Microbiological characterization of aquatic microbiomes targeting taxonomical marker genes and antibiotic resistance genes of opportunistic bacteria

Photolysis of four β‑lactam antibiotics under simulated environmental conditions: Degradation, transformation products and antibacterial activity

β‑Lactam antibiotics are among the most widely used antibiotics in human medicine and their effects on the aquatic environment - concerning bacterial resistance - are controversially discussed. This study focused on the photolysis of the four β‑lactam antibiotics - amoxicillin, ampicillin, penicillin V and piperacillin - under simulated environmental conditions. It was observed that all investigated β‑lactam antibiotics are photolytically degradable by simulated sunlight (1 kW/m²) with half-lives between 3.2 and 7.0 h. Structure elucidation of transformation products performed with liquid chromatography coupled to high resolution mass spectrometry showed that the hydrolysis of the β‑lactam ring is the primary transformation reaction, followed by the elimination of carboxylic and dimethyl thiazolidine carboxylic acid. Growth inhibition tests on Bacillus subtilis showed the loss of bactericide activity of irradiated solutions of amoxicillin, ampicillin and piperacillin, suggesting the transformation of the β‑lactam ring is responsible for the antibiotic effect. In contrast, the solutions of penicillin V did not show any decline of the antibacterial activity after photolytic degradation, probably due to the formation of still active epimers.

Impact of the particulate matter from wastewater discharge on the abundance of antibiotic resistance genes and facultative pathogenic bacteria in downstream river sediments

Wastewater treatment plants (WWTPs) are point sources for both, the release of antibiotic resistance genes (ARGs) and the discharge of antibiotics (ABs) into the environment. While it is well established that ARGs emission by WWTPs leads to an ARGs increase in receiving rivers, also the role of sub-inhibitory AB concentrations in this context is being discussed. However, the results obtained in this study suggest that, at environmental concentrations, ABs do not have an effect on resistance selection. Instead, we emphasize the significance of ARG transport and, in that respect, highlight the relevance of wastewater particles and associated microorganisms. We can show that ARGs (ermB, bla_TEM,tetM, qnrS) as well as facultative pathogenic bacteria (FPB) (enterococci, Pseudomonas aeruginosa, Acinetobacter baumannii) inside the particulate fraction of WWTP effluent are very likely to remain in the riverbed of the receiving water due to sedimentation. Moreover, ARG and FPB abundances measured in the particulate fraction strongly correlated with the delta ARG and FPB abundances measured in the receiving river sediment (downstream compared to upstream) (R² = 0.93, p < 0.05). Apparently, the sheer amount of settleable ARGs and FPB from WWTP effluent is sufficient, to increase abundances in the receiving riverbed by 0.5 to 2 log units.

Quantitative Occurrence of Antibiotic Resistance Genes among Bacterial Populations from Wastewater Treatment Plants Using Activated Sludge

Wastewater treatment plants (WWTPs) are an important reservoir in the development of drug resistance phenomenon and they provide a potential route of antibiotic resistance gene (ARGs) dissemination in the environment. The aim of this study was to assess the role of WWTPs in the spread of ARGs. Untreated and treated wastewater samples that were collected from thirteen Polish WWTPs (applying four different modifications of activated sludge–based treatment technology) were analyzed. The quantitative occurrence of genes responsible for the resistance to beta-lactams and tetracyclines was determined using the real-time PCR method. Such genes in the DNA of both the total bacterial population and of the E. coli population were analyzed. Among the tested genes that are responsible for the resistance to beta-lactams and tetracyclines, blaOXA and blaTEM and tetA were dominant, respectively. This study found an insufficient reduction in the quantity of the genes that are responsible for antibiotic resistance in wastewater treatment processes. The results emphasize the need to monitor the presence of genes determining antibiotic resistance in the wastewater that is discharged from treatment plants, as they can help to identify the hazard that treated wastewater poses to public health.

Performance of secondary wastewater treatment methods for the removal of contaminants of emerging concern implicated in crop uptake and antibiotic resistance spread: A review

