Seasonal variations in export of antibiotic resistance genes and bacteria in runoff from an agricultural watershed in Iowa

Effects of hydrothermal treatment on the reduction of antibiotic-resistant Escherichia coli and antibiotic resistance genes and the fertilizer potential of liquid product from cattle manure

In this study, the reduction in the abundance of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) and the fertilizer potential of liquid products from hydrothermally treated cattle manure were investigated. Hydrothermal treatment (HTT) was conducted under different reaction temperatures (125, 150, 175 and 200 °C) and retention times (60, 90 and 120 min). The total organic carbon (TOC) and total nitrogen (TN) of the liquid product increased with increasing reaction temperature. The germination index (GI), a measure of the percentage of germination, exceeded 90 % at 125, 150, and 175 °C in diluted samples, while it decreased to 18 % at 200 °C. Although a longer retention time contributed to an increase in TOC of liquid products, it did not increase the GI values. The liquid product should be diluted or adjusted before use as fertilizer to prevent phytotoxicity. In our analysis of ARB and ARGs, E. coli and antibiotic-resistant E. coli were completely reduced after HTT, except for the operating conditions of 125 °C and 60 min. Although both a higher reaction temperature and longer retention time tended to be better for the reduction of ARGs and intI1, it was found that the longer retention time is much more effective than the higher reaction temperature. The reduction of target ARGs and intI1 was 2.9-log under175 °C and 120 min. Comprehensively considering the fertilizer potential of liquid product and the reduction of ARB and ARGs, 175 °C of reaction temperature and 120 min of retention time of operating conditions for HTT were recommended.

Temporal variations of antimicrobial resistance genes in aerosols: A one-year monitoring at the puy de Dôme summit (Central France)

The recent characterization of antibiotic resistance genes (ARGs) in clouds evidenced that the atmosphere actively partakes in the global spreading of antibiotic resistance worldwide. Indeed, the outdoor atmosphere continuously receives large quantities of particles of biological origins, emitted from both anthropogenic or natural sources at the near Earth's surface. Nonetheless, our understanding of the composition of the atmospheric resistome, especially at mid-altitude (i.e. above 1000 m a.s.l.), remains largely limited. The atmosphere is vast and highly dynamic, so that the diversity and abundance of ARGs are expected to fluctuate both spatially and temporally. In this work, the abundance and diversity of ARGs were assessed in atmospheric aerosol samples collected weekly between July 2016 and August 2017 at the mountain site of puy de Dôme (1465 m a.s.l., central France). Our results evidence the presence of 33 different subtypes of ARGs in atmospheric aerosols, out of 34 assessed, whose total concentration fluctuated seasonally from 59 to 1.1 × 105 copies m-3 of air. These were heavily dominated by genes from the quinolone resistance family, notably the qepA gene encoding efflux pump mechanisms, which represented >95 % of total ARGs concentration. Its abundance positively correlated with that of bacteria affiliated with the genera Kineococcus, Neorhizobium, Devosia or Massilia, ubiquitous in soils. This, along with the high abundance of Sphingomonas species, points toward a large contribution of natural sources to the airborne ARGs. Nonetheless, the increased contribution of macrolide resistance (notably the erm35 gene) during winter suggests a sporadic diffusion of ARGs from human activities. Our observations depict the atmosphere as an important vector of ARGs from terrestrial sources. Therefore, monitoring ARGs in airborne microorganisms appears necessary to fully understand the dynamics of antimicrobial resistances in the environment and mitigate the threats they may represent.

Heterotrophic bacteria in drinking water: evaluating antibiotic resistance and the presence of virulence genes

