Airborne antibiotics, antimicrobial resistance, and bacterial pathogens in a commercial composting facility: Transmission and exposure risk.

Multiple elements associated with antimicrobial resistance in compost may escape into the air during the composting process, including antibiotic resistance genes (ARGs), human pathogenic bacteria (HPBs), and even antibiotics. Although antibiotics play a critical role in the evolution of resistance in HPBs, no information is available on airborne antibiotics in composting facilities. In this study, we systematically quantified airborne antibiotics, ARGs, and HPBs in comparison with those in compost. The burden of antibiotics in the air reached 4.17 ± 2.71 × 102 ng/g, significantly higher than that in compost. The concentration of ARGs (102 copies/g) in air also increased compared with that in compost. Concentrations of target contaminants in air were affected by temperature, organic matter, and heavy metals. Co-occurrence network analysis revealed the connectivity and complexity of antibiotics, ARGs, and HPBs were greater in air than in compost. The maximum daily antibiotic intake dose was up to 1.18 × 10-1ng/d/kg, accompanied by considerable inhalation levels of ARGs and HPBs. Our results reveal the severity of airborne antimicrobial resistance (AMR) elements in composting facilities, highlight the non-negligible amount of antibiotics and their co-existence with ARGs and HPBs, and shed light on the potential role of airborne antibiotics in the evolution of environmental AMR.

Research on antibiotic resistance genes in wild and artificially bred green turtles (Chelonia mydas).

Sea turtles, vital to marine ecosystems, face population decline. Artificial breeding is a recovery strategy, yet it risks introducing antibiotic resistance genes (ARGs) to wild populations and ecosystems. This study employed metagenomic techniques to compare the distribution characteristics of ARGs in the guts of wild and artificially bred green turtles (Chelonia mydas). The findings revealed that the total abundance of ARGs in C. mydas that have been artificially bred was significantly higher than that in wild individuals. Additionally, the abundance of mobile genetic elements (MGEs) co-occurring with ARGs in artificially bred C. mydas was significantly higher than in wild C. mydas. In the analysis of bacteria carrying ARGs, wild C. mydas exhibited greater bacterial diversity. Furthermore, in artificially bred C. mydas, we discovered 23 potential human pathogenic bacteria (HPB) that contain antibiotic resistance genes. In contrast, in wild C. mydas, only one type of HPB carrying an antibiotic resistance gene was found. The findings of this study not only enhance our understanding of the distribution and dissemination of ARGs within the gut microbial communities of C. mydas, but also provide vital information for assessing the potential impact of releasing artificially bred C. mydas on the spread of antibiotic resistance.

Assessing the pig microbial health impacts of smallholder farming.

The livestock industry has long been a hotspot environment for antibiotic resistance genes, with smallholder farming still holding a significant position in pig farming. However, the microbial antibiotic resistance and pathogen risks in pigs under the smallholder farming model remain unclear. We systematically analyzed the antibiotic resistance and microbial composition of pig feces from smallholder and large-scale farming models in Sichuan. The results indicated a lower abundance of antibiotic resistance genes (ARGs) and similar microbial composition in smallholder farming compared to large-scale farming. Beneficial bacteria were more abundant in small-scale farming, whereas large-scale farming exhibited more ARGs, virulence genes, and human pathogenic bacteria (HPBs), including ESBL Escherichia coli strains closely related to human strains, indicating higher zoonotic risk. The findings suggest that smallholder farming presents a relatively better microbial composition and resistance profile, highlighting its advantages over large-scale farming in terms of pig and human health. It is noteworthy that a considerable proportion of HPBs carrying ARGs still exist in the feces from smallholder farming, and given the openness of fecal handling, there remains a high risk of transmitting ARGs and pathogens to humans.

Deciphering the impact of organic loading rate and digestate recirculation on the occurrence patterns of antibiotics and antibiotic resistance genes in dry anaerobic digestion of kitchen waste.

