Potential pathogenic microorganisms in rural wastewater treatment process: Succession characteristics, concentration variation, source exploration, and risk assessment

Pathogenic microorganisms can cause infection, sepsis, and other diseases in humans. Although municipal wastewater plants are important sources and sinks for potential pathogenic microorganisms, data on rural wastewater treatment processes are limited. The proximity of rural wastewater facilities to human settlements and the trend toward wastewater resourcing could pose risks to humans. Here, a typical village in southern China was selected to analyze potential pathogenic microorganisms in wastewater, sewage sludge, and aerosols during the collection, treatment, and discharge of domestic wastewater. The succession characteristics and concentration variations of potential pathogenic microorganisms throughout the wastewater treatment process were identified using high-throughput sequencing and culture methods. Bacteria-associated health risks in facility aerosols were estimated based on average daily dose rates from inhalation and dermal exposure. Lower amounts of pathogenic bacteria and pathogenic fungi were detected in the effluent of the 1-ton treatment scale and the 10-ton treatment scale facilities, compared to those in the influent. Pathogen effluent concentrations were significantly lower than influent concentrations after treatment in rural wastewater facilities. 16 and 29 potential pathogenic bacteria and fungi were detected in aerosols from wastewater treatment facilities, respectively. Furthermore, the potential pathogen concentrations were higher than those in the background air. Aerobic units are the main source of pathogen emissions from aerosols. There were 42 potential pathogenic bacteria and 34 potential pathogenic fungi in the sewage sludge. Biochemical units were the main source of potential pathogens in sewage sludge, and more potential airborne pathogens originated from wastewater. In rural wastewater resourcing processes with greater pollutant exposure, the effluent of rural wastewater treatment facilities (WWTFs), downstream rivers, and facility aerosols, could be important potential sources of microbial risk. Inhalation is the main pathway of human exposure to airborne bacteria. Therefore, more attention should be focused on microbiological risk in rural wastewater treatment processes.

Effects of cadmium exposure on gut microbiota and antibiotic resistance genes in Haliotis diversicolor abalone

Heavy metals in soil, water, and industrial production can affect the antibiotic resistance of bacteria. Antibiotic resistance in gut microbiota has been extensively researched. The effects of cadmium (Cd) was investigated on the gut microbiota and antibiotic resistance genes (ARGs) of Haliotis diversicolor, a commercially important abalone species. By exposing H. diversicolor to four concentrations of Cd (0 μg L-1 (control), 6.5 μg L-1 (low), 42.25 μg L-1 (medium), and 274.63 μg L-1 (high)) for 30 and 60 days, 16 types of ARG (aadA-01, aadA-02, cfr, dfrA1, ermB, floR, folA, mecA, sul2, tetB-01, tetC-01, tetD-01, tetG-01, tetM-02, tetQ, vanC-01), and 1213 genus and 27 phylum microbiomes were detected. ARGs can be resistant to aminoglycoside, beta-lactamase, macrolide-lincosamide-streptogramin B, multidrug, florfenicol, macrolide, sulfonamides, tetracyclines, and vancomycin. Cadmium exposure significantly alters the abundance of tetC-01, tetB-01, tetQ, sul2, and aadA-01. About 5% (61) of genus-level microorganisms were significantly affected by Cd exposure. Microbiota alpha and beta diversities in the 60-day 42.25 μg L-1 Cd treatment differed significantly from those in other treatments. In addition, 26 pathogens were detected, and two pathogens (Vibrio and Legionella) were significantly affected by Cd exposure. Significant correlations between pathogens and ARGs increased with increased Cd concentration after 60 days of Cd exposure. Cadmium exposure may cause gut microbiota disturbance in H. diversicolor and increase the likelihood of ARG transfer to pathogens, increasing potential ecological and economic risks.

Soil plastisphere interferes with soil bacterial community and their functions in the rhizosphere of pepper (Capsicum annuum L.)

With a growing number of research reports on microplastics (MPs), there is increasing concern regarding MPs-induced contamination in soil ecological systems. Notwithstanding, the interaction between the plastisphere and rhizosphere microbial hotspots in soil-plant systems, as well as the diversity and composition of plastisphere microbial communities in such systems, remain largely unexplored. This study evaluated the response of rhizosphere bacterial communities to MPs at three growth stages of pepper and examined the bacterial communities present on MPs (plastisphere). The 16 S rRNA revealed that, under the stress of MPs, the Chao1 and Shannon index of the pepper soil bacterial community decreased. Meanwhile the relative abundance of Actinobacteriota was decreased, and that of Proteobacteria was increased. Furthermore, the plastisphere serves as a unique microbial habitat (niche) that recruits the colonization of specific bacterial groups, including potential plastic-degrading bacteria and potential pathogens (e.g., Massilia and Pseudomonas). Simultaneously, the plastisphere recruits specific bacteria that may impact the rhizosphere soil bacterial communities, thus indirectly affecting plant growth. Functional prediction using PICRUSt2 revealed higher activity in the plastisphere for Metabolism of terpenoids and polyketides, Human diseases, and Xenobiotics biodegradation and metabolism. Notably, the human diseases metabolic pathway exhibited increased activity, suggesting potential ecological risks associated with pathogens. These results highlighted that the plastisphere serves as a unique microbial habitat (niche) in the soil ecological systems, recruiting specific bacteria and potentially interfering with the surrounding soil microbial community, thereby influencing the functional characteristics of the soil ecological systems.