Heterotrophic bacteria, impacting those with infections or compromised immunity, pose heightened health risks when resistant to antibiotics. This study investigates heterotrophic plate count bacteria in water from North West-C (NWC) and North West-G (NWG) facilities, revealing prevalent β-hemolysis (NWC 82.5%, NWG 86.7%), enzyme production (98%), and antibiotic resistance, especially in NWC. NWG exhibits variations in hemolysin (P = 0.013), lipase (P = 0.009), and DNase activity (P = 0.006). Antibiotics, including ciprofloxacin, persist throughout treatment, with high resistance to β-lactams and trimethoprim (47%-100%), predominantly in NWC. Multiple antibiotic resistance index indicates that 90% of values exceed 0.20, signifying isolates from high antibiotic usage sources. Whole genome sequencing reveals diverse antibiotic resistance genes in heterotrophic strains, emphasizing their prevalence and health risks in water.IMPORTANCEThis study's findings are a stark reminder of a significant health concern: our water sources harbor antibiotic-resistant heterotrophic bacteria, which can potentially cause illness, especially in individuals with weakened immune systems or underlying infections. Antibiotic resistance among these bacteria is deeply concerning, as it threatens the effectiveness of antibiotics, critical for treating various infections. Moreover, detecting virulence factors in a notable proportion of these bacteria highlights their elevated risk to public health. This research underscores the immediate need for enhanced water treatment processes, rigorous water quality monitoring, and the development of strategies to combat antibiotic resistance in the environment. Safeguarding the safety of our drinking water is imperative to protect public health and mitigate the spread of antibiotic-resistant infections, making these findings a compelling call to action for policymakers and public health authorities alike.

Portable biosensor combining CRISPR/Cas12a and loop-mediated isothermal amplification for antibiotic resistance gene ermB in wastewater

Wastewater is among the main sources of antibiotic resistance genes (ARGs) in the environment, but effective methods to quickly assess ARGs on-site in wastewater are lacking. Here, using the typical ARG ermB as the target, we report a portable biosensor combining CRISPR/Cas12a and loop-mediated isothermal amplification (LAMP) for the detection of ARGs. Six primers of LAMP and the crRNA of CRISPR/Cas12a were first designed to be preamplification with LAMP and lead Cas12a to recognize the ermB via base pairing. Due to the trans-cleavage activity of CRISPR/Cas12a after amplicon recognition, ssDNA probes modified with reporter molecules were used to implement a visual assay with lateral flow test strips and fluorescence. After a simple nucleic acid extraction with magnetic beads, the constructed biosensor possesses excellent sensitivity and selectivity as low as 2.75 × 103 copies/μL using fluorescence and later flow strips in wastewater. We further evaluated the community-wide prevalence of ermB in wastewater influent and found high mass loads of ermB during different months. This user-friendly and low-cost biosensor is applicable for rapid on-site ARG detection, providing a potential point-of-use method for rapid assessments of ARG abundance in wastewater from large city areas with many wastewater treatment plants and in resource-limited rural areas.

Simultaneous stream assessment of antibiotics, bacteria, antibiotic resistant bacteria, and antibiotic resistance genes in an agricultural region of the United States

Antimicrobial resistance (AMR) is now recognized as a leading global threat to human health. Nevertheless, there currently is a limited understanding of the environment's role in the spread of AMR and antibiotic resistance genes (ARGs). In 2019, the U.S. Geological Survey conducted the first statewide assessment of antibiotic resistant bacteria (ARB) and ARGs in surface water and bed sediment collected from 34 stream locations across Iowa. Environmental samples were analyzed for a suite of 29 antibiotics and plated on selective media for 15 types of bacteria growth; DNA was extracted from culture growth and used in downstream polymerase chain reaction (PCR) assays for the detection of 24 ARGs. ARGs encoding resistance to antibiotics of clinical importance to human health and disease prevention were prioritized as their presence in stream systems has the potential for environmental significance. Total coliforms, Escherichia coli (E. coli), and staphylococci were nearly ubiquitous in both stream water and stream bed sediment samples, with enterococci present in 97 % of water samples, and Salmonella spp. growth present in 94 % and 67 % of water and bed sediment samples. Bacteria enumerations indicate that high bacteria loads are common in Iowa's streams, with 23 (68 %) streams exceeding state guidelines for primary contact for E. coli in recreational waters and 6 (18 %) streams exceeding the secondary contact advisory level. Although antibiotic-resistant E. coli growth was detected from 40 % of water samples, vancomycin-resistant enterococci (VRE) and penicillinase-resistant Staphylococcus aureus (MRSA) colony growth was detected from nearly all water samples. A total of 14 different ARGs were detected from viable bacteria cells from 30 Iowa streams (88 %, n = 34). Study results provide the first baseline understanding of the prevalence of ARB and ARGs throughout Iowa's waterways and health risk potential for humans, wildlife, and livestock using these waterways for drinking, irrigating, or recreating.