Organic loading rate (OLR) is crucial for determining the stability of dry anaerobic digestion (AD). Digestate recirculation contributes to reactor stability and enhances methane production. Nevertheless, the understanding of how OLR and digestate recirculation affect the abundance and diversity of antibiotics and antibiotic resistance genes (ARGs), as well as the mechanisms involved in the dissemination of ARGs, remains limited. This study thoroughly investigated this critical issue through a long-term pilot-scale experiment. The metabolome analyses revealed the enrichment of various antibiotics, such as aminoglycoside, tetracycline, and macrolide, under low OLR conditions (OLR ≤ 4.0 g·VS/L·d) and the reactor instability. Antibiotics abundance decreased by approximately 19.66-31.69 % during high OLR operation (OLR ≥ 6.0 g·VS/L·d) with digestate recirculation. The metagenome analyses demonstrated that although low OLR promoted reactor stability, it facilitated the proliferation of antibiotic-resistant bacteria, such as Pseudomonas, and triggered functional profiles related to ATP generation, oxidative stress response, EPS secretion, and cell membrane permeability, thereby facilitating horizontal gene transfer (HGT) of ARGs. However, under stable operation at an OLR of 6.0 g·VS/L·d, there was a decrease in ARGs abundance but a notable increase in human pathogenic bacteria (HPB) and mobile genetic elements (MGEs). Subsequently, during reactor instability, the abundance of ARGs and HPB increased. Notably, during digestate recirculation at OLR levels of 6.0 and 7.0 g·VS/L·d, the process attenuated the risk of ARGs spread by reducing the diversity of ARGs hosts, minimizing interactions among ARGs hosts, ARGs, and MGEs, and weakening functional profiles associated with HGT of ARGs. Overall, digestate recirculation aids in reducing the abundance of antibiotics and ARGs under high OLR conditions. These findings provide advanced insights into how OLR and digestate recirculation affect the occurrence patterns of antibiotics and ARGs in dry AD.

The hidden threat: Comprehensive assessment of antibiotic and disinfectant resistance in commercial pig slaughterhouses.

The presence of antibiotic resistance genes (ARGs), disinfectant resistance genes (DRGs), and pathogens in animal food processing environments (FAPE) poses a significant risk to human health. However, knowledge of the contamination and risk profiles of a typical commercial pig slaughterhouse with periodic disinfectant applications is limited. By creating the overall metagenomics-based behavior and risk profiles of ARGs, DRGs, and microbiomes in a nine-section pig slaughterhouse, an important FAPE in China. A total of 454 ARGs and 84 DRGs were detected in the slaughterhouse with resistance genes for aminoglycosides and quaternary ammonium compounds, respectively. The entire slaughtering chain is a hotspot for pathogens, including 83 human pathogenic bacteria (HPB), with 47 core HPB. In addition, 68 high-risk ARGs were significantly correlated with 55 HPB, 30 of which were recognized as potential bacteria co-resistant to antibiotics and disinfectants, confirm a three-fold risk of ARGs, DRGs, and pathogens prevailing throughout the chain. Pre-slaughter pig house (PSPH) was the major risk source for ARGs, DRGs, and HPB. Moreover, 75 Escherichia coli and 47 Proteus mirabilis isolates showed sensitivity to potassium monopersulfate and sodium hypochlorite, suggesting that slaughterhouses should use such related disinfectants. By using whole genome multi-locus sequence typing and single nucleotide polymorphism analyses, genetically closely related bacteria were identified across distinct slaughter sections, suggesting bacterial transmission across the slaughter chain. Overall, this study underscores the critical role of the PSPH section as a major source of HPB, ARGs, and DRGs contamination in commercial pig slaughterhouses. Moreover, it highlights the importance of addressing clonal transmission and cross-contamination of antibiotic- and disinfectant-resistant bacteria within and between slaughter sections. These issues are primarily attributed to the microbial load carried by animals before slaughter, carcass handling, and content exposure during visceral treatment. Our findings provide valuable insights for One Health-oriented slaughterhouse management practices.

Exploring the dynamics of antibiotic resistome on plastic debris traveling from the river to the sea along a representative estuary based on field sequential transfer incubations.

