remains largely unknown. In this study, different types of samples including groundwater and its potential contamination sources from aboveground (pig feces, wastewater, and soil) from both working and abandoned swine feedlots in southern China were collected and subjected to metagenomic sequencing and ARB isolation. The source tracking based on metagenomic analysis revealed that 56-95 % of ARGs in groundwater was attributable to aboveground sources. Using metagenomic assembly, we found that 45 ARGs predominantly conferring resistance to aminoglycosides, sulfonamides, and tetracyclines could be transferred from the aboveground sources to groundwater, mostly through plasmid-mediated horizontal gene transfer. Furthermore, the full-length nucleotide sequences of sul1, tetA, and TEM-1 detected in ARB isolates exhibited the close evolutionary relationships between aboveground sources and groundwater. Some isolated strains of antibiotic-resistant Pseudomonas spp. from aboveground sources and groundwater had the high similarity (average nucleotide identity > 99 %). Notably, the groundwater-borne ARGs were identified as mainly carried by bacterial pathogens, potentially posing risks to human and animal health. Overall, this study underscores the dissemination of ARGs from aboveground sources to groundwater in animal farms and associated risks.

Occurrence, fate, and risk assessment of antibiotics in conventional and advanced drinking water treatment systems: From source to tap

The occurrence and removal of 38 antibiotics from nine classes in two drinking water treatment plants (WTPs) were monitored monthly over one year to evaluate the efficiency of typical treatment processes, track the source of antibiotics in tap water and assess their potential risks to ecosystem and human health. In both source waters, 18 antibiotics were detected at least once, with average total antibiotic concentrations of 538.5 ng/L in WTP1 and 569.3 ng/L in WTP2. The coagulation/flocculation and sedimentation, sand filtration and granular activated carbon processes demonstrated limited removal efficiencies. Chlorination, on the other hand, effectively eliminated antibiotics by 48.7 ± 11.9%. Interestingly, negative removal was observed along the distribution system, resulting in a significant antibiotic presence in tap water, with average concentrations of 131.5 ng/L in WTP1 and 362.8 ng/L in WTP2. Source tracking analysis indicates that most antibiotics in tap water may originate from distribution system. The presence of antibiotics in raw water and tap water posed risks to the aquatic ecosystem. Untreated or partially treated raw water could pose a medium risk to infants under six months. Water parameters, for example, temperature, total nitrogen and total organic carbon, can serve as indicators to estimate antibiotic occurrence and associated risks. Furthermore, machine learning models were developed that successfully predicted risk levels using water quality parameters. Our study provides valuable insights into the occurrence, removal and risk of antibiotics in urban WTPs, contributing to the broader understanding of antibiotic pollution in water treatment systems.

The detailed analysis of the microbiome and resistome of artisanal blue-veined cheeses provides evidence on sources and patterns of succession linked with quality and safety traits

BACKGROUND

Artisanal cheeses usually contain a highly diverse microbial community which can significantly impact their quality and safety. Here, we describe a detailed longitudinal study assessing the impact of ripening in three natural caves on the microbiome and resistome succession across three different producers of Cabrales blue-veined cheese.

RESULTS

Both the producer and cave in which cheeses were ripened significantly influenced the cheese microbiome. Lactococcus and the former Lactobacillus genus, among other taxa, showed high abundance in cheeses at initial stages of ripening, either coming from the raw material, starter culture used, and/or the environment of processing plants. Along cheese ripening in caves, these taxa were displaced by other bacteria, such as Tetragenococcus, Corynebacterium, Brevibacterium, Yaniella, and Staphylococcus, predominantly originating from cave environments (mainly food contact surfaces), as demonstrated by source-tracking analysis, strain analysis at read level, and the characterization of 613 metagenome-assembled genomes. The high abundance of Tetragenococcus koreensis and Tetragenococcus halophilus detected in cheese has not been found previously in cheese metagenomes. Furthermore, Tetragenococcus showed a high level of horizontal gene transfer with other members of the cheese microbiome, mainly with Lactococcus and Staphylococcus, involving genes related to carbohydrate metabolism functions. The resistome analysis revealed that raw milk and the associated processing environments are a rich reservoir of antimicrobial resistance determinants, mainly associated with resistance to aminoglycosides, tetracyclines, and β-lactam antibiotics and harbored by aerobic gram-negative bacteria of high relevance from a safety point of view, such as Escherichia coli, Salmonella enterica, Acinetobacter, and Klebsiella pneumoniae, and that the displacement of most raw milk-associated taxa by cave-associated taxa during ripening gave rise to a significant decrease in the load of ARGs and, therefore, to a safer end product.

CONCLUSION

Overall, the cave environments represented an important source of non-starter microorganisms which may play a relevant role in the quality and safety of the end products. Among them, we have identified novel taxa and taxa not previously regarded as being dominant components of the cheese microbiome (Tetragenococcus spp.), providing very valuable information for the authentication of this protected designation of origin artisanal cheese. Video Abstract.

Organic pollutants adsorbed on microplastics: Potential indicators for source appointment of microplastics

Pollution by microplastics (MPs) has caused potential threats to the environment. Understanding the sources of MPs in the environment can help control their emissions and reduce environmental risks. Source apportionment of MPs has been conducted according to the characteristics of MPs themselves (such as types of polymers and morphological characteristics). However, the specificity and resolution of the appointments of sources need to be improved. Organic pollutants adsorbed on MPs can be used as a novel and reliable indicator to identify the source of MPs in the environment. In the present work, the analytical methods of MPs and organic pollutants adsorbed on MPs were critically reviewed, and the occurrence of organic pollutants and factors influencing their adsorption on MPs were discussed. Furthermore, the potential applications of organic pollutants adsorbed on MPs as indicators for determining the sources of MPs were highlighted. The study would help recognize the sources of MPs, which will support efforts aimed at reducing their emissions and further pollution of the ecosystem.

Establishing a fingerprinting method for fast catheter identification in HDR brachytherapy in vivo dosimetry

PURPOSE

To use quantities measurable during in vivo dosimetry to build unique channel identifiers, that enable detection of brachytherapy errors.

MATERIALS AND METHODS

Treatment plan of 360 patients with prostate cancer who underwent high-dose-rate brachytherapy (range, 16-25 catheters; mean, 17) were used. A single point virtual dosimeter was placed at multiple positions within the treatment geometry, and the source-dosimeter distance and dwell time were determined for each dwell position in each catheter. These values were compared across all catheters, dwell position by dwell position, simulating a treatment delivery. A catheter was considered uniquely identified if, for a given dwell position, no other catheters had the same measured values. The minimum number of dwell positions needed to identify a specific catheter and the optimal dosimeter location uniquely were determined. The radial (r) and vertical (z) dimensions of the source-dosimeter distance were also examined for their utility in discriminating catheters.

RESULTS

Using a virtual dosimeter with no uncertainties, all catheters were identified in 359 of the 360 cases with 9 dwell position measurements. When only the dwell time were measured, all catheters were uniquely identified after 1 dwell position. With a 2-mm spatial accuracy (r,z), all catheters were identified in 94% of the plans. Simultaneous measurement of source-dosimeter distance and dwell time ensured full catheter identification in all plans ranging from 2 to 6 dwell positions. The number of dwell positions needed to uniquely identify all catheters was lower when the distance from the implant center was higher.

CONCLUSIONS

The most efficient fingerprinting approach involved combining source-dosimeter distance (i.e., source tracking) and dwell time. The further the dosimeter is placed from the center of the implant the better it can uniquely identify catheters.

Mobile genetic elements affect the dissemination of antibiotic resistance genes (ARGs) of clinical importance in the environment

The prevalence of antibiotic resistance genes (ARGs) in the environment is a quintessential One Health issue that threats both human and ecosystem health; however, the source and transmission of ARGs, especially clinically important ARGs (CLIARGs), in the environment have not yet been well studied. In the present study, shotgun metagenomic approaches were used to characterize the microbiome, resistome, and mobilome composition in human feces and six different environment sample types in South China. Overall, the resistome harbored 157 CLIARGs, with specific ARG hotspots (e.g., human feces, wastewater treatment plants, livestock manure and wastewater) excreting significantly higher abundance of CLIARGs compared with the natural environment. A redundancy analysis (RDA) was performed and revealed that the bacterial community compositions and mobile genetic elements (MGEs) explained 55.08% and 34.68% of the variations in ARG abundance, respectively, indicating that both bacterial community and MGEs are key contributors to the maintenance and dissemination of CLIARGs in the environment. The network analysis revealed non-random co-occurrence patterns between 200 bacterial genera and 147 CLIARGs, as well as between 135 MGEs and 123 CLIARGs. In addition to numerous co-shared CLIARGs among different sample types, the source tracking program based on the FEAST probabilistic model was used to estimate the relative contributions of the CLIARGs from potential sources to the natural environment. The source tracking analysis results delineated that mobilome, more than microbiome, contributed CLIARG transmission from those ARG hotspots into natural environment, and the MGEs in WWTPs seem to play the most significant role in the spread of CLIARGs to the natural environment (average contribution 32.9%-46.4%). Overall, this study demonstrated the distribution and dissemination of CLIARGs in the environment, and aimed to better inform strategies to control the spread of CLIARGs into the natural environment.