Antibiotics and their associations with antibiotic resistance genes and microbial communities in estuarine and coastal sediment of Quanzhou Bay, Southeast China

The antibiotic concentrations spanned from 11.2 to 173.8 ng/g, with quinolones and tetracyclines being observed to be prevalent. The amount of microbial biomass as determined by Phospholipid fatty acid (PLFA) ranged from 2.92 to 10.99 mg kg-1, with G- bacteria dominating. A total of 254 distinct ARGs and 10 MEGs were identified, with multidrug ARGs having the highest relative abundance (1.18 × 10-2 to 3.00 × 10-1 copies/16S rRNA gene copies), while vancomycin and sulfonamide resistance genes were the least abundant. Results from canonical-correlation analyses combined with redundancy analysis indicated that macrolides were significantly related to the shifts of microbial community structure in sediments, particularly in G+ bacteria that were more sensitive to antibiotic residues. It was observed that sulfonamide ARGs had a greater correlation with residual antibiotics than other ARGs. This study provided a field evidence that multiple residual antibiotics from coastal sites could cause fundamental shifts in microbial community and their associated ARGs.

Characteristics of antibiotic resistance gene distribution in rainfall runoff and combined sewer overflow

Rainfall runoff and combined sewer overflow (CSO) converge with organic waste, nutrients, and microbes from the ground and wastewater. These pollutants promote the spread and transformation of antibiotic resistance genes (ARGs). In this study, four rainfall runoff and one CSO outfall were chosen, and samples were collected to explore the occurrence and distribution of ARGs. The ARGs were extracted from suspended solids and analyzed using metagenomic sequencing. A total of 888 ARG subtypes, belonging to 17 ARG types, were detected in all samples. Eleven ARG types were shared by all the samples. Multidrug resistance genes had the highest relative abundance. Their total relative abundance reached 1.07 ratio (ARG copy number/16S rRNA gene copy number) and comprised 46.6% of all the ARGs. In all samples, the CSO outfall had the highest total relative abundance (8.25 × 10^-1 ratio) of ARGs, with a ratio ranging ND (not detected)-3.78 × 10^-1 ratio. Furthermore, the relationship between ARG types and environmental factors was determined using redundancy analysis. The results showed that chemical organic demand (COD) and bacterial abundance were positively correlated with most ARG types, including multidrug, bacitracin, aminoglycoside, β-lactam, tetracycline, and sulfonamide. NH₃-N, TN, and TP were positively correlated with rifamycin, fosmidomycin, and vancomycin resistance genes. The relationship among the ARG subtypes was investigated using network analyses. The multidrug resistance gene subtypes had the highest frequency of co-occurrence. This study provides insights into the occurrence and distribution of ARGs under non-point source pollution and may contribute to the control of ARGs.

Antimicrobial resistance in dairy slurry tanks: A critical point for measurement and control

Waste from dairy production is one of the largest sources of contamination from antimicrobial resistant bacteria (ARB) and genes (ARGs) in many parts of the world. However, studies to date do not provide necessary evidence to inform antimicrobial resistance (AMR) countermeasures. We undertook a detailed, interdisciplinary, longitudinal analysis of dairy slurry waste. The slurry contained a population of ARB and ARGs, with resistances to current, historical and never-used on-farm antibiotics; resistances were associated with Gram-negative and Gram-positive bacteria and mobile elements (ISEcp1, Tn916, Tn21-family transposons). Modelling and experimental work suggested that these populations are in dynamic equilibrium, with microbial death balanced by fresh input. Consequently, storing slurry without further waste input for at least 60 days was predicted to reduce ARB spread onto land, with > 99 % reduction in cephalosporin resistant Escherichia coli. The model also indicated that for farms with low antibiotic use, further reductions are unlikely to reduce AMR further. We conclude that the slurry tank is a critical point for measurement and control of AMR, and that actions to limit the spread of AMR from dairy waste should combine responsible antibiotic use, including low total quantity, avoidance of human critical antibiotics, and choosing antibiotics with shorter half-lives, coupled with appropriate slurry storage.