Contaminants of emerging concern (CEC) discharged in effluents of wastewater treatment plants (WWTPs), not specifically designed for their removal, pose serious hazards to human health and ecosystems. Their impact is of particular relevance to wastewater disposal and re-use in agricultural settings due to CEC uptake and accumulation in food crops and consequent diffusion into the food-chain. This is the reason why the chemical CEC discussed in this review have been selected considering, besides recalcitrance, frequency of detection and entity of potential hazards, their relevance for crop uptake. Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) have been included as microbial CEC because of the potential of secondary wastewater treatment to offer conditions favourable to the survival and proliferation of ARB, and dissemination of ARGs. Given the adverse effects of chemical and microbial CEC, their removal is being considered as an additional design criterion, which highlights the necessity of upgrading conventional WWTPs with more effective technologies. In this review, the performance of currently applied biological treatment methods for secondary treatment is analysed. To this end, technological solutions including conventional activated sludge (CAS), membrane bioreactors (MBRs), moving bed biofilm reactors (MBBRs), and nature-based solutions such as constructed wetlands (CWs) are compared for the achievable removal efficiencies of the selected CEC and their potential of acting as reservoirs of ARB&ARGs. With the aim of giving a picture of real systems, this review focuses on data from full-scale and pilot-scale plants treating real urban wastewater. To achieve an integrated assessment, technologies are compared considering also other relevant evaluation parameters such as investment and management costs, complexity of layout and management, present scale of application and need of a post-treatment. Comparison results allow the definition of design and operation strategies for the implementation of CEC removal in WWTPs, when agricultural reuse of effluents is planned.

Reduction of Antibiotic Resistant Bacteria During Conventional and Advanced Wastewater Treatment, and the Disseminated Loads Released to the Environment

The occurrence of new chemical and microbiological contaminants in the aquatic environment has become an issue of increasing environmental concern. Thus, wastewater treatment plants (WWTPs) play an important part in the distribution of so-called new emerging pathogens and antibiotic resistances. Therefore, the daily loads released by the WWTP were calculated including a model system for the distribution of these loads within the receiving water body. UV-, as well as ozone-treatment in separate or in combination for wastewater treatment were under investigation aiming at the reduction of these loads. Here, the impact of these treatments on the DNA integrity via antibody staining and PCR efficiencies experiments were included. All three facultative pathogenic bacteria [enterococci (23S rRNA), Pseudomonas aeruginosa (ecfX), and Escherichia coli (yccT)] and seven clinically relevant antibiotic resistance genes (ARGs) (mecA (methicillin resistance gene), ctx-M32 (β- lactame resistance gene), ermB (erythromycine resistance gene), bla_TEM (β- lactame resistance gene), sul1 (sulfonamide resistance gene), vanA (vancomycin resistance gene), and intI1 (Integrase1 gene) associated with mobile genetic elements were detected in wastewaters. Different reduction efficiencies were analyzed during advanced wastewater treatments. ARGs were still found to be present in the effluents under the parameters of 1.0 g ozone per g dissolved organic carbon (DOC) and 400 J/m², like ctx-M32, ermB, bla_TEM, sul1, and intI1. Especially UV radiation induced thymidine dimerization which was analyzed via antibody mediated detection in the metagenome of the natural wastewater population. These specific DNA alterations were not observed during ozone treatment and combinations of UV/ozone treatment. The dimerization or potential other DNA alterations during UV treatment might be responsible for a decreased PCR efficiency of the 16S rRNA amplicons (176, 490, and 880 bp fragments) from natural metagenomes compared to the untreated sample. This impact on PCR efficiencies was also observed for the combination of ozone and UV treatment.

Metagenomics Reveals the Impact of Wastewater Treatment Plants on the Dispersal of Microorganisms and Genes in Aquatic Sediments

Wastewater treatment plants (WWTPs) release treated effluent containing mobile genetic elements (MGEs), antibiotic resistance genes (ARGs), and microorganisms into the environment, yet little is known about their influence on nearby microbial communities and the retention of these factors in receiving water bodies. Our research aimed to characterize the genes and organisms from two different WWTPs that discharge into Lake Michigan, as well as from surrounding lake sediments to determine the dispersal and fate of these factors with respect to distance from the effluent outfall. Shotgun metagenomics coupled to distance-decay analyses showed a higher abundance of genes identical to those in WWTP effluent genes in sediments closer to outfall sites than in sediments farther away, indicating their possible WWTP origin. We also found genes attributed to organisms, such as those belonging to Helicobacteraceae, Legionellaceae, Moraxellaceae, and Neisseriaceae, in effluent from both WWTPs and decreasing in abundance in lake sediments with increased distance from WWTPs. Moreover, our results showed that the WWTPs likely influence the ARG composition in lake sediments close to the effluent discharge. Many of these ARGs were located on MGEs in both the effluent and sediment samples, indicating a relatively broad propensity for horizontal gene transfer (HGT). Our approach allowed us to specifically link genes to organisms and their genetic context, providing insight into WWTP impacts on natural microbial communities. Overall, our results suggest a substantial influence of wastewater effluent on gene content and microbial community structure in the sediments of receiving water bodies.