Metagenomic analysis of antibiotic-resistance genes and viruses released from glaciers into downstream habitats

Glaciers serve as effective reservoirs of antibiotic resistance genes (ARGs) and viruses for millions of years. Climate change and anthropogenic activity have accelerated the melting of glaciers, but the patterns of release of ARGs and viruses from melting glaciers into downstream habitats remain unknown. We analyzed 171 metagenomic samples from glaciers and their downstream habitats and found that the abundance and diversity of ARGs were higher in glaciers (polar and plateau glaciers) than downstream habitats (Arctic Ocean, Qinghai Lake, and Yangtze River Basin), with the diversity of viruses having the opposite pattern. Proteobacteria and Actinobacteria were the main potential hosts of ARGs and viruses, and the richness of ARGs carried by the hosts was positively correlated with viral abundance, suggesting that the transmission of viruses in the hosts could disseminate ARGs. Source tracking indicated that >18 % of the ARGs and >25 % of the viruses detected in downstream habitats originated from glaciers, demonstrating that glaciers could be one of the potential sources of ARGs and viruses in downstream habitats. Increased solar radiation and emission of carbon dioxide mainly influenced the release of the ARGs and viruses from glaciers into downstream habitats. This study provides a systematic insight demonstrating the release of ARGs and viruses from the melting glaciers, potentially increasing ecological pressure.

Marine sediments are identified as an environmental reservoir for Escherichia coli: comparing signature-based and novel amplicon sequencing approaches for microbial source tracking

Viable Escherichia coli were detected in sediments near a point of wastewater discharge in a marine coastal environment in Sweden. Since high concentrations were found in the sediments nearest the pipe, this suggested that treated wastewater effluent was the source of the microbes. In order to examine this hypothesis, different bioinformatics approaches were applied using 16S rRNA gene V3-V4 amplicon sequences from the sediments. Both signature-based source tracking using sequence libraries describing known sources of fecal water pollution (SourceTracker); and, a curated source tracking method, indicated that sediments were contaminated with wastewater. The results from the curated approach were independently confirmed using differential abundance analysis (DESeq2). A number of taxa originating from wastewater were identified which can be used to describe contamination of the sediments, and examine the spread of these specific taxa, even at low relative abundance, along the urban coast. Sequences of phylum Bacteroidetes (such as Bacteroides and Prevotella) and Firmicutes (such as Romboutsia) increased in sediments with higher concentrations of E. coli. In addition, sequences from Trichococcus are proposed as an indicator for treated wastewater. All three source tracking approaches, and the detection of viable E. coli, suggest that urban sediments can be a reservoir for indicator bacteria.

Fate, risk and sources of antibiotic resistome and its attenuation dynamics in the river water-sediment system: Field and microcosm study

Antibiotic resistance genes (ARGs) in rivers have received widespread attentions. Deciphering the fate and spread mechanisms of ARGs in river system can contribute to the design of effective strategies for reducing resistome risk in the environment. Although some studies have reported the prevalence and distribution of ARGs in rivers worldwide, few have systematically explored their fates, sources and risks in river water-sediment system. Also, the role of natural sunlight on the attenuation and fate of ARGs in river remains to be demonstrated. To fill the gaps, field investigation and microcosm experiment have been conducted in this study to reveal the fate, risk, source-sink relationship and attenuation dynamics of ARGs in an urban river water-sediment system, by utilizing high-throughput sequencing-based metagenomic assembly analysis and machine-learning-based source tracking tool. In all, 527 unique ARGs belonging to 29 antimicrobial classes were identified in the river. Relatively, the level of ARGs in the sediments were significantly higher (p < 0.05) than that in the waters. Variance partitioning analysis indicated the biotic and abiotic factors co-governed the riverine resistome, totally explaining 76% and 83% variations of ARGs in the waters and sediments, respectively. Microcosm experiment under natural light and dark condition showed that light induced the decay of ARGs in the waters and might promote their transfers from waters to sediments, which were also confirmed by the attenuation dynamics of bacteria in the experimental water-sediment system. Notably, the co-occurrences of ARGs with MGEs and VFs on the same contigs suggested resistome risk in the river, and relatively, the risk scores in the sediments were significantly higher (p < 0.05) than those in the waters. Source apportionment with metagenomic resistome signatures showed the Wenyu River was the most dominant contributor of ARGs in the downstream, with average contributions of 44.5% and 40.8% in the waters and sediments, respectively.

Insights into the circular: The cryptic plasmidome and its derived antibiotic resistome in the urban water systems

Plasmids have been a concern in the dissemination and evolution of antibiotic resistance in the environment. In this study, we investigated the total pool of plasmids (plasmidome) and its derived antibiotic resistance genes (ARGs) in different compartments of urban water systems (UWSs) in three European countries representing different antibiotic usage regimes. We applied a direct plasmidome approach using wet-lab methods to enrich circular DNA in the samples, followed by shotgun sequencing and in silico contig circularisation. We identified 9538 novel sequences in a total of 10,942 recovered circular plasmids. Of these, 66 were identified as conjugative, 1896 mobilisable and 8970 non-mobilisable plasmids. The UWSs' plasmidome was dominated by small plasmids (≤10 Kbp) representing a broad diversity of mobility (MOB) types and incompatibility (Inc) groups. A shared collection of plasmids from different countries was detected in all treatment compartments, and plasmids could be source-tracked in the UWSs. More than half of the ARGs-encoding plasmids carried mobility genes for mobilisation/conjugation. The richness and abundance of ARGs-encoding plasmids generally decreased with the flow, while we observed that non-mobilisable ARGs-harbouring plasmids maintained their abundance in the Spanish wastewater treatment plant. Overall, our work unravels that the UWS plasmidome is dominated by cryptic (i.e., non-mobilisable, non-typeable and previously unknown) plasmids. Considering that some of these plasmids carried ARGs, were prevalent across three countries and could persist throughout the UWSs compartments, these results should alarm and call for attention.

Contrasting copper concentrations and isotopic compositions in two Great Lakes watersheds

Copper (Cu) stable isotopes can elucidate the biogeochemical controls and sources governing Cu dynamics in aquatic environments, but their application in larger rivers and catchments remains comparatively scarce. Here, we use major and trace element hydrogeochemical data, Cu isotope analyses, and mixing modeling, to assess Cu loads and sources in two major river systems in Ontario, Canada. In both the Spanish River and Trent River catchments, aqueous hydrochemical compositions appeared reasonably consistent, but Cu concentrations were more variable spatially. In the Spanish River, waters near (historic) industrial mining activities displayed positive Cu isotope compositions (δ65CuSRM-976 between +0.75 ‰ and +1.01 ‰), but these signatures were gradually attenuated downstream by mixing with natural background waters (δ65Cu -0.65 ‰ to -0.16 ‰). In contrast, Trent River waters exhibited more irregular in-stream Cu isotope patterns (δ65Cu from -0.75 ‰ to +0.21 ‰), beyond the variability in Cu isotope signatures observed for adjacent agricultural soils (δ65Cu between -0.26 ‰ and +0.30 ‰) and lacking spatial correlation, reflective of the more diffuse sourcing and entwined endmember contributions to Cu loads in this catchment. This work shows that metal stable isotopes may improve our understanding of the sources and baseline dynamics of metals, even in large river systems.

Municipal separate storm sewer system (MS4) dry weather flows and potential flow sources as assessed by conventional and advanced bacterial analyses

Municipal separate storm sewer systems (MS4s) function in urbanized areas to convey flows during both wet weather (i.e., stormwater) and dry weather (i.e., urban runoff as well as subsurface sources of flow) to receiving waters. While urban stormwater is known to contain microbial and chemical pollutants, MS4 dry weather flows, or non-stormwater discharges (NSWDs), are much less studied, although they are also known to contain pollutants, especially when these flows include raw sewage. In addition, some natural NSWDs (e.g., from groundwater infiltrating MS4 pipes) are critical for aquatic habitat protection. Thus, it is important to distinguish NSWD sources to prevent non-natural flows while retaining natural waters (i.e., groundwater). Here, MS4 dry weather flows were assessed by analyzing water samples from MS4 outfalls across multiple watersheds and water provider service areas in south Orange County, CA; potential NSWD sources including sewage, recycled water, potable water, and groundwater were sampled and analyzed for their likely contributions to overall NSWDs. Geochemical and microbiological water quality indicators, as well as bacterial communities, differed across NSWDs, yet water quality within most locations did not vary significantly diurnally or by sampling date. Meanwhile, NSWD source waters had distinctly different bacterial taxa abundances and specific bacterial genera. Shared geochemical and microbial characteristics of certain sources and outfall flows suggested the contributions of sources to outfall flows. The average proportions by sources contributing to MS4 outfalls were further estimated by SourceTracker and FEAST, respectively. The results of this study highlight the use of multiple tools when assessing chemical and microbiological water quality to predict sources of NSWDs contributing to urban MS4 flows during dry weather. This information can be used to support management actions to reduce unnatural and high risk sources of dry weather drainage while preserving natural sources important to environmental health in downstream receiving waters.

