Selective pressure of antibiotic pollution on bacteria of importance to public health

Sewage sludge fertilization affects microbial community structure and its resistome in agricultural soils

Global sewage sludge production is rapidly increasing, and its safe disposal is becoming an increasingly serious issue. One of the main methods of municipal sewage sludge management is based on its agricultural use. The wastewater and sewage sludge contain numerous antibiotic resistance genes (ARGs), and its microbiome differs significantly from the soil microbial community. The aim of the study was to assess the changes occurring in the soil microbial community and resistome after the addition of sewage sludge from municipal wastewater treatment plant (WWTP) in central Poland, from which the sludge is used for fertilizing agricultural soils on a regular basis. This study used a high-throughput shotgun metagenomics approach to compare the microbial communities and ARGs present in two soils fertilized with sewage sludge. The two soils represented different land uses and different physicochemical and granulometric properties. Both soils were characterized by a similar taxonomic composition of the bacterial community, despite dissimilarities between soils properties. Five phyla predominated, viz. Planctomycetes, Actinobacteria, Proteobacteria, Chloroflexi and Firmicutes, and they were present in comparable proportions in both soils. Network analysis revealed that the application of sewage sludge resulted in substantial qualitative and quantitative changes in bacterial taxonomic profile, with most abundant phyla being considerably depleted and replaced by Proteobacteria and Spirochaetes. In addition, the ratio of oligotrophic to copiotrophic bacteria substantially decreased in both amended soils. Furthermore, fertilized soils demonstrated greater diversity and richness of ARGs compared to control soils. The increased abundance concerned mainly genes of resistance to antibiotics most commonly used in human and animal medicine. The level of heavy metals in sewage sludge was low and did not exceed the standards permitted in Poland for sludge used in agriculture, and their level in fertilized soils was still inconsiderable.

Horizontal gene transfer plays a crucial role in the development of antibiotic resistance in an antibiotic-free shrimp farming system

Antibiotic selective pressure in aquaculture systems often results in the antibiotic resistance genes (ARGs) proliferation. Nonetheless, a paucity of data exists concerning the mechanisms of ARGs development in aquaculture systems without the influences of antibiotics. This study utilized metagenomic approaches to elucidate the dynamics and transfer mechanisms of ARGs throughout the aquaculture of Pacific white shrimp. A marked change in the resistome was observed throughout the aquaculture without antibiotics. The total ARGs relative abundance increased from 0.05 to 0.33 by day 90 of cultivation, with even higher in mixed wastewater (0.44). Both bacterial communities and mobile genetic elements play pivotal roles in the development of ARGs. Metagenome-assembled genomes showed enrichment of environmentally intrinsic ARGs on chromosomes including macB and mdtK. The plasmid-mediated horizontal transfer was recognized as a principal factor contributing to the rise of ARGs, particularly for tetG and floR, and this led to an escalation of resistance risk, peaking at a risks core of 35.43 on day 90. This study demonstrates that horizontal gene transfer plays a crucial role in ARGs development without antibiotic pressure, which can provide a theoretical foundation for controlling ARGs proliferation in aquaculture systems.

Species sensitivity distribution for nonylphenol: Acute toxicity and ecological risk in Bohai Region

Nonylphenol (NP), a main byproduct of nonylphenol polyethoxylates (NPEs) degradation, is prevalent across diverse environmental settings. Given its widespread presence, evaluating the ecological risks associated with NP in coastal waters and sediments is essential for the protection of the marine environment. This study evaluates the acute toxicity of NP on ten representative aquatic species from the Bohai Sea, determining the Aquatic Life Criteria (ALC) through two distinct methods. The Criteria Maximum Concentration (CMC) for NP in seawater was established at 12.0 μg/L, with a Predicted No-Effect Concentration (PNEC) for water at 15.2 μg/L and for sediment at 33.3 μg/kg. Additionally, a tiered ecological risk assessment (ERA) of both surface seawater and sediment in the Bohai Sea revealed significant ecological risks at various sediment sites. These results offer crucial insights for assessing the ecological risks to coastal ecosystem and provide foundational data necessary for informed environmental protection and management strategies.

A critical meta-analysis of predicted no effect concentrations for antimicrobial resistance selection in the environment

Antimicrobial resistance (AMR) is one of the greatest threats to human health with a growing body of evidence demonstrating that selection for AMR can occur at environmental antimicrobial concentrations. Understanding the concentrations at which selection for resistance may occur is critical to help inform environmental risk assessments and highlight where mitigation strategies are required. A variety of experimental and data approaches have been used to determine these concentrations. However, there is minimal standardisation of existing approaches and no consensus on the relative merits of different methods. We conducted a semi-systematic literature review to collect and critically appraise available minimal selective concentration (MSC) and predicted no effect concentration for resistance (PNECR) data and the approaches used to derive them. There were 21 relevant articles providing 331 selective concentrations, ranging from 0.00087 µg/L (ciprofloxacin) to 2000 µg/L (carbenicillin). Meta-analyses of these data found that selective concentrations are highly compound-dependent, and only a subset of all antimicrobials have been the focus of most of the research. The variety of approaches that have been used, knowledge gaps and future research priorities were identified, as well as recommendations for those considering the selective risks of antimicrobials in the environment.

Coagulase-negative staphylococci from bovine milk: Antibiogram profiles and virulent gene detection

BACKGROUND

Coagulase-negative Staphylococcus species are an emerging cause of intramammary infection, posing a significant economic and public health threat. The aim of this study was to assess the occurrence of coagulase-negative Staphylococcus species in bovine milk and dairy farms in Northwestern Ethiopia and to provide information about their antibiotic susceptibility and virulence gene profiles.

METHODS

The cross-sectional study was conducted from February to August 2022. Coagulase-negative Staphylococcus species were isolated from 290 milk samples. Species isolation and identification were performed by plate culturing and biochemical tests and the antimicrobial susceptibility pattern of each isolate was determined by the Kirby-Bauer disc diffusion test. The single-plex PCR was used to detect the presence of virulent genes. The STATA software version 16 was used for data analysis. The prevalence, proportion of antimicrobial resistance and the number of virulent genes detected from coagulase-negative Staphylococcus species were analyzed using descriptive statistics.

RESULTS

Coagulase-negative Staphylococcus species were isolated in 28.6%, (95% CI: 23.5-34.2) of the samples. Of these, the S. epidermidis, S. sciuri, S. warneri, S. haemolyticus, S. simulans, S. chromogens, S. cohnii, and S. captis species were isolated at the rates of 11, 5.2, 3.4, 3.1, 3.1, 1, 1, and 0.7% respectively. All the isolates showed a high percentage (100%) of resistance to Amoxicillin, Ampicillin, and Cefotetan and 37.5% of resistance to Oxacillin. The majority (54.2%) of coagulase-negative isolates also showed multidrug resistance. Coagulase-negative Staphylococcus species carried the icaD, pvl, mecA, hlb, sec, and hla virulent genes at the rates of 26.5%, 22.1%, 21.7%, 9.6%, 9.6% and 8.4% respectively.

CONCLUSION

The present study revealed that the majority of the isolates (54.2%) were found multidrug-resistant and carriage of one or more virulent and enterotoxin genes responsible for intramammary and food poisoning infections. Thus, urgent disease control and prevention measures are warranted to reduce the deleterious impact of coagulase-negative species. To the best of our knowledge, this is the first study in Ethiopia to detect coagulase-negative Staphylococcus species with their associated virulent and food poisoning genes from bovine milk.

The Role of Wastewater Treatment Plants in Dissemination of Antibiotic Resistance: Source, Measurement, Removal and Risk Assessment

Antibiotic Resistance Genes (ARGs) are contaminants of emerging concern with marked potential to impact public and environmental health. This review focusses on factors that influence the presence, abundance, and dissemination of ARGs within Wastewater Treatment Plants (WWTPs) and associated effluents. Antibiotic-Resistant Bacteria (ARB) and ARGs have been detected in the influent and the effluent of WWTPs worldwide. Different levels of wastewater treatment (primary, secondary, and tertiary) show different degrees of removal efficiency of ARGs, with further differences being observed when ARGs are captured as intracellular or extracellular forms. Furthermore, routinely used molecular methodologies such as quantitative polymerase chain reaction or whole genome sequencing may also vary in resistome identification and in quantifying ARG removal efficiencies from WWTP effluents. Additionally, we provide an overview of the One Health risk assessment framework, as well as future strategies on how WWTPs can be assessed for environmental and public health impact.

