Detection of clinically relevant antibiotic-resistance genes in municipal wastewater using real-time PCR (TaqMan)

Visual and photoelectrochemical analysis of antibiotic resistance genes enabled by surface-engineered ZIF-8@Au cascade nanozymes

The aggravation of antibiotic resistance genes (ARGs) in the environment has posed a significant global health crisis. Accurate evaluation of ARGs levels in a facile manner is a pressing issue for environmental surveillance. Here, we demonstrate a unique dumbbell-shaped cascade nanozyme for visual/photoelectrochemical (PEC) dual-mode detection of ARGs. Gold nanoparticles (AuNPs) with tunable exposed facets are controllably anchored onto ZIF-8 dodecahedrons, exhibiting glucose oxidase (GOx)-like (ZIF-8@Au/G) and peroxidase (POD)-like (ZIF-8@Au/P) activities. Upon the occurrence of ARGs, an asymmetric cascade-amplified "dumbbell" configuration is spontaneously generated via target-induced DNA hybridization, comprising GOx-like ZIF-8@Au/G with capture DNA on one side and POD-like ZIF-8@Au/P with signal DNA on the opposite side. Such a cascade nano-system can efficiently oxidize colorless 2, 2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) into its green oxidation state and synergistically decompose H2O2, realizing colorimetric/PEC dual-mode ARGs detection with a detection limit of 0.112 nM. The applicability of the present bioassay is validated through measuring ARGs in real sludge samples. This work suggests the possibility to rationally design task-specific nanozymes and develop target-responsive nano-cascade assays for environmental monitoring.

One-pot, one-step, label-free miRNA detection method based on the structural transition of dumbbell probe

In this study, we present a one-pot, one-step, label-free miRNA detection method through a structural transition of a specially designed dumbbell-shape probe, initiating a rolling circle transition (RCT). In principle, target miRNA binds to right loop of the dumbbell probe (DP), which allows structural change of the DP to circular form, exposing a sequence complementary to the T7 promoter (T7p) previously hidden within the stem. This exposure allows T7 RNA polymerase to initiate RCT, producing a repetitive Mango aptamer sequence. TO1-biotin, fluorescent dye, binds to the aptamer, inducing a detectable enhancement of fluorescence intensity. Without miR-141, the DP stays closed, RCT is prevented, and the fluorescence intensity remains low. By employing this novel strategy, target miRNA was successfully identified with a detection of 73 pM and a dynamic linear range of 0-10 nM. Additionally, the method developed enables one-pot, one-step, and label-free detection of miRNA, demonstrating potential for point-of-care testing (POCT) applications. Furthermore, the practical application of the designed technique was demonstrated by reliably detecting the target miRNA in the human serum sample. We also believe that the conceived approach could be widely used to detect not only miRNAs but also diverse biomolecules by simply replacing the detection probe.

Amplidiff: an optimized amplicon sequencing approach to estimating lineage abundances in viral metagenomes

BACKGROUND

Metagenomic profiling algorithms commonly rely on genomic differences between lineages, strains, or species to infer the relative abundances of sequences present in a sample. This observation plays an important role in the analysis of diverse microbial communities, where targeted sequencing of 16S and 18S rRNA, both well-known hypervariable genomic regions, have led to insights into microbial diversity and the discovery of novel organisms. However, the variable nature of discriminatory regions can also act as a double-edged sword, as the sought-after variability can make it difficult to design primers for their amplification through PCR. Moreover, the most variable regions are not necessarily the most informative regions for the purpose of differentiation; one should focus on regions that maximize the number of lineages that can be distinguished.

RESULTS

Here we present AmpliDiff, a computational tool that simultaneously finds highly discriminatory genomic regions in viral genomes of a single species, as well as primers allowing for the amplification of these regions. We show that regions and primers found by AmpliDiff can be used to accurately estimate relative abundances of SARS-CoV-2 lineages, for example in wastewater sequencing data. We obtain errors that are comparable with using whole genome information to estimate relative abundances. Furthermore, our results show that AmpliDiff is robust against incomplete input data and that primers designed by AmpliDiff also bind to genomes sampled months after the primers were selected.

CONCLUSIONS

With AmpliDiff we provide an effective, cost-efficient alternative to whole genome sequencing for estimating lineage abundances in viral metagenomes.

Antibiotic resistance in livestock, environment and humans: One Health perspective

Antibiotic resistance (AR) is a complex, multifaceted global health issue that poses a serious threat to livestock, humans, and the surrounding environment. It entails several elements and numerous potential transmission routes and vehicles that contribute to its development and spread, making it a challenging issue to address. AR is regarded as an One Health issue, as it has been found that livestock, human, and environmental components, all three domains are interconnected, opening up channels for transmission of antibiotic resistant bacteria (ARB). AR has turned out to be a critical problem mainly because of the overuse and misuse of antibiotics, with the anticipation of 10 million annual AR-associated deaths by 2050. The fact that infectious diseases induced by ARB are no longer treatable with antibiotics foreshadows an uncertain future in the context of health care. Hence, the One Health approach should be emphasized to reduce the impact of AR on livestock, humans, and the environment, ensuring the longevity of the efficacy of both current and prospective antibiotics.

Development of a highly sensitive TaqMan method based on multi-probe strategy: its application in ASFV detection

The establishment of high sensitive detection method for various pathogenic microorganisms remains constantly concerned. In the present study, multi-probe strategy was first systematically investigated followed by establishing a highly sensitive TaqMan real-time fluorescent quantitative PCR (qPCR) method for detecting African swine fever virus (ASFV). Briefly, four probes based on the B646L gene of ASFV were designed and the effects of different combinations of the probes in a single TaqMan qPCR assay on the detection sensitivity were investigated. As less as 0.5-5 copies/μl of the ASFV gene was detected by the established TaqMan qPCR assay. Furthermore, plasmid harboring the B646L in water samples could be concentrated 1000 times by ultrafiltration to enable a highly sensitive detection of trace viral nucleic acids. Moreover, no cross-reactivity was observed with other common clinical swine viruses such as PCV2, PCV3, PCV4, PEDV, PDCoV, CSFV, PRRSV, and PRV. When detecting 173 clinical porcine serum samples, the coincidence rate between the developed method and WOAH (World Organization of Animal Health) recommended method was 100%. This study might provide an integrated strategy to achieve higher detection sensitivity of trace pathogenic microorganisms and applicably sensitive TaqMan-based qPCR assays.

Simultaneous extraction and detection of DNA and RNA from viruses, prokaryotes, and eukaryotes in wastewater using a modified COPMAN

Wastewater surveillance can offer a comprehensive grasp of infectious disease prevalence and human health because wastewater contains various human-derived microbial pathogens, including viruses, bacteria, and fungi. However, methods capable of simultaneous detection of multiple groups of targets in the automated systems and large-scale surveillance are still under development. Here, we demonstrated the modification, involving the addition of bead-beating, to the existing COPMAN (COagulation and Proteolysis method using MAgnetic beads for detection of Nucleic acids in wastewater) enabled enhanced detection of various microorganisms, including SARS-CoV-2. The modified method, termed bead-beating COPMAN (BB-COPMAN), was evaluated through spike-and-recovery experiments and comparative analysis against three previously reported methods for simultaneous DNA/RNA detection. Our study targeted a range of microorganisms, including enveloped and non-enveloped RNA viruses (SARS-CoV-2, PMMoV), a DNA virus (crAssphage), archaea, gram-negative and gram-positive bacteria (E. coli, Lachnospiraceae), antibiotic resistance gene (ampC), and fungi (Candida albicans). The recovery rates of BB-COPMAN for gram-negative and gram-positive bacteria were 17 and 2.1-fold higher, respectively, compared to the method for DNA/RNA detection. Additionally, BB-COPMAN exhibited the highest extraction efficiency among the tested methods, achieving 1.2-5.7 times more DNA and 1.1-69 times more RNA yield on average. BB-COPMAN allowed the detection of SARS-CoV-2 from all nine samples and PMMoV at concentrations 39-97 times higher than other methods. Moreover, BB-COPMAN detected larger amounts of DNA for four out of six DNA targets than the previously reported DNA/RNA detection method. These results demonstrated that BB-COPMAN enables enhanced detection of multiple targets in a single flow of nucleic acid extraction, making the method well-suited for automated systems. In conclusion, BB-COPMAN is a promising method in wastewater surveillance for assessing the prevalence of wide range of pathogenic microorganisms.