Fecal-related anthropogenic sources are key determinants of lake microbiomes through microbial source tracking

Lake microbiomes are essential indicators of lake health and are strongly influenced by allochthonous microbial communities from various sources within the watershed. However, quantifying the contributions of multiple inputs to lake microbiomes is challenging because of the complex nature of river‒lake systems and the presence of many untraceable sources. Here, Jianhu Lake‒‒a geographically simple and closed plateau lake in southwestern China, was surveyed to disentangle the contributions of five distinct sources (three input rivers that receive town sewage, stormwater runoff, and creek spring water, as well as two nonpoint sources, duck ponds and dry farmland) to the overall lake microbiomes. We found that feces-loading sources, namely town sewage and duck aquaculture, accounted for 48.7% of the total variations in lake microbiomes. In contrast, the combined contribution of the remaining three sources amounted to 13.21%, despite these less-influential sources (e.g., stormwater runoff) may introduce an even larger volume of allochthonous materials into the lake. In addition, approximately 38.1% of the variations in the lake microbiomes were attributed to unknown sources. Sewage effluents also caused a significant loss of lake microbial diversity, and there was a tendency for large-scale microbial homogeneity in lake sediments that resembled those from duck ponds. We then used a targeted approach to track host-specific fecal pollution, and found that human feces were the primary source, followed by ruminant and chicken/duck feces, all of which can be successfully traced back to the feces-loading sources. In our further modelling of sediment transport from three rivers into the whole lake, we observed a significant relationship between sediment accumulation and adsorbed microorganisms only for the sewage-receiving river. Together, lines of evidence indicate that both point and nonpoint fecal-related anthropogenic sources possess discriminatory power for shaping microbial geographic patterns of the lake, posing threats to the survival of local indigenous lake microbiomes.

Six-probe scintillator dosimeter for treatment verification in HDR-brachytherapy

BACKGROUND

In vivo dosimetry (IVD) is gaining interest for treatment delivery verification in HDR-brachytherapy. Time resolved methods, including source tracking, have the ability both to detect treatment errors in real time and to minimize experimental uncertainties. Multiprobe IVD architectures holds promise for simultaneous dose determinations at the targeted tumor and surrounding healthy tissues while enhancing measurement accuracy. However, most of the multiprobe dosimeters developed so far either suffer from compactness issues or rely on complex data post-treatment.

PURPOSE

We introduce a novel concept of a compact multiprobe scintillator detector and demonstrate its applicability in HDR-brachytherapy. Our fabricated seven-fiber probing system is sufficiently narrow to be inserted in a brachytherapy needle or in a catheter.

METHODS

Our multiprobe detection system results from the parallel implementation of six miniaturized inorganic Gd2 O2 S:Tb scintillator detectors at the end of a bundle of seven fibers, one fiber is kept bare to assess the stem effect. The resulting system, which is narrower than 320 microns, is tested with a MicroSelectron 9.14 Ci Ir-192 HDR afterloader, in a water phantom. The detection signals from all six probes are simultaneously read with a sCMOS camera (at a rate of 0.06 s). The camera is coupled to a chromatic filter to cancel Cerenkov signal induced within the fibers upon exposure. By implementing an aperiodic array of six scintillating cells along the bundle axis, we first determine the range of inter-probe spacings leading to optimal source tracking accuracy (first tracking method). Then, three different source tracking algorithms involving all the scintillating probes are tested and compared. In each of these four methods, dwell positions are assessed from dose measurements and compared to the treatment plan. Dwell time is also determined and compared to the treatment plan.

RESULTS

The optimum inter-probe spacing for an accurate source tracking ranges from 15 to 35 mm. The optimum detection algorithm consists of adding the readout signals from all detector probes. In that case, the error to the planned dwell positions is of 0.01 ± 0.14 mm and 0.02 ± 0.29 mm at spacings between the source and detector axes of 5.5 and 40 mm, respectively. Using this approach, the average deviations to the expected dwell time are of- 0.006 ± 0.009 $-0.006\,\pm \,0.009$ s and- 0.008 ± 0.058 $-0.008\, \pm 0.058$ s, at spacings between source and probe axes of 5.5 and 20 mm, respectively.

CONCLUSIONS

Our six-probe Gd2 O2 S:Tb dosimeter coupled to a sCMOS camera can perform time-resolved treatment verification in HDR brachytherapy. This detection system of high spatial and temporal resolutions (0.25 mm and 0.06 s, respectively) provides a precise information on the treatment delivery via a dwell time and position verification of unmatched accuracy.

Anthropogenic contributions to antibiotic resistance gene pollution in household drinking water revealed by machine-learning-based source-tracking

Although the presence of antibiotic resistance genes (ARGs) in drinking water and their potential horizontal gene transfer to pathogenic microbes are known to pose a threat to human health, their pollution levels and potential anthropogenic sources are poorly understood. In this study, broad-spectrum ARG profiling combined with machine-learning-based source classification SourceTracker was performed to investigate the pollution sources of ARGs in household drinking water collected from 95 households in 47 cities of eight countries/regions. In total, 451 ARG subtypes belonging to 19 ARG types were detected with total abundance in individual samples ranging from 1.4 × 10-4 to 1.5 × 10° copies per cell. Source tracking analysis revealed that many ARGs were highly contributed by anthropogenic sources (37.1%), mainly wastewater treatment plants. The regions with the highest detected ARG contribution from wastewater (∼84.3%) used recycled water as drinking water, indicating the need for better ARG control strategies to ensure safe water quality in these regions. Among ARG types, sulfonamide, rifamycin and tetracycline resistance genes were mostly anthropogenic in origin. The contributions of anthropogenic sources to the 20 core ARGs detected in all of the studied countries/regions varied from 36.6% to 84.1%. Moreover, the anthropogenic contribution of 17 potential mobile ARGs identified in drinking water was significantly higher than other ARGs, and metagenomic assembly revealed that these mobile ARGs were carried by diverse potential pathogens. These results indicate that human activities have exacerbated the constant input and transmission of ARGs in drinking water. Our further risk classification framework revealed three ARGs (sul1, sul2 and aadA) that pose the highest risk to public health given their high prevalence, anthropogenic sources and mobility, facilitating accurate monitoring and control of anthropogenic pollution in drinking water.

Mass-Suite: a novel open-source python package for high-resolution mass spectrometry data analysis

Mass-Suite (MSS) is a Python-based, open-source software package designed to analyze high-resolution mass spectrometry (HRMS)-based non-targeted analysis (NTA) data, particularly for water quality assessment and other environmental applications. MSS provides flexible, user-defined workflows for HRMS data processing and analysis, including both basic functions (e.g., feature extraction, data reduction, feature annotation, data visualization, and statistical analyses) and advanced exploratory data mining and predictive modeling capabilities that are not provided by currently available open-source software (e.g., unsupervised clustering analyses, a machine learning-based source tracking and apportionment tool). As a key advance, most core MSS functions are supported by machine learning algorithms (e.g., clustering algorithms and predictive modeling algorithms) to facilitate function accuracy and/or efficiency. MSS reliability was validated with mixed chemical standards of known composition, with 99.5% feature extraction accuracy and ~ 52% overlap of extracted features relative to other open-source software tools. Example user cases of laboratory data evaluation are provided to illustrate MSS functionalities and demonstrate reliability. MSS expands available HRMS data analysis workflows for water quality evaluation and environmental forensics, and is readily integrated with existing capabilities. As an open-source package, we anticipate further development of improved data analysis capabilities in collaboration with interested users.

Performance of bacterial and mitochondrial qPCR source tracking methods: A European multi-center study

With the advent of molecular biology diagnostics, different quantitative PCR assays have been developed for use in Source Tracking (ST), with none of them showing 100% specificity and sensitivity. Most studies have been conducted at a regional level and mainly in fecal slurry rather than in animal wastewater. The use of a single molecular assay has most often proven to fall short in discriminating with precision the sources of fecal contamination. This work is a multicenter European ST study to compare bacterial and mitochondrial molecular assays and was set to evaluate the efficiency of nine previously described qPCR assays targeting human-, cow/ruminant-, pig-, and poultry-associated fecal contamination. The study was conducted in five European countries with seven fecal indicators and nine ST assays being evaluated in a total of 77 samples. Animal fecal slurry samples and human and non-human wastewater samples were analyzed. Fecal indicators measured by culture and qPCR were generally ubiquitous in the samples. The ST qPCR markers performed at high levels in terms of quantitative sensitivity and specificity demonstrating large geographical application. Sensitivity varied between 73% (PLBif) and 100% for the majority of the tested markers. On the other hand, specificity ranged from 53% (CWMit) and 97% (BacR). Animal-associated ST qPCR markers were generally detected in concentrations greater than those found for the respective human-associated qPCR markers, with mean concentration for the Bacteroides qPCR markers varying between 8.74 and 7.22 log10 GC/10 mL for the pig and human markers, respectively. Bacteroides spp. and mitochondrial DNA qPCR markers generally presented higher Spearman's rank coefficient in the pooled fecal samples tested, particularly the human fecal markers with a coefficient of 0.79. The evaluation of the performance of Bacteroides spp., mitochondrial DNA and Bifidobacterium spp. ST qPCR markers support advanced pollution monitoring of impaired aquatic environments, aiming to elaborate strategies for target-oriented water quality management.