Relevance of the Adjuvant Effect between Cellular Homeostasis and Resistance to Antibiotics in Gram-Negative Bacteria with Pathogenic Capacity: A Study of Klebsiella pneumoniae

Antibiotic resistance has become a global issue. The most significant risk is the acquisition of these mechanisms by pathogenic bacteria, which can have a severe clinical impact and pose a public health risk. This problem assumes that bacterial fitness is a constant phenomenon and should be approached from an evolutionary perspective to develop the most appropriate and effective strategies to contain the emergence of strains with pathogenic potential. Resistance mechanisms can be understood as adaptive processes to stressful conditions. This review examines the relevance of homeostatic regulatory mechanisms in antimicrobial resistance mechanisms. We focus on the interactions in the cellular physiology of pathogenic bacteria, particularly Gram-negative bacteria, and specifically Klebsiella pneumoniae. From a clinical research perspective, understanding these interactions is crucial for comprehensively understanding the phenomenon of resistance and developing more effective drugs and treatments to limit or attenuate bacterial sepsis, since the most conserved adjuvant phenomena in bacterial physiology has turned out to be more optimized and, therefore, more susceptible to alterations due to pharmacological action.

From remote to urbanized: Dispersal of antibiotic-resistant bacteria under the aspect of anthropogenic influence

Antibiotic resistance is a growing global concern, but our understanding of the spread of resistant bacteria in remote regions remains limited. While some level of intrinsic resistance likely contributes to reduced susceptibility to antimicrobials in the environment, it is evident that human actions, particularly the (mis)use of antibiotics, play a significant role in shaping the environmental resistome, even in seemingly distant habitats like glacier ice sheets. Our research aims to bridge this knowledge gap by investigating the direct influence of human activities on the presence of antibiotic-resistant bacteria in various habitats. To achieve a comprehensive assessment of anthropogenic impact across diverse and seemingly isolated sampling sites, we developed an innovative approach utilizing Corine Land Cover data and heatmaps generated from sports activity trackers. This method allowed us to make meaningful comparisons across relatively pristine environments. Our findings indicate a noteworthy increase in culturable antibiotic-resistant bacteria with heightened human influence, as evidenced by our analysis of glacier, snow, and lake water samples. Notably, the most significant concentrations of antibiotic-resistant and multidrug-resistant microorganisms were discovered in two highly impacted sampling locations, namely the Tux Glacier and Gas Station Ellmau.

Evolution Under Thermal Stress Affects Escherichia coli's Resistance to Antibiotics

Exposure to both antibiotics and temperature changes can induce similar physiological responses in bacteria. Thus, changes in growth temperature may affect antibiotic resistance. Previous studies have found that evolution under antibiotic stress causes shifts in the optimal growth temperature of bacteria. However, little is known about how evolution under thermal stress affects antibiotic resistance. We examined 100+ heat-evolved strains of Escherichia coli that evolved under thermal stress. We asked whether evolution under thermal stress affects optimal growth temperature, if there are any correlations between evolving in high temperatures and antibiotic resistance, and if these strains' antibiotic efficacy changes depending on the local environment's temperature. We found that: (1) surprisingly, most of the heat-evolved strains displayed a decrease in optimal growth temperature and overall growth relative to the ancestor strain, (2) there were complex patterns of changes in antibiotic resistance when comparing the heat-evolved strains to the ancestor strain, and (3) there were few significant correlations among changes in antibiotic resistance, optimal growth temperature, and overall growth.

Genome-wide transcriptional profiling and functional analysis of long noncoding RNAs and mRNAs in chicken macrophages associated with the infection of avian pathogenic E. coli

BACKGROUND

Avian pathogenic E. coli (APEC) can cause localized or systemic infections, collectively known as avian colibacillosis, resulting in huge economic losses to poultry industry globally per year. In addition, increasing evidence indicates that long non-coding RNAs (lncRNAs) play a critical role in regulating host inflammation in response to bacterial infection. However, the role of lncRNAs in the host response to APEC infection remains unclear.

RESULTS

Here, we found 816 differentially expressed (DE) lncRNAs and 1,798 DE mRNAs in APEC infected chicken macrophages by RNAseq. The identified DE lncRNA-mRNAs were involved in Toll like receptor signaling pathway, VEGF signaling pathway, fatty acid metabolism, phosphatidylinositol signaling system, and other types of O-glycan biosynthesis. Furthermore, we found the novel lncRNA TCONS_00007391 as an important immune regulator in APEC infection was able to regulate the inflammatory response by directly targeting CD86.

CONCLUSION

These findings provided a better understanding of host response to APEC infection and also offered the potential drug targets for therapy development against APEC infection.

Environmentally Friendly Degradation and Detoxification of Rifampicin by a Bacterial Laccase and Hydrogen Peroxide

Antibiotics are micropollutants accumulating in our rivers and wastewaters, potentially leading to bacterial antibiotic resistance, a worldwide problem to which there is no current solution. Here, we have developed an environmentally friendly two-step process to transform the antibiotic rifampicin (RIF) into non-antimicrobial compounds. The process involves an enzymatic oxidation step by the bacterial CotA-laccase and a hydrogen peroxide bleaching step. NMR identified rifampicin quinone as the main product of the enzymatic oxidation. Growth of Escherichia coli strains in the presence of final degradation products (FP) and minimum inhibitory concentration (MIC) measurements confirmed that FP are non-anti-microbial compounds, and bioassays suggest that FP is not toxic to eukaryotic organisms. Moreover, competitive fitness assays between susceptible and RIF-resistant bacteria show that susceptible bacteria is strongly favoured in the presence of FP. Our results show that we have developed a robust and environmentally friendly process to effectively remediate rifampicin from antibiotic contaminated environments.

Review of emerging contaminants in green stormwater infrastructure: Antibiotic resistance genes, microplastics, tire wear particles, PFAS, and temperature

Green stormwater infrastructure is a growing management approach to capturing, infiltrating, and treating runoff at the source. However, there are several emerging contaminants for which green stormwater infrastructure has not been explicitly designed to mitigate and for which removal mechanisms are not yet well defined. This is an issue, as there is a growing understanding of the impact of emerging contaminants on human and environmental health. This paper presents a review of five emerging contaminants - antibiotic resistance genes, microplastics, tire wear particles, PFAS, and temperature - and seeks to improve our understanding of how green stormwater infrastructure is impacted by and can be designed to mitigate these emerging contaminants. To do so, we present a review of the source and transport of these contaminants to green stormwater infrastructure, specific treatment mechanisms within green infrastructure, and design considerations of green stormwater infrastructure that could lead to their removal. In addition, common removal mechanisms across these contaminants and limitations of green infrastructure for contaminant mitigation are discussed. Finally, we present future research directions that can help to advance the use of green infrastructure as a first line of defense for downstream water bodies against emerging contaminants of concern.

Development of a national antibiotic multimetric index for identifying watersheds vulnerable to antibiotic pollution

Improved surveillance of antibiotics and antibiotic resistance (AR) throughout the environment is an important aspect of the prevention and control of threats posed to human and ecological health. In response to field investigations often limited by resources and time, this study aims to develop a systematic approach to assess watershed vulnerability to antibiotic pollution and AR by integrating modeling and field studies. The national antibiotic pollution vulnerability index was developed to identify watersheds most impacted by antibiotic sources. The index incorporates multiple metrics representing antibiotic pollution driven by both agricultural activities and municipal wastewater (i.e. outpatient antibiotic prescriptions, wastewater treatment plant effluent flow, stream order and dilution factor of effluent-receiving streams, manure application, and animal facilities), alongside climate change indicators (i.e., temperature, precipitation, and runoff). The pollution index was applied at a state level in North Carolina to identify the most-impacted watersheds and inform site selection for targeted field study quantifying azithromycin, ciprofloxacin, sulfamethoxazole, and trimethoprim concentrations. Modeled-informed sites in NC demonstrated the highest reported concentrations of azithromycin, trimethoprim, and sulfamethoxazole compared to previous NC studies, confirming the index effectiveness in identifying watersheds with higher antibiotic concentrations. At the national scale, watersheds relatively more vulnerable to antibiotic pollution are predominantly located in the Midwest, South, and Northeast regions of the U.S., with Iowa and Indiana being the most impacted states. Climate change is expected to exacerbate watershed vulnerability to agriculture-driven AR in the Midwest and Northeast due to an increase in precipitation and mean temperature coupled with intense agricultural activities. In addition, due to climate change-induced reductions in precipitation and runoff, watersheds in the Midwest, Mid-Atlantic, and South Central are dominantly at higher risk of effluent-driven AR occurrences. We have disseminated the developed indices as open-source online tools to aid in prioritizing strategies to mitigate AR occurrence across the U.S.

The Challenge of Overcoming Antibiotic Resistance in Carbapenem-Resistant Gram-Negative Bacteria: "Attack on Titan"

The global burden of bacterial resistance remains one of the most serious public health concerns. Infections caused by multidrug-resistant (MDR) bacteria in critically ill patients require immediate empirical treatment, which may not only be ineffective due to the resistance of MDR bacteria to multiple classes of antibiotics, but may also contribute to the selection and spread of antimicrobial resistance. Both the WHO and the ECDC consider carbapenem-resistant Enterobacteriaceae (CRE), carbapenem-resistant Pseudomonas aeruginosa (CRPA), and carbapenem-resistant Acinetobacter baumannii (CRAB) to be the highest priority. The ability to form biofilm and the acquisition of multiple drug resistance genes, in particular to carbapenems, have made these pathogens particularly difficult to treat. They are a growing cause of healthcare-associated infections and a significant threat to public health, associated with a high mortality rate. Moreover, co-colonization with these pathogens in critically ill patients was found to be a significant predictor for in-hospital mortality. Importantly, they have the potential to spread resistance using mobile genetic elements. Given the current situation, it is clear that finding new ways to combat antimicrobial resistance can no longer be delayed. The aim of this review was to evaluate the literature on how these pathogens contribute to the global burden of AMR. The review also highlights the importance of the rational use of antibiotics and the need to implement antimicrobial stewardship principles to prevent the transmission of drug-resistant organisms in healthcare settings. Finally, the review discusses the advantages and limitations of alternative therapies for the treatment of infections caused by these "titans" of antibiotic resistance.