Comparison of concentration and extraction workflows for qPCR quantification of intI1 and vanA in untreated wastewater

Quantitative polymerase chain reaction (qPCR) measurement of antibiotic resistance genes (ARGs) in untreated municipal wastewater may prove useful in combating the antimicrobial resistance crisis. However, harmonizing and optimizing qPCR-based workflows is essential to facilitate comparisons across studies, and includes achieving highly-effective ARG capture through efficient concentration and extraction procedures. In the current study, combinations of sample volume, membrane types and DNA extraction kits within filtration and centrifugation-based workflows were used to quantify 16S ribosomal RNA (16S rRNA), class 1 integron-integrase gene (intI1) and an ARG encoding resistance to vancomycin (vanA) in untreated wastewater sampled from three wastewater treatment plants (WWTPs). Highly abundant 16S rRNA and intI1 were detected in 100 % of samples from all three WWTPs using both 2 and 20 mL sample volumes, while lower prevalence vanA was only detected when using the 20 mL volume. When filtering 2 mL of wastewater, workflows with 0.20-/0.40-μm polycarbonate (PC) membranes generally yielded greater concentrations of the three targets than workflows with 0.22-/0.45-μm mixed cellulose ester (MCE) membranes. The improved performance was diminished when the sample volume was increased to 20 mL. Consistently greater concentrations of 16S rRNA, intI1 and vanA were yielded by filtration-based workflows using PC membranes combined with a DNeasy PowerWater (DPW) Kit, regardless of the sample volume used, and centrifugation-based workflows with DNeasy Blood & Tissue Kit for 2-mL wastewater extractions. Within the filtration-based workflows, the DPW kit yielded more detection and quantifiable results for less abundant vanA than the DNeasy PowerSoil Pro Kit and FastDNA™ SPIN Kit for Soil. These findings indicate that the performance of qPCR-based workflows for surveillance of ARGs in wastewater varies across targets, sample volumes, concentration methods and extraction kits. Workflows must be carefully considered and validated considering the target ARGs to be monitored.

Quaternary ammonium-based coating of textiles is effective against bacteria and viruses with a low risk to human health

While the global healthcare system is slowly recovering from the COVID-19 pandemic, new multi-drug-resistant pathogens are emerging as the next threat. To tackle these challenges there is a need for safe and sustainable antiviral and antibacterial functionalized materials. Here we develop an 'easy-to-apply' procedure for the surface functionalization of textiles, rendering them antiviral and antibacterial and assessing the performance of these textiles. A metal-free quaternary ammonium-based coating was applied homogeneously and non-covalently to hospital curtains. Abrasion, durability testing, and aging resulted in little change in the performance of the treated textile. Additionally, qualitative and quantitative antibacterial assays on Staphylococcus aureus, Pseudomonas aeruginosa, and Acinetobacter baumanii revealed excellent antibacterial activity with a CFU reduction of 98-100% within only 4 h of exposure. The treated curtain was aged 6 months before testing. Similarly, the antiviral activity tested according to ISO-18184 with murine hepatitis virus (MHV) showed > 99% viral reduction with the functionalized curtain. Also, the released active compounds of the coating 24 ± 5 µg mL-1 revealed no acute in vitro skin toxicity (IC50: 95 µg mL-1) and skin sensitization. This study emphasizes the potential of safe and sustainable metal-free textile coatings for the rapid antiviral and antibacterial functionalization of textiles.

Identification of DNA variants at ultra-low variant allele frequencies via Taq polymerase cleavage of wild-specific blockers

Detecting mutations related to tumors holds immense clinical significance for cancer diagnosis and treatment. However, the presence of highly redundant wild DNA poses a challenge for the advancement of low-copy mutant ctDNA genotyping in cancer cases. To address this, a Taqman qPCR strategy to identify rare mutations at low variant allele fractions (VAFs) has been developed. This strategy combines mutant-specific primers with wild-specific blockers. Diverging from other blocker-mediated PCRs, which rely on primer-induced strand displacement or the use of modified oligos resistant to Taq polymerase, our innovation is built upon the cleavage of specific blockers by Taq polymerase. Given its unique design, which does not hinge on strand displacement or base modification, we refer to this novel method as unmodified-blocker cleavage PCR (UBC-PCR). Multiple experiments consistently confirmed that variant distinction was improved significantly by introduction of 5' unmatched blockers into the reaction. Moreover, UBC-PCR successfully detected mutant DNA at VAFs as low as 0.01% across six different variant contexts. Multiplex UBC-PCR was also performed to identify a reference target and three mutations with a sensitivity of 0.01% VAFs in one single tube. In profiling the gene status from 12 lung cancer ctDNA samples and 22 thyroid cancer FNA DNA samples, UBC-PCR exhibited a 100% concordance rate with ddPCR and a commercial ARMS kit, respectively. Our work demonstrates that UBC-PCR can identify low-abundance variants with high sensitivity in multiplex reactions, independent of strand displacement and base modification. This strategy holds the potential to significantly impact clinical practice and precision medicine.

Antibiotic resistances from slaughterhouse effluents and enhanced antimicrobial blue light technology for wastewater decontamionation

The frequencies of 6 different facultative pathogenic bacteria of the ESKAPE group (priority list WHO) and a total of 14 antibiotic resistance genes (ARGs) with different priorities for human medicine were quantified in wastewaters of poultry and pig slaughterhouses using molecular biological approaches. Raw sewage from poultry and pig slaughterhouses was found to be contaminated not only with facultative pathogenic bacteria but also with various categories of clinically relevant ARGs, including ARGs against the reserve antibiotics group. The concentration of the different gene targets decreased after on-site conventional biological or advanced oxidative wastewater treatments, but was not eliminated. Hence, the antimicrobial BlueLight (aBL) in combination with a porphyrin photo-sensitizer was studied with ESKAPE bacteria and real slaughterhouse wastewaters. The applied broad LED-based blue light (420-480 nm) resulted in groups of sensitive, intermediate, and non-sensitive ESKAPE bacteria. The killing effect of aBL was increased in the non-sensitive bacteria Klebsiella pneumoniae and Enterococcus faecium due to the addition of porphyrins in concentrations of 10-6 M. Diluted slaughterhouse raw wastewater was treated with broad spectrum aBL and in combination with porphyrin. Here, the presence of the photo-sensitizer enhanced the aBL biocidal impact.

qSanger: Quantification of Genetic Variants in Bacterial Cultures by Sanger Sequencing

Genetic variations such as mutations and recombinations arise spontaneously in all cultured organisms. Although it is possible to identify nonneutral mutations by selection or counterselection, the identification of neutral mutations in a heterogeneous population usually requires expensive and time-consuming methods such as quantitative or droplet polymerase chain reaction and high-throughput sequencing. Neutral mutations could even become dominant under changing environmental conditions enforcing transitory selection or counterselection. We propose a novel method, which we called qSanger, to quantify DNA using amplitude ratios of aligned electropherogram peaks from mixed Sanger sequencing reads. Plasmids expressing enhanced green fluorescent protein and mCherry fluorescent markers were used to validate qSanger both in vitro and in cotransformed Escherichia coli via quantitative polymerase chain reaction and fluorescence quantifications. We show that qSanger allows the quantification of genetic variants, including single-base natural polymorphisms or de novo mutations, from mixed Sanger sequencing reads, with substantial reduction of labor and costs compared to canonical approaches.