Deciphering community assembly and succession in sequencing batch moving bed biofilm reactor: Differentiation between attached and suspended communities

Elucidating community assembly and succession is crucial to understanding the ecosystem functioning. Herein, the ecological processes underpinning community assembly and succession were studied to uncover the respective ecological functions of attached biofilms and suspended biomass in a sequencing batch moving bed biofilm reactor. Compared with suspended biomass, attached biofilms presented higher relative abundances of Nitrospira (2.94 %) and Nitrosomonas (1.25 %), and contributed to 66.89 ± 11.37 % and 68.11 ± 12.72 % of nitrification and denitrification activities, respectively. The microbial source tracking result demonstrated that early formation of suspended biomass was dominated by the seeding effect of detached biofilms in the start-up period (days 0-30), while self-growth of previous suspended biomass was eventually outcompeted the seeding effect when the reactor stabilized (days 31-120). Null model and ecological network analysis further suggested distinctive ecological processes underpinning the differentiation between attached and suspended communities in the same reactor. Specifically, in the start-up period, positive interactions facilitated early formation of attached (73.84 %) and suspended communities (59.41 %), while homogenous selection (88.89 %) and homogenizing dispersal (65.71 %) governed assembly of attached and suspended communities, respectively. When the reactor stabilized, attached and suspended communities showed low composition turnover as reflected by dominant homogenizing dispersal, while they presented distinctive trends of interspecies interactions. This study sheds light on discrepant ecological processes governing community differentiation of attached biofilms and suspended biomass, which would provide ecological insights into the regulation of hybrid ecosystems.

Contribution of soil bacteria to the atmosphere across biomes

The dispersion of microorganisms through the atmosphere is a continual and essential process that underpins biogeography and ecosystem development and function. Despite the ubiquity of atmospheric microorganisms globally, specific knowledge of the determinants of atmospheric microbial diversity at any given location remains unresolved. Here we describe bacterial diversity in the atmospheric boundary layer and underlying soil at twelve globally distributed locations encompassing all major biomes, and characterise the contribution of local and distant soils to the observed atmospheric community. Across biomes the diversity of bacteria in the atmosphere was negatively correlated with mean annual precipitation but positively correlated to mean annual temperature. We identified distinct non-randomly assembled atmosphere and soil communities from each location, and some broad trends persisted across biomes including the enrichment of desiccation and UV tolerant taxa in the atmospheric community. Source tracking revealed that local soils were more influential than distant soil sources in determining observed diversity in the atmosphere, with more emissive semi-arid and arid biomes contributing most to signatures from distant soil. Our findings highlight complexities in the atmospheric microbiota that are relevant to understanding regional and global ecosystem connectivity.

SNV-FEAST: microbial source tracking with single nucleotide variants

Elucidating the sources of a microbiome can provide insight into the ecological dynamics responsible for the formation of these communities. Source tracking approaches to date leverage species abundance information; however, single nucleotide variants (SNVs) may be more informative because of their high specificity to certain sources. To overcome the computational burden of utilizing all SNVs for a given sample, we introduce a novel method to identify signature SNVs for source tracking. Signature SNVs used as input into a previously designed source tracking algorithm, FEAST, can more accurately estimate contributions than species and provide novel insights, demonstrated in three case studies.

First evidence and potential sources of novel brominated flame retardants and BDE 209 in the deepest ocean

Organic anthropogenic pollutants reach even the deepest parts of the oceans, i.e., the hadal trenches. We here presented the concentrations, influencing factors, and potential sources of polybrominated diphenyl ethers (PBDEs) and novel brominated flame retardants (NBFRs) in hadal sediments and amphipods from the Mariana, Mussau and New Britain trenches. Results showed that BDE 209 was the dominant PBDEs congener and DBDPE was the dominant NBFRs. No significant correlation was found between TOC contents and PBDEs or NBFRs levels in sediment. Lipid content and body length were the potential important factors affecting variation in pollutant concentrations in the carapace & muscle of amphipods, while the pollution levels of viscera were mainly affected by the sex and lipid content. PBDEs and NBFRs might reach trench surface seawater through long-range atmospheric transport and oceans currents but with little contribution from the Great Pacific Garbage Patch. Determination of carbon and nitrogen isotopes indicated that the pollutants were transported and accumulated in amphipods and sediment via different pathways. PBDEs and NBFRs in the hadal sediments were generally transported via the settling of sediment particles of either marine or terrigenous origin whereas in amphipods they accumulated via feeding on animal carrion through the food web. This is the first study reporting on BDE 209 and NBFR contaminations in hadal settings and provide new insight on influencing factors and sources of PBDEs and NBFRs in the deepest oceans.

Microplastic pollution in the offshore sea, rivers and wastewater treatment plants in Jiangsu coastal area in China

Offshore areas are particularly important in recognizing microplastics pollution because they are sinks of land imports and sources of ocean microplastics. This study investigated the pollution and distribution of microplastics in the offshore Sea, rivers and wastewater treatment plants (WWTPs) in Jiangsu coastal area in China. Results showed that microplastics were widely present in the offshore area, with an average abundance of 3.1-3.5 items/m³. Significantly higher abundance was present in rivers (3.7-5.9 item/m³), municipal WWTPs (13.7 ± 0.5 item/m³), and industrial WWTPs (19.7 ± 1.2 item/m³). The proportion of small-sized microplastics (1-3 mm) increased from WWTPs (53%) to rivers (64%) and the offshore area (53%). Polyamide (PA), polyethylene (PE), polyvinyl chloride (PVC), polypropylene (PP), polystyrene (PS), and rayon (RA) were dominant types of microplastics. Both living and industrial sources contributed to the prevalent microplastics in the offshore Sea. Redundancy analysis showed that small-sized microplastics (1-3 mm) were positively correlated to total phosphorus (TP), while large-sized microplastics (3-5 mm) were positively correlated to TP and NH₃-N. The abundance of PE, PP and PVC microplastics were positively correlated to TP and total nitrogen (TN), thus nutrients could be indicators of microplastics pollution in the offshore area.

Unraveling multifunction of low-temperature Daqu in simultaneous saccharification and fermentation of Chinese light aroma type liquor

Chinese liquor is produced by a representative simultaneous saccharification and fermentation process. Daqu, as a starter of Chinese liquor fermentation, affects both saccharification and fermentation. However, it is still unclear how Daqu contributed to the simultaneous saccharification and fermentation process. Here, using Chinese light aroma type liquor as a case, we identified low-temperature Daqu-originated enzymes and microorganisms that contributed to the simultaneous saccharification and fermentation using metaproteomic analysis combined with amplicon sequencing analysis. α-Amylase and glucoamylase accounted for 95 % of total saccharifying enzymes and were identified as key saccharifying enzymes. Lichtheimia was the key producer of these two enzymes (> 90 %) in low-temperature Daqu. Daqu contributed 90 % α-amylase and 99 % glucoamylase to the initial liquor fermentation. These two enzymes decreased by 35 % and 49 % until day 15 in liquor fermentation. In addition, Daqu contributed key microbial genera (91 % Saccharomyces, 6.5 % Companilactobacillus) and key enzymes (37 % alcohol dehydrogenase, 40 % lactic acid dehydrogenase, 56 % aldehyde dehydrogenase) related with formations of ethanol, lactic acid and flavour compounds to the initial liquor fermentation. The average relative abundances of these fermentation-related key microorganisms and enzymes increased by 2.78 times and 1.29 times till day 15 in liquor fermentation, respectively. It indicated that Daqu provided saccharifying enzymes for starch hydrolysis, and provided both enzymes and microorganisms associated with formations of ethanol, lactic acid and flavour compounds for liquor fermentation. This work illustrated the multifunction of low-temperature Daqu in the simultaneous saccharification and fermentation of Chinese light aroma type liquor. It would facilitate improving liquor fermentation by producing high-quality Daqu.

Assessment of plasmids for relating the 2020 Salmonella enterica serovar Newport onion outbreak to farms implicated by the outbreak investigation

BACKGROUND

The Salmonella enterica serovar Newport red onion outbreak of 2020 was the largest foodborne outbreak of Salmonella in over a decade. The epidemiological investigation suggested two farms as the likely source of contamination. However, single nucleotide polymorphism (SNP) analysis of the whole genome sequencing data showed that none of the Salmonella isolates collected from the farm regions were linked to the clinical isolates-preventing the use of phylogenetics in source identification. Here, we explored an alternative method for analyzing the whole genome sequencing data driven by the hypothesis that if the outbreak strain had come from the farm regions, then the clinical isolates would disproportionately contain plasmids found in isolates from the farm regions due to horizontal transfer.