CRISPR-Cas-Based Antimicrobials: Design, Challenges, and Bacterial Mechanisms of Resistance

The emergence of antibiotic-resistant bacterial strains is a source of public health concern across the globe. As the discovery of new conventional antibiotics has stalled significantly over the past decade, there is an urgency to develop novel approaches to address drug resistance in infectious diseases. The use of a CRISPR-Cas-based system for the precise elimination of targeted bacterial populations holds promise as an innovative approach for new antimicrobial agent design. The CRISPR-Cas targeting system is celebrated for its high versatility and specificity, offering an excellent opportunity to fight antibiotic resistance in pathogens by selectively inactivating genes involved in antibiotic resistance, biofilm formation, pathogenicity, virulence, or bacterial viability. The CRISPR-Cas strategy can enact antimicrobial effects by two approaches: inactivation of chromosomal genes or curing of plasmids encoding antibiotic resistance. In this Review, we provide an overview of the main CRISPR-Cas systems utilized for the creation of these antimicrobials, as well as highlighting promising studies in the field. We also offer a detailed discussion about the most commonly used mechanisms for CRISPR-Cas delivery: bacteriophages, nanoparticles, and conjugative plasmids. Lastly, we address possible mechanisms of interference that should be considered during the intelligent design of these novel approaches.

Phenotypic characterization and epidemiology of extended-spectrum β-lactamase-producing Enterobacteriaceae strains from urinary tract infections in Garoua, Cameroon

Background and objectives

The emergence of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) is causing increased morbidity and mortality around the world as a result of therapeutic failures. ESBL-E are priority pathogens due to their multidrug resistance (MDR). In Northern Cameroon, ESBL-producing bacteria, particularly in urinary tract infections (UTIs), are being increasingly isolated. This study aimed to retrospectively determine the prevalence of multi-drug resistant ESBL strains isolated from UTIs in Northern Cameroon and to evaluate the effectiveness of the ATB UR Gallery of BioMérieux in diagnosing ESBL-E in clinical settings.

Methods

Standard microbiology protocols and statistical tools were utilized to identify ESBL-producing bacteria and characterize their phenotypic susceptibility and resistance profiles in the study population.

Results

Out of the 144 enterobacteria isolates successfully cultured, 59 (41%) were identified as MDR strains. The ATB UR EU gallery identified 33 (23%) multi-drug resistant ESBL-producing strains, while the double synergy test identified 35 strains without disc reconciliation and 38 strains after reconciliation. The most prevalent ESBL-E isolate was Escherichia coli, accounting for 77.1% of the isolates, followed by Klebsiella pneumoniae (20%) and Enterobacter aerogenes (2.9%). Additionally, the study revealed the emergence of Imipenem resistance (5.7%), a critical last-resort antibiotic. However, all ESBL strains were sensitive to Fosfomycin (FSF/FOS), demonstrating its potential as an effective therapeutic option. Moreover, 37% of the ESBL producers exhibited co-resistance to over 20 different antibiotics.

Conclusion

This study provides valuable insights into the prevalence and susceptibility patterns of ESBL-E associated with UTIs in Northern Cameroon. These insights emphasizes the importance of implementing appropriate treatment guidelines and antimicrobial stewardship measures to mitigate the spread and impact of MDR ESBL-producing strains on public health.

Determination of the fate of antibiotic resistance genes and the response mechanism of plants during enhanced antibiotic degradation in a bioelectrochemical-constructed wetland system

Chloramphenicol (CAP) has a high concentration and detection frequency in aquatic environments due to its insufficient degradation in traditional biological wastewater treatment processes. In this study, bioelectrochemical assistant-constructed wetland systems (BES-CWs) were developed as advanced processes for efficient CAP removal, in which the degradation and transfer of CAP and the fate of antibiotic resistance genes (ARGs) were evaluated. The CAP removal efficiency could reach as high as 90.2%, while the removed CAP can be partially adsorbed and bioaccumulated in plants, significantly affecting plant growth. The vertical gene transfer and horizontal gene transfer increased the abundance of ARGs under high voltage and CAP concentrations. Microbial community analysis showed that CAP pressure and electrical stimulation selected the functional bacteria to increase CAP removal and antibiotic resistance. CAP degradation species carrying ARGs could increase their opposition to the biotoxicity of CAP and maintain system performance. In addition, ARGs are transferred into the plant and upward, which can potentially enter the food chain. This study provides an essential reference for enhancing antibiotic degradation and offers fundamental support for the underlying mechanism and ARG proliferation during antibiotic biodegradation.

Efficient photo-Fenton reaction for tetracycline and antibiotic resistant bacteria removal using hollow Fe-doped In2O3 nanotubes: From theoretical research to practical application

The low exposure of active sites and the slow electron transfer rate still restrict the wide application of the photo-Fenton system of Fe-based photocatalyst in practical water treatment. Herein, we prepared a hollow Fe-doped In₂O₃ nanotube (h-Fe-In₂O₃) catalyst for activating hydrogen peroxide (H₂O₂) to remove tetracycline (TC) and antibiotic resistant bacteria (ARB). Incorporation of Fe could shorten the band gap and increase the absorption capacity of visible light. Meanwhile, the increase of electron density at the Fermi level promotes the interfacial electron transport. The large specific surface area of the tubular structure exposes more Fe active site and the Fe-O-In site reduces the energy barrier of H₂O₂ activation, resulting in more and faster formation of hydroxyl radicals (•OH). After continuous operation for 600 min, the h-Fe-In₂O₃ reactor still can remove 85% TC and about 3.5 log ARB in secondary effluent, showing good stability and durability for practical wastewater treatment.

Quantification and antibiotic resistance risk assessment of chlorination-residual viable/VBNC Escherichia coli and Enterococcus in on-site hospital wastewater treatment system

On-site hospital wastewater treatment system widely applying chlorination has been regarded as an important barrier to curb the dissemination of antibiotic resistance. Chlorination-residual viable and viable but non-culturable (VBNC) bacteria probably lead to overestimate the effect of disinfection, while their antibiotic resistance risks imported from hospital effluents to municipal pipe network may be ignored. In this study, we quantified viable/VBNC Escherichia coli and Enterococcus in chlorination of an on-site hospital wastewater treatment system and assessed their antibiotic resistance risks. The numbers of viable/VBNC Escherichia coli and Enterococcus in raw wastewater were detected as high as 5.76-6.34/5.76-6.33 and 5.44-5.76/5.44-5.75 log₁₀(cells/mL). Meanwhile, high proportions of antibiotic-resistant Escherichia coli and Enterococcus to culturable Escherichia coli and Enterococcus were observed, especially carrying ampicillin resistance (22.25-41.70 % and 28.09-54.05 %). Chlorination could remove 0.44-1.88-/0.43-1.88- and 0.29-1.29-/0.28-1.28-log of viable/VBNC and complete culturable Escherichia coli and Enterococcus, but cause antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) to be released outside cells, and possibly further enhance the antibiotic resistance of viable bacteria. Low detections of antibiotics suggested that the occurrence of antibiotic-resistant bacteria (ARB) may not be accompanied by the corresponding antibiotics. Different sampling months had some impacts on above results, while the results were basically stable at different sampling times of hospital daily working period. The high release rates (11.26-13.02 and 11.59-12.98 log₁₀(cells/h)) and cumulative amounts (15.41-16.12 and 15.75-16.14 log₁₀(cells)) of chlorination-residual viable/VBNC Escherichia coli and Enterococcus indirectly assessed the potential risks of bacterial antibiotic resistance entering municipal pipe network. Additionally, the contributions from the corresponding antibiotic ceftazidime, ciprofloxacin, and vancomycin with the cumulative amounts of 2.57-4.85, 5.73-7.50, and 5.21-7.14 kg should also be taken seriously. Residual chlorine could serve as an important signal indicator for the risk assessment.