Growth and prevalence of antibiotic-resistant bacteria in microplastic biofilm from wastewater treatment plant effluents

It is accepted that Microplastic (MP) biofilms accumulates antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) in water. ARB/ARGs and MPs are emerging pollutants of concern due to various associated health risks. The objective of this study was to 1) investigate the ARB community in a pilot-scale wastewater treatment plant (WWTP) effluent, 2) to study and visualize the ARB/ARGs in MP biofilm grown in WWTP effluent and tap water, and 3) to analyze microplastic adherent ARB/ARGs in the biofilm and planktonic ARB/ARGs in the filtrate under controlled conditions. Results indicated the dominance of Pseudomonas, Aeromonas, and Bacillus among isolated ARB in WWTP effluent. Representative resistance strains were incubated in 300 mL water containing commercial polystyrene beads of 300550 μm diameter (MP) in a series of batch experiments. Microbiological, molecular, and microscopic analyses were performed by enumeration, 16srRNA, real-time polymerase chain reaction (qPCR), and Field Emission-Scanning Electron Microscopy (FEG-SEM) techniques. The analyzed viable ARB indicated an increasing trend in MP biofilms between days 3 and 5. It further decreased on days 7 and 9. The prevalence of ARB in the filtrate and MP biofilm varied as a function of time and TOC level, while no significant impacts were observed for minor temperature variation, low antibiotic pressure, and increased MP mass with few exceptions. Relative abundance of ARGs (vanA, sul1) and integron integrase gene (intl1) in MP biofilm were significantly different across different TOC levels, time, and antibiotic pressure. ARGs and intl1 were detected in the MP biofilm in tap water and WWTP effluent on day 30.

Application of Nucleotide-Based Kinetic Modeling Approaches to Predict Antibiotic Resistance Gene Degradation during UV- and Chlorine-Based Wastewater Disinfection Processes: From Bench- to Full-Scale

This study investigated antibiotic resistance gene (ARG) degradation kinetics in wastewaters during bench- and full-scale treatment with UV light and chlorine─with the latter maintained as free available chlorine (FAC) in low-ammonia wastewater and converted into monochloramine (NH₂Cl) in high-ammonia wastewater. Twenty-three 142-1509 bp segments (i.e., amplicons) of seven ARGs (blt, mecA, vanA, tet(A), ampC, bla_NDM, bla_KPC) and the 16S rRNA gene from antibiotic resistant bacteria (ARB) strains Bacillus subtilis, Staphylococcus aureus, Enterococcus faecium, Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae were monitored as disinfection targets by qPCR. Rate constants for ARG and 16S rRNA gene amplicon degradation by UV, FAC, and NH₂Cl were measured in phosphate buffer and used to expand and validate several recently developed approaches to predict DNA segment degradation rate constants based solely on their nucleotide contents, which were then applied to model ARG degradation during bench-scale treatment in buffer and wastewater matrixes. Kinetics of extracellular and intracellular ARG degradation by UV and FAC were well predicted up to ∼1-2-log₁₀ elimination, although with decreasing accuracy at higher levels for intracellular genes, while NH₂Cl yielded minimal degradation under all conditions (agreeing with predictions). ARB inactivation kinetics varied substantially across strains, with intracellular gene degradation lagging cell inactivation in each case. ARG degradation levels observed during full-scale disinfection at two wastewater treatment facilities were consistent with bench-scale measurements and predictions, where UV provided ∼1-log₁₀ ARG degradation, and chlorination of high-ammonia wastewater (dominated by NH₂Cl) yielded minimal ARG degradation.

Geospatial Patterns of Antimicrobial Resistance Genes in the US EPA National Rivers and Streams Assessment Survey

Antimicrobial resistance (AR) is a serious global problem due to the overuse of antimicrobials in human, animal, and agriculture sectors. There is intense research to control the dissemination of AR, but little is known regarding the environmental drivers influencing its spread. Although AR genes (ARGs) are detected in many different environments, the risk associated with the spread of these genes to microbial pathogens is unknown. Recreational microbial exposure risks are likely to be greater in water bodies receiving discharge from human and animal waste in comparison to less disturbed aquatic environments. Given this scenario, research practitioners are encouraged to consider an ecological context to assess the effect of environmental ARGs on public health. Here, we use a stratified, probabilistic survey of nearly 2000 sites to determine national patterns of the anthropogenic indicator class I integron Integrase gene (intI1) and several ARGs in 1.2 million kilometers of United States (US) rivers and streams. Gene concentrations were greater in eastern than in western regions and in rivers and streams in poor condition. These first of their kind findings on the national distribution of intI1 and ARGs provide new information to aid risk assessment and implement mitigation strategies to protect public health.

The Revolution of Lateral Flow Assay in the Field of AMR Detection

The global spread of antimicrobial resistant (AMR) bacteria represents a considerable public health concern, yet their detection and identification of their resistance mechanisms remain challenging. Optimal diagnostic tests should provide rapid results at low cost to enable implementation in any microbiology laboratory. Lateral flow assays (LFA) meet these requirements and have become essential tools to combat AMR. This review presents the versatility of LFA developed for the AMR detection field, with particular attention to those directly triggering β-lactamases, their performances, and specific limitations. It considers how LFA can be modified by detecting not only the enzyme, but also its β-lactamase activity for a broader clinical sensitivity. Moreover, although LFA allow a short time-to-result, they are generally only implemented after fastidious and time-consuming techniques. We present a sample processing device that shortens and simplifies the handling of clinical samples before the use of LFA. Finally, the capacity of LFA to detect amplified genetic determinants of AMR by isothermal PCR will be discussed. LFA are inexpensive, rapid, and efficient tools that are easy to implement in the routine workflow of laboratories as new first-line tests against AMR with bacterial colonies, and in the near future directly with biological media.

Antimicrobial Resistance Monitoring of Water Environments: A Framework for Standardized Methods and Quality Control

Antimicrobial resistance (AMR) is a grand societal challenge with important dimensions in the water environment that contribute to its evolution and spread. Environmental monitoring could provide vital information for mitigating the spread of AMR; this includes assessing antibiotic resistance genes (ARGs) circulating among human populations, identifying key hotspots for evolution and dissemination of resistance, informing epidemiological and human health risk assessment models, and quantifying removal efficiencies by domestic wastewater infrastructure. However, standardized methods for monitoring AMR in the water environment will be vital to producing the comparable data sets needed to address such questions. Here we sought to establish scientific consensus on a framework for such standardization, evaluating the state of the science and practice of AMR monitoring of wastewater, recycled water, and surface water, through a literature review, survey, and workshop leveraging the expertise of academic, governmental, consulting, and water utility professionals.

Antimicrobial Resistance Monitoring of Water Environments: A Framework for Standardized Methods and Quality Control

Antimicrobial resistance (AMR) is a grand societal challenge with important dimensions in the water environment that contribute to its evolution and spread. Environmental monitoring could provide vital information for mitigating the spread of AMR; this includes assessing antibiotic resistance genes (ARGs) circulating among human populations, identifying key hotspots for evolution and dissemination of resistance, informing epidemiological and human health risk assessment models, and quantifying removal efficiencies by domestic wastewater infrastructure. However, standardized methods for monitoring AMR in the water environment will be vital to producing the comparable data sets needed to address such questions. Here we sought to establish scientific consensus on a framework for such standardization, evaluating the state of the science and practice of AMR monitoring of wastewater, recycled water, and surface water, through a literature review, survey, and workshop leveraging the expertise of academic, governmental, consulting, and water utility professionals.