The environmental risks arising from ubiquitous microplastics or plastic debris (PD) acting as carriers of antibiotic resistance genes (ARGs) have attracted widespread attention. Enormous amounts of plastic waste are transported by rivers and traverse estuaries into the sea every year. However, changes in the antibiotic resistome within the plastisphere (the biofilms formed on PD) as PD travels through estuaries are largely unknown. In this study, we performed sequential migration incubations for PD along Haihe Estuary to simulate the natural process of PD floating from rivers to the ocean. Metagenomic sequencing and analysis techniques were used to track microbial communities and antibiotic resistome on migrating PD and in seawater representing the marine environment. The total relative gene copies of ARGs on traveling PD remained stable. As migration between greatly varied waters, additional ARG subtypes were recruited to the plastisphere. Above 80 % ARG subtypes identified in the plastisphere were persistent throughout the migration, and over 30 % of these persistent ARGs were undetected in seawater. The bacterial hosts composition of ARGs on PD progressively altered as transported downstream. Human pathogenic bacteria carrying ARGs (HPBs-ARG) exhibited decreasing trends in abundance and species number during transfer. Individual HPBs-ARG persisted on transferred PD and were absent in seawater samples, comprising Enterobacter cloacae, Klebsiella pneumoniae, Mycobacterium tuberculosis, and Vibrio parahaemolyticus. Based on all detected ARGs and HPBs-ARG, the Projection Pursuit model was applied to synthetically evaluate the potential risks of antibiotic resistance on migrating PD. Diminished risks on PD were observed upon the river-to-sea journey but consistently remained significantly higher than in seawater. The potential risks posed to marine environments by drifting PD as dispersal vectors for antibiotic resistance deserve greater attention. Our results provide initial insights into the dynamics or stability of antibiotic resistome on PD crossing distinct aquatic systems in field estuaries.

Polyol synthesis of one-dimensional Ag nanowires for the photocatalytic degradation of textile dye and effective removal of microbes.

Due to the excess release of hazardous pollutants to the environment, the quest for the synthesis of effective nanomaterials for wastewater treatment is never-ending. Present study reports the polyol synthesis of Ag NWs of ~ 85 nm diameter and average length of 4.08 µm using PVP and ethylene glycol. The experimental data on the methylene blue dye degradation substantiated the photocatalytic efficiency of Ag NWs (88% degradation in 120 min). Furthermore, the Ag NWs exhibited microbial load reducing property in air conditioner condensate water (ACW) within a time period of 60 min. Also, the anti-bacterial effect of Ag NWs was estimated using two human pathogenic bacterial strains, namely Staphylococcus aureus and Bacillus cereus. The antibacterial potential of Ag NWs against Staphylococcus aureus and Bacillus cereus was revealed significant with an inhibition zone size of 14 ± 0.1 mm and 9 ± 0.1 mm, respectively. Hence, the present work validates the potential efficiency of Ag NWs in the degradation of textile dyes and reduction of microbial population.

The interaction between extracellular polymeric substances and corrosion products in pipes shaped different bacterial communities and the effects of micropollutants.

There are growing concerns over the effects of micropollutants on biofilms formation and antibiotic resistance gene (ARGs) transmission in drinking water distribution pipes. However, there was no reports about the influence of the interaction between extracellular polymeric substances (EPS) and corrosion products on biofilms formation. Our results indicated that the abundance of quorum sensing (QS)-related genes, polysaccharide and amino acids biosynthesis genes of EPS was 6747-8055 TPM, 2221-2619 TPM, and 1461-1535 TPM in biofilms of cast iron pipes, respectively, which were higher than that of stainless steel pipes. The two-dimensional correlation spectroscopy (2D-COS) analysis of attenuated total reflectance-Fourier transform infrared spectrometry (ATR-FTIR) results indicated that polysaccharide of EPS was more easily adsorbed onto the corrosion products of cast iron pipes. Therefore, more human pathogenic bacteria (HPB) carrying ARGs were formed in biofilms of cast iron pipes. The amide I and amide II components and phosphate moieties of EPS were more susceptible to the corrosion products of stainless steel pipes. Thus, more bacteria genera carrying mobile genetic elements (MGE)-ARG were formed in biofilms of stainless steel pipes due to more abundance of QS-related genes, amino acids biosynthesis genes of EPS and the functional genes related to lipid metabolism. The enrichment of dimethyl phthalate (DMP), perfluorooctanoic acid (PFOA) and sulfadiazine (SUL) in corrosion products induced upregulation of QS and EPS-related genes, which promoted bacteria carrying different ARGs growth in biofilms, inducing more microbial risks.

Metagenomic and Machine Learning Meta-Analyses Characterize Airborne Resistome Features and Their Hosts in China Megacities.