Awareness and Knowledge of Antimicrobial Resistance, Antimicrobial Stewardship and Barriers to Implementing Antimicrobial Susceptibility Testing among Medical Laboratory Scientists in Nigeria: A Cross-Sectional Study

Background: Antimicrobial resistance (AMR) is now considered one of the greatest global health threats. This is further compounded by a lack of new antibiotics in development. Antimicrobial stewardship programmes can improve and optimize the use of antibiotics, thereby increasing the cure rates of antibiotic treatment and decreasing the problem of AMR. In addition, diagnostic and antimicrobial stewardships in the pathology laboratories are useful tools to guide clinicians on patient treatment and to stop the inappropriate use of antibiotics in empirical treatment or narrow antibiotics. Medical Laboratory Scientists are at the forefront of performing antibiotics susceptibility testing in pathology laboratories, thereby helping clinicians to select the appropriate antibiotics for patients suffering from bacterial infections. Methods: This cross-sectional study surveyed personal antimicrobial usage, the knowledge and awareness on AMR, and antimicrobial stewardship, as well as barriers to antimicrobial susceptibility testing among medical laboratory scientists in Nigeria using pre-tested and validated questionnaires administered online. The raw data were summarized and exported in Microsoft Excel and further analyzed using IBM SPSS version 26. Results: Most of the respondents were males (72%) and 25-35 years old (60%). In addition, the BMLS degree was the highest education qualification most of the respondents (70%) achieved. Of the 59.2% of the respondents involved in antibiotics susceptibility testing, the disc diffusion method was the most commonly used (67.2%), followed by PCR/Genome-based detection (5.2%). Only a small percentage of respondents used the E-test (3.4%). The high cost of testing, inadequate laboratory infrastructure, and a lack of skilled personnel are the major barriers to performing antibiotics susceptibility testing. A higher proportion of a good AMR knowledge level was observed in male respondents (75%) than females (42.9%). The knowledge level was associated with the respondent's gender (p = 0.048), while respondents with a master's degree were more likely to possess a good knowledge level of AMR (OR: 1.69; 95% CI: 0.33, 8.61). Conclusion: The findings of this study indicate that Nigerian medical laboratory scientists had moderate awareness of AMR and antibiotic stewardship. It is necessary to increase investments in laboratory infrastructure and manpower training, as well as set up an antimicrobial stewardship programme to ensure widespread antibiotics susceptibility testing in hospitals, thereby decreasing empirical treatment and the misuse of antibiotics.

Genomic and functional characterization of carbapenem-resistant Klebsiella pneumoniae from hospital wastewater

BACKGROUND

The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) attracted extensive attention. Information on CRKP from hospital wastewater (HWW) is limited. The aims of this study were to investigate the genomic characteristics and to evaluate the survivability characteristics of 11 CRKP from HWW in a Chinese teaching hospital in Fujian province.

RESULTS

A total of 11 CRKP from HWW were recovered in this study. All CRKP from HWW were resistant to most antibiotics. Comparative genetic analysis demonstrated that all CRKP isolates were clustered into the three distinct phylogenetic clades and clade 2 and clade 3 were mixtures of samples collected from both HWW and clinical settings. Varieties of resistance genes, virulence genes and plasmid replicon types were detected in CRKP from HWW. In vitro transfer of bla_KPC-2 was successful for 3 bla_KPC-2-positive CRKP from HWW with high conjugation frequency. Our study demonstrated that the genetic environments of bla_KPC-2 shared core structure with ISKpn27-bla_KPC-2-ISKpn6. Group analysis showed that CRKP from HWW had a lower survivability in serum compared to clinical CRKP (p < 005); and CRKP from HWW had no significant difference in survivability in HWW compared to clinical CRKP (p > 005).

CONCLUSIONS

We analyzed the genomic and survivability characteristics of CRKP from HWW in a Chinese teaching hospital. These genomes represent a significant addition of genomic data from the genus and could serve as a valuable resource for future genomic studies about CRKP from HWW.

Effect of composted pig manure, biochar, and their combination on antibiotic resistome dissipation in swine wastewater-treated soil

The prevalence of antibiotic resistance genes (ARGs), owing to irrigation using untreated swine wastewater, in vegetable-cultivated soils around swine farms poses severe threats to human health. Furthermore, at the field scale, the remediation of such soils is still challenging. Therefore, here, we performed field-scale experiments involving the cultivation of Brassica pekinensis in a swine wastewater-treated soil amended with composted pig manure, biochar, or their combination. Specifically, the ARG and mobile genetic element (MGE) profiles of bulk soil (BS), rhizosphere soil (RS), and root endophyte (RE) samples were examined using high-throughput quantitative polymerase chain reaction. In total, 117 ARGs and 22 MGEs were detected. Moreover, we observed that soil amendment using composted pig manure, biochar, or their combination decreased the absolute abundance of ARGs in BS and RE after 90 days of treatment. However, the decrease in the abundance of ARGs in RS was not significant. We also observed that the manure and biochar co-application showed a minimal synergistic effect. To clarify this observation, we performed network and Spearman correlation analyses and used structure equation models to explore the correlations among ARGs, MGEs, bacterial composition, and soil properties. The results revealed that the soil amendments reduced the abundances of MGEs and potential ARG-carrying bacteria. Additionally, weakened horizontal gene transfer was responsible for the dissipation of ARGs. Thus, our results indicate that composted manure application, with or without biochar, is a useful strategy for soil nutrient supplementation and alleviating farmland ARG pollution, providing a justification for using an alternative to the common agricultural practice of treating the soil using only untreated swine wastewater. Additionally, our results are important in the context of soil health for sustainable agriculture.

Metagenomic profiling of antibiotic resistance genes in Red Sea brine pools

Antibiotic resistance (AR) is an alarming global health concern, causing an annual death rate of more than 35,000 deaths in the US. AR is a natural phenomenon, reported in several pristine environments. In this study, we report AR in pristine Red Sea deep brine pools. Antimicrobial resistance genes (ARGs) were detected for several drug classes with tetracycline and macrolide resistance being the most abundant. As expected, ARGs abundance increased in accordance with the level of human impact with pristine Red Sea samples having the lowest mean ARG level followed by estuary samples, while activated sludge samples showed a significantly higher ARG level. ARG hierarchical clustering grouped drug classes for which resistance was detected in Atlantis II Deep brine pool independent of the rest of the samples. ARG abundance was significantly lower in the Discovery Deep brine pool. A correlation between integrons and ARGs abundance in brine pristine samples could be detected, while insertion sequences and plasmids showed a correlation with ARGs abundance in human-impacted samples not seen in brine pristine samples. This suggests different roles of distinct mobile genetic elements (MGEs) in ARG distribution in pristine versus human-impacted sites. Additionally, we showed the presence of mobile antibiotic resistance genes in the Atlantis II brine pool as evidenced by the co-existence of integrases and plasmid replication proteins on the same contigs harboring predicted multidrug-resistant efflux pumps. This study addresses the role of non-pathogenic environmental bacteria as a silent reservoir for ARGs, and the possible horizontal gene transfer mechanism mediating ARG acquisition.

Evidence of Bacterial Community Coalescence between Freshwater and Discharged tpm-Harboring Bacterial Taxa from Hospital and Domestic Wastewater Treatment Plants among Epilithic Biofilms

The ability of WWTP outflow bacteria at colonizing rock surfaces and contributing to the formation of river epilithic biofilms was investigated. Bacterial community structures of biofilms (b-) developing on rocks exposed to treated wastewaters (TWW) of a hospital (HTWW) and a domestic (DTWW) clarifier, and to surface waters of the stream located at 10 m, 500 m, and 8 km from the WWTP outlet, were compared. Biofilm bacterial contents were analyzed by cultural approaches and a tpm-based DNA metabarcoding analytical scheme. Co-occurrence distribution pattern analyses between bacterial datasets and eighteen monitored pharmaceuticals were performed. Higher concentrations of iohexol, ranitidine, levofloxacin, and roxithromycin were observed in the b-HTWW while atenolol, diclofenac, propranolol, and trimethoprim were higher in the b-DTWW. MPN growth assays showed recurrent occurrences of Pseudomonas aeruginosa and Aeromonas caviae among these biofilms. An enrichment of multi-resistant P. aeruginosa cells was observed in the hospital sewer line. P. aeruginosa MPN values were negatively correlated to roxithromycin concentrations. The tpm DNA metabarcoding analyses confirmed these trends and allowed an additional tracking of more than 90 species from 24 genera. Among the recorded 3082 tpm ASV (amplicon sequence variants), 41% were allocated to the Pseudomonas. Significant differences through ANOSIM and DESeq2 statistical tests were observed between ASV recovered from b-HTWW, b-DTWW, and epilithic river biofilms. More than 500 ASV were found restricted to a single sewer line such as those allocated to Aeromonas popoffii and Stenotrophomonas humi being strictly found in the b-HTWW file. Several significant correlations between tpm ASV counts per species and pharmaceutical concentrations in biofilms were recorded such as those of Lamprocystis purpurea being positively correlated with trimethoprim concentrations. A tpm source tracking analysis showed the b-DTWW and b-HTWW tpm ASV to have contributed, respectively, at up to 35% and 2.5% of the epilithic river biofilm tpm-taxa recovered downstream from the WWTP outlet. Higher contributions of TWW taxa among epilithic biofilms were recorded closer to the WWTP outlet. These analyses demonstrated a coalescence of WWTP sewer communities with river freshwater taxa among epilithic biofilms developing downstream of a WWTP outlet.