Cascade Filtration With PCR Detection and Field-Flow-Fractionation Online With ICP-MS for the Characterization of DNA Interaction With Suspended Particulate Matter

The variety of applied antibiotics in animal and human medicine results in the release, development, and spread of relevant numbers of antibiotic resistance genes (ARGs) in the environment. The majority of ARGs are present in intracellular forms (in bacteria). Neglected aspects are extracellular variants of ARGs (eARGs) and their fragments, which have been detected in surface-water samples and sediments. The stability of eARGs is expected to be low; however, binding to particulate matter is likely to improve their stability and also affect their transport and dissemination behavior. Few studies have investigated DNA particle interactions, mostly via indirect characterization of adduct formation in model systems but not in real environmental matrices. Therefore, our study aims at a novel approach for direct characterization of desoxyribonucleic acid (DNA) particle interactions using both cascade filtration and field-flow fractionation. Cascade filtration with quantitative polymerase chain reaction (qPCR) detection indicated retention of ARGs on filters with much larger pore sizes supporting the hypothesis of ARG-particle interactions. However, artifacts from membrane clogging or DNA–membrane interaction cannot be excluded. Consequently, asymmetric flow field-flow fractionation was investigated as an alternative separation technique with the advantage of particle separation in a thin channel, reducing the risk of artifacts. The key method parameters, membrane composition, molecular weight cut off, and carrier composition, were systematically investigated using a calf-thymus DNA-spiked surface-water sample as a model. The results clearly showed a shift in the elution time of clay particles suggesting the presence of DNA–clay adducts. Multi-element detection by inductively coupled plasma mass spectrometry (ICP-MS) enabled monitoring of clay via the Al, Fe, and Si signals and DNA via the P signal. Matching peak profiles for the new fraction in the fractograms of the ARG and DNA-spiked water sample support adduct formation. Further evidence was provided by a novel post-channel filtration approach for the separation of free DNA from DNA–clay adducts.

Antimicrobial resistance- Do we share more than companionship with our dogs?

Aims

To investigate and compare antimicrobial resistance genes (ARGs) in faeces from cohabiting dogs and owners.

Methods and Results

DNA from faecal samples from 35 dogs and 35 owners was screened for the presence of 34 clinically relevant ARGs using high throughput qPCR. In total, 24 and 25 different ARGs were present in the dog and owner groups, respectively. The households had a mean of 9.9 ARGs present, with dogs and owners sharing on average 3.3 ARGs. ARGs were shared significantly more in households with dogs over 6 years old (3.5, interquartile range 2.75–5.0) than in households with younger dogs (2.5, interquartile range 2.0–3.0) (p = 0.02). Dogs possessed significantly more mecA and aminoglycoside resistance genes than owners.

Conclusions

Dogs and owners can act as reservoirs for a broad range of ARGs belonging to several antimicrobial resistance classes. A modest proportion of the same resistance genes were present in both dogs and owners simultaneously, indicating that ARG transmission between the dog and human gut is of minor concern in the absence of antimicrobial selection.

Significance and Impact of the Study

This study provides insight into the common dog and human gut resistomes, contributing to an improved knowledge base in risk assessments regarding ARG transmission between dogs and humans.

Antibiotic resistance in the viral fraction of dairy products and a nut-based milk

Phages, the most abundant biological entities in the biosphere, can carry different bacterial genes, including those conferring antibiotic resistance. In this study, dairy products were analyzed by qPCR for the presence of phages and phage particles containing antibiotic resistance genes (ARGs). Eleven ARGs were identified in 50 samples of kefir, yogurt, milk, fresh cheese and nut-based milk (horchata), purchased from local retailers in Barcelona. Propagation experiments showed that at least some of the phages isolated from these samples infected Escherichia coli WG5, which was selected as the host strain because it does not contain prophages or ARGs in its genome. Electron microscopy revealed that the phage particles showed morphologies compatible with the Myoviridae and Siphoviridae families. Our results show that dairy products contain ARGs within infectious phage particles and may therefore serve as a reservoir of ARGs that can be mobilized to susceptible hosts, both in the food matrix and in the intestinal tract after ingestion.

Reduction of antibiotic-resistant-E. coli, -K. pneumoniae, -A. baumannii in aged-sludge of membrane bioreactor treating hospital wastewater

A pilot-scale of membrane bioreactor (MBR) had functioned without sludge withdrawal for six months, proposed to minimize antibiotic-resistant bacteria (ARB) dissemination from hospital wastewater. With this proposal, an aging sludge in MBR has concerned as preserved-severe multidrug-resistant microorganisms. Thus, this study aims to investigate resistance alteration of ARB in the aging-sludge compared to that in the wastewater. Escherichia coli (EC), Klebsiella pneumoniae (KP), and Acinetobacter baumannii (AB) were antimicrobial-resistant indicators. In wastewater, AB showed the highest concentration followed by KP and EC, respectively, while an inverse order of those species showed in MBR-aging sludge. 60-isolates of each species per sample were tested on 8-antibiotics (AMAB) and 19-antibiotics (AMEC&AMKP) to evaluate antimicrobial resistance (AM) potency. The results show that high ARB variation of 0 to 100% population among those ARB had shown in the wastewater, while a significant reduction of those ARB population in MBR-aged-sludge had appeared surprisingly (P < 0.05). For example, the AMEC population of sludge to influent was <0.5 as of ESBL, Cefoperazone, Cefquinome, Imipenem, Gentamicin, Enrofloxacin, and Marbofloxacin. Among the three species studied, AB showed the highest antibiotic-resistant reduction of 8 antibiotics (100%), followed by KP (17 antibiotics, 99.44%) and EC (16 antibiotics, 88.89%), respectively. High dissolved oxygen levels and prolonged sludge age were possibly contributing to the reduction of those ARB in the MBR. This study gives a new point of view on potential ARB population reduction via the appropriate MBR operation.

Shotgun metagenomics assessment of the resistome, mobilome, pathogen dynamics and their ecological control modes in full-scale urban wastewater treatment plants

The conventional activated sludge (CAS) process has limited capacity to remove pathogenic microorganisms and antibiotic resistance genes (ARGs), compared to membrane bioreactors (MBRs). However, the full extent of pathogenic microbial fraction, resistome (antibiotic and biocide resistance genes, ARGs and BRGs) and mobilome (mobile genetic elements, MGE) of urban wastewater treatment plant (UWTP) influents and effluents remains unknown. Thus, the fate of putative pathogenic bacteria, ARGs and potential co-occurrence patterns with BRGs, MGEs and bacterial-predatory microorganisms was determined in two full-scale UWTPs, a MBR and a CAS system, using shotgun metagenomics. Both UWTPs significantly reduced the BOD₅ (99.4-99.9%), COD (97.6-99.4%) and TSS (98.9-99.9%). MBR was more effective in reducing the abundance and diversity of pathogen-containing taxa, with 4 and 30 taxa enriched in MBR and CAS effluents, respectively. MBR treatment favored resistance genes associated with triclosan, whereas CAS effluents contained ARGs associated with antibiotics of clinical importance. Correlations between putative pathogenic bacteria, ARG/BRGs/MGEs and bacterial-predatory microorganisms suggested that: (i) opportunistic pathogens (Clostridia, Nocardia) may acquire ARGs against first-line treatments and (ii) bacteriophages may act as a biogenic mechanism of pathogen removal. These findings reinforce the MBR capacity to retain pathogenic components, hence reducing potential health risks associated with treated wastewater reuse.

Discriminatory Detection of ssDNA by Surface-Enhanced Raman Spectroscopy (SERS) and Tree-Based Support Vector Machine (Tr-SVM)

We report label-free detection of 86-base single-stranded DNA (ssDNA) gene segments by surface-enhanced Raman spectroscopy (SERS). The use of a slippery liquid infused porous (SLIP) membrane induced aggregation of 43 nm gold nanoparticles and ssDNA upon pin-free droplet evaporation. The combined SLIPSERS approach generates significant numbers of SERS hot-spots and enabled detection at the 100 nM level of mecA and intI1 gene segments-two genes of interest in the context of antibiotic resistance. Tree-based multiclass support vector machine (Tr-SVM) classifiers were built to discriminate SERS spectra of 12 different gene sequences obtained by SLIPSERS: mecA, intI1, as well as analogues of mecA and intI1, respectively, with 2-10 base mismatches, and two random sequences. The trained predictive Tr-SVM classifiers correctly identified each gene sequence with a prediction accuracy of ∼90%. This study illustrates a novel means for discriminatory label-free SERS detection of ssDNA enabled by Tr-SVM.