RESULTS

SNP analysis confirmed that the clinical isolates formed a single, nearly-clonal clade with evidence for ancestry in California going back a decade. The clinical clade had a large core genome (4,399 genes) and a large and sparsely distributed accessory genome (2,577 genes, at least 64% on plasmids). At least 20 plasmid types occurred in the clinical clade, more than were found in the literature for Salmonella Newport. A small number of plasmids, 14 from 13 clinical isolates and 17 from 8 farm isolates, were found to be highly similar (> 95% identical)-indicating they might be related by horizontal transfer. Phylogenetic analysis was unable to determine the geographic origin, isolation source, or time of transfer of the plasmids, likely due to their promiscuous and transient nature. However, our resampling analysis suggested that observing a similar number and combination of highly similar plasmids in random samples of environmental Salmonella enterica within the NCBI Pathogen Detection database was unlikely, supporting a connection between the outbreak strain and the farms implicated by the epidemiological investigation.

CONCLUSION

Horizontally transferred plasmids provided evidence for a connection between clinical isolates and the farms implicated as the source of the outbreak. Our case study suggests that such analyses might add a new dimension to source tracking investigations, but highlights the need for detailed and accurate metadata, more extensive environmental sampling, and a better understanding of plasmid molecular evolution.

Antibiotic resistome in groundwater and its association with mountain springs and river

The distribution of antibiotic resistance genes (ARGs) in water sources potentially threatens drinking water safety. However, the sources of antibiotic resistome in groundwater are still under-investigated. Here, we evaluated the profiles of antibiotic resistome in peri-urban groundwater and its associated water sources (river and mountain spring) to characterize the antibiotic resistome from natural water sources on groundwater resistome. A total of 261 antibiotic resistome were detected in groundwater, mountain spring, and river samples. The relative abundances of ARGs and mobile genetic elements (MGEs) were significantly higher in the river samples than in spring water and groundwater samples. The resistome profiles were similar between groundwater and spring water but differed from the river samples. According to source tracking results, the groundwater resistome was likely to be derived from springs (28.0%-50.0%) and rivers (28.6%-48.6%), which share the same trend for the source tracking of bacterial communities. Bacterial α-diversity, bacterial β-diversity, and MGEs directly or indirectly affected the ARGs in groundwater samples. Although the abundance of groundwater resistome was not elevated by river and spring water, groundwater resistomes were diverse and may be derived from both river and spring water. We highlight the importance of groundwater resistome and its association with potential water sources, providing a better understanding and basis for the effective control of the ARG proliferation and dissemination in groundwater from exogenous water bodies in the future.

Wholegenome sequencing as the gold standard approach for control of Listeria monocytogenes in the food chain

Listeria monocytogenes has been implicated in numerous outbreaks and related deaths of listeriosis. In food production, L. monocytogenes occurs in raw food material and above all, through postprocessing contamination. The use of next-generation sequencing technologies such as whole-genome sequencing (WGS) facilitates foodborne outbreak investigations, pathogen source tracking and tracing geographic distributions of different clonal complexes, routine microbiological/epidemiological surveillance of listeriosis, and quantitative microbial risk assessment. WGS can also be used to predict various genetic traits related to virulence, stress, or antimicrobial resistance, which can be of great benefit for improving food safety management as well as public health.

Dissemination of antibiotic resistance genes from landfill leachate to groundwater

Landfill leachate, a highly concentrated organic wastewater containing diverse microorganisms and various heavy metals, has become an important reservoir of antibiotic resistance genes (ARGs). In this study, a total of 203 unique ARGs and 10 mobile genetic elements (MGEs) were identified from collected landfill leachate and groundwater. The number and abundance (normalized and absolute) of antibiotic resistome in effluent of leachate treatment plants decreased significantly compared to influent. The abundance of ARGs in groundwater increased as the distance from the leachate basin decreased. Fast expectation-maximization microbial source tracking (FEAST) showed that up to 96 % of ARGs in groundwater (GW3) may originate from nearby leachate, suggesting that ARGs in leachate can penetrate and spread into the groundwater environment. A significant correlation between ARGs and bacterial communities was identified. Together with network analysis showing the 12 bacterial taxa co-occurring with seven classes of antibiotic-associated ARGs, our results revealed the diverse potential microbial hosts of ARGs in water samples around the landfill sites. Heavy metals, bacterial community and MGEs were the driving factors shaping the ARGs patterns in the water samples, with their interactions explaining 57 % of ARGs variations. Our results provide an understanding of the distribution and dissemination of ARGs from landfill leachate to the nearby groundwater and suggest a comprehensive impact assessment of ARGs in aquatic environments of landfills.

Skin microbiota interact with microbes on office surfaces

The indoor environment is recognized as a potential contributor to human health impacts through resident microbiomes. Indoor surface microbial communities are formed from several sources, environmental and anthropogenic. In this study, we characterized the bacterial and fungal communities from various sources typical of a working office environment including dust, fingers, and computer keyboards and mice. The composition of the dust bacterial community was significantly different from the other tested surfaces (P < 0.05), whereas the dust fungal community was only significantly different from fingers (P < 0.05). Bacterial and fungal communities were both shaped by deterministic processes, and bacterial communities had a higher migration rate. Results of a network analysis showed that the microbial community interactions of keyboards and mice were mainly competitive. Fast expectation-maximization microbial source tracking (FEAST) identified the sources of > 70 % of the keyboard and mouse microbial communities. Biomarkers for each sample types were identified by LDA Effect Size (LEfSE) analysis, some of which were soil-derived and potential anthropogenic pathogens, indicating the potential for exchange of microbes among outdoor, human and indoor surfaces. The current study shows that the source of microorganisms at the office interface is highly traceable and that their migration is linked to human activity. The migration of potentially pathogenic microbes were identified, emphasising the importance of personal hygiene.

Prevalence, antibiotic resistance, and molecular epidemiology of Listeria monocytogenes isolated from imported foods in China during 2018 to 2020

A total of 1797 imported food samples collected during 2018 to 2020 were investigated for Listeria monocytogenes. Antibiotic susceptibility tests and whole genome sequencing analysis were performed for the obtained isolates. The overall prevalence of L. monocytogenes was 5.62 %; the highest prevalence was observed for pork (13.65 %), followed by fish (6.25 %), sheep casing (6.06 %), chicken (3.61 %), and beef (2.06 %). Geographical differences in prevalence were also observed for pork. Resistance to oxacillin (39.33 %) and clindamycin (16.85 %) was common, whereas resistance rates for other antibiotics were relatively low, ranging from 0 % to 6.74 %. Pork and fish isolates showed resistance to more antibiotics than beef isolates. Tetracycline and chloramphenicol resistance phenotypes strongly correlated with genotypes. The predominant serogroup was 1/2a, 3a, at 44.44 %, while the percentages of three other serogroups were similar and relatively lower, from 17.28 % to 19.75 %. Significant genetic differences were observed among lineage I and II isolates. LIPI-3 was carried by 19.75 % (16/81) of isolates and LIPI-4 by 6.17 % (5/81); all were lineage I. The stress survival island was present in 31.03 % (9/29) of lineage I and 83.02 % (44/53) of lineage II. Benzalkonium chloride tolerance genes were carried by 10.34 % (3/29) of lineage I and 23.08 % (12/52) of lineage II isolates. A total of 25 sequence types (STs) were identified, among which one was novel; ST9 and ST121 were the most prevalent. Disparate distribution of STs among food types was observed, and geographical and food related characteristics were also found for some STs. Hypervirulent STs, such as ST1, ST4 and ST6, belonged to 4b,4e,4e; carried LIPI-3 and/or LIPI-4; and some even were ECI or ECII; while only one carried SSI or BC tolerance genes. In contrast, hypo-virulent STs such as ST9 and ST121 carried SSI and BC tolerance genes, while none had LIPI-3/LIPI-4. Certain STs were detected frequently from a particular food of a particular country for a long time, indicating more attention should be given to these special persistent isolates. These findings are valuable for source tracking, prevention and control of L. monocytogenes in the global food chain.

Variation in the diversity of bacterial communities and potential sources of fecal contamination of beaches in the Huron to Erie corridor

Understanding the diversity of bacteria and E.coli levels at beaches is important for managing health risks. This study compared temporal changes of the bacterial communities of Belle Isle Beach (Detroit, MI) and Sand Point Beach (Windsor, ONT), both located near the Lake St. Clair origin of the Detroit River. Water samples collected 4 days/week for 12 weeks in summer, were subjected to 16S rRNA analysis of amplicon sequencing and E. coli enumeration. Bacterial communities changed over time, as determined by cluster dendrogram analysis, exhibiting different communities in July and August than in June and different communities at the two beaches. After June, alpha diversity decreased and relative abundance of Enterobacter (Gammaproteobacteria) increased at Sand Point; whereas, Belle Isle maintained its alpha diversity and dominance by Betaproteobacteria and Actinobacteria. Contamination at both beaches is dominated by birds (23% to 50% of samples), while only ∼10% had evidence of human-associated bacteria. High E. coli at both beaches was often associated with precipitation. Nearshore sampling counts were higher than waist-deep sampling counts. Despite the dynamic changes in bacterial communities between the two beaches, this analysis based on 16S rRNA amplicon sequencing is able to provide information about bacterial types associated with high E. coli levels and to use bacterial sequences to more precisely determine sources and health relevance of contaminants.