Advances of non-thermal plasma discharge technology in degrading recalcitrant wastewater pollutants. A comprehensive review

With development and urbanization, the amount of wastewater generated due to human activities drastically increases yearly, causing water pollution and intensifying the already worsened water crisis. Although convenient, conventional wastewater treatment methods such as activated sludge, stabilization ponds, and adsorption techniques cannot fully eradicate the complex and recalcitrant contaminants leading to toxic byproducts generation. Recent advancements in wastewater treatment techniques, specifically non-thermal plasma technology, have been extensively investigated for the degradation of complex pollutants in wastewater. Non-thermal plasma is an effective alternative for degrading and augmenting the biodegradability of recalcitrant pollutants due to its ability to generate reactive species in situ. This article critically reviews the non-thermal plasma technology, considering the plasma discharge configuration and reactor types. Furthermore, the influence of operational parameters on the efficiency of the plasma systems and the reactive species generated by the system during discharge has gained significant interest and hence been discussed. Also, the application of non-thermal plasma technology for the degradation of pharmaceuticals, pesticides, and dyes and the inactivation of microbial activities are outlined in this review article. Additionally, optimistic applications involving the combination of non-thermal plasma and catalysts and pilot and industrial-scale projects utilizing non-thermal plasma technology have been addressed. Concluding perceptions on the challenges and future perspectives of the non-thermal technology on wastewater treatment are accentuated. Overall, this review outlines a comprehensive understanding of the non-thermal plasma technology for recalcitrant pollutant degradation from a scientific perspective providing detailed instances for reference.

Fluoroquinolone Residues in the Environment Rapidly Induce Heritable Fluoroquinolone Resistance in Escherichia coli

Extensive antibiotic use increases the environmental presence of their residues and may accelerate the development of antibiotic resistance, although this remains poorly understood at environmentally relevant concentrations. Herein, susceptible Escherichia coli K12 was continuously exposed to five antibiotics at such concentrations for 100 days. The de novo-evolved mutants rapidly obtained fluoroquinolone resistance within 10 days, as indicated by the 4- and 16-fold augmentation of minimum inhibitory concentrations against enrofloxacin and ciprofloxacin, respectively. Moreover, the mutants maintained heritable fluoroquinolone resistance after the withdrawal of antibiotics for 30 days. Genomic analysis identified Asp87Gly or Ser83Leu substitutions in the gyrA gene in the mutants. Transcriptomics data showed that the transcriptional response of the mutants to fluoroquinolones was primarily involved in biofilm formation, cellular motility, porin, oxidative stress defense, and energy metabolism. Homologous recombination and molecular docking revealed that mutations of gyrA primarily mainly conferred fluoroquinolone resistance, while mutations at different positions of gyrA likely endowed different fluoroquinolone resistance levels. Collectively, this study revealed that environmentally relevant concentrations of antibiotics could rapidly induce heritable antibiotic resistance; therefore, the discharge of antibiotics into the environment should be rigorously controlled to prevent the development of antibiotic resistance.

How do freshwater microalgae and cyanobacteria respond to antibiotics?

Antibiotic pollution is an emerging environmental challenge. Residual antibiotics from various sources, including municipal and industrial wastewater, sewage discharges, and agricultural runoff, are continuously released into freshwater environments, turning them into reservoirs that contribute to the development and spread of antibiotic resistance. Thus, it is essential to understand the impacts of antibiotic residues on aquatic organisms, especially microalgae and cyanobacteria, due to their crucial roles as primary producers in the ecosystem. This review summarizes the effects of antibiotics on major biological processes in freshwater microalgae and cyanobacteria, including photosynthesis, oxidative stress, and the metabolism of macromolecules. Their adaptive mechanisms to antibiotics exposure, such as biodegradation, bioadsorption, and bioaccumulation, are also discussed. Moreover, this review highlights the important factors affecting the antibiotic removal pathways by these organisms, which will promote the use of microalgae-based technology for the removal of antibiotics. Finally, we offer some perspectives on the opportunities for further studies and applications.

A Systematic Review of Culture-Based Methods for Monitoring Antibiotic-Resistant Acinetobacter, Aeromonas, and Pseudomonas as Environmentally Relevant Pathogens in Wastewater and Surface Water

PURPOSE OF REVIEW

Mounting evidence indicates that habitats such as wastewater and environmental waters are pathways for the spread of antibiotic-resistant bacteria (ARB) and mobile antibiotic resistance genes (ARGs). We identified antibiotic-resistant members of the genera Acinetobacter, Aeromonas, and Pseudomonas as key opportunistic pathogens that grow or persist in built (e.g., wastewater) or natural aquatic environments. Effective methods for monitoring these ARB in the environment are needed to understand their influence on dissemination of ARB and ARGs, but standard methods have not been developed. This systematic review considers peer-reviewed papers where the ARB above were cultured from wastewater or surface water, focusing on the accuracy of current methodologies.

RECENT FINDINGS

Recent studies suggest that many clinically important ARGs were originally acquired from environmental microorganisms. Acinetobacter, Aeromonas, and Pseudomonas species are of interest because their ability to persist and grow in the environment provides opportunities to engage in horizontal gene transfer with other environmental bacteria. Pathogenic strains of these organisms resistant to multiple, clinically relevant drug classes have been identified as an urgent threat. However, culture methods for these bacteria were generally developed for clinical samples and are not well-vetted for environmental samples. The search criteria yielded 60 peer-reviewed articles over the past 20 years, which reported a wide variety of methods for isolation, confirmation, and antibiotic resistance assays. Based on a systematic comparison of the reported methods, we suggest a path forward for standardizing methodologies for monitoring antibiotic resistant strains of these bacteria in water environments.

Ecology, more than antibiotics consumption, is the major predictor for the global distribution of aminoglycoside-modifying enzymes

Antibiotic consumption and its abuses have been historically and repeatedly pointed out as the major driver of antibiotic resistance emergence and propagation. However, several examples show that resistance may persist despite substantial reductions in antibiotic use, and that other factors are at stake. Here, we study the temporal, spatial, and ecological distribution patterns of aminoglycoside resistance, by screening more than 160,000 publicly available genomes for 27 clusters of genes encoding aminoglycoside-modifying enzymes (AME genes). We find that AME genes display a very ubiquitous pattern: about 25% of sequenced bacteria carry AME genes. These bacteria were sequenced from all the continents (except Antarctica) and terrestrial biomes, and belong to a wide number of phyla. By focusing on European countries between 1997 and 2018, we show that aminoglycoside consumption has little impact on the prevalence of AME-gene-carrying bacteria, whereas most variation in prevalence is observed among biomes. We further analyze the resemblance of resistome compositions across biomes: soil, wildlife, and human samples appear to be central to understand the exchanges of AME genes between different ecological contexts. Together, these results support the idea that interventional strategies based on reducing antibiotic use should be complemented by a stronger control of exchanges, especially between ecosystems.

Comparative selective pressure potential of antibiotics in the environment

To guide both environmental and public health policy, it is important to assess the degree of antibiotic resistance selection pressure under measured environmental concentrations (MECs), and to compare the efficacy of different mitigation strategies to minimize the spread of resistance. To this end, the resistance selection and enrichment potential due to antibiotic emissions into the environment must be analysed from a life cycle perspective, for a wide range of antibiotics, and considering variations in the underlying fitness costs between different resistance mutations and genes. The aim of this study is to consistently derive fitness cost-dependent minimum selective concentrations (MSCs) from readily available bacterial inhibition data and to build MSC-based species sensitivity distributions (SSDs). These are then used to determine antibiotic-specific resistance selection concentrations predicted to promote resistance in 5% of exposed bacterial species (RSC₅). Using a previously developed competition model, we provide estimated MSC₁₀ endpoints for 2,984 antibiotic and bacterial species combinations; the largest set of modelled MSCs available to date. Based on constructed SSDs, we derive RSC₅ for 128 antibiotics with four orders of magnitude difference in their 'selective pressure potential' in the environment. By comparing our RSC₅ to MECs, we highlight specific environmental compartments (e.g. hospital and wastewater effluents, lakes and rivers), as well as several antibiotics (e.g. ciprofloxacin, norfloxacin, enrofloxacin, and tetracycline), to be scrutinized for their potential role in resistance selection and dissemination. In addition to enabling comparative risk screening of the selective pressure potential of multiple antibiotics, our SSD-derived RSC₅ provide the point of departure for calculating new life cycle-based characterization factors for antibiotics to compare mitigation strategies, thereby contributing towards a 'One-Health' approach to tackling the global antibiotic resistance crisis.