Mitigating Antibiotic Resistance Genes in Wastewater by Sequential Treatment with Novel Nanomaterials

Wastewater (WW) has been widely recognized as the major sink of a variety of emerging pathogens (EPs), antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs), which may disseminate and impact wider environments. Improving and maximizing WW treatment efficiency to remove these microbial hazards is fundamentally imperative. Despite a variety of physical, biological and chemical treatment technologies, the efficiency of ARG removal is still far from satisfactory. Within our recently accomplished M-ERA.NET project, novel functionalized nanomaterials, i.e., molecularly imprinted polymer (MIP) films and quaternary ammonium salt (QAS) modified kaolin microparticles, were developed and demonstrated to have significant EP removal effectiveness on both Gram-positive bacteria (GPB) and Gram-negative bacteria (GNB) from WW. As a continuation of this project, we took the further step of exploring their ARG mitigation potential. Strikingly, by applying MIP and QAS functionalized kaolin microparticles in tandem, the ARGs prevalent in wastewater treatment plants (WWTPs), e.g., blaCTXM, ermB and qnrS, can be drastically reduced by 2.7, 3.9 and 4.9 log (copies/100 mL), respectively, whereas sul1, tetO and mecA can be eliminated below their detection limits. In terms of class I integron-integrase I (intI1), a mobile genetic element (MGE) for horizontal gene transfer (HGT), 4.3 log (copies/100 mL) reduction was achieved. Overall, the novel nanomaterials exhibit outstanding performance on attenuating ARGs in WW, being superior to their control references. This finding provides additional merit to the application of developed nanomaterials for WW purification towards ARG elimination, in addition to the proven bactericidal effect.

Characterization of methicillin-resistant Staphylococcus aureus strains in sewage treatment plants in Tehran, Iran

Multidrug-resistant Staphylococcus aureus strains have been commonly found in hospitals and communities causing wide ranges of infections among humans and animals. Typing of these strains is a key factor to reveal their clonal dissemination in different regions. We investigated the prevalence and dissemination of different clonal groups of S. aureus with resistance phenotype to multiple antibiotics in two sewage treatment plants (STPs) in Tehran, Iran over four sampling occasions. A total of 576 S. aureus were isolated from the inlet, sludge and outlet. Of these, 80 were identified as methicillin-resistant S. aureus (MRSA) and were further characterized using a combination of Phene Plate (PhP) typing, staphylococcal cassette chromosome mec (SCCmec), ccr types, prophage and antibiotic-resistant profiling. In all, eight common type (CT) and 13 single PhP type were identified in both STPs, with one major CT accounting for 38.8% of the MRSA strains. These strains belonged to three prophage patterns and five prophage types with SCCmec type III being the predominant type. Resistance to 11 out of the 17 antibiotics tested was significantly (P < 0.0059) higher among the MRSA isolates than methicillin-sensitive S. aureus (MSSA) strains. The persistence of the strains in samples collected from the outlet of both STPs was 31.9% for MRSA and 23.1% for MSSA. These data indicated that while the sewage treatment process, in general, is still useful for removing most MRSA populations, some strains with SCCmec type III may have a better ability to survive the STP process.

Fate and removal of bacteria and antibiotic resistance genes in horizontal subsurface constructed wetlands: Effect of mixed vegetation and substrate type

This study aimed to investigate the influence of cropping method and substrate type on the fate and the removal of bacterial and antibiotic resistance genes (ARGs) indicators from primary wastewater by constructed wetlands (CWs) during startup and maturation stages. Four small-scale CWs differing in their plantation pattern (monoculture vs. polyculture) and substrate type were constructed and operated under field conditions. While for bacteria, the greatest impact of the cropping method and substrate type on removal was during the startup stage rather than the maturation stage, for ARGs, such impact was significant at both stages. During startup, the removal efficiencies of heterotrophic bacteria, fecal coliforms, E. coli, 16S rRNA genes and lacZ increased with the operation time. At maturation, the removal efficiencies were constant and were within the range of 89.2-99.4%, 93.7-98.9%, 89-98.8%, 94.1-99.6% and 92.9-98.7%, respectively. The removal efficiencies of intl1, tetM, intl1, sul1, ermB and total ARGs were also increased with the operation time. However, they were ARG type and configuration-dependent; at maturation they ranged between 50.7%-89.4%, 85.9%-97%, 49.6%-92.9%, 58.2%-96.7% and 79.9-94.3%, respectively. The tuff-filled serially planted CW was also the only one capable of removing these genes at similar high efficiency. Metagenomic analysis showed that none of the ARGs was among the most common ARGs in water and biofilm samples; rather most ARGs belonged to bacterial efflux transporter superfamilies. Although ARGs were removed, they were still detected in substrate biofilm and their relative concentrations were increased in the effluents. While the removal of both bacteria and ARGs was higher during summer compared to winter, the season had no effect on the removal pattern of ARGs. Hence, combination of the serial plantation with substrate having high surface area is a potential strategy that can be used to improve the performance of CWs.

Degradation Kinetics of Antibiotic Resistance Gene mecA of Methicillin-Resistant Staphylococcus aureus (MRSA) during Water Disinfection with Chlorine, Ozone, and Ultraviolet Light

Degradation kinetics of antibiotic resistance genes (ARGs) by free available chlorine (FAC), ozone (O₃), and UV₂₅₄ light (UV) were investigated in phosphate buffered solutions at pH 7 using a chromosomal ARG (mecA) of methicillin-resistant Staphylococcus aureus (MRSA). For FAC, the degradation rates of extracellular mecA (extra-mecA) were accelerated with increasing FAC exposure, which could be explained by a two-step FAC reaction model. The degradation of extra-mecA by O₃ followed second-order reaction kinetics. The degradation of extra-mecA by UV exhibited tailing kinetics, which could be described by a newly proposed kinetic model considering cyclobutane pyrimidine dimer (CPD) formation, its photoreversal, and irreversible (6-4) photoproduct formation. Measured rate constants for extra-mecA increased linearly with amplicon length for FAC and O₃, or with number of intrastrand pyrimidine doublets for UV, which enabled prediction of degradation rate constants of extra-mecA amplicons based on sequence length and/or composition. In comparison to those of extra-mecA, the observed degradation rates of intracellular mecA (intra-mecA) were faster for FAC and O₃ at low oxidant exposures but significantly slower at high exposures for FAC and UV. Differences in observed extra- and intracellular kinetics could be due to decreased DNA recovery efficiency and/or the presence of MRSA aggregates protected from disinfectants.

Assessment of Full-Scale Indirect Potable Water Reuse in El Port de la Selva, Spain

In 2015, the town of El Port de la Selva in Spain implemented soil-aquifer treatment (SAT) using tertiary treated wastewater effluents to replenish the local potable aquifer. This study evaluated the initial phase of this indirect potable water reuse system including a characterization of hydraulic conditions in the aquifer and monitoring of microbial contaminants and 151 chemicals of emerging concern (CECs). The combined treatment resulted in very low abundances of indicator bacteria, enteric viruses and phages in the monitoring wells after three days of infiltration and a reduction of antibiotic microbial resistance to background levels of local groundwater. After tertiary treatment, 94 CECs were detected in the infiltration basin of which 15 chemicals exceeded drinking water thresholds or health-based monitoring trigger levels. Although SAT provided an effective barrier for many chemicals, 5 CECs were detected above health-based threshold levels in monitoring wells after short hydraulic retention times. However, additional attenuation is expected due to dilution prior to abstraction via downstream drinking water wells and during granular activated carbon (GAC) filtration, which was recently installed to mitigate residual CECs. Overall, the results demonstrate that indirect potable water reuse can be a reliable option for smaller communities, if related risks from microbial and chemical contaminants are adequately addressed by tertiary treatment and subsequent SAT, providing sufficient hydraulic retention times for pathogen decay and CEC removal.