Urban greenspace types influence the microbial community assembly and antibiotic resistome more in the phyllosphere than in the soil

Urban greenspace (UGS) is recognized to confer significant societal benefits, but few studies explored the microbial communities and antibiotic resistance genes (ARGs) from different urban greenspace types. Here, we collected leaf and soil samples from forest, greenbelt, and parkland to analyze microbial community assembly and ARG profile. For phyllosphere fungal community, the α-diversity was higher in forest, compared to those in greenbelt and parkland. Moreover, urban greenspace types altered the community assembly. Stochastic processes had a greater effect on phyllosphere fungal community in greenbelt and parkland, while in forest they were dominated by deterministic processes. In contrast, no significant differences in bacterial community diversity, community assembly were observed between the samples collected from different urban greenspace types. A total of 153 ARGs and mobile genetic elements (MGEs) were detected in phyllosphere and soil with resistance to the majority classes of antibiotics commonly applied to humans and animals. Structural equation model further revealed that a direct association between greenspace type and ARGs in the phyllosphere even after considering the effects of all other factors simultaneously. Our findings provide new insights into the microbial communities and antibiotic resistome of urban greenspaces and the potential risk linked with human health.

Characteristics of aerosols from swine farms: A review of the past two-decade progress

With the rapid development of large-scale and intensive swine production, the emission of aerosols from swine farms has become a growing concern, attracting extensive attention. While aerosols are found in various environments, those from swine farms are distinguished from human habitats, such as residential, suburban, and urban areas. In order to gain a comprehensive understanding of aerosols from swine farms, this paper reviewed relevant studies conducted between 2000 and 2022. The main components, concentrations, and size distribution of the aerosols were systematically reviewed. The differences between aerosols from swine farms and human living and working environments were compared. Finally, the sources, influencing factors, and reduction technologies for aerosols from swine farms were thoroughly elucidated. The results demonstrated that the concentrations of aerosols inside swine farms varied considerably, and most exceeded safety thresholds. However, further exploration is needed to fully understand the difference in airborne microorganism community structure and particles with small sizes (<1 μm) between swine farms and human living and working environments. More airborne bacterial and viruses were adhered to large particles in swine houses, while the proportion of airborne fungi in the respirable fraction was similar to that of human living and working environments. In addition, swine farms have a higher abundance and diversity of potential pathogens, airborne resistant microorganisms and resistant genes compared to the human living and working environments. The aerosols of swine farms mainly originated from sources such as manure, feed, swine hair and skin, secondary production, and waste treatment. According to the source analysis and factors influencing aerosols in swine farms, various technologies could be employed to mitigate aerosol emissions, and some end-of-pipe technologies need to be further improved before they are widely applied. Swine farms are advised not to increase aerosol concentration in human living and working environments, in order to decrease the impact of aerosols from swine farms on human health and restrain the spread of airborne potential pathogens. This review provides critical insights into aerosols of swine farms, offering guidance for taking appropriate measures to enhance air quality inside and surrounding swine farms.

Deciphering the distribution of microbial communities and potential pathogens in the household dust

The reliance of modern society on indoor environments increasing has made them crucial sites for human exposure to microbes. Extensive research has identified ecological drivers that influence indoor microbial assemblages. However, few studies have examined the dispersion of microbes in different locations of identical indoor environments. In this study, we employed PacBio Sequel full-length amplicon sequencing to examine the distribution of microbes at distinct locations in a single home and to identify the potential pathogens and microbial functions. Microbial communities differed considerably among the indoor sampling sites (P < 0.05). In addition, bacterial diversity was influenced by human activities and contact with the external environment at different sites, whereas fungal diversity did not significantly differ among the sites. Potential pathogens, including bacteria and fungi, were significantly enriched on the door handle (P < 0.05), suggesting that door handles may be hotpots for potential pathogens in the household. A high proportion of fungal allergens (34.37 %-56.50 %), which can cause skin diseases and asthma, were observed. Co-occurrence network analysis revealed the essential ecological role of microbial interactions in the development of a healthy immune system. Overall, we revealed the differences in microbial communities at different sampling sites within a single indoor environment, highlighting the distribution of potential pathogens and ecological functions of microbes, and providing a new perspective and information for assessing indoor health from a microbiological viewpoint.

Contribution of pollution gradient to the sediment microbiome and potential pathogens in urban streams draining into Lake Victoria (Kenya)

In sub-Saharan Africa (SSA), urban rivers/streams have long been subjected to anthropogenic pollution caused by urbanization, resulting in significantly altered chemical and biological properties of surface water and sediments. However, little is known about the diversity and structure of river microbial community composition and pathogens, as well as how they respond to anthropogenic inputs. High-throughput 16S rRNA amplicon sequencing and PICRUSt predictive function profiling were used in this study to conduct a comprehensive analysis of the spatial bacterial distribution and metabolic functions in sediment of two urban streams (Kisat and Auji) flowing through Kisumu City, Kenya. Results revealed that sediment samples from the highly urbanized mid and lower stream catchment zones of both streams had significantly higher levels of total organic carbon (TOC), total nitrogen (TN), total phosphorous (TP) than the less urbanized upper catchment zone, and were severely polluted with toxic heavy metals lead (Pb), cadmium (Cd), and copper (Cu). Differential distribution of Actinobacteria, Proteobacteria, Chloroflexi, and Verrucomicrobia in sediment bacterial composition was detected along stream catchment zones. The polluted mid and lower catchment zones were rich in Actinobacteria and Proteobacteria, as well as a variety of potential pathogenic taxa such as Corynebacterium, Staphylococcus, Cutibacterium, Turicella, Acinetobacter, and Micrococcus, as well as enteric bacteria such as Faecalibacterium, Shewanella, Escherichia, Klebsiella, Enterococcus, Prevotella, Legionella, Vibrio and Salmonella. Furthermore, PICRUSt metabolic inference analysis revealed an increasing enrichment in the sediments of genes associated with carbon and nitrogen metabolism, disease pathogenesis, and virulence. Environmental factors (TOC, Pb, Cd, TN, pH) and geographical distance as significant drivers of sediment bacterial community assembly, with the environmental selection to play a dominant role. In polluted river catchment zone sediment samples, Pb content was the most influential sediment property, followed by TOC and Cd content. Given the predicted increase in urbanization in SSA, further alteration of surface water and sediment microbiome due to urban river pollution is unavoidable, with potential long-term effects on ecosystem function and potential health hazards. As a result, this study provides valuable information for ecological risk assessment and management of urban rivers impacted by diffuse and point source anthropogenic inputs, which is critical for future proactive and sustainable urban waste management, monitoring, and water pollution control in low-income countries.