Coexistence of antibiotic resistance genes, fecal bacteria, and potential pathogens in anthropogenically impacted water

Microbial indicators are often used to monitor microbial safety of aquatic environments. However, information regarding the correlation between microbial indicators and ecotoxicological factors such as potential pathogens and antibiotic resistance genes (ARGs) in anthropogenically impacted waters remains highly limited. Here, we investigated the bacterial community composition, potential pathogens, ARGs diversity, ARG hosts, and horizontal gene transfer (HGT) potential in urban river and wastewater samples from Chaohu Lake Basin using 16S rRNA and metagenomic sequencing. The composition of the microbial community and potential pathogens differed significantly in wastewater and river water samples, and the total relative abundance of fecal indicator bacteria was positively correlated with the total relative abundance of potential pathogens (p < 0.001 and Pearson's r = 0.758). Network analysis indicated that partial ARG subtypes such as dfrE, sul2, and PmrE were significantly correlated with indicator bacteria (p < 0.05 and Pearson's r > 0.6). Notably, Klebsiella was the indicator bacteria significantly correlated with 4 potential pathogens and 14 ARG subtypes. ARGs coexisting with mobile gene elements were mainly found in Thauera, Pseudomonas, Escherichia, and Acinetobacter. Next-generation sequencing (NGS) can be used to conduct preliminary surveys of environmental samples to access potential health risks, thereby facilitating water resources management.

Inactivation of Antibiotic-Resistant Bacteria in Wastewater by Ozone-Based Advanced Water Treatment Processes

The inactivating effect of ozone (O₃)-based advanced oxidation processes (AOPs) (O₃/H₂O₂, O₃/UV, and O₃/UV/H₂O₂ systems) on antimicrobial-resistant bacteria (AMRB) and antimicrobial-susceptible bacteria (AMSB) in sewage treatment plant (STP) wastewater was investigated. The AMRB were grouped into six classes: carbapenem-resistant Enterobacteriaceae (CRE), extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae (ESBL-E), multidrug-resistant Acinetobacter (MDRA), multidrug-resistant Pseudomonas aeruginosa (MDRP), methicillin-resistant Staphylococcus aureus (MRSA), and vancomycin-resistant Enterococcus (VRE); these classes constituted the World Health Organization (WHO) global priority list of AMRB. The results indicate that O₃-based advanced wastewater treatment inactivated all AMRB and AMSB (>99.9%) after 10 min of treatment, and significant differences (p < 0.5) were not observed in the disinfection of AMRB and AMSB by each treatment. Altered taxonomic diversity of micro-organisms based on 16S rRNA gene sequencing via O₃/UV and O₃/UV/H₂O₂ treatment showed that advanced wastewater treatments not only inactivated AMRB but also removed antimicrobial resistance genes (AMRGs) in the wastewater. Consequently, this study recommends the use of advanced wastewater treatments for treating the STP effluent, reducing environmental pollution, and alleviating the potential hazard to human health caused by AMRB, AMSB, and infectious diseases. Overall, this study provides a new method for assessing environmental risks associated with the spread of AMRB and AMSB in aquatic environments, while keeping the water environment safe and maintaining human health.

A Review on Constructed Treatment Wetlands for Removal of Pollutants in the Agricultural Runoff

Constructed wetland (CW) is a popular sustainable best management practice for treating different wastewaters. While there are many articles on the removal of pollutants from different wastewaters, a comprehensive and critical review on the removal of pollutants other than nutrients that occur in agricultural field runoff and wastewater from animal facilities, including pesticides, insecticides, veterinary medicine, and antimicrobial-resistant genes are currently unavailable. Consequently, this paper summarized recent findings on the occurrence of such pollutants in the agricultural runoff water, their removal by different wetlands (surface flow, subsurface horizontal flow, subsurface vertical flow, and hybrid), and removal mechanisms, and analyzed the factors that affect the removal. The information is then used to highlight the current research gaps and needs for resilient and sustainable treatment systems. Factors, including contaminant property, aeration, type, and design of CWs, hydraulic parameters, substrate medium, and vegetation, impact the removal performance of the CWs. Hydraulic loading of 10–30 cm/d and hydraulic retention of 6–8 days were found to be optimal for the removal of agricultural pollutants from wetlands. The pollutants in agricultural wastewater, excluding nutrients and sediment, and their treatment utilizing different nature-based solutions, such as wetlands, are understudied, implying the need for more of such studies. This study reinforced the notion that wetlands are effective for treating agricultural wastewater (removal > 90%) but several research questions remain unanswered. More long-term research in the actual field utilizing environmentally relevant concentrations to seek actual impacts of weather, plants, substrates, hydrology, and other design parameters, such as aeration and layout of wetland cells on the removal of pollutants, are needed.