Performance of Layer-by-Layer-Modified Multibore® Ultrafiltration Capillary Membranes for Salt Retention and Removal of Antibiotic Resistance Genes

Polyether sulfone Multibore^® ultrafiltration membranes were modified using polyelectrolyte multilayers via the layer-by-layer (LbL) technique in order to increase their rejection capabilities towards salts and antibiotic resistance genes. The modified capillary membranes were characterized to exhibit a molecular weight cut-off (at 90% rejection) of 384 Da. The zeta-potential at pH 7 was −40 mV. Laboratory tests using single-fiber modified membrane modules were performed to evaluate the removal of antibiotic resistance genes; the LbL-coated membranes were able to completely retain DNA fragments from 90 to 1500 nt in length. Furthermore, the pure water permeability and the retention of single inorganic salts, MgSO₄, CaCl₂ and NaCl, were measured using a mini-plant testing unit. The modified membranes had a retention of 80% toward MgSO₄ and CaCl₂ salts, and 23% in case of NaCl. The modified membranes were also found to be stable against mechanical backwashing (up to 80 LMH) and chemical regeneration (in acidic conditions and basic/oxidizing conditions).

Antibiotic resistance levels in soils from urban and rural land uses in Great Britain

Although soil is one of the largest microbial diversity reservoirs, the processes that define its microbial community dynamics are not fully understood. Improving our understanding of the levels of antibiotic resistance in soils with different land uses in Great Britain is not only important for the protection of animal health (including humans), but also for gaining an insight into gene transfer levels in microbial communities. This study looked at the levels of antibiotic-resistant bacteria (ARB) able to survive inhibitory concentrations of chloramphenicol, erythromycin and vancomycin, as well as subinhibitory (10 µg ml⁻¹) erythromycin concentrations. Soils from nine different sites across Great Britain with three distinct land uses (agricultural, urban and semi-natural) were sampled and the percentage of ARB was calculated for each site. Statistical analyses confirmed a significant difference in the level of ARB found in agricultural land compared to urban or semi-natural sites. The results also showed that resistance levels to vancomycin and chloramphenicol in the agricultural and urban sites sampled were significantly higher than those for erythromycin, whilst in semi-natural sites all three antibiotics show similar resistance levels. Finally, although the levels of resistance to a subinhibitory (10 µg ml⁻¹) erythromycin concentration were significantly higher across land use types when compared to the levels of resistance to an inhibitory (20 µg ml⁻¹) concentration, these were much less marked in soil from agricultural land compared to that from urban or semi-natural land use soil.

Antibiotic Resistance Genes in Phage Particles from Antarctic and Mediterranean Seawater Ecosystems

Anthropogenic activities are a key factor in the development of antibiotic resistance in bacteria, a growing problem worldwide. Nevertheless, antibiotics and resistances were being generated by bacterial communities long before their discovery by humankind, and might occur in areas without human influence. Bacteriophages are known to play a relevant role in the dissemination of antibiotic resistance genes (ARGs) in aquatic environments. In this study, five ARGs (bla_TEM, bla_CTX-M-1, bla_CTX-M-9, sul1 and tetW) were monitored in phage particles isolated from seawater of two different locations: (i) the Mediterranean coast, subjected to high anthropogenic pressure, and (ii) the Antarctic coast, where the anthropogenic impact is low. Although found in lower quantities, ARG-containing phage particles were more prevalent among the Antarctic than the Mediterranean seawater samples and Antarctic bacterial communities were confirmed as their source. In the Mediterranean area, ARG-containing phages from anthropogenic fecal pollution might allow ARG transmission through the food chain. ARGs were detected in phage particles isolated from fish (Mediterranean, Atlantic, farmed, and frozen), the most abundant being β-lactamases. Some of these particles were infectious in cultures of the fecal bacteria Escherichia coli. By serving as ARG reservoirs in marine environments, including those with low human activity, such as the Antarctic, phages could contribute to ARG transmission between bacterial communities.

Characteristics of the antibiotic resistance genes in the soil of medical waste disposal sites

The inappropriate disposal of medical waste allows bacteria to acquire antibiotic resistance, which results in a threat to public health. Antibiotic resistance gene (ARG) profiles were determined for 45 different soil samples containing medical waste and 15 nearby soil samples as controls. Besides physical and chemical analyses (i.e., dry matter content, pH value, and metal content), the genomes of microorganisms from the soil samples were extracted for high-throughput sequencing. ARG abundances of these samples were obtained by searching the metagenomic sequences against the antibiotic resistance gene database and the copies of ARGs per copy of the 16S rRNA gene at different levels were assessed. The results showed medical waste accumulation significantly enriched the contents of Cu, Cr, Pb, and As in the tested soil samples. Compared to the controls, the samples collected from areas containing medical waste were significantly enriched (p < 0.05, t-test) with ARGs annotated as sulfonamide and multidrug resistance genes, and in particular, the subtypes sul1 and sul2 (sulfonamide resistance genes), and multidrug_transporter (multidrug resistance gene). Moreover, the ARGs of the samples from the polluted areas were more diverse than those of the control samples (p < 0.05, t-test). The comparatively higher abundance and diversity of ARGs in contaminated soil pose a potential risk to human health.

Antibiotic Resistance Genes Occurrence in Wastewaters from Selected Pharmaceutical Facilities in Nigeria

The proliferation of antibiotic-resistant bacteria (ARB) and the prevalence of antibiotic resistance genes (ARGs) in wastewaters are well-established factors that contribute to the reduced potency of antibiotics used in healthcare worldwide. The human health risk associated with the proliferation of ARB and ARGs need to be understood in order to design mitigation measures to combat their dissemination. Using the PCR analysis of genomic DNA, the prevalence of 41 ARGs active against the commonly used six classes of antibiotics was evaluated in 60 bacterial isolates obtained from pharmaceutical wastewaters in Nigeria. The ARGs most frequently detected from the bacterial isolates in each of the antibiotic classes under study include catA1 (58.3%); sulI (31.7%); tet(E) (30%); aac(3)-IV (28.3%); ermC (20%); blaTEM, blaCTX-M, blaNDM-1 at 18.3% each; which encode for resistance to chloramphenicol, sulfonamides, tetracycline, aminoglycoside, macrolide-lincosamide-streptogramin and β-lactams and penicillins, respectively. Acinetobacter spp., accession number MH396735 expressed the highest number of ARGs of all the bacterial isolates, having at least one gene that encodes for resistance to all the classes of antibiotics in the study. This study highlights wide distribution of ARB and ARGs to the antibiotics tested in the wastewater, making pharmaceutical wastewater reservoirs of ARGs which could potentially be transferred from commensal microorganisms to human pathogens.

Stochasticity in microbiology: managing unpredictability to reach the Sustainable Development Goals

Pure (single) cultures of microorganisms and mixed microbial communities (microbiomes) have been important for centuries in providing renewable energy, clean water and food products to human society and will continue to play a crucial role to pursue the Sustainable Development Goals. To use microorganisms effectively, microbial engineered processes require adequate control. Microbial communities are shaped by manageable deterministic processes, but also by stochastic processes, which can promote unforeseeable variations and adaptations. Here, we highlight the impact of stochasticity in single culture and microbiome engineering. First, we discuss the concepts and mechanisms of stochasticity in relation to microbial ecology of single cultures and microbiomes. Second, we discuss the consequences of stochasticity in relation to process performance and human health, which are reflected in key disadvantages and important opportunities. Third, we propose a suitable decision tool to deal with stochasticity in which monitoring of stochasticity and setting the boundaries of stochasticity by regulators are central aspects. Stochasticity may give rise to some risks, such as the presence of pathogens in microbiomes. We argue here that by taking the necessary precautions and through clever monitoring and interpretation, these risks can be mitigated.