Plastisphere showing unique microbiome and resistome different from activated sludge

Plastisphere (the biofilm on microplastics) in wastewater treatment plants (WWTPs) may enrich pathogens and antibiotic resistance genes (ARGs) which can cause risks to the ecological environment by discharging into receiving waters. However, the microbiome and resistome of plastisphere in activated sludge (AS) systems remain inconclusive. Here, metagenome was applied to investigate the microbial composition, functions and ARGs of the Polyvinyl chloride (PVC) plastisphere in lab-scale reactors, and revealed the effects of tetracycline (TC) and/or Cu(II) pressures on them. The results indicated that the plastisphere provided a new niche for microbiota showing unique functions distinct from the AS. Particularly, various potentially pathogenic bacteria tended to enrich in PVC plastisphere. Moreover, various ARGs were detected in plastisphere and AS, but the plastisphere had more potential ARGs hosts and a stronger correlation with ARGs. The ARGs abundances increased after exposure to TC and/or Cu(II) pressures, especially tetracycline resistance genes (TRGs), and the results further showed that TRGs with different resistance mechanisms were separately enriched in plastisphere and AS. Furthermore, the exogenous pressures from Cu(II) or/and TC also enhanced the association of potential pathogens with TRGs in PVC plastisphere. The findings contribute to assessing the potential risks of spreading pathogens and ARGs through microplastics in WWTPs.

Spatiotemporal variations of microbial assembly, interaction, and potential risk in urban dust

Community and composition of dust-borne microbes would affect human health and are regulated by microbial community assembly. The dust in kindergarten is always collected to evaluate the microbial exposure of children, yet the microbial assembly, their interactions, and potential pathogens in kindergarten dust remain unclear. Here, we aim to investigate the microbial community assembly and structures, and potential bacterial pathogens in outdoor dust of kindergartens, and reveal the factors influencing the assembly and composition of microbial community. A total of 118 urban dust samples were collected on the outdoor impervious surfaces of 59 kindergartens from different districts of Xiamen in January and June 2020. We extracted microbial genomic DNA in these dusts and characterized the microbial (i.e., bacteria and fungi) community compositions and diversities using target gene-based (16S rRNA genes for bacterial community and ITS 2 regions for fungal community) high-throughput sequencing. Potential bacterial pathogens were identified and the interactions between microbes were determined through a co-occurrence network analysis. Our results showed the predominance of Actinobacteria and α-Proteobacteria in bacterial communities and Capnodiales in fungal communities. Season altered microbial assembly, composition, and interactions, with both bacterial and fungal communities exhibiting a higher heterogeneity in summer than those in winter. Although stochastic processes predominated in bacterial and fungal community assembly, the season-depended environmental factors (e.g., temperature) and interactions between microbes play important roles in dust microbial community assembly. Potential bacterial pathogens were detected in all urban dust, with significantly higher relative abundance in summer than that in winter. These results indicated that season exerted more profound effects on microbial community composition, assembly, and interactions, and suggested the seasonal changes of potential risk of microbes in urban dust. Our findings provide new insights into microbial community, community assembly, and interactions between microbes in the urban dust, and indicate that taxa containing opportunistic pathogens occur commonly in urban dust.

The occurrence of potential pathogenic bacteria on international ships' ballast water at Yangshan Port, Shanghai, China

Ballast water is a primary vector for the global transfer of non-indigenous species, which threaten the balance of aquatic ecosystems. The second-generation high-throughput sequencing (HTS) and culture method (by the first-generation sequencing technology) were used to explore pathogens in ballast water from international ships on the routes of China-Australia (AU), China-Europe (E) and China-America (AM). No significant differences in dominant bacteria among ballast water samples from different routes. Thirty-four pathogens were detected in all samples by HTS, including Acinetobacter lwoffii, Brevundimonas vesicular and Pseudomonas sp., etc., while nine pathogens were detected by culture, including Pseudoalteromonas piscicida, Rhodococcus erythropolis and Vibrio alginolyticus, etc. All ballast water carried a potential bacteriological risk to Yangshan Port. The abundance of pathogens was significant affected by holding time, temperature, salinity and NH₄. Detection of pathogens as much as possible through different technologies is desirable, more pathogens could provide beneficial information for enhancing ballast water management.