Per- and polyfluoroalkyl substances (PFAS) in river discharge: Modeling loads upstream and downstream of a PFAS manufacturing plant in the Cape Fear watershed, North Carolina

The Cape Fear River is an important source of drinking water in North Carolina, and many drinking water intakes in the watershed are affected by per- and polyfluoroalkyl substances (PFAS). We quantified PFAS concentrations and loads in river water upstream and downstream of a PFAS manufacturing plant that has been producing PFAS since 1980. River samples collected from September 2018 to February 2021 were analyzed for 13 PFAS at the upstream station and 43-57 PFAS downstream near Wilmington. Frequent PFAS sampling (daily to weekly) was conducted close to gauging stations (critical to load estimation), and near major drinking water intakes (relevant to human exposure). Perfluoroalkyl acids dominated upstream while fluoroethers associated with the plant made up about 47% on average of the detected PFAS downstream. Near Wilmington, Σ₄₃PFAS concentration averaged 143 ng/L (range 40-377) and Σ₄₃PFAS load averaged 3440 g/day (range 459-17,300), with 17-88% originating from the PFAS plant. LOADEST was a useful tool in quantifying individual and total quantified PFAS loads downstream, however, its use was limited at the upstream station where PFAS levels in the river were affected by variable inputs from a wastewater treatment plant. Long-term monitoring of PFAS concentrations is warranted, especially at the downstream station. Results suggest a slight downward trend in PFAS levels downstream, as indicated by a decrease in flow-weighted mean concentrations and the best-fitting LOADEST model. However, despite the cessation of PFAS process wastewater discharge from the plant in November 2017, and the phase-out of perfluorooctane sulfonic acid (PFOS) and perfluorooctanoic acid (PFOA) in North America, both fluoroethers and legacy PFAS continue to reach the river in significant quantities, reflecting groundwater discharge to the river and other continuing inputs. Persistence of PFAS in surface water and drinking water supplies suggests that up to 1.5 million people in the Cape Fear watershed might be exposed.

Conurbation size drives antibiotic resistance along the river

With growing concerns about antibiotic resistance, the tracking of antibiotic resistance genes (ARGs) in urban waterways will facilitate our increased understanding of the impact of urbanization on ARGs dissemination. In the current study, we assessed the ARGs profiles and antibiotic resistome in water samples along the Jiulong River basin, a distance of 250 km, to better understand the impact of anthropogenic activities. A total of 244 ARGs and 12 MGEs were detected from 21 sampling sites. Both relative and absolute abundance of the observed resistome decreased with increasing distance from urban areas. Ordinary least-squares (OLS) regression revealed that both the relative and absolute resistome abundance were positively correlated with city size. The resistome had several inputs and outputs and Fast Expectation Maximization Microbial Source Tracking (FEAST), suggested that the majority of the antibiotic resistome originated from anthropogenic activities. A total of 8 ARGs and 20 microbial OTUs were considered as biomarkers that differentiated the location of sampling sites. Bacterial communities were significantly correlated with ARGs according to Procrustes analysis and Mantel test, which was also supported by a co-occurrence network. Variation partitioning analysis revealed that ARG profiles were driven by multiple factors. Although antibiotic resistome abundance significantly increased near urban conurbations, overall resistome abundance decreased as the river flowed downstream. Our study highlights the effect of conurbation size on antibiotic resistance profiles within the river basin and the potential resilience of rivers to recover from ARGs contamination.

Monitoring microbial communities in intensive care units over one year in China

Healthcare-associated infections (HAIs) seriously threaten patient health in intensive care units (ICUs). Profiling the microbial composition and diversity in ICU is important to prevent HAI-related spreading. Given that microbial communities vary across different environments, the time-scale characteristics of pathogens in ICUs have not been explored in China. In our study, to study the bacterial communities of two different ICUs in China, we proceeded dynamic monitoring using 16S rRNA sequencing for a whole year among the bed sheets, bed rails, shared pulse oximeters, bedside lockers, nurses' hands, floor, and carts. Our results showed that the microbial composition significantly changed within months. Significant differences in alpha and beta diversities were also observed among the 12 sampling months in each ICU. Additionally, we found the persistence of several HAI-related bacteria, including Acinetobacter, Pseudomonas, Staphylococcus, Escherichia, and Enterococcus. Source tracking analysis showed that most bacteria in both ICUs came from buildings or human skin. With deep investigations of hospital microbial surveillance on a long-term time-scale, we hope that these results will provide constructive guidelines to prevent the spread of HAIs in ICUs.

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

Antibiotic resistance genes (ARGs) are receiving increasing concerns due to the antibiotic resistance crisis. Nevertheless, little is known about the spatial behavior and sources of extracellular ARGs (eARGs) in the chlorinated drinking water distribution systems (DWDSs). Here, tap water was continuously collected to reveal the occurrence of both eARGs and intracellular ARGs (iARGs) along a chlorinated DWDS. Afterward, the correlation between eARGs, eDNA-releasing communities, and communities of planktonic bacteria was further analyzed. The eARG concentration decreased significantly, whereas the proportion of vanA and bla_NDM-1 increased. Further, the diversity of the eDNA-releasing community increased markedly with increasing distance from the drinking water treatment plant (DWTP). Moreover, the dominant eDNA-releasing bacteria shifted from Acinetobacter, Pseudomonas, and Methylobacterium-Methylorubrum in finished water from the DWTP to Bacteroides, Faecalibacterium, Staphylococcus, and Parabacteroides in the DWDS. In terms of eARG source, thirty genera were significantly correlated with seven types of eARGs that resulted from the lysis of dead planktonic bacteria and detached biofilms. Conversely, the iARGs concentration increased, whereas the biodiversity of the planktonic bacteria community decreased in the sampling points along the DWDSs. Our findings provide critical insights into the spatial behavior and sources of eARGs, highlighting the health risks associated with ARGs in DWDSs.

Toward shotgun metagenomic approaches for microbial source tracking sewage spills based on laboratory mesocosms

Little is known about the genomic diversity of the microbial communities associated with raw municipal wastewater (sewage), including whether microbial populations specific to sewage exist and how such populations could be used to improve source attribution and apportioning in contaminated waters. Herein, we used the influent of three wastewater treatment plants in Atlanta, Georgia (USA) to perturb laboratory freshwater mesocosms, simulating sewage contamination events, and followed these mesocosms with shotgun metagenomics over a 7-day observational period. We describe 15 abundant non-redundant bacterial metagenome-assembled genomes (MAGs) ubiquitous within all sewage inocula yet absent from the unperturbed freshwater control at our analytical limit of detection. Tracking the dynamics of the populations represented by these MAGs revealed varied decay kinetics, depending on (inferred) phenotypes, e.g., anaerobes decayed faster than aerobes under the well-aerated incubation conditions. Notably, a portion of these populations showed decay patterns similar to those of common markers, Enterococcus and HF183. Despite the apparent decay of these populations, the abundance of β-lactamase encoding genes remained high throughout incubation relative to the control. Lastly, we constructed genomic libraries representing several different fecal sources and outline a bioinformatic approach which leverages these libraries for identifying and apportioning contamination signal among multiple probable sources using shotgun metagenomic data.

Seasonal disparities and source tracking of airborne antibiotic resistance genes in Handan, China

The transmission of airborne antibiotic resistance genes (ARGs) loaded on particle is a significant global public health concern. Up to date, the dispersal pattern of airborne ARGs remains unclear despite their critical role in multiregional transmission. In this study, airborne ARGs loaded on fine particulate matter (PM_2.5) and source tracking based on the airflow trajectories were performed by the potential source contribution function (PSCF) and concentration weighted trajectory (CWT) model. The results show that the absolute abundance of ARG subtypes were generally twice times higher in the winter season than that in the summer season, which could be attributable to winter haze events with high particulate matter concentrations in Handan. Exogenous input from serious haze events and local release of ARGs loaded on PM_2.5 of air masses may cause higher levels of ARGs in the winter. Moreover, based on the positive correlation between the abundance of ARGs and PM_2.5 concentration, a source tracing model of airborne ARGs was proposed to the estimate of ARGs release and dissemination. This study highlights airborne ARGs transmission loaded on PM_2.5 of air masses, which facilitating the global spread of antibiotic resistance.