Urban ambient air contains a cocktail of antibiotic resistance genes (ARGs) emitted from various anthropogenic sites. However, what is largely unknown is whether the airborne ARGs exhibit site-specificity or their pathogenic hosts persistently exist in the air. Here, by retrieving 1.2 Tb metagenomic sequences (n = 136), we examined the airborne ARGs from hospitals, municipal wastewater treatment plants (WWTPs) and landfills, public transit centers, and urban sites located in seven of China's megacities. As validated by the multiple machine learning-based classification and optimization, ARGs' site-specificity was found to be the most apparent in hospital air, with featured resistances to clinical-used rifamycin and (glyco)peptides, whereas the more environmentally prevalent ARGs (e.g., resistance to sulfonamide and tetracycline) were identified being more specific to the nonclinical ambient air settings. Nearly all metagenome-assembled genomes (MAGs) that possessed the site-featured resistances were identified as pathogenic taxa, which occupied the upper-representative niches in all the neutrally distributed airborne microbial community (P < 0.01, m = 0.22-0.50, R2 = 0.41-0.86). These niche-favored putative resistant pathogens highlighted the enduring antibiotic resistance hazards in the studied urban air. These findings are critical, albeit the least appreciated until our study, to gauge the airborne dimension of resistomes' features and fates in urban atmospheric environments.

Response behavior of antibiotic resistance genes and human pathogens to slope gradient and position: An environmental risk analysis in sloping cultivated land.

Soils, especially in farmlands, are key media for the transmission of antibiotic resistance genes (ARGs) and their hosts from the environment to humans. Sloping farmland is an important agricultural resource, but there lack of studies on the fate and risk of ARGs in sloping land. Also, the behavior and drivers of ARGs in response to slope gradient and position are unclear. Here, metagenomics was used to investigate the profiles of ARGs, mobile genetic elements, and microbial communities in soils from lands of five slope gradients (5°, 10°, 15°, 20°, and 25°) with two slope positions (uphill and downhill). Results showed that while the abundance (except 15°) and diversity (except 20°) of ARGs increased as the slope gradient increased, the diversity of ARGs with health risk, especially the high-risk ones, decreased. For slope positions, abundant and diverse ARGs were more likely to accumulate at downhill. Furthermore, 52 bacterial genera and 12 human pathogenic bacteria (HPB) species were identified as the potential hosts for ARGs with high risk, and abundant HPB species were also detected in the soils with low gradients at downhill. Moreover, the structural equation model analysis revealed that the slope gradient and the slope position have both direct and indirect effects on the abundance of ARGs. Further correlation analysis revealed that the slope gradient has a positive effect (p < 0.05) on nitrite nitrogen in the soils. Also, the slope position has a negative effect (p < 0.05) on total phosphorus and microbial nitrogen, while positively affected (p < 0.05) on particulate nitrogen and microbial carbon, which were the key factors driving the behavior of ARGs. Overall, this study provided comprehensive information on ARGs with health risks and their potential pathogenic hosts in sloping farmland. It can be important for controlling antibiotic resistance transmission and be consistent with the One Health framework.

Aerosolization behavior of antimicrobial resistance in animal farms: a field study from feces to fine particulate matter.

Antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in animal feces can be released into the atmosphere via aerosolization, posing a high health risk to farm workers. So far, little attention has been paid to the characterization of the aerosolization process. In this study, fecal and fine particulate matter (PM2.5) samples were collected from 20 animal farms involving swine, cattle, layers, and broilers, and the ARGs, ARB, and human pathogenic bacteria (HPB) were loaded in these two media. The results showed that approximately 70% of ARGs, 60% of ARBs, and 43% of HPBs were found to be preferential aerosolization. The bioaerosolization index (BI) of target 30 ARGs varied from 0.04 to 460.07, and the highest value was detected from tetW. The highest BI values of erythromycin- and tetracycline-resistant bacteria were for Kocuria (13119) and Staphylococcus (24746), respectively, and the distribution of BI in the two types of dominant ARB was similar. Regarding the bioaerosolization behavior of HPB, Clostridium saccharolyticum WM1 was the most easily aerosolized pathogen in swine and broiler farms, and Brucella abortus strain CNM 20040339 had the highest value in cattle and layer farms. Notably, the highest BI values for ARGs, ARB, and HPB were universally detected on chicken farms. Most ARGs, ARB, and HPB positively correlated with animal age, stocking density, and breeding area. Temperature and relative humidity have significant effects on the aerosolization behavior of targets, and the effects of these two parameters on the same target are usually opposite. The results of this study provide a basis for a better understanding of the contribution of animal feces to airborne ARGs and HPBs in farms, as well as for controlling the transport of the fecal microbiome to the environment through the aerosolization pathway.