Membrane-covered composting significantly decreases methane emissions and microbial pathogens: Insight into the succession of bacterial and fungal communities

In this study, the effects of semipermeable membrane-covered on methane emissions and potential pathogens during industrial-scale composting of the solid fraction of dairy manure were investigated. The results showed that the oxygen concentration in the membrane-covered group (CT) was maintained above 10 %, and the cumulative methane emission in CT was >99 % lower than that in the control group (CK). Microbial analysis showed that the bacterial genus Thermus and the fungal genus Mycothermus were dominant in CT, and the richness and diversity of the bacterial community were greater than those of the fungal community. At the end of the composting, the relative abundance of potential bacterial pathogens in CT was 32.59 % lower than that in CK, and the relative abundance of potential fungal pathogens in each group was <2 %. Structural equation models revealed that oxygen concentration was a major factor influencing the bacterial diversity in CT, and the increase of oxygen concentration could limit methane emissions by inhibiting the growth of anaerobic bacteria. Therefore, membrane-covered composting could effectively improve compost safety and reduce methane emissions by regulating microbial community structure.

Corpse decomposition of freshwater economic fish leads to similar resistomes and the enrichment of high-risk antibiotic resistance genes in different water types

Animal carcass decay produces many poisonous metabolites and chemical pollutants, which pose potential ecological risks to the aquatic environment and human health. However, the effects of animal cadaver decomposition on high-risk antibiotic resistance genes (ARGs) and potential pathogens in different water types are still unknown. In this study, fifteen freshwater economic fish (Carassius auratus) corpses were put into three types of water (i.e., pond water, tap water, and domestic sewage) for a 100-day decomposition. Next generation sequencing and HT-qPCR were used to illustrate how corpse decomposition affected microbial communities and ARG profiles. Our results revealed that fish corpse degradation caused similar resistomes and microbiome in different water types. MLSB (Macrolide-Lincosamide-Streptogramin B), β-lactamase, sulfonamide, tetracycline resistance genes and transposase genes in the experimental groups were increased. Among them, tetracycline resistance genes were enriched by 224 to 136,218-fold during the process of corpse degradation. Furthermore, high-risk ARGs (ermB, floR and dfrA1), which resist to MLSB, multidrug and sulfonamide respectively, were significantly enriched in the cadaver groups and had co-occurrence patterns with opportunistic pathogens, such as Bacteroidetes, which was more than 37 times in carcass groups than that in control groups. The study is able to draw a general conclusion that cadaver decomposition of freshwater economic fish deteriorates the aquatic environment by affecting high-risk ARGs and pathogenic microorganisms regardless of water types, which poses potential threats to human health. Therefore, timely management and treatment of animal carcasses is of great significance to the protection of water environment.

Antibiotic resistance of airborne bacterial populations in a hospital environment

Bacteria in a hospital environment potentially cause hospital-acquired infections (HAIs), particularly in immunocompromised individuals. Treatments of HAIs with antibiotics, however, are ineffective due to the emergence of antibiotic-resistant bacteria (ARB). This study aims to identify airborne bacteria in a tertiary hospital in Malaysia and screen for their resistance to commonly used broad-spectrum antibiotics. Airborne bacteria were sampled using active sampling at the respiratory ward (RW), physician clinic (PC) and emergency department (ED). Physical parameters of the areas were recorded, following the Industry Code of Practice on Indoor Air Quality 2010 (ICOP IAQ 2010). Bacterial identification was based on morphological and biochemical tests. Antibiotic resistance screening was carried out using the Kirby-Bauer disk diffusion method. Results showed that the highest bacterial population was found in the highest density occupancy area, PC (1024 ± 54 CFU/m³), and exceeded the acceptable limit. Micrococcus spp., Staphylococcus aureus, α- and β-Streptococcus spp., Bacillus spp. and Clostridium spp. colonies were identified at the sampling locations. The antibiotic resistance screening showed a vast percentage of resistance amongst the bacterial colonies, with resistance to ampicillin observed as the highest percentage (Micrococcus spp.: 95.2%, S. aureus: 100%, Streptococcus spp.: 75%, Bacillus spp.: 100% and Clostridium spp.: 100%). This study provides awareness to healthcare practitioners and the public on the status of the emergence of ARB in a hospital environment. Early detection of bacterial populations and good management of hospital environments are important prevention measures for HAI.

Succession and change of potential pathogens in the co-composting of rural sewage sludge and food waste

Composting is an effective way to prevent and control the spread of pathogenic microorganisms which could put potential risk to humans and environment, from rural solid waste, especially sewage sludge and food waste. In the study, we aim to analyze the changes of pathogenic bacteria during the co-composting of rural sewage sludge and food waste. The results showed that only 27 pathogenic bacteria were detected after composting, compared to 50 pathogenic bacteria in the raw mixed pile. About 74% of pathogen concentrations dropped below 1000 copies/g after composting. Lactobacillus, Bacillus, Paenibacillus and Comamonas were the core pathogenic bacteria in the compost, of which concentrations were all significantly lower than that in the raw mixed pile at the end of composting. The concentration of Lactobacillus decreased to 3.03 × 10³ copies/g compared to 0 d with 1.25 × 10⁹ copies/g by the end of the composting, while that of Bacillus, Paenibacillus and Comamonas decreased to 2.77 × 10⁴ copies/g, 2.13 × 10⁴ copies/g and 3.38 × 10² copies/g, respectively, with 1.26 × 10⁷ copies/g, 4.71 × 10⁶ copies/g, 1.69 × 10⁸ copies/g on 0 d. Redundancy analysis (RDA) indicated that physicochemical factors and substances could affect the changes of pathogenic bacteria during composting, while temperature was the key influencing factor. In addition, certain potential pathogenic bacteria, such as Bacteroides-Bifidobacterium, show statistically strong and significant co-occurrence during composting, which may increase the risk of multiple infections and also influence their distribution. These findings provide a theoretical reference for biosafety prevention and control in the treatment and disposal of rural solid waste.