Synergistic role of in-situ Zr-doping and cobalt oxide cocatalysts on photocatalytic bacterial inactivation and organic pollutants removal over template-free Fe2O3 nanorods

Herein, we synthesized in-situ Zr-doped Fe₂O₃ NRs photocatalyst by successive simple hydrothermal and air quenching methods. The synergistic roles of CoO_x (1 wt%) and Zr-doping on bacteria inactivation and model organic pollutants over Fe₂O₃ NRs photocatalyst were studied in detail. Initially, rod-like Zr ((0-8) %)-doped Fe₂O₃ NRs were produced via a hydrothermal method. CoO_x was loaded onto the Zr ((0-8) %)-doped Fe₂O₃ NRs) surface by a wet impregnation approach. The Zr-doping conditions and CoO_x loadings were judiciously optimized, and a highly photoactive CoO_x(1 wt%)/Zr(6%)-doped Fe₂O₃ NRs photocatalyst was developed. The CoO_x(1 wt%) loaded Zr(6%)-doped Fe₂O₃ NRs photocatalyst revealed 99.4% inactivation efficiency compared with (0, 4 and 8)% Zr-doped Fe₂O₃ NRs, respectively. After CoO_x(1 wt%)/Zr(6%)-doped Fe₂O₃ NRs photocatalyst treatment, Bio-TEM images of bacterial cells showed extensive morphological deviations in cell membranes, compared with the non-treated ones. Additionally, the optimum CoO_x(1 wt%)/Zr(6%)-doped Fe₂O₃ NRs photocatalyst exhibited 99.2% BPA and 98.3% orange II dye degradation after light radiation for 3 h. This work will provide a rapid method for the development of photostable catalyst materials for bacterial disinfection and organic degradation.

Designing benign molecules: The influence of O-acetylated glucosamine-substituents on the environmental biodegradability of fluoroquinolones

Antibiotics are detected worldwide in the aquatic environment, with continuously rising concentrations. Antibiotics in the environment have the potential to damage ecosystems and contribute to the development of resistance. Whilst a few antibiotics, such as some β-lactams, are eliminated by effluent treatment, others, such as fluoroquinolones, are not or just partially removed and enter the environment. Therefore, approaches are needed to tackle those problems at the compound level. Benign by design (BbD), an important part of green pharmacy, has the goal to integrate environmental fate and end-of-use considerations at the very beginning, i.e., into the design of active pharmaceutical ingredients. Hence, pharmaceuticals should be designed to be sufficiently active and stable during storage and usage but should degrade after excretion into the environment, so that they cannot cause any adverse effects. Fluoroquinolones (FQs) are important broad-spectrum antibiotics. They are known to be persistent in the environment and to be neither inactivated nor degraded or even mineralized during sewage treatment. The addition of new substituents via amidation, like glucosamine moieties, at the carboxylic group of FQs, led to better antimicrobial activity compared to its parent compounds against various microorganisms. To investigate if the addition of sugar moieties could improve the overall environmental biodegradability of FQs, eight novel quinolone and fluoroquinolone analogs conjugated with 1,3,4,6-Tetra-O-acetyl-β-d-glucosamine and 2-deoxy-d-glucopyranose have been investigated regarding their ready biodegradability (OECD 301D/F) and their degradation pathways have been analyzed. According to the OECD 301D test, none of the substances could be classified as readily biodegradable. However, the O-acetyl analogs did undergo a partial degradation of the O-acetyl glucosamine moiety, via stepwise deacetylation and the degradation of the whole glucosamine moiety. The degradation resulted in Fluoroquinolone-3-carboxamide derivatives. Those insights could be further used as input for fragment-based design of benign APIs that will degrade once they reached the environment.

Predicting selection for antimicrobial resistance in UK wastewater and aquatic environments: Ciprofloxacin poses a significant risk

Antimicrobial resistance (AMR) is a threat to human and animal health, with the environment increasingly recognised as playing an important role in AMR evolution, dissemination, and transmission. Antibiotics can select for AMR at very low concentrations, similar to those in the environment, yet their release into the environment, e.g., from wastewater treatment plants, is not currently regulated. Understanding the selection risk antibiotics pose in wastewater and receiving waters is key to understanding if environmental regulation of antibiotics is required. We investigated the risk of selection occurring in UK wastewater and receiving waters by determining where measured environmental concentration data (n = 8187) for four antibiotics (ciprofloxacin, azithromycin, clarithromycin, and erythromycin) collected in England and Wales 2015-2018 (sites n = 67) exceeded selective concentration thresholds derived from complex microbial community evolution experiments undertaken previously. We show that selection for AMR by ciprofloxacin is likely to have occurred routinely in England and Wales wastewater during the 2015-2018 period, with some seasonal and regional trends. Wastewater treatment reduces the selection risk posed by ciprofloxacin significantly, but not completely, and predicted risk in surface waters remains high in several cases. Conversely, the potential risks posed by the macrolides (azithromycin, clarithromycin, and erythromycin) were lower than those posed by ciprofloxacin. Our data demonstrate further action is needed to prevent selection for AMR in wastewater, with environmental quality standards for some antibiotics required in the future, and that selection risk is not solely a concern in low/middle income countries.

Effect of temperature, pH, and soil texture on pirlimycin fate in dairy manure-amended soils

Antibiotics applied to soil through application of manure are of increasing concern due to their adverse environmental impacts, including their potential contribution to the development of antibiotic resistance in the environment. Two 90-d laboratory incubation studies were conducted to determine the effects of temperature (10 or 21 °C), pH (5, 7, 9), and soil texture (sandy loam, loam) on the persistence of two antibiotics (pirlimycin and cephapirin) applied to soils with dairy manure amendment. Dairy manure from treated and untreated cows was used as the source for this study. However, cephapirin was not detected in manure used for the study. Initial manure pH affected pirlimycin concentration of the manure, and there were differences in initial soil concentration between soil types. In the temperature experiment, pirlimycin concentration was significantly affected by temperature and soil type. In the 10 °C treatments, pirlimycin concentration initially decreased at 7 d but increased to levels similar to 0 d concentrations at 14 d, indicating possible deconjugation of pirlimycin ribonucleotide adducts in the manure applied. Although the loam soil type had a higher pirlimycin concentration in the temperature experiment at 0 d and 14 d, concentrations decreased below the sandy loam soil at 56 d and continued in the 90-d sampling period. Pirlimycin dissipation from dairy manure-amended soils was enhanced by higher temperature and finer soil texture, both of which could affect development of resistance genes if soil microbes are exposed to pirlimycin for longer periods of time.

Effects of Trophic Level and Land Use on the Variation of Animal Antibiotic Resistome in the Soil Food Web

In recent years, it has been increasingly recognized that soil animals are hidden reservoirs of antibiotic resistance genes (ARGs) and play a vital role in spreading ARGs in soil ecosystems. However, little is known about the variation of ARGs among different animals in the soil food web and effects of trophic levels and land uses on them. We characterized the antibiotic resistomes of 495 soil animal samples collected from six regions across China, including two different land uses. A total of 265 ARGs were detected in all animal samples, and relative abundances of ARGs in animals were significantly higher than in soils. In addition, significant differences in ARGs were observed among different animal groups. Twelve common ARGs were identified among all animal groups, accounting for 17.4% of total ARGs abundance. A positive and significant correlation was found between δ¹⁵N values (trophic level) and total ARGs abundance in animals. The relative abundance of ARGs in the soil food web from arable land was higher than forest land. Changes in soil antibiotics may indirectly affect animal resistome by altering soil ARGs. This study suggests that the risk of ARGs spreading through the food web is greater in arable than in forest ecosystems.

The source, fate and prospect of antibiotic resistance genes in soil: A review

Antibiotic resistance genes (ARGs), environmental pollutants of emerging concern, have posed a potential threat to the public health. Soil is one of the huge reservoirs and propagation hotspot of ARGs. To alleviate the potential risk of ARGs, it is necessary to figure out the source and fate of ARGs in the soil. This paper mainly reviewed recent studies on the association of ARGs with the microbiome and the transmission mechanism of ARGs in soil. The compositions and abundance of ARGs can be changed by modulating microbiome, soil physicochemical properties, such as pH and moisture. The relationships of ARGs with antibiotics, heavy metals, polycyclic aromatic hydrocarbons and pesticides were discussed in this review. Among the various factors mentioned above, microbial community structure, mobile genetic elements, pH and heavy metals have a relatively more important impact on ARGs profiles. Moreover, human health could be impacted by soil ARGs through plants and animals. Understanding the dynamic changes of ARGs with influencing factors promotes us to develop strategies for mitigating the occurrence and dissemination of ARGs to reduce health risks.

A tiered probabilistic approach to assess antibiotic ecological and resistance development risks in the fresh surface waters of China

Exposure to antibiotics can result in not only ecotoxicity on aquatic organisms but also the development of antibiotic resistance. In the study, the ecotoxicity data and minimum inhibitory concentrations of the antibiotics were screened to derive predicted no-effect concentrations of ecological (PNEC_eco) and resistance development risks (PNEC_res) for 36 antibiotics in fresh surface waters of China. The derived PNEC_eco and PNEC_res values were ranged from 0.00175 to 2351 μg/L and 0.037-50 μg/L, respectively. Antibiotic ecological and resistance development risks were geographically widespread, especially in the Yongding River, Daqing River, and Ziya River basins of China. Based on the risk quotients, 11 and 14 of 36 target antibiotics were at high ecological risks and high resistance development risks in at least one basin, respectively. The higher tiered assessments provided more detailed risk descriptions by probability values and β-lactams (penicillin and amoxicillin) were present at the highest levels for ecological and resistance development risks. Although there was uncertainty based on the limited data and existing methods, this study can indicate the overall situation of the existing risk levels and provide essential insights and data supporting antibiotic management.