Removal of Antibiotic Resistance Genes at Two Conventional Wastewater Treatment Plants of Louisiana, USA

Wastewater treatment plants (WWTPs) represent all known types of antibiotic resistance mechanisms and are considered as the critical points for the spread of antibiotic resistance genes (ARGs). The purpose of this study is to investigate the removal of a Class 1 integrase gene (intI1) and a selected set of ARGs (blaTEM, ermF, mecA, and tetA) at two conventional WWTPs by using chlorination in Louisiana, USA. We collected 69 wastewater samples (23 each from influent, secondary effluent, and final effluent) and determined the concentrations of ARGs by using quantitative polymerase chain reaction. All tested ARGs, except for mecA, were detected in 83–96% and 30–65% of influent and final effluent samples, respectively. Although the ARGs underwent approximately 3-log10 reduction, two WWTPs on an average still released 3.3 ± 1.7 log10 copies/mL of total ARGs studied in the effluents. Chlorination was found to be critical in the significant reduction of total ARGs (p < 0.05). Correlation analysis and the ability of intI1 to persist through the treatment processes recommend the use of intI1 as a marker of ARGs in effluents to monitor the spread of antibiotic resistance in effluents. Our study suggests that conventional WWTPs using chlorination do not favor the proliferation of antibiotic resistance bacteria and ARGs during wastewater treatment.

Evaluation of antibiotic resistance dissemination by wastewater treatment plant effluents with different catchment areas in Germany

The study quantified the abundances of antibiotic resistance genes (ARGs) and facultative pathogenic bacteria (FPB) as well as one mobile genetic element in genomic DNA via qPCR from 23 different wastewater treatment plant (WWTP) effluents in Germany. 12 clinically relevant ARGs were categorized into frequently, intermediately, and rarely occurring genetic parameters of communal wastewaters. Taxonomic PCR quantifications of five FPB targeting Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, Acinetobacter baumannii, and enterococci were performed. The WWTPs differed in their catchment areas being impacted by hospitals, food processing companies, or housing areas only. The total discharges of the analyzed ARGs and FPB were found to cluster independently of the sizes of the WWTPs with a maximum difference of two log units within one cluster. Initially, quantitative data evaluations revealed no significant difference between ARG categories and WWTP catchment areas. More distinct correlations became obvious with a Pearson correlation approach, where each single taxonomic marker is compared to each ARG target. Here, increased correlation of FPB (i.e. E. coli, K. pneumoniae, P. aeruginosa, and enterococci) with clinically relevant ARGs of the category of rarely occurring resistance genes (bla_NDM-1, vanA) was found in WWTP effluents being influenced by hospital wastewaters.

Microbial and Viral Communities and Their Antibiotic Resistance Genes Throughout a Hospital Wastewater Treatment System

Antibiotic resistance poses a serious threat to global public health, and antibiotic resistance determinants can enter natural aquatic systems through discharge of wastewater effluents. Hospital wastewater in particular is expected to contain high abundances of antibiotic resistance genes (ARGs) compared to municipal wastewater because it contains human enteric bacteria that may include antibiotic-resistant organisms originating from hospital patients, and can also have high concentrations of antibiotics and antimicrobials relative to municipal wastewater. Viruses also play an important role in wastewater treatment systems since they can influence the bacterial community composition through killing bacteria, facilitating transduction of genetic material between organisms, and modifying the chromosomal content of bacteria as prophages. However, little is known about the fate and connections between ARGs, viruses, and their associated bacteria in hospital wastewater systems. To address this knowledge gap, we characterized the composition and persistence of ARGs, dsDNA viruses, and bacteria from influent to effluent in a pilot-scale hospital wastewater treatment system in Israel using shotgun metagenomics. Results showed that ARGs, including genes conferring resistance to antibiotics of high clinical relevance, were detected in all sampling locations throughout the pilot-scale system, with only 16% overall depletion of ARGs per genome equivalent between influent and effluent. The most common classes of ARGs detected throughout the system conferred resistance to aminoglycoside, cephalosporin, macrolide, penam, and tetracycline antibiotics. A greater proportion of total ARGs were associated with plasmid-associated genes in effluent compared to in influent. No strong associations between viral sequences and ARGs were identified in viral metagenomes from the system, suggesting that phage may not be a significant vector for ARG transfer in this system. The majority of viruses in the pilot-scale system belonged to the families Myoviridae, Podoviridae, and Siphoviridae. Gammaproteobacteria was the dominant class of bacteria harboring ARGs and the most common putative viral host in all samples, followed by Bacilli and Betaproteobacteria. In the total bacterial community, the dominant class was Betaproteobacteria for each sample. Overall, we found that a variety of different types of ARGs and viruses were persistent throughout this hospital wastewater treatment system, which can be released to the environment through effluent discharge.

The Occurrence of Antibiotic Resistance Genes in an Urban River in Nepal

Urban rivers affected by anthropogenic activities can act as reservoirs of antibiotic resistance genes (ARGs). This study aimed to describe the occurrence of selected ARGs (blaTEM, ermF, mecA, and tetA) and a class 1 integron (intI1) in an urban river in Nepal. A total of 18 water samples were collected periodically from upstream, midstream, and downstream sites along the Bagmati River over a 1-year period. All ARGs except mecA and intI1 were consistently detected by a quantitative polymerase chain reaction in the midstream and downstream sites, with concentrations ranging from 3.1 to 7.8 log copies/mL. ARG abundance was significantly lower at the upstream site (p < 0.05), reflecting the impact of anthropogenic activities on increasing concentrations of ARGs at midstream and downstream sites. Our findings demonstrate the presence of clinically relevant ARGs in the urban river water of Nepal, suggesting a need for mitigating strategies to prevent the spread of antibiotic resistance in the environment.

Higher normalized concentrations of tetracycline resistance found in ballast and harbor water compared to ocean water

Although ballast water is a known vector for the global transport of microorganisms, the Ballast Water Management Convention only sets limits for indicator organisms and does not consider antibiotic resistance genes (ARGs). Herein, we examined the concentration of indicator organisms and prevalence of three ARGs (sul1, tet (M), and vanA) in a total of 53 ballast, 21 harbor, and 8 ocean samples collected in Singapore, China, South Africa, and California. E. coli was found in significantly higher concentrations in ballast samples obtained in Singapore and China compared to South Africa (Singapore, p = 0.040) and California (Singapore, p < 0.001; China, p = 0.038). Harbor samples from China had significantly higher concentrations of E. coli than Singapore (p = 0.049) and California (p = 0.001). When compared to ocean samples, there were significantly higher concentrations of normalized tet(M) in ballast samples from California (p = 0.011) and Singapore (p = 0.019) and in harbor samples from California (p = 0.018), Singapore (p = 0.010), and South Africa (p = 0.008). These findings suggest that microbial loads significantly differ among ports. Furthermore, certain ARGs are enriched in ballast and harbor waters when compared to ocean water, which suggests that ballast waters have the potential to either transport higher concentrations of certain ARGs or that ballast tank conditions may exert selective pressure for some ARGs.

Selective enrichment of bacterial pathogens by microplastic biofilm

Microplastics have been found to be ubiquitous in freshwater ecosystems, providing a novel substrate for biofilm formation. Here, we incubated biofilm on microplastics and two natural substrates (rock and leaf) under a controlled environment to investigate the differences of microbial community structure, antibiotic resistance gene (ARG) profiles, and ARG microbial hosts between biofilms on three types of substrates. Results from high-throughput sequencing of 16S rRNA gene revealed that microplastic biofilm had a distinctive community structure. Network analyses suggested that microplastic biofilm possessed the highest node connected community, but with lower average path length, network diameter and modularity compared with biofilm on two natural particles. Metagenomic analyses further revealed microplastic biofilm with broad-spectrum and distinctive resistome. Specifically, according to taxonomic annotation of ARG microbial hosts, two opportunisitic human pathogens (Pseudomonas monteilii, Pseudomonas mendocina) and one plant pathogen (Pseudomonas syringae) were detected only in the microplastic biofilm, but not in biofilms formed on natural substrates. Our findings suggest that microplastic is a novel microbial niche and may serve as a vector for ARGs and pathogens to new environment in river water, generating freshwater environmental risk and exerting adverse impacts on human health.