Behaviors of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) during the pilot-scale biophysical drying treatment of sewage sludge: Reduction of ARGs and enrichment of MRGs

Biophysical drying (BPD) is one of the best alternatives for reducing the moisture content from sewage sludge by utilizing biological heat from aerobic reactions. However, the fate of emerging pollutants during BPD process is largely unknown. In this study, the fates of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) were investigated during a pilot-scale BPD treatment of sewage sludge. A total of 20 types (388 subtypes) of ARGs and 16 types (364 subtypes) of MRGs were detected by metagenomic sequencing and annotation. The total abundance of ARGs decreased from 1.78 ± 0.13 copies/16S rRNA to 0.55 ± 0.01 copies/16S rRNA while the total abundance of MRGs increased from 3.81 ± 0.01 copies/16S rRNA to 6.30 ± 0.02 copies/16S rRNA, showing the distinct behaviors of ARGs and MRGs during BPD process. The ARGs were effectively reduced during the mesophilic and thermophilic stages of BPD process and the reduction of ARGs fitted the first-order kinetic model (p < 0.01). Microbial community analysis showed that the abundance of potential pathogens also decreased during BPD process. On the contrary, the abundances of most MRG subtypes (78.3%) were enriched during BPD process with up to 122-fold change, implying the potential threats for the end product of BPD process. These results together indicate that although the ARGs and potential pathogens can be effectively reduced during BPD process, the safety for the end product still needs to be considered due to the enrichment of MRGs.

Heavy metals and microbiome are negligible drivers than mobile genetic elements in determining particle-attached and free-living resistomes in the Yellow River

Suspended particles in water can shelter both microorganisms and contaminants. However, the emerging pollutants antibiotic resistance genes (ARGs) in free-living (FL) or particle-attached (PA) bacteria in aquatic environments are less explored. In this study, we compared the free-living and particle-attached ARGs during four seasons in the Yellow River using high-throughput quantitative PCR techniques and 16S rRNA gene sequencing. Our results demonstrated that both the free-living water and particles were dominated by tetracycline and beta-lactamase resistance genes. The PA-ARGs had a higher absolute abundance than FL-ARGs in the Yellow River, regardless of the season. Both PA-ARGs and FL-ARGs had the highest absolute abundance and diversity during winter. Mobile genetic elements (MGEs) were the dominant driver for both size-fractionated ARGs. However, the microbiome had less influence on PA-ARG profiles than the FL-ARG profiles, while the effects of the heavy metals on ARGs were negligible. The community assembly of both FL-ARG and PA-ARG can be explained by neutral processes. Several opportunistic pathogens (e.g., Escherichia coli) associated with human health exhibited a higher relative abundance in the particles than during a free-living lifestyle. Parts of these pathogens were potential ARG hosts. As such, it is important to monitor the ARGs and opportunistic pathogens from size-fractionated bacteria and develop targeted strategies to manage ARG dissemination and opportunistic pathogens to ensure public health.

Seasonal distribution of antibiotic resistance genes in the Yellow River water and tap water, and their potential transmission from water to human

The prevalence and transmission of antibiotic resistance genes (ARGs) and opportunistic pathogens in water environments can pose great threat to public health. However, the dissemination of ARGs and opportunistic pathogens from water environments to humans has been poorly explored. Here, we employed 16S rRNA gene sequencing and high-throughput quantitative PCR techniques to explore the seasonal distribution of ARGs and opportunistic pathogens in the Yellow River water (source water) and tap water, as well as their relationships with healthy humans at Lanzhou, China. Physiochemical analysis was applied to detect water quality parameters and heavy metal contents. The absolute abundance and diversity of ARGs in the Yellow River and tap water demonstrated distinct seasonal patterns. In winter, the Yellow river water had the highest ARG abundance and diversity, while tap water owned the lowest. Mobile genetic elements (MGEs) were the predominant driver of ARG profiles in both the Yellow river and tap water. Null model analysis showed that ARG assembly in the Yellow River was more influenced by stochastic processes than tap water and this was independent of seasons. Total organic carbon and arsenic contents exhibited positive correlations with many ARGs. Opportunistic pathogens Aeromonas and Pseudomonas may be potential hosts for ARGs. Approximately 80% of detected ARGs were shared between water samples and the human gut. These persistent ARGs could not be entirely eliminated through drinking water treatment processes. Thus, it is crucial to protect sources of tap water from anthropogenic pollution and improve water treatment technologies to reduce the dissemination of ARGs and ensure drinking-water biosafety for human health.

Prevalence, Drug Resistance, and Virulence Genes of Potential Pathogenic Bacteria in Pasteurized Milk of Chinese Fresh Milk Bar

Fresh Milk Bar (FMB), an emerging dairy retail franchise, is used to instantly produce and sell pasteurized milk and other dairy products in China. However, the quality and safety of pasteurized milk in FMB have received little attention. The objective of this study was to investigate the prevalence, antimicrobial resistance, and virulence genes of Escherichia coli, Staphylococcus aureus, and Streptococcus in 205 pasteurized milk samples collected from FMBs in China. Four (2.0%) isolates of E. coli, seven (3.4%) isolates of S. aureus, and three (1.5%) isolates of Streptococcus agalactiae were isolated and identified. The E. coli isolates were resistant to amikacin (100%), streptomycin (50%), and tetracycline (50%). Their detected resistance genes include aac(3)-III (75%), blaTEM (25%), aadA (25%), aac(3)-II (25%), catI (25%), and qnrB (25%). The S. aureus isolates were mainly resistant to penicillin G (71.4%), trimethoprim-sulfamethoxazole (71.4%), kanamycin (57.1%), gentamicin (57.1%), amikacin (57.1%), and clindamycin (57.1%). blaZ (42.9%), mecA (28.6%), ermB (14.3%), and ermC (14.3%) were detected as their resistance genes. The Streptococcus strains were mainly resistant to tetracycline (66.7%) and contained the resistance genes pbp2b (33.3%) and tetM (33.3%). The virulence genes eae and stx2 were only found in one E. coli strain (25%), sec was detected in two S. aureus strains (28.6%), and bca was detected in one S. agalactiae strain (33.3%). The results of this study indicate that bacteria with drug resistance and virulence genes isolated from the pasteurized milk of FMB are a potential risk to consumers' health.