Fate characteristics, exposure risk, and control strategy of typical antibiotics in Chinese sewerage system: A review

In China, the sewerage system plays an essential role in antibiotic removal; however, the fate profiles of antibiotics in sewers are not well understood, and risk identification throughout the sewerage system is inadequate. Based on the extensive detection results for typical groups of antibiotics in the discharge sources, influent and effluent from wastewater treatment plants (WWTPs), and excess sludge, a comprehensive evaluation was conducted to reveal the elimination profiles of the antibiotics, identify the fate characteristics in both sewers and WWTPs, assess the exposure risk levels, and propose a control strategy. The total concentration (based on the median concentrations of the target antibiotics) in aqueous waters was estimated to decrease from 7383.4 ng/L at the discharge source to 886.6 ng/L in the WWTP effluent, among which 69.6% was reduced by sewers and 18.4% was reduced by WWTPs. Antibiotic reduction in sewers was a combined effect of dilution, physiochemical reactions, sorption, biodegradation, and retransformation, and the A2O-MBR + ozonation process in the WWTPs exhibited superior performance in diminishing antibiotics. Notably, accumulated antibiotics in the excess sludge posed a high risk to natural environments (with a risk quotient of approximately 13.0), and the potential risk during combined sewer overflows (CSOs) was undetermined. Thus, enhanced sludge treatment techniques, accurate risk prediction, and proper precautions at CSOs are required to mitigate potential risk. A novel scheme involving an accurate estimation of discharge loads, preliminary treatment of highly concentrated discharge sources, and synergic control in sewers was proposed to eliminate antibiotics at the front end of pipes.

Insights into highly effective catalytic persulfate activation on oxygen-functionalized mesoporous carbon for ciprofloxacin degradation

Nanocarbons have been demonstrated as promising carbon catalysts for substituting metal-based catalysts for the green treatment of wastewater. In this study, oxygen-functionalized mesoporous carbon (OCMK-3) was prepared by wet oxidation and exhibited high catalytic performance against ciprofloxacin (CIP) by activation of persulfate. The effects of environmental parameters (pH, temperature, coexisting ions) and process parameters (temperature, sodium persulfate concentration, catalyst agent dosage, initial concentration) on the removal of CIP were investigated. Compared with the pristine ordered mesoporous carbon (CMK-3), the removal efficiency of CIP by OCMK-3 was increased by 32% under optimal conditions. This rise in activity was attributed to the increase in oxygen-containing functional groups, porosity, and specific surface area of OCMK-3 with improved structural defects and electron transfer efficiency. Furthermore, based on active species scavenging experiments, a dual-pathway mechanism of the radical and nonradical pathways was discovered. The rational degradation pathway of CIP was investigated based on liquid chromatography-mass spectrometry (LC-MS). In addition, the OCMK-3/PS system exhibited high decomposition efficiency in pharmaceutical wastewater treatment. This study provides an in-depth mechanism for the degradation of organic pollutants by carbon-based PS-AOPs and provides theoretical support for further studies.

Occurrence of E. coli and antibiotic-resistant E. coli in the southern watershed of Lake Biwa, including in wastewater treatment plant effluent and inflow rivers

The emergence of antibiotic-resistant bacteria (ARB) and their antibiotic resistance genes (ARGs) poses a serious challenge to human, animal, and environmental health worldwide. ARB can spread into the environment via various sources and routes. In this study, we investigated the occurrence of antibiotic-resistant E. coli in the southern watershed of Lake Biwa. Two-year monitoring of antibiotic-resistant E. coli was carried out in the southern part of Lake Biwa and inflow rivers and at three WWTPs around the southern part of the lake. Concentrations of E. coli in waters that are resistant to ampicillin (AMP), cefotaxime (CTX), ceftazidime (CAZ), levofloxacin (LVFX), tetracycline (TC), and amikacin (AMK) were measured using the culture method. Of these antibiotic-resistant E. coli, AMP-resistant E. coli were found at the highest prevalence, followed by LVFX, CTX, CAZ, TC, and AMK-resistant in both the influent and effluent of WWTPs. These resistance patterns in wastewater are the same as those in clinical samples in Japan. The numbers of antibiotic-resistant E. coli decreased by around a factor of 1000 during the wastewater treatment processes, but the rates clearly increased, suggesting that selection for antibiotic resistance might occur during the wastewater treatment process. AMP-resistant and TC-resistant E. coli were also detected in Lake Biwa and inflow rivers, which suggests that antibiotic resistance might come from not only WWTPs but also livestock farms and small-scale wastewater treatment facilities located in the river catchment.

Accumulation of antibiotic resistance genes in pakchoi (Brassica chinensis L.) grown in chicken manure-fertilized soil amended with fresh and aged biochars

Biochar has been used to alleviate the contamination of antibiotic resistance genes (ARGs) in soil and to inhibit ARGs transfer from soil to plants. However, the effect of aged biochar on ARGs abundance in soil and ARGs enrichment in plants are scarcely investigated. In this study, a pot experiment was conducted to compare the effects of fresh and aged biochars on the accumulation of five typical ARGs including tetX, tetW, sul2, ermB, and intI1 in a chicken manure-fertilized soil and in pakchoi (Brassica chinensis L.). Results showed that both biochars significantly decreased the abundance of tetW, sul2, and ermB and increased the abundance of tetX and intI1 in soil. However, the accumulation of all tested ARGs in pakchoi were significantly decreased by both biochars. At the lower addition rate (1%), the fresh biochar was superior to the aged biochar in decreasing the accumulation of some genes (tetW, tetX, and sul2) in pakchoi, whereas an opposite tendency was observed for other genes (ermB and intI1). As the addition rate increased to 2%, the difference between the two biochars diminished, and a similar capacity of decreasing ARGs transfer was observed. The reduction in ARGs accumulation in pakchoi was highly related to the type of ARGs, the biochar addition level, and the aging of biochar. Our results provide insights into the naturally aged biochar on the fate of ARGs in a soil-plant system.

A qnrD-Plasmid Promotes Biofilm Formation and Class 1 Integron Gene Cassette Rearrangements in Escherichia coli

Bacteria within biofilms may be exposed to sub-minimum inhibitory concentrations (sub-MICs) of antibiotics. Cell-to-cell contact within biofilms facilitates horizontal gene transfers and favors induction of the SOS response. Altogether, it participates in the emergence of antibiotic resistance. Aminoglycosides at sub-MICs can induce the SOS response through NO accumulation in E. coli carrying the small plasmid with the quinolone resistance qnrD gene (pDIJ09-518a). In this study, we show that in E. coli pDIJ09-518a, the SOS response triggered by sub-MICs of aminoglycosides has important consequences, promoting genetic rearrangement in class 1 integrons and biofilm formation. We found that the integrase expression was increased in E. coli carrying pDIJ09-518a in the presence of tobramycin, which was not observed for the WT isogenic strain that did not carry the qnrD-plasmid. Moreover, we showed that biofilm production was significantly increased in E. coli WT/pDIJ09-518a compared to the WT strain. However, such a higher production was decreased when the Hmp-NO detoxification pathway was fully functional by overexpressing Hmp. Our results showing that a qnrD-plasmid can promote biofilm formation in E. coli and potentiate the acquisition and spread of resistance determinants for other antibiotics complicate the attempts to counteract antibiotic resistance and prevention of biofilm development even further. We anticipate that our findings emphasize the complex challenges that will impact the decisions about antibiotic stewardship, and other decisions related to retaining antibiotics as effective drugs and the development of new drugs.

Tiered ecological risk assessment of nonylphenol and tetrabromobisphenol A in the surface waters of China based on the augmented species sensitivity distribution models

The ecological risks of nonylphenol (NP) and tetrabromobisphenol A (TBBPA) have received continued attention owing to their large consumption, frequently detection, adverse effects on the reproductive fitness, and lack of risk assessment technical systems. The geometric mean of the median concentrations of NP in the 22 surface waters was 0.278 μg/L, and TBBPA in the seven surface waters was 0.014 μg/L in China. The species sensitivity distribution (SSD) models were augmented by extrapolated reproductive toxicity data of native species to reduce uncertainty. The SSD models and the hazardous concentrations for 5% of species exhibited good robustness and reliability using the bootstrap method and minimum sample size determination. The acute and reproductive predicted no-effect concentrations (PNECs) were derived as 9.88 and 0.187 μg/L for NP, and 56.6 and 0.0878 μg/L for TBBPA, respectively. The risk quotients indicated that 11 of 22 locations for NP, and 3 of 7 locations for TBBPA were at high ecological risk levels based on the reproductive PNECs. Furthermore, the higher tier ecological risk assessment (ERA) based on potential affected fraction and joint probability curves indicated that the ecological risks in the four of above locations needed further concern. The ERA based on both the acute and reproductive toxicity is essential for assessing the ecological risks of NP and TBBPA, otherwise using acute PNECs only may result in an underestimation of ecological risk. The developed tiered ERA method and its framework can provide accurate, detailed, quantitative, locally applicable, and economically technical support for ERA of typical endocrine-disrupting chemicals in China.