Formulation and Evaluation of Amikacin Sulfate Loaded Dextran Nanoparticles against Human Pathogenic Bacteria.

Amikacin sulfate-loaded dextran sulfate sodium nanoparticles were formulated, lyophilized (LADNP), and then analyzed. The LADNP had a -20.9 ± 8.35 mV zeta potential, PDI of 0.256, and % PDI of 67.7. The zeta average nano size of LADNP was 317.9 z. d.nm, while the dimension of an individual particle was 259.3 ± 73.52 nm, and nanoparticle conductivity in colloidal solution was 2.36 mS/cm. LADNP has distinct endothermic peaks at temperatures at 165.77 °C, according to differential scanning calorimetry (DSC). The thermogravimetric analysis (TGA) showed the weight loss of LADNP, which was observed as 95% at 210.78 °C. XRD investigation on LADNP exhibited distinct peaks at 2θ as 9.6°, 10.4°, 11.4°, 18.9°, 20.3°, 24.4°, 28.2°, 33.2°, 38.9°, and 40.4° confirming crystalline structure. The amikacin release kinetics from LADNP revealed zero order kinetics with a linear release showed zero order kinetics with 37% of drug release in 7 h and had an R2 value of 0.99. The antibacterial effect of LADNP showed broad-spectrum activity against tested human pathogenic bacteria. The preset study demonstrated that LADNP is a promising antibacterial agent.

Effects of freeze-thaw dynamics and microplastics on the distribution of antibiotic resistance genes in soil aggregates.

This is the first study investigating the effects of freeze-thaw (FT) and microplastics (MPs) on the distribution of antibiotic resistance genes (ARGs) in soil aggregates (i.e., soil basic constituent and functional unit) via microcosm experiments. The results showed that FT significantly increased the total relative abundance of target ARGs in different aggregates due to the increase in intI1 and ARG host bacteria. However, polyethylene MPs (PE-MPs) hindered the increase in ARG abundance caused by FT. The host bacteria carrying ARGs and intI1 varied with aggregate size, and the highest number of hosts was observed in micro-aggregates (<0.25 mm). FT and MPs altered host bacteria abundance by affecting aggregate physicochemical properties and bacterial community and enhanced multiple antibiotic resistance via vertical gene transfer. Although the dominant factors affecting ARGs varied with aggregate size, intI1 was a co-dominant factor in various-sized aggregates. Furthermore, other than ARGs, FT, PE-MPs, and their integration promoted the proliferation of human pathogenic bacteria in aggregates. These findings suggested that FT and its integration with MPs significantly affected ARG distribution in soil aggregates. They amplified antibiotic resistance environmental risks, contributing to a profound understanding of soil antibiotic resistance in the boreal region.

Mechanisms of Antimicrobial Peptides from Bagasse against Human Pathogenic Bacteria.

Nonedible agricultural wastes (agricultural wastes, agro-industrial wastes, and fishery wastes) were chosen as potential sources of antimicrobial peptides and evaluated for antibacterial efficiency against human pathogens. Specifically, protein hydrolysates were first obtained by hydrolysis with pepsin. Filtrated peptides smaller than 3 kDa were then purified by C18 reversed-phase chromatography, cation exchange chromatography, and off-gel fractionation. NanoLC-MS/MS was used to investigate the amino acid sequences of active peptide candidates. Five candidate peptides were finally chosen for chemical synthesis and evaluation of growth inhibition against human pathogenic bacteria. Two synthetic peptides from bagasse, NLWSNEINQDMAEF (Asn-Leu-Trp-Ser-Asn-Glu-Ile-Asn-Gln-Asp-Met-Ala-Glu-Phe) and VSNCL (Val-Ser-Asn-Cys-Leu), showed the most potent antibacterial activity against three pathogens: Pseudomonas aeruginosa, Bacillus subtilis, and Burkholderia cepacia. The antibacterial mechanisms of these peptides were then examined using shotgun proteomics, which revealed their effects to involve both intracellular-active and membrane-active mechanisms. Further investigation and modification of peptides are needed to increase the efficiency of these peptides against human pathogens.