Infectious phage particles packaging antibiotic resistance genes found in meat products and chicken feces

Bacteriophages can package part of their host's genetic material, including antibiotic resistance genes (ARGs), contributing to a rapid dissemination of resistances among bacteria. Phage particles containing ARGs were evaluated in meat, pork, beef and chicken minced meat, and ham and mortadella, purchased in local retailer. Ten ARGs (bla_TEM, bla_CTX-M-1, bla_CTX-M-9, bla_OXA-48, bla_VIM, qnrA, qnrS, mecA, armA and sul1) were analyzed by qPCR in the phage DNA fraction. The genes were quantified, before and after propagation experiments in Escherichia coli, to evaluate the ability of ARG-carrying phage particles to infect and propagate in a bacterial host. According to microbiological parameters, all samples were acceptable for consumption. ARGs were detected in most of the samples after particle propagation indicating that at least part of the isolated phage particles were infectious, being sul1the most abundant ARG in all the matrices followed by β-lactamase genes. ARGs were also found in the phage DNA fraction of thirty-seven archive chicken cecal samples, confirming chicken fecal microbiota as an important ARG reservoir and the plausible origin of the particles found in meat. Phages are vehicles for gene transmission in meat that should not be underestimated as a risk factor in the global crisis of antibiotic resistance.

Dissemination prevention of antibiotic resistant and facultative pathogenic bacteria by ultrafiltration and ozone treatment at an urban wastewater treatment plant

Conventional wastewater treatment is not sufficient for the removal of hygienically relevant bacteria and achieves only limited reductions. This study focuses on the reduction efficiencies of two semi-industrial ultrafiltration units operating at a large scale municipal wastewater treatment plant. In total, 7 clinically relevant antibiotic resistance genes, together with 3 taxonomic gene markers targeting specific facultative pathogenic bacteria were analysed via qPCR analyses before and after advanced treatment. In parallel with membrane technologies, an ozone treatment (1 g ozone/g DOC) was performed for comparison of the different reduction efficiencies. Both ultrafiltration units showed increased reduction efficiencies for facultative pathogenic bacteria and antibiotic resistance genes of up to 6 log units, resulting mostly in a strong reduction of the bacterial targets. In comparison, the ozone treatment showed some reduction efficiency, but was less effective compared with ultrafiltration due to low ozone dosages frequently used for micro-pollutant removal at municipal wastewater treatment plants. Additionally, metagenome analyses demonstrated the accumulation of facultative pathogenic bacteria, antibiotic resistance genes, virulence factor genes, and metabolic gene targets in the back flush retentate of the membranes, which opens further questions about retentate fluid material handling at urban wastewater treatment plants.

Global distribution and current research of AmpC beta-lactamase genes in aquatic environments: A systematic review

AmpC beta-lactamase genes are some of the most common antibiotic resistance genes and require special attention once they have become mobilised. The detection of these genes is well documented in clinical settings. However, there is insufficient knowledge of both plasmid and genomic AmpC genes in aquatic environments. This systematic review aimed to determine the extent of the knowledge gap in the literature regarding the prevalence of AmpC beta-lactamase genes in aquatic systems. Using selected criteria, a total of 27 databases were searched for applicable peer-reviewed journal articles. No date and language restrictions were applied. Journal articles that highlighted the detection of AmpC beta-lactamase genes in environmental aquatic systems, including wastewater treatment plants, were included. Of the 950 literature sources that were identified, 50 were selected for full text analysis based on predetermined criteria. Studies on AmpC genes detection were traced in 23 countries. These studies focused on surface water (24), wastewater (17), sea water (4) and both surface and wastewater (5). Most studies did not specifically aim to detect AmpC genes, but to detect antibiotic resistance genes in general. Presently no surveillance protocols, standardised detection methods or environmental limits exist for these genes and, due to a paucity of research in this field, it is unlikely that such systems will be implemented in the near future. The implications and dynamics of AmpC genes in aquatic systems remain unclear and require intense research to ensure the sustainability of environmental systems and human health.

Longitudinal Comparison of Bacterial Diversity and Antibiotic Resistance Genes in New York City Sewage

Urban sewage or wastewater is a diverse source of bacterial growth, as well as a hot spot for the development of environmental antibiotic resistance, which can in turn influence the health of the residents of the city. As part of a larger study to characterize the urban New York City microbial metagenome, we collected raw sewage samples representing three seasonal time points spanning the five boroughs of NYC and went on to characterize the microbiome and the presence of a range of antibiotic resistance genes. Through this study, we have established a baseline microbial population and antibiotic resistance abundance in NYC sewage which can prove to be very useful in studying the load of antibiotic usage, as well as for developing effective measures in antibiotic stewardship.

Bacterial resistance to antibiotics is a pressing health issue around the world, not only in health care settings but also in the community and environment, particularly in crowded urban populations. The aim of our work was to characterize the microbial populations in sewage and the spread of antibiotic resistance within New York City (NYC). Here, we investigated the structure of the microbiome and the prevalence of antibiotic resistance genes in raw sewage samples collected from the fourteen NYC Department of Environmental Protection wastewater treatment plants, distributed across the five NYC boroughs. Sewage, a direct output of anthropogenic activity and a reservoir of microbes, provides an ecological niche to examine the spread of antibiotic resistance. Taxonomic diversity analysis revealed a largely similar and stable bacterial population structure across all the samples, which was found to be similar over three time points in an annual cycle, as well as in the five NYC boroughs. All samples were positive for the presence of the seven antibiotic resistance genes tested, based on real-time quantitative PCR assays, with higher levels observed for tetracycline resistance genes at all time points. For five of the seven genes, abundances were significantly higher in May than in February and August. This study provides characteristics of the NYC sewage resistome in the context of the overall bacterial populations.

IMPORTANCE Urban sewage or wastewater is a diverse source of bacterial growth, as well as a hot spot for the development of environmental antibiotic resistance, which can in turn influence the health of the residents of the city. As part of a larger study to characterize the urban New York City microbial metagenome, we collected raw sewage samples representing three seasonal time points spanning the five boroughs of NYC and went on to characterize the microbiome and the presence of a range of antibiotic resistance genes. Through this study, we have established a baseline microbial population and antibiotic resistance abundance in NYC sewage which can prove to be very useful in studying the load of antibiotic usage, as well as for developing effective measures in antibiotic stewardship.

Effects of sample preservation and DNA extraction on enumeration of antibiotic resistance genes in wastewater

With the growing application of high-throughput sequencing-based metagenomics for profiling antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs), comparison of sample pretreatment and DNA extraction methods are needed to move toward standardized comparisons among laboratories. Three widely employed DNA extraction methods (FastDNA® Spin Kit for Soil, PowerSoil® DNA Isolation Kit and ZR Fecal DNA MiniPrep), with and without preservation in 50% ethanol and freezing, were applied to the influent, activated sludge and effluent of two WWTPs, in Hong Kong and in the USA. Annotated sequences obtained from the DNA extracted using the three kits shared similar taxonomy and ARG profiles. Overall, it was found that the DNA yield and purity, and diversity of ARGs captured were all highest when applying the FastDNA SPIN Kit for Soil for all three WWTP sample types investigated here (influent, activated sludge, effluent). Quantitative polymerase chain reaction of 16S rRNA genes confirmed the same trend as DNA extraction yields and similar recovery of a representative Gram-negative bacterium (Escherichia coli). Moreover, sample fixation in ethanol, deep-freezing and overseas shipment had no discernable effect on ARG profiles, as compared to fresh samples. This approach serves to inform future efforts toward global comparisons of ARG distributions in WWTPs.