Characterization of fungal communities on shared bicycles in Southwest China

BACKGROUND

The widespread use of shared bicycles has increased the demand and sanitary requirements for shared bicycles. Previous studies have identified potentially pathogenic bacteria on the surfaces of shared bicycles, but fungal communities have not been investigated.

METHODS

We sampled shared-bicycle handles and saddles from five selected locations in a metropolis (Chengdu, China, n = 98) and used surrounding air deposition samples as controls (n = 12). Full-length ITS sequencing and multiple bioinformatic analyses were utilized to reveal fungal community structures and differences.

RESULTS

Aspergillus was dominant on both the handles and saddles of shared bicycles, and Alternaria and Cladosporium were the most abundant families in the air samples. Significant differences in fungal community structures were found among the three groups. The handle samples contained higher abundances of Aureobasidium melanogenum and Filobasidium magnum than the saddle and air samples. The saddle samples had a higher abundance of Cladosporium tenuissimum than the other two sample types (P < 0·05). A higher abundance of fungal animal pathogens on shared-bicycle surfaces than in air by FUNGuild (P < 0·05). Moreover, the co-occurrence network of fungi on handles was more stable than that on saddles.

CONCLUSION

There were more potential pathogens, including Aspergillus pseudoglaucus, Aureobasidium melanogenum, Kazachstania pintolopesii, Filobasidium magnum, Candida tropicalis, and Malassezia globose were found on shared bicycles than in air, suggesting that hands should not contact mucous membrane after cycling, especially in susceptible individuals, and hygiene management of shared bicycles should be given more attention by relevant organizations worldwide.

The aerobiome uncovered: Multi-marker metabarcoding reveals potential drivers of turn-over in the full microbial community in the air

Air is a major conduit for the dispersal of organisms at the local and the global scale. Most research has focused on the dispersal of plants, vertebrates and human disease agents. However, the air represents a key dispersal medium also for bacteria, fungi and protists. Many of those represent potential pathogens of animals and plants and have until now gone largely unrecorded. Here we studied the turnover in composition of the entire aerobiome, the collective diversity of airborne microorganisms. For that we performed daily analyses of all prokaryotes and eukaryotes (including plants) using multi-marker high-throughput sequencing for a total of three weeks. We linked the resulting communities to local weather conditions, to assess determinants of aerobiome composition and distribution. We observed hundreds of microbial taxa, mostly belonging to spore-forming organisms including fungi, but also protists. Additionally, we detected many potential human- and plant-pathogens. Community composition fluctuated on a daily basis and was linked to concurrent weather conditions, particularly air pressure and temperature. Using network analyses, we identified taxonomically diverse groups of organisms with correlated temporal dynamics. In part, this was due to co-variation with environmental conditions, while we could also detect specific host-parasite interactions. This study provides the first full inventory of the aerobiome and identifies putative drivers of its dynamics in terms of taxon composition. This knowledge can help develop early warning systems against pathogens and improve our understanding of microbial dispersal.

Microbial community and antibiotic resistance genes of biofilm on pipes and their interactions in domestic hot water system

This study aimed to explore the dynamics of microbial communities and antibiotic resistance genes (ARGs) during biofilm formation on polypropylene random (PPR), polyvinyl chloride and stainless steel pipes in domestic hot water system (DHWS), as well as their interactions. Full-scale classification was used to divide abundant and rare genera with 0.1% and 1% as the thresholds. The biofilm community structure presented a temporal pattern, which was mainly determined by conditionally rare or abundant taxa (CRAT) and conditionally rare taxa (CRT). The dynamics of microbial community during biofilm formation were observed, and the effect of pipe material on conditionally abundant taxa (CAT) and CRAT was greater than CRT and rare taxa (RT). CRAT showed the most complex internal associations and were identified as the core taxa. Notably, CRT and RT with low relative abundance, also played an important role in the network. For potential pathogens, 17 genera were identified in this study, and their total relative abundance was the highest (3.6-28.9%) in PPR samples. Enterococcus of CRAT was the dominant potential pathogen in young biofilms. There were 36 more co-exclusion patterns (140) observed between potential pathogens and nonpathogenic bacteria than co-occurrence (104). A total of 38 ARGs were predicted, and 109 negative and 165 positive correlations were detected between them. Some potential pathogens (Escherichia/Shigella and Burkholderia) and nonpathogenic bacteria (Meiothermus and Sphingopyxis) were identified as the possible hosts of ARGs. This study is helpful for a comprehensive understanding of the biofilm microbial community and ARGs, and provides a reference for the management and biosafety guarantee of newly-built DHWS.