Effects of micron-scale zero valent iron on behaviors of antibiotic resistance genes and pathogens in thermophilic anaerobic digestion of waste activated sludge.

This work investigated the metagenomics-based behavior and risk of antibiotic resistance genes (ARGs), and their potential hosts during thermophilic anaerobic digestion (TAD) of waste activated sludge, enhanced by micron-scale zero valent iron (mZVI). Tests were conducted with 0, 25, 100, and 250 mg mZVI/g total solids (TS). Results showed that up to 7.3% and 4.8% decrease in ARGs' abundance and diversity, respectively, were achieved with 100 mg mZVI/g TS. At these conditions, ARGs with health risk in abundance and human pathogenic bacteria (HPB) diversity were also decreased by 8.3% and 3.6%, respectively. Additionally, mZVI reduced abundance of 72 potential pathogenic supercarriers for ARGs with high health risk by 2.5%, 5.0%, and 6.1%, as its dosage increased. Overall, mZVI, especially at 100 mg/g TS, can mitigate antibiotic resistance risk in TAD. These findings are important for better understanding risks of ARGs and their pathogenic hosts in ZVI-enhanced TAD of solid wastes.

Metagenomic insights into dietary remodeling of gut microbiota and antibiotic resistome in meat rabbits.

The gut microbiota is a repository of antibiotic resistance genes (ARGs), which may affect the health of humans and animals. The intestinal flora is affected by many factors but it is unclear how the intestinal microflora and antibiotic resistome in rabbits might change under dietary intervention. Feeding with lettuce led to the amplification and transfer of exogenous ARGs in the intestinal flora, but there were no significant differences when fed lettuces grown with different manure types. For example, the lsaC of lettuce fed with bovine, chicken and pig manure without adding organic fertilizer increased by 0.143, 0.151, 0.179 and 0.169 logs respectively after 4 weeks, and the efrB also increased by 0.074, 0.068, 0.079 and 0.106 logs respectively. Network analysis showed that Clostridium_ sensu_ stricto_ 18 was a potential host of type 6 virulence factor genes (VFGs). Mantel analysis showed that ARGs were directly influenced by mobile genetic elements (MGEs) and VFGs. Thus, feeding rabbits lettuce grown with different manure types contribute to the transmission of ARGs by remodeling the intestinal microenvironment. In addition, diet may affect exogenous ARGs to change the intestinal antibiotic resistome and possibly threaten health.

The Impact of Harsh Stratospheric Conditions on Survival and Antibiotic Resistance Profile of Non-Spore Forming Multidrug Resistant Human Pathogenic Bacteria Causing Hospital-Associated Infections.

Bacteria are constantly being lifted to the stratosphere due to air movements caused by weather phenomena, volcanic eruptions, or human activity. In the upper parts of the atmosphere, they are exposed to extremely harsh and mutagenic conditions such as UV and space radiation or ozone. Most bacteria cannot withstand that stress, but for a fraction of them, it can act as a trigger for selective pressure and rapid evolution. We assessed the impact of stratospheric conditions on the survival and antibiotic resistance profile of common non-spore-forming human pathogenic bacteria, both sensitive and extremely dangerous multidrug-resistant variants, with plasmid-mediated mechanisms of resistance. Pseudomonas aeruginosa did not survive the exposure. In the case of strains that were recovered alive, the survival was extremely low: From 0.00001% of Klebsiella pneumoniae carrying the ndm-1 gene and methicillin-resistant Staphylococcus aureus mecA-positive with reduced susceptibility to vancomycin (MRSA/VISA), to a maximum of 0.001% of K. pneumoniae sensitive to all common antibiotics and S. aureus sensitive to vancomycin (MRSA/VSSA). We noticed a tendency towards increased antibiotic susceptibility after the stratospheric flight. Antimicrobial resistance is a current real, global, and increasing problem, and our results can inform current understandings of antibiotic resistance mechanisms and development in bacteria.

Deciphering risks of resistomes and pathogens in intensive laying hen production chain.