MaxiCalc: A tool for online dosimetric evaluation of source-tracking based treatment verification in HDR brachytherapy

PURPOSE

Source tracking is becoming a more widely used approach in HDR brachytherapy treatment verification. While it provides a sensitive method to detect deviations from the treatment plan during delivery, it does not show the clinical significance of any detected changes. By incorporating a tool that calculates volumetric doses and DVH indices from measurements, source tracking systems can be expanded to assess dosimetric significance of any deviations from the plan.

METHODS

The source tracking dose calculation tool, MaxiCalc, was developed in MATLAB. Validation was performed by comparing doses and DVH indices calculated in MaxiCalc to those calculated by the clinical TPS, for several test plans and 10 clinical plans. Clinical implementation was demonstrated by calculating volumetric doses from a clinical source tracking event.

RESULTS

MaxiCalc showed excellent agreement with the clinical TPS for point and volumetric doses (mean difference < 0.01% and 0.1% respectively). MaxiCalc calculates dosimetrically equivalent plans to the TPS with agreement < 0.3% for all DVH indices except PTV V200%. Small differences seen for the clinical source tracking event were consistent with the known tracking uncertainties enabling them to be quantified for clinical decision making. Calculations are fast, enabling real-time use.

CONCLUSIONS

MaxiCalc is an independent tool that calculates doses and DVH indices from dwells measured with any clinical HDR brachytherapy source tracking system. This extends the capabilities of source tracking systems from determining discrepancies in positions or times during delivery to assessing the dosimetric impact of any detected deviations, allowing for more comprehensive treatment verification and evaluation.

Quantitative fatty acid signature analysis (QFASA) in indoor dust: Implication for tracking indoor source accumulation of organic pollutant exposure

Indoor dust has been used as a proxy for estimating human indoor pollutant exposure risks, yet source identification remains challenging. This study tentatively investigated whether quantitative fatty acid signature analysis (QFASA) of dust, could be applied to indicate sources and their respective contributions for a major class of indoor organic pollutants organophosphate flame retardants (OPFRs). We observed significant correlations between OPFR concentrations and lipid content (p < 0.05) in house dusts. Using 15 signature fatty acids (FAs) in various indoor sources and the QFASA model, we found that clothing (39.1% in Australia and 36.5% in China) was the predominant contributing vector of dust OPFR followed by cooking oil and pet hair. Among these sources, clothing materials were proposed to be important vectors introducing organic pollutants to the indoor environment. Our QFASA contribution estimation analyses allowed for accurate prediction of most OPFR concentrations in clothing, validating our findings that clothing materials may serve as important carrier for OPFRs in indoor migration. This is the first study attempting to identify sources of organic pollutants using QFASA in an indoor setting and will provide important insight into the transfer of organic pollutants in indoor environment.

Tracing the sources of phosphorus along the salinity gradient in a coastal estuary using multi-isotope proxies

Eutrophication in coastal water has compromised ecosystem services. Identification of phosphorus (P) sources and their load contributions are required for the development of effective nutrient management plans. In this research, multi-isotope proxies were applied to track P sources and evaluate their relative contributions in Love Creek, a coastal estuary in Delaware. The isotope values of carbon (ca. -22‰), nitrogen (ca.+6‰), and phosphate oxygen (ca.+18‰) of agricultural soils under different agricultural practices are generally similar even though their concentrations are distinctly different from forest soils (δ¹³C: ca. -27‰; δ¹³N: ca.+2‰; δ¹⁸O_P: ca.+22‰). Comparison of these parameters among potential land sources (agricultural soils, forest soils, septic wastes, and plant debris) and sink (colloids in water) revealed that the plant debris and soils from forest sources are likely dominant sources of P in freshwater sites. The contribution of terrestrial P sources gradually decreased along the salinity gradient and agricultural soil sources gradually dominanted in the saline water portion of the creek. The variations of P loads due to weather-related discharge, changing land use and activities, and seasons were high and reflected the limitation of accurate estimation of sources. Overall, these results provide improved insights into potential sources and biogeochemical processes in the estuary, which are expected to be useful for water quality monitoring programs.

Occurrence and distribution of microbial pollutants in coastal areas of the Adriatic Sea influenced by river discharge

The transport of a variety of pollutants from agricultural, industrial and urbanised areas makes rivers major contributors to the contamination of coastal marine environments. Too little is known of their role in carrying pathogens to the coast. We used DNA-based metabarcoding data to describe the microbial community composition in seawater and sediment collected in front of the estuary of the Tronto, the Chienti and the Esino, three Italian rivers with different pollution levels that empty into the north-central Adriatic Sea, and to detect and measure within these communities the relative abundance of microbial pollutants, including traditional faecal indicators and alternative faecal and sewage-associated pollutants. We then applied the FORENSIC algorithm to distinguish human from non-human sources of microbial pollution and FAPROTAX to map prokaryotic clades to established metabolic or other ecologically relevant functions. Finally, we searched the dataset for other common pathogenic taxa. Seawater and sediment contained numerous potentially pathogenic bacteria, mainly faecal and sewage-associated. The samples collected in front of the Tronto estuary showed the highest level of contamination, likely sewage-associated. The pathogenic signature showed a weak but positive correlation with some nutrients and strong correlations with some polycyclic aromatic hydrocarbons. This study confirms that rivers transport pathogenic bacteria to the coastal sea and highlights the value of expanding the use of HTS data, source tracking and functional identification tools to detect microbial pollutants and identify their sources with a view to gaining a better understanding of the pathways of sewage-associated discharges to the sea.

Elucidation of fecal inputs into the River Tagus catchment (Portugal) using source-specific mitochondrial DNA, HAdV, and phage markers

Determining the source of fecal contamination in a water body is important for the application of appropriate remediation measures. However, it has been suggested in the extant literature that this can best be achieved using a 'toolbox' of molecular- and culture-based methods. In response, this study deployed three indicators (Escherichia coli (EC), intestinal enterococci (IE) and somatic coliphages (SC)), one culture-dependent human marker (Bacteroides (GB-124) bacteriophage) and five culture-independent markers (human adenovirus (HAdV), human (HMMit), cattle (CWMit), pig (PGMit) and poultry (PLMit) mitochondrial DNA markers (mtDNA)) within the River Tagus catchment (n = 105). Water samples were collected monthly over a 13-month sampling campaign at four sites (impacted by significant specific human and non-human inputs and influenced by differing degrees of marine and freshwater mixing) to determine the dominant fecal inputs and assess geographical, temporal, and meteorological (precipitation, UV, temperature) fluctuations. Our results revealed that all sampling sites were not only highly impacted by fecal contamination but that this contamination originated from human and from a range of agricultural animal sources. HMMit was present in a higher percentage (83%) and concentration (4.20 log GC/100 mL) than HAdV (32%, 2.23 log GC/100 mL) and GB-124 bacteriophage with the latter being detected once. Animal mtDNA markers were detected, with CWMit found in 73% of samples with mean concentration of 3.74 log GC/100 mL. Correlation was found between concentrations of fecal indicators (EC, IE and SC), CWMit and season. Levels of CWMit were found to be related to physico-chemical parameters, such as temperature and UV radiation, possibly as a result of the increasing presence of livestock outside in warmer months. This study provides the first evaluation of such a source-associated 'toolbox' for monitoring surface water in Portugal, and the conclusions may inform future implementation of surveillance and remediation strategies for improving water quality.

Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads

BACKGROUND

Whole genome sequencing of cultured pathogens is the state of the art public health response for the bioinformatic source tracking of illness outbreaks. Quasimetagenomics can substantially reduce the amount of culturing needed before a high quality genome can be recovered. Highly accurate short read data is analyzed for single nucleotide polymorphisms and multi-locus sequence types to differentiate strains but cannot span many genomic repeats, resulting in highly fragmented assemblies. Long reads can span repeats, resulting in much more contiguous assemblies, but have lower accuracy than short reads.

RESULTS

We evaluated the accuracy of Listeria monocytogenes assemblies from enrichments (quasimetagenomes) of naturally-contaminated ice cream using long read (Oxford Nanopore) and short read (Illumina) sequencing data. Accuracy of ten assembly approaches, over a range of sequencing depths, was evaluated by comparing sequence similarity of genes in assemblies to a complete reference genome. Long read assemblies reconstructed a circularized genome as well as a 71 kbp plasmid after 24 h of enrichment; however, high error rates prevented high fidelity gene assembly, even at 150X depth of coverage. Short read assemblies accurately reconstructed the core genes after 28 h of enrichment but produced highly fragmented genomes. Hybrid approaches demonstrated promising results but had biases based upon the initial assembly strategy. Short read assemblies scaffolded with long reads accurately assembled the core genes after just 24 h of enrichment, but were highly fragmented. Long read assemblies polished with short reads reconstructed a circularized genome and plasmid and assembled all the genes after 24 h enrichment but with less fidelity for the core genes than the short read assemblies.

CONCLUSION

The integration of long and short read sequencing of quasimetagenomes expedited the reconstruction of a high quality pathogen genome compared to either platform alone. A new and more complete level of information about genome structure, gene order and mobile elements can be added to the public health response by incorporating long read analyses with the standard short read WGS outbreak response.