Temporal succession of water microbiomes and resistomes during carcass decomposition in a fish model

Carcass decomposition in water may cause serious environmental pollution, which poses a great threat to water quality and public health. However, water microbial community succession and antibiotic resistance genes (ARGs) during carcass decomposition process are less explored. Using high-throughput sequencing and high-throughput quantitative PCR techniques, the temporal succession of water bacterial communities and ARGs profiles in experimental groups (fish carcasses) and control groups (no carcasses) containing two different types of water (the Yellow River water and tap water) in different successional stages were studied. Our results showed that NH₃-N concentration in the corpse groups has greatly risen and exceeded more than 28 times on average over the safety thresholds of water quality. Some potential pathogenic genera Comamonas, Bacteroides and Pseudomonas significantly increased during carcass decomposition process. The bacterial communities of the Yellow River water and tap water in the experimental groups exhibited similar succession patterns, and community dissimilarities between the two groups decreased and smaller over time, indicating that bacterial community convergence. NH₃-N, NO₃-N and time were three most important factors in determining bacteria community structures. The influence of water type on corpse bacterial community structures was significant but weak. The gene copy number of seven detected ARGs (cmlA1-01, floR, sul1, sul2, tetG-01, tetM-01 and tetQ) in the experimental groups was more abundant than that in the control groups. The ARGs concentrations in the corpse groups were even enriched 19-fold (minimum) to 148-fold (maximum) compared to the gene tetQ of the Yellow River water in the control groups on the initial stage. Redundancy analysis (RDA) indicated that Bacteroidetes and Firmicutes were significantly correlated with all detected ARGs. This study emphasizes that cadaver degradation leads to the deterioration of nitrogen pollution, the abundance increase of potential pathogens, and the transfer of ARGs from dead animals to water environment, thereby uncovering the harmful effects of related water pollution for human health.

Response of high-, mid- and low-abundant taxa and potential pathogens to eight disinfection methods and their interactions in domestic hot water system

Eight disinfection methods were applied to control biofilm contamination in domestic hot water system. The inactivation efficiency, responses of high- (≥1%), mid- (0.1% ~ 1%) and low-abundant taxa (≤0.1%) to disinfection, and interactions within and across three sub-communities were investigated. Ultraviolet was the most effective disinfection method for total bacteria and Escherichia coli, and chlorine dioxide had the highest inactivation efficiency on heterotrophic bacteria, while silver ions exhibited poor performance on all of them. At the phylum level, the responses of microorganisms to eight disinfection methods were different, but Proteobacteria and Firmicutes dominated in most samples. Eight disinfection methods had a greater impact on the proportion of high- and mid-abundant taxa than that of low-abundant taxa, and led to dissimilar transformations of genera among high-, mid- and low-abundant taxa in each sample. High-, mid- and low-abundant taxa of different samples showed similar structures and were roughly clustered into three Groups. Moreover, high-abundant taxa had more complex internal interactions than mid- and low-abundant taxa, and mainly presented co-occurrence patterns. The associations between high- and low-abundant taxa were close, and some low-abundant genera were identified as hub bacteria, such as Paracoccus, Thioalkalispira and Flavitalea. Furthermore, a total of 23 potential pathogens were detected in this study, and they mainly showed positive interactions, with Mycobacteria and Streptococcus as keystone genera. These results highlight the dissimilar responses of high-, mid- and low-abundant taxa to disinfection, and the critical role of some low-abundant genera in the microbial network, as well as the co-occurrence patterns among potential pathogens.

Response of bacterial regrowth, abundant and rare bacteria and potential pathogens to secondary chlorination in secondary water supply system

This study investigated the effects of secondary chlorination on bacterial regrowth, microbial communities (abundant and rare taxa) and bacterial functions of pipe wall biofilm and bulk water in simulated secondary water supply system (SWSS). Continuous secondary chlorination was more effective than short-term secondary chlorination to control the bacterial regrowth in both biofilm and water samples. Bacterial diversity slightly reduced after continuous secondary chlorination, and 19.27% of the total operational taxonomic units (OTUs) were shared by biofilm and water samples, with Bacillus as the dominant genus. Abundant and rare taxa exhibited different community structures. Proteobacteria and candidate division WPS-1 predominated in abundant and rare phyla were sensitive to chlorine, while Firmicutes, Acidobacteria and Bacteroidetes, exhibited relative strong chlorine resistance. The abundant genera in control sample (e.g., Bosea, Sphingobium and Gemmata) exhibited poor tolerance to chlorine, while Bacillus in biofilm and Defluviimonas in water were the main chlorine-resistant genera. Moreover, the composition of rare genera in each sample was obviously different. Furthermore, a total of 18 potential pathogens were detected with Pseudomonas as the dominant genus, most of which were significantly reduced after disinfection. There were mainly positive interactions among potential pathogenic bacteria, with Enterococcus, Legionella and Vibrio as the hub genera as revealed by network analysis. Similar bacterial functions in both biofilm and water were observed with metabolism as the predominant bacterial function, while, human disease function only accounted for 1.07% of bacterial functions. These results highlighted the importance of continuous secondary chlorination for controlling biosafety of SWSS and identified the dissimilar responses of abundant and rare bacteria to the disinfection, as well as the co-occurrence patterns among potential pathogens, improving our understanding of bacterial communities in SWSS.

Phyllosphere of Submerged Plants in Bathing Lakes as a Reservoir of Fungi-Potential Human Pathogens

This study analysed whether the littoral zone in the immediate vicinity of bathing sites retains potentially pathogenic yeasts on the phyllosphere surface and to what extent the species composition of microfungi in the phyllosphere and in surface waters is similar. The research was carried out in selected lakes located within the administrative boundaries of the city of Olsztyn, the largest city in the Masurian Lake District (NE Poland). The experiment was conducted in three summer seasons near bathing sites in three lakes, which are the most popular as recreational sites (Lake Kortowskie, Lake Tyrsko, and Lake Skanda). Microfungi isolated from the phyllosphere of 13 plant species of the littoral zone from dropped leaves of coast plants with no disease symptoms were used as the study material. The isolated fungi were identified in accordance with the accepted diagnostic procedures applied in mycological laboratories. A total of 36 yeast species of 16 genera were identified. Fungi found earlier at the bathing sites of the lakes were identified in 60% of the cases. Nine species were categorised as class BSL-2 fungi. This study provides a valuable complement of data concerning the natural composition of the littoral microbiota.