IMPORTANCE Wastewater treatment plants (WWTPs) release their effluent into aquatic environments. Although treated, effluent retains many genes and microorganisms that have the potential to influence the receiving water in ways that are poorly understood. Here, we tracked the genetic footprint, including genes specific to antibiotic resistance and mobile genetic elements and their associated organisms, from WWTPs to lake sediments. Our work is novel in that we used metagenomic data sets to comprehensively evaluate total gene content and the genetic and taxonomic context of specific genes in environmental samples putatively impacted by WWTP inputs. Based on two different WWTPs with different treatment processes, our findings point to an influence of WWTPs on the presence, abundance, and composition of these factors in the environment.

Occurrence of antimicrobial agents, drug-resistant bacteria, and genes in the sewage-impacted Vistula River (Poland)

Antimicrobial agents (antimicrobials) are a group of therapeutic and hygienic agents that either kill microorganisms or inhibit their growth. Their occurrence in surface water may reveal harmful effects on aquatic biota and challenge microbial populations. Recently, there is a growing concern over the contamination of surface water with both antimicrobial agents and multidrug-resistant bacteria. The aim of the study was the determination of the presence of selected antimicrobials at specific locations of the Vistula River (Poland), as well as in tap water samples originating from the Warsaw region. Analysis was performed using the liquid chromatography-electrospray ionization-tandem mass spectrometry method. In addition, the occurrence of drug-resistant bacteria and resistance genes was determined using standard procedures. This 2-year study is the first investigation of the simultaneous presence of antimicrobial agents, drug-resistant bacteria, and genes in Polish surface water. In Poland, relatively high concentrations of macrolides are observed in both surface and tap water. Simultaneous to the high macrolide levels in the environment, the presence of the erm B gene, coding the resistance to macrolides, lincosamides, and streptogramin, was detected in almost all sampling sites. Another ubiquitous gene was int1, an element of the 5'-conserved segment of class 1 integrons that encode site-specific integrase. Also, resistant isolates of Enterococcus faecium and Enterococcus faecalis and Gram-negative bacteria were recovered. Multidrug-resistant bacteria isolates of Gram-negative and Enterococcus were also detected. The results show that wastewater treatment plants (WWTP) are the main source of most antimicrobials, resistant bacteria, and genes in the aquatic environment, probably due to partial purification during wastewater treatment processes.

Prevalence of antibiotic resistance genes from effluent of coastal aquaculture, South Korea

The wide use of antibiotics in aquaculture for prophylactic and therapeutic purposes can potentially lead to the prevalence of antibiotic resistance genes (ARGs). This study reports for the first time the profile of ARGs from effluents of coastal aquaculture located in South Jeolla province and Jeju Island, South Korea. Using quantitative PCR (qPCR), twenty-two ARGs encoding tetracycline resistance (tetA, tetB, tetD, tetE, tetG, tetH, tetM, tetQ, tetX, tetZ, tetBP), sulfonamide resistance (sul1, sul2), quinolone resistance (qnrD, qnrS, aac(6')-Ib-cr), β-lactams resistance (bla_TEM, bla_CTX, bla_SHV), macrolide resistance (ermC), florfenicol resistance (floR) and multidrug resistance (oqxA) and a class 1 integrons-integrase gene (intI1) were quantified. In addition, Illumina Miseq sequencing was applied to investigate microbial community differences across fish farm effluents. Results from qPCR showed that the total number of detected ARGs ranged from 4.24 × 10^-3 to 1.46 × 10^-2 copies/16S rRNA gene. Among them, tetB and tetD were predominant, accounting for 74.8%-98.0% of the total ARGs. Furthermore, intI1 gene showed positive correlation with tetB, tetD, tetE, tetH, tetX, tetZ tetQ and sul1. Microbial community analysis revealed potential host bacteria for ARGs and intI1. Two genera, Vibrio and Marinomonas belonging to Gammaproteobacteria, showed significant correlation with tetB and tetD, the most dominant ARGs in all samples. Also, operational taxonomic units (OTUs)-based network analysis revealed that ten OTUs, classified into the phyla Proteobacteria, Cyanobacteria/Chloroplast, Bacteroidetes, Verrucomicrobia and an unclassified phylum, were potential hosts of tetracycline resistance genes (i.e., tetA, tetG, tetH, tetM, tetQ and tetZ). Further systematic monitoring of ARGs is warranted for risk assessment and management of antibacterial resistance from fish farm effluents.