Anti-Virulence Activity of 3,3′-Diindolylmethane (DIM): A Bioactive Cruciferous Phytochemical with Accelerated Wound Healing Benefits

Antimicrobial resistance is among the top global health problems with antibacterial resistance currently representing the major threat both in terms of occurrence and complexity. One reason current treatments of bacterial diseases are ineffective is the occurrence of protective and resistant biofilm structures. Phytochemicals are currently being reviewed for newer anti-virulence agents. In the present study, we aimed to investigate the anti-virulence activity of 3,3′-diindolylmethane (DIM), a bioactive cruciferous phytochemical. Using a series of in vitro assays on major Gram-negative pathogens, including transcriptomic analysis, and in vivo porcine wound studies as well as in silico experiments, we show that DIM has anti-biofilm activity. Following DIM treatment, our findings show that biofilm formation of two of the most prioritized bacterial pathogens Acinetobacter baumannii and Pseudomonas aeruginosa was inhibited respectively by 65% and 70%. Combining the antibiotic tobramycin with DIM enabled a high inhibition (94%) of P. aeruginosa biofilm. A DIM-based formulation, evaluated for its wound-healing efficacy on P. aeruginosa-infected wounds, showed a reduction in its bacterial bioburden, and wound size. RNA-seq was used to evaluate the molecular mechanism underlying the bacterial response to DIM. The gene expression profile encompassed shifts in virulence and biofilm-associated genes. A network regulation analysis showed the downregulation of 14 virulence-associated super-regulators. Quantitative real-time PCR verified and supported the transcriptomic results. Molecular docking and interaction profiling indicate that DIM can be accommodated in the autoinducer- or DNA-binding pockets of the virulence regulators making multiple non-covalent interactions with the key residues that are involved in ligand binding. DIM treatment prevented biofilm formation and destroyed existing biofilm without affecting microbial death rates. This study provides evidence for bacterial virulence attenuation by DIM.

Genomic Characteristics of Recently Recognized Vibrio cholerae El Tor Lineages Associated with Cholera in Bangladesh, 1991 to 2017

Comparative genomic analysis of Vibrio cholerae El Tor associated with endemic cholera in Asia revealed two distinct lineages, one dominant in Bangladesh and the other in India. An in-depth whole-genome study of V. cholerae El Tor strains isolated during endemic cholera in Bangladesh (1991 to 2017) included reference genome sequence data obtained online. Core genome phylogeny established using single nucleotide polymorphisms (SNPs) showed V. cholerae El Tor strains comprised two lineages, BD-1 and BD-2, which, according to Bayesian phylodynamic analysis, originated from paraphyletic group BD-0 around 1981. BD-1 and BD-2 lineages overlapped temporally but were negatively associated as causative agents of cholera during 2004 to 2017. Genome-wide association study (GWAS) revealed 140 SNPs and 31 indels, resulting in gene alleles unique to BD-1 and BD-2. Regression analysis of root to tip distance and year of isolation indicated early BD-0 strains at the base, whereas BD-1 and BD-2 subsequently emerged and progressed by accumulating SNPs. Pangenome analysis provided evidence of gene acquisition by both BD-1 and BD-2, of which six crucial proteins of known function were predominant in BD-2. BD-1 and BD-2 diverged and have distinctively different genomic traits, namely, heterogeneity in VSP-2, VPI-1, mobile elements, toxin encoding elements, and total gene abundance. In addition, the observed phage-inducible chromosomal island-like element (PLE1), and SXT ICE elements (ICETET) in BD-2 presumably provided a fitness advantage for the lineage to outcompete BD-1 as the etiological agent of endemic cholera in Bangladesh, with implications for global cholera epidemiology. IMPORTANCE Cholera is a global disease with specific reference to the Bay of Bengal Ganges Delta where Vibrio cholerae O1 El Tor, the causative agent of the disease showed two circulating lineages, one dominant in Bangladesh and the other in India. Results of an in-depth genomic study of V. cholerae associated with endemic cholera during the past 27 years (1991 to 2017) indicate emergence and succession of the two lineages, BD-1 and BD-2, arising from a common ancestral paraphyletic group, BD-0, comprising the early strains and short-term evolution of the bacterium in Bangladesh. Among the two V. cholerae lineages, BD-2 supersedes BD-1 and is predominant in the most recent endemic cholera in Bangladesh. The BD-2 lineage contained significantly more SNPs and indels, and showed richness in gene abundance, including antimicrobial resistance genes, gene cassettes, and PLE to fight against bacteriophage infection, acquired over time. These findings have important epidemic implications on a global scale.

Emerging nanotechnologies for targeting antimicrobial resistance

Antimicrobial resistance is a leading cause of mortality worldwide. Without newly approved antibiotics and antifungals being brought to the market, resistance is being developed to the ones currently available to clinicians. The reason is the applied evolutionary pressure to bacterial and fungal species due to the wide overuse of common antibiotics and antifungals in clinical practice and agriculture. Biofilms harbour antimicrobial-resistant subpopulations, which make their antimicrobial treatment even more challenging. Nanoparticle-based technologies have recently been shown to successfully overcome antimicrobial resistance in both planktonic and biofilms phenotypes. This results from the combination of novel nanomaterial research and classic antimicrobial therapies which promise to deliver a whole new generation of high-performance active nanocarrier systems. This review discusses the latest developments of promising nanotechnologies with applications against resistant pathogens and evaluates their potential and feasibility for use in novel antimicrobial therapies.

Antimicrobial resistance management in Pacific Island countries: Current status, challenges, and strategic solutions

Antimicrobial resistance (AMR) is currently recognized as a major emerging threat to human and animal health. The burden of antimicrobial-resistant infections affects the economy in developed and developing countries. There is a rapid rise in AMR in human and veterinary medicine globally. AMR profiles are poorly documented in Fiji, and limited data are accessible. Fiji currently has no national veterinary antibiotic resistance surveillance network or regulations and guidelines on veterinary drug use. However, available literature shows that although human drugs are better managed than veterinary drugs, the knowledge is still constrained and dispersed. Furthermore, Fiji was chosen as a case study to develop a prototype AMR surveillance and control in the Pacific region. Pacific Island countries share similar geographic and climatic conditions. Currently, the Australian Centre for International Agricultural Research has funded an AMR project that addresses some gaps in managing AMR in the region. The project is the first to adopt the One Health approach to research the AMR in humans, animals, and the Pacific region's environment. Combating AMR needs human health and veterinary personnel to work with all other stakeholders. Continuous surveillance for resistant clinical isolates in humans and animals and the development of appropriate policy intervention measures in human and veterinary drug use are necessary to alleviate AMR burden. Therefore, there is a need to educate farmers, human patients, and the public on the fight against AMR. In addition, AMR data are necessary to develop effective AMR control strategies. This review gives a comprehensive information assessment on AMR in Fiji and the other South Pacific Islands in relation to global trends. Suggestions on the most appropriate ways of effectively managing AMR in Fiji have been made.

The dissemination of antibiotics and their corresponding resistance genes in treated effluent-soil-crops continuum, and the effect of barriers

Irrigation with treated effluent is expanding as freshwater sources diminish, but hampered by growing concerns of pharmaceuticals contamination, specifically antibiotics and resistance determinants. To evaluate this concern, freshwater and effluent were applied to an open field that was treated with soil barriers including plastic mulch together with surface and subsurface drip irrigation, cultivating freshly eaten crops (cucumbers or melons) for two consecutive growing seasons. We hypothesized that the effluent carries antibiotics and resistance determinants to the drip-irrigated soil and crops regardless of the treatment. To test our hypothesis, we monitored for antibiotics abundance (erythromycin, sulfamethoxazole, tetracycline, chlortetracycline, oxytetracycline, amoxicillin, and ofloxacin) and their corresponding resistance genes (ermB, ermF, sul1, tetW, tetO, bla_TEM and qnrB), together with class 1 integron (intl1), and bacterial 16S rRNA, in water, soil, and crop samples taken over two years of cultivation. The results showed that an array of antibiotics and their corresponding resistance genes were detected in the effluent but not the freshwater. Yet, there were no significant differences in the distribution or abundance of antibiotics and resistance genes, regardless of the irrigation water quality, or crop type (p > 0.05), but plastic-covered soil irrigated with effluent retained the antibiotics oxytetracycline and ofloxacin (p < 0.05). However, we could not detect significant correlations between the detected antibiotics and the corresponding resistance genes. Overall, our findings disproved our hypothesis suggesting that treated effluent may not carry antibiotics resistance genes to the irrigated soil and crops yet, plastic mulch covered soil retain some antibiotics that may inflict long term contamination.