Characteristics and exposure risks of potential pathogens and toxic metal(loid)s in aerosols from wastewater treatment plants

Aerosols from wastewater treatment plants (WWTPs) are considered to be potentially hazardous to on-site employees and surrounding residents. However, their harmful components and their effects remain poorly understood. In this study, the characteristics, responsible factors, sources and exposure risks of potential pathogens and toxic metal(loid)s in aerosols from four WWTPs were investigated. There were 21 potential pathogens and 15 toxic metal(loid)s detected in the aerosols. Arcobacter and Fe were the dominant taxa responsible for the dissimilarity of the potential pathogen population and toxic metal(loid) composition between the aerosols and the wastewater/sludge, respectively. Both meteorological factors and sources affected pathogen and toxic metal(loid) composition. The potential pathogens and toxic metal(loid)s in indoor aerosols mainly originated from wastewater/sludge, while those in outdoor aerosols originated from wastewater/sludge and ambient air. The highest respirable fraction (<3.30 μm) concentrations and proportions were detected at the aeration units. Non-carcinogenic and carcinogenic risks of toxic metal(loid)s for both adults and children were found within and/or around WWTPs, and non-carcinogenic risks of bacteria for children were found at downwind, suggesting the need for active safeguard procedures, such as that employees wear masks and work clothes, covering the main emission sites, and collecting and destroying of aerosols.

Bacteria detected in the genital tract, semen or pre-ejaculatory fluid of Swedish stallions from 2007 to 2017

Background

Although artificial insemination (AI) was developed as a means of controlling disease transmission, pathogens can still be transmitted to females in semen used for AI. In addition, bacteria can cause deterioration in sperm quality during storage. Semen becomes contaminated by the male’s normal bacterial flora as it passes out of the reproductive tract but potential pathogens may also contaminate the semen. Therefore, semen samples from stallions to be used for AI are tested before the breeding season to minimize transmission of pathogens to inseminated mares. In Sweden, semen samples are tested at the National Veterinary Institute, Uppsala (SVA). For the present study, a retrospective analysis was made of potentially pathogenic bacteria isolated from samples submitted to the SVA from 2007 to 2017.

Results

In our study, Taylorella equigenitalis was found infrequently (53 out of 25,512 samples), representing 11 out of 2308 stallions. If T. equigenitalis was detected, the stallions were treated with antibiotics and re-tested later in the same year. Klebsiella pneumoniae and beta haemolytic streptococci were the most commonly found potential pathogens, whereas Pseudomonas aeruginosa was also isolated occasionally. There were considerable differences in the number of species isolated each year.

Conclusions

Potential pathogens were identified in relatively few of the samples submitted to SVA during this period, with T. equigenitalis not being identified since 2015. Of the other potential pathogens, K. pneumoniae and beta haemolytic streptococci were the most common. The information is relevant for determining guidelines on the testing and treatment of stallions before breeding.

Do different livestock dwellings on single grassland share similar faecal microbial communities?

Huge numbers of microorganisms reside in livestock faeces and constitute one of the most complex microbial ecosystems. Here, faecal microbial communities of three typical livestock in Xilingol steppe grassland, i.e. sheep, cattle, and horse, were investigated by Illumina MiSeq sequencing and quantitative real-time polymerase chain reaction (qPCR). Firmicutes and Bacteroidetes comprised the majority of bacterial communities in three livestock faeces. Sordariomycetes, Leotiomycetes, and Dothideomycetes were dominant in fungal communities, as well as Methanobacteria and Methanomicrobia were dominant in archaeal communities in three livestock faeces. Similar fungal community dominated in these samples, with 95.51% of the sequences falling into the overlap of three livestock faeces. In contrast, bacterial communities were quite variable among three different livestock faeces, but a similar community was observed in sheep and cattle faeces. Nearly all the archaea were identified as methanogens, whilst the most diverse and abundant methanogens were detected in cattle faeces. Potential pathogens including Bacteroides spp., Desulfovibrio spp., and Fusarium spp. were also detected in livestock faeces. Overall, this study provides the first detailed microbial comparison of typical livestock faeces dwelling on single grassland, and may be help guide management strategies for livestock grazing and grassland restoration.

Functional genera, potential pathogens and predicted antibiotic resistance genes in 16 full-scale wastewater treatment plants treating different types of wastewater

This study aimed to investigate the bacterial communities and antibiotic resistance genes (ARGs) in 16 wastewater treatment plants (WWTPs) treating municipal, industrial and mixed wastewater. Wastewater types showed obvious effects on bacterial communities and functions. Nitrosomonas, Nitrospira, Hyphomicrobium and Accumulibacter were the main functional genera. Mycobacterium was the dominant potential pathogens. A total of 69 ARGs were obtained, and the dominant ARGs subtypes were similar in different WWTPs. Efflux pumps were the most common resistance mechanisms. Copper and zinc resistance genes were the main metal resistance genes (MRGs). Wastewater types affected the distributions of ARGs and MRGs, and they were more similar in industrial and mixed wastewater. The co-occurrence of ARGs existed within or across ARG types, and they were also positively linked to MRGs, some functional and pathogenic genera or environmental factors. This study furthers the understanding of interactions between bacterial communities, ARGs and MRGs in different WWTPs.