Antimicrobial resistance in integrated agroecosystems: State of the science and future opportunities

As the Journal of Environmental Quality (JEQ) celebrates 50 years of publication, the division of environmental microbiology is one of the newest additions to the journal. During this time, significant advances in understanding of the interconnected microbial community and impact of the microbiome on natural and designed environmental systems have occurred. In this review, we highlight the intractable challenge of antimicrobial resistance (AMR) on humans, animals, and the environment, with particular emphasis on the role of integrated agroecosystems and by highlighting contributions published in JEQ. From early studies of phenotypic resistance of indicator organisms in waters systems to current calls for integrating AMR assessment across "One Health," publications in JEQ have advanced our understanding of AMR. As we reflect on the state of the science, we emphasize future opportunities. First, integration of phenotypic and molecular tools for assessing environmental spread of AMR and human health risk continues to be an urgent research need for a one health approach to AMR. Second, monitoring AMR levels in manure is recommended to understand inputs and potential spread through agroecosystems. Third, baseline knowledge of AMR levels is important to realize the impact of manure inputs on water quality and public health risk; this can be achieved through background monitoring or identifying the source-related genes or organisms. And finally, conservation practices designed to meet nutrient reduction goals should be explored for AMR reduction potential.

Antimicrobial-resistant bacteria in international travelers

PURPOSE OF REVIEW

Antimicrobial resistance (AMR) in bacteria poses a major risk to global public health, with many factors contributing to the observed increase in AMR. International travel is one recognized contributor. The purpose of this review is to summarize current knowledge regarding the acquisition, carriage and spread of AMR bacteria by international travelers.

RECENT FINDINGS

Recent studies have highlighted that travel is an important risk factor for the acquisition of AMR bacteria, with approximately 30% of studied travelers returning with an acquired AMR bacterium. Epidemiological studies have shown there are three major risk factors for acquisition: travel destination, antimicrobial usage and travelers' diarrhea (TD). Analyses have begun to illustrate the AMR genes that are acquired and spread by travelers, risk factors for acquisition and carriage of AMR bacteria, and local transmission of imported AMR organisms.

SUMMARY

International travel is a contributor to the acquisition and dissemination of AMR organisms globally. Efforts to reduce the burden of AMR organisms should include a focus on international travelers. Routine genomic surveillance would further elucidate the role of international travel in the global spread of AMR bacteria.

Agricultural land-use change exacerbates the dissemination of antibiotic resistance genes via surface runoffs in Lake Tai Basin, China

Agricultural runoff is an important antibiotic resistance genes (ARGs) dissemination pathway from farmlands to water environment, however few studies have focused on the influence of agricultural land-use change on the pattern of ARGs in runoff and assess the health risk to public. Lake Tai Basin which experiences agricultural land-use change was selected to elucidate this concern. Our findings revealed that the pattern of ARGs was more diverse and the gene abundance was higher in orchard runoffs by comparison with conventional cropland runoffs. Co-occurrence network analysis between mobile genetic elements and ARGs demonstrated that after agricultural land-use change, ARG dissemination via runoffs became more threatened. In addition, this study illustrated the correlations between the antibiotic resistome and microbiome in runoffs, finding that non-dominant microbial taxa were the limiting factor which determined the pattern of ARGs in surface runoffs. In summary, the pattern and dissemination risk of ARGs in the surface runoff after agricultural land-use change in Lake Tai Basin were clarified via this study.