Antimicrobial resistance (AMR) and pathogens derived from food animals and their associated environments have emerged as challenging threats to humans from a health perspective, but our understanding of these risks and their key prevention and control points in the current intensive breeding industry remains poor. By creating an integral composition and risk profile of the resistome and microbiome through metagenomics in feces, flies, dust, sewage, and soil along the four-stage laying hen production chain, we found that the whole production chain is a hotspot for antimicrobial resistance genes (ARGs) with 374 known subtypes and pathogens, including 157 human pathogenic bacteria (HPB). Feces and flies were identified as major risk sources for these contaminations. Also, we confirmed a twin-risk of AMR and pathogenicity prevailing throughout the chain, but with different frequencies in each stage; thus, high-risk ARGs in the young chicken stage and highly prioritized HPB in the chick stage contributed 37.33 % to the total AMR risk and 36.36 % to the pathogenic risks, respectively, thus rendering the two stages to be the key prevention points. Moreover, the prevalence of 112 binned ARG supercarriers (for example, Klebsiella pneumoniae harboring 20 ARGs) was unraveled along the production chain, especially in feces, flies, and dust, and 87 potential hosts exhibited high pathogenic risk, high-risk AMR, or both, with 262 ARGs and 816 virulence factor genes. Overall, this study provides first-hand comprehensive data on high-risk ARGs and their pathogenic hosts in the intensive laying hen production chain, and thus is fundamentally important for developing new measures to help control the global AMR crisis induced through the animal-environment-human pathway.

Implications for assessing sludge hygienization: Differential responses of the bacterial community, human pathogenic bacteria, and fecal indicator bacteria to sludge pretreatment-anaerobic digestion.

Sewage sludge is the byproduct of wastewater treatment plants, which host enormous diversity of microbes including potential pathogens. However, there are still challenges in assessing hygienization during sludge stabilization due to the complex relationships between dominant microbes and human pathogenic bacteria (HPB), and the accuracy of fecal indicator bacteria (FIB) is also disputed. Here, the responses of the bacterial community, HPB, and FIB to sludge pretreatment-anaerobic digestion (AD) were comprehensively compared using culture-based and 16S rRNA gene molecular analysis methodologies. Bacterial and HPB communities differed in response to sludge pretreatment-AD. AD drove the variation of bacterial community, but led to the convergence of HPB communities in pretreated sludge, indicating the existence of ecological niches that favors HPB dissemination in digesters. The correlation analysis indicated that FIB was suitable for characterizing general pathogen removal instead of showing the real pattern of HPB (i.e., each HPB), implying the need for comprehensive assessment approaches. Moreover, AD-related parameters including pH, total solids destruction, and methane yield were found to play important role in assessing pathogen inactivation given their correlation. This work provides theoretical basis for the selection of appropriate sludge stabilization approaches and future supervision of biosolids biosafety, which finally benefits human health.

Co-occurrence of phthalate esters and perfluoroalkyl substances affected bacterial community and pathogenic bacteria growth in rural drinking water distribution systems.

The adverse health effects of phthalate esters (PAEs) and perfluoroalkyl substances (PFAS) in drinking water have attracted considerable attention. Our study investigated the effects of PAEs and PFAS on the bacterial community and the growth of potential human pathogenic bacteria in rural drinking water distribution systems. Our results showed that the total concentration of PAEs and PFAS ranged from 1.02 × 102 to 1.65 × 104 ng/L, from 4.40 to 1.84 × 102 ng/L in rural drinking water of China, respectively. PAEs concentration gradually increased and PFAS slowly decreased along the pipeline distribution, compared to concentrations in the effluents of rural drinking water treatment plants. The co-occurrence of higher concentrations of PAEs and PFAS changed the structure and function of the bacterial communities found within these environments. The bacterial community enhanced their ability to respond to fluctuating environmental conditions through up-regulation of functional genes related to extracellular signaling and interaction, as well as genes related to replication and repair. Under these conditions, co-occurrence of PAEs and PFAS promoted the growth of potential human pathogenic bacteria (HPB), therefore increasing the risk of the development of associated diseases among exposed persons. The main HPB observed in this study included Burkholderia mallei, Mycobacterium tuberculosis, Klebsiella pneumoniae, Acinetobacter calcoaceticus, Escherichia coli, and Pseudomonas aeruginosa. Contaminants including particles, microorganisms, PAEs and PFAS were found to be released from corrosion scales and deposits of pipes and taps, resulting in the increase of the cytotoxicity and microbial risk of rural tap water. These results are important to efforts to improve the safety of rural drinking water.