Spatiotemporal variations and source tracking of antibiotics in an ecological aquaculture farm in Southern China

Although the occurrence and distribution of antibiotics in aquatic environments and reared organisms have been widely reported, the spatiotemporal variations and sources of antibiotics throughout the rearing period of aquaculture remain unclear. In this study, the concentrations and spatiotemporal variations of antibiotics in water sources, pond water, sediment, feed, and reared shrimp samples during three rearing periods in an ecological shrimp farm in Southern China were investigated. The water, sediment, and feed samples were found to contain twelve, nine, and four types of antibiotics, respectively, and the concentration of erythromycin-H₂O was the highest among these antibiotics. No target antibiotics were detected in the reared shrimp samples from this typical shrimp farm, which employed ecological rearing with no antibiotic use throughout the rearing processes. The total concentrations of antibiotics in water source were 1.96-40.58 times higher than those in pond water. A significant decrease in the total antibiotic concentrations of the pond water was observed, while a significant increase was observed in sediment during each rearing period (p < 0.05), suggesting that antibiotics transferred from the water phase to the sediment phase in the farm. Redundancy analysis demonstrated that the chemical oxygen demand was negatively correlated with the concentration of the target antibiotics in the water samples during three rearing periods (p < 0.05). The results of calculations conducted using the concentrations of antibiotics in the water source, pond water, sediment, and feed samples detected in this study indicated that the water source was likely to be the main source of antibiotics in the rearing ponds. This study can provide a better understanding of the spatiotemporal variations and sources of antibiotics in aquaculture.

Spatiotemporal variations in chromophoric dissolved organic matter (CDOM) in a mixed land-use river: Implications for surface water restoration

A challenge for current surface water restoration and management in China is acquiring the source information for complex pollution scenarios in order to develop effective control strategies. As an important part of dissolved organic matter, chromophoric dissolved organic matter (CDOM) contains unique chemical signals related to various pollution sources. Spectral methods such as fluorescence excitation-emission matrices coupled with parallel factor analysis enable rapid and low-cost CDOM characterization for source tracking. In this study, a typical small-sized river flowing through mixed land-use regions in southeastern China, the Lujiang River, was investigated to determine the responses of CDOM to spatiotemporal factors. The effects of land-use patterns were reflected by the fluorescent components of terrestrial and sewage substances. A high and stable proportion of terrestrial-like components (C1 + C2) in each sampling period (i.e., March: 47.6 ± 5.7% and October: 44.3 ± 2.7%) indicated a high input of non-point source (NPS) pollution from both agriculture and urban areas. In addition, the difference in solar radiation intensity induced by climate and air quality changes was also reflected by variability in the photodegradation product component (C3) of terrestrial precursors between October (24.8 ± 2.6%) and March (4.5 ± 2.0%), suggesting that terrestrial components could be a sensitive indicator for NPS pollutant monitoring. Increased sewage impact in downstream regions was reflected by a spike in the tryptophan-like component (C4); temporal variations in C4 (paired t-Test, p < 0.005) also indicated that sewage substances were more prone to removal by microbial activity in warmer seasons. The dynamics of C4 could serve as a good indicator of sewage disposal performance. The results of this study demonstrate that CDOM data have important practical applications for existing water restoration campaigns in southeastern China, as well as substantial potential for routine water quality monitoring.

Paper product production identified as the main source of per- and polyfluoroalkyl substances (PFAS) in a Norwegian lake: Source and historic emission tracking

The entirety of the sediment bed in lake Tyrifjorden, Norway, is contaminated by per- and polyfluoroalkyl substances (PFAS). A factory producing paper products and a fire station were investigated as possible sources. Fire station emissions were dominated by the eight carbon perfluoroalkyl sulfonic acid (PFSA), perfluorooctanesulfonic acid (PFOS), from aqueous film forming foams. Factory emissions contained PFOS, PFOS precursors (preFOS and SAmPAP), long chained fluorotelomer sulfonates (FTS), and perfluoroalkyl carboxylic acids (PFCA). Concentrations and profiles in sediments and biota indicated that emissions originating from the factory were the main source of pollution in the lake, while no clear indication of fire station emissions was found. Ratios of linear-to branched-PFOS increased with distance from the factory, indicating that isomer profiles can be used to trace a point source. A dated sediment core contained higher concentrations in older sediments and indicated that two different PFAS products have been used at the factory, referred to here as Scotchban and FTS mixture. Modelling, based on the sediment concentrations, indicated that 42-189 tons Scotchban, and 2.4-15.6 tons FTS mixture, were emitted. Production of paper products may be a major PFAS point source, that has generally been overlooked. It is hypothesized that paper fibres released from such facilities are important vectors for PFAS transport in the aquatic environment.

Comparison of pollutant source tracking approaches: Heavy metals deposited on urban road surfaces as a case study

A range of source tracking approaches have been developed to identify sources in the environmental pollution research field. A comparison of source tracking approaches is essential for a better understanding and practical applications of these approaches. This study compared the commonly used source tracking approaches, namely positive matrix factorization (PMF), Unmix, flag element ratio (FER), and chemical mass-balance based stochastic approach (SCMD). A case study was illustrated for tracing heavy metals (Pb, Zn, Cr, Cu, and Ni) attached to road deposited sediments, which can significantly influence urban road stormwater quality. The results indicated that the accuracy of PMF and Unmix are affected by the number of chemical species used and whether useful markers can be identified for particular sources. However, this does not have an essential influence on FER and SCMD. PMF and Unmix are easier on data preparation and calculation processes but more difficult for source identification process than FER and SCMD. This study also provided recommendations related to the selection of source tracking approach based on different study scenarios and result requirements. These study results are able to provide important guidance for undertaking effective source tracking and devising environmental pollution mitigations.

Source tracking of antibiotic resistance genes in the environment - Challenges, progress, and prospects

Antibiotic resistance has become a global public health concern, rendering common infections untreatable. Given the widespread occurrence, increasing attention is being turned toward environmental pathways that potentially contribute to antibiotic resistance gene (ARG) dissemination outside the clinical realm. Studies during the past decade have clearly proved the increased ARG pollution trend along with gradient of anthropogenic interference, mainly through marker-ARG detection by PCR-based approaches. However, accurate source-tracking has been always confounded by various factors in previous studies, such as autochthonous ARG level, spatiotemporal variability and environmental resistome complexity, as well as inherent method limitation. The rapidly developed metagenomics profiles ARG occurrence within the sample-wide genomic context, opening a new avenue for source tracking of environmental ARG pollution. Coupling with machine-learning classification, it has been demonstrated the potential of metagenomic ARG profiles in unambiguously assigning source contribution. Through identifying indicator ARG and recovering ARG-host genomes, metagenomics-based analysis will further increase the resolution and accuracy of source tracking. In this review, challenges and progresses in source-tracking studies on environmental ARG pollution will be discussed, with specific focus on recent metagenomics-guide approaches. We propose an integrative metagenomics-based framework, in which coordinated efforts on experimental design and metagenomic analysis will assist in realizing the ultimate goal of robust source-tracking in environmental ARG pollution.

Effect of Pichia on shaping the fermentation microbial community of sauce-flavor Baijiu

In spontaneous food fermentation processes, environmental microbiota affects the yield and quality of the fermentation productions. Although the importance of environmental microbiota has been highlighted, the ecological processes that how the environmental microbiota affects the fermentation microbial community are poorly understood. To study the effect of the environmental microbiota on community assembly, the sources of microbiota and the ecological processes of the fermentation were characterized in sauce-flavor Baijiu. Results showed that the process of sauce-flavor Baijiu making could be divided into three phases according to fermentation parameters. Heap fermentation (phase I) was an important period for rapid temperature rise, substrate utilization and production accumulation. The microbial community of heap fermentation was characterized by decrease of diversity and rapid succession of community structure. Virgibacillus, Kroppenstedtia, Bacillus and Oceanobacillus were predominant in the initial heap fermentation, while Lactobacillus was predominant during the later stage. Pichia was the predominant fungal genus during the whole fermentation process. Then, SourceTracker results showed that Daqu provided 95.6% of the bacterial community and 28.10% of the fungal community to heap fermentation, whereas the environments (indoor ground and tools) provided 71.9% of the fungal communities (mainly Pichia) to heap fermentation. Next, the results revealed that the temperature, ethanol and microbial interaction of Pichia synergistically drove the dynamic of the microbial community during the heap fermentation process. Pichia was proved to be the heat-resistant fungi and strong competitor based on growth in different temperature and competition assays in vitro. Finally, the quick succession of heap fermentation microbiota increased the enrichment of volatile flavors such as acids and esters. Our comprehensive methods shows that Pichia, which mainly comes from the environment, can construct the microbial community of Baijiu fermentation, and highlights the importance of environmental microbiota in attempts to control and promote the formation of Baijiu fermentation microbial community. This systematic study of environmental microbiota is valuable for quality control and management during spontaneous fermentation.