Tracking antibiotic resistance gene transfer at all seasons from swine waste to receiving environments

Antibiotic resistance genes (ARGs) in livestock farms have attracted a growing attention with potential effects on human health. As one of the most important organic fertilizer, swine waste provided an ideal environment for understanding the dissemination and accumulation of ARGs in agricultural ecosystems. Here we conducted a year-round follow-up trace from swine waste to receiving environments, with the purpose of revealing the contamination profiles and ecological risks of ARGs at different seasons. Results indicated that a variety of common ARGs and even high-risk ARGs (i.e., bla_ampC, bla_OXA-1, bla_TEM-1 and mcr-1) were prevalent from swine waste to farmland soil, with changing in various degrees from season to season. Regarding the occurrence pattern of ARGs, tetracycline resistance genes (tet-ARGs) were predominant genes at four seasons in all fresh pig feces, swine manure, manured soil and wastewater. The levels of most ARGs in solid waste were reduced at a different degree via natural composting, and the removal effect was best in summer, while ARGs decreased poorly after wastewater treatment, especially in winter (up to 10^-1 copies/16S copies in the residual level), which increased the possibility of propagation to receiving environment. This concern was also validated by the investigation on farmland environment with long-term application of manure, where causing an increase in ARG abundances in soils (approximately 0.9-32.7 times). To our knowledge, this study is the first to demonstrate the distribution pattern of ARGs from swine waste to its receiving farmland environment at all seasons on this integrity chain.

On-site chlorination responsible for effective disinfection of wastewater from hospital

Both hospital effluent and a model sewage treatment plant (STP) wastewater prepared by mixing STP influent and STP secondary effluent at a volume ratio of 1:9 were directly treated with chlorine for investigation of their effects on disinfection of antimicrobial-resistant bacteria (AMRB) and antimicrobial-susceptible bacteria (AMSB). The overall results indicate that the chlorine disinfection effectively inactivated the majority of AMRB and AMSB, expect for MRSA and Staphylococcus aureus in both wastewaters. No significant differences could further be observed in the taxonomic diversity of micro-organisms after the treatment. The degrees of disinfection given by the direct chlorination were comparable to those attained by combination of conventional activated sludge process and additional chlorine treatment at the STP. The results of this study evoked a recommendation to operate local chlorination treatment directly for the wastewater from medicinal facilities prior to its flow into the STP as sewage. Although additional disinfection treatment at the STP seems necessary to remove the recalcitrant MRSA and Staphylococcus aureus, the present study desirably contributes to a great reduction of the loads of STP and urgent prevention of spreading of infectious diseases in the present state.

Antimicrobial resistance genes are enriched in aerosols near impacted urban surface waters in La Paz, Bolivia

Antibiotic resistance poses a major global health threat. Understanding emergence and dissemination of antibiotic resistance in environmental media is critical to the design of control strategies. Because antibiotic resistance genes (ARGs) may be aerosolized from contaminated point sources and disseminated more widely in localized environments, we assessed ARGs in aerosols in urban La Paz, Bolivia, where wastewater flows in engineered surface water channels through the densely populated urban core. We quantified key ARGs and a mobile integron (MI) via ddPCR and E. coli spp. as a fecal indicator by culture over two years during both the rainy and dry seasons in sites near wastewater flows. ARG targets represented major antibiotic groups-tetracyclines (tetA), fluoroquinolines (qnrB), and beta-lactams (blaTEM)-and an MI (intI1) represented the potential for mobility of genetic material. Most air samples (82%) had detectable targets above the experimentally determined LOD: most commonly blaTEM and intI1 (68% and 47% respectively) followed by tetA and qnrB (17% and 11% respectively). ARG and MI densities in positive air samples ranged from 1.3 × 101 to 6.6 × 104 gene copies/m3 air. Additionally, we detected culturable E. coli in the air (52% of samples <1 km from impacted surface waters) with an average density of 11 CFU/m3 in positive samples. We observed decreasing density of blaTEM with increasing distance up to 150 m from impacted surface waters. To our knowledge this is the first study conducting absolute quantification and a spatial analysis of ARGs and MIs in ambient urban air of a city with contaminated surface waters. Environments in close proximity to urban wastewater flows in this setting may experience locally elevated concentrations of ARGs, a possible concern for the emergence and dissemination of antimicrobial resistance in cities with poor sanitation.