Vancomycin-resistant enterococci with vanA gene in treated municipal wastewater and their association with human hospital strains

Vancomycin-resistant enterococci (VRE) are pathogens of increasing medical importance. In Brno, Czech Republic, we collected 37 samples from the effluent of a wastewater treatment plant (WWTP), 21 surface swabs from hospital settings, and 59 fecal samples from hospitalized patients and staff. Moreover, we collected 284 gull cloacal swabs from the colony situated 35km downstream the WWTP. Samples were cultured selectively. Enterococci were identified using MALDI-TOF MS, phenotypically tested for susceptibility to antibiotics, and by PCR for occurrence of resistance and virulence genes. Pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST) were used to examine genotypic diversity. VRE carrying the vanA gene were found in 32 (86%, n=37) wastewater samples, from which we obtained 49 isolates: Enterococcus faecium (44) and Enterococcus gallinarum (2), Enterococcus casseliflavus (2), and Enterococcus raffinosus (1). From 33 (69%) of 48 inpatient stool samples, we obtained 39 vanA-carrying VRE, which belonged to E. faecium (33 isolates), Enterococcus faecalis (4), and Enterococcus raffinosus (2). Nearly one-third of the samples from hospital surfaces contained VRE with the vanA gene. VRE were not detected among gulls. Sixty-seven (84%, n=80) E. faecium isolates carried virulence genes hyl and/or esp. Virulence of E. faecalis was encoded by gelE, asa1, and cylA genes. A majority of the E. faecium isolates belonged to the clinically important sequence types ST17 (WWTP: 10 isolates; hospital: 4 isolates), ST18 (9;8), and ST78 (5;0). The remaining isolates belonged to ST555 (2;0), ST262 (1;6), ST273 (3;0), ST275 (1;0), ST549 (2;0), ST19 (0;1), ST323 (3;0), and ST884 (7;17). Clinically important enterococci carrying the vanA gene were almost continually detectable in the effluent of the WWTP, indicating insufficient removal of VRE during wastewater treatment and permanent shedding of these antibiotic resistant pathogens into the environment from this source. This represents a risk of their transmission to the environment.

Characterization of Metagenomes in Urban Aquatic Compartments Reveals High Prevalence of Clinically Relevant Antibiotic Resistance Genes in Wastewaters

The dissemination of antimicrobial resistance (AMR) is an escalating problem and a threat to public health. Comparative metagenomics was used to investigate the occurrence of antibiotic resistant genes (ARGs) in wastewater and urban surface water environments in Singapore. Hospital and municipal wastewater (n = 6) were found to have higher diversity and average abundance of ARGs (303 ARG subtypes, 197,816 x/Gb) compared to treated wastewater effluent (n = 2, 58 ARG subtypes, 2,692 x/Gb) and surface water (n = 5, 35 subtypes, 7,985 x/Gb). A cluster analysis showed that the taxonomic composition of wastewaters was highly similar and had a bacterial community composition enriched in gut bacteria (Bacteroides, Faecalibacterium, Bifidobacterium, Blautia, Roseburia, Ruminococcus), the Enterobacteriaceae group (Klebsiella, Aeromonas, Enterobacter) and opportunistic pathogens (Prevotella, Comamonas, Neisseria). Wastewater, treated effluents and surface waters had a shared resistome of 21 ARGs encoding multidrug resistant efflux pumps or resistance to aminoglycoside, macrolide-lincosamide-streptogramins (MLS), quinolones, sulfonamide, and tetracycline resistance which suggests that these genes are wide spread across different environments. Wastewater had a distinctively higher average abundance of clinically relevant, class A beta-lactamase resistant genes (i.e., blaKPC, blaCTX-M, blaSHV, blaTEM). The wastewaters from clinical isolation wards, in particular, had a exceedingly high levels of blaKPC-2 genes (142,200 x/Gb), encoding for carbapenem resistance. Assembled scaffolds (16 and 30 kbp) from isolation ward wastewater samples indicated this gene was located on a Tn3-based transposon (Tn4401), a mobilization element found in Klebsiella pneumonia plasmids. In the longer scaffold, transposable elements were flanked by a toxin-antitoxin (TA) system and other metal resistant genes that likely increase the persistence, fitness and propagation of the plasmid in the bacterial host under conditions of stress. A few bacterial species (Enterobacter cloacae, Klebsiella pneumoniae, Citrobacter freundii, Pseudomonas aeruginosa) that were cultured from the isolation ward wastewaters on CHROMagar media harbored the blaKPC-2 gene. This suggests that hospital wastewaters derived from clinical specialty wards are hotspots for the spread of AMR. Assembled scaffolds of other mobile genetic elements such as IncQ and IncF plasmids bearing quinolone resistance genes (qnrS1, qnrS2) and the class A beta-lactamase gene (blaTEM-1) were recovered in wastewater samples which may aid the transfer of AMR.

Fate of antimicrobial resistance genes in response to application of poultry and swine manure in simulated manure-soil microcosms and manure-pond microcosms

This study aimed to determine the occurrence, abundance, and fate of nine important antimicrobial resistance genes (ARGs) (sul1, sul2, tetB, tetM, ermB, ermF, fexA, cfr, and Intl1) in the simulated soil and pond microcosms following poultry and swine manure application. Absolute quantitative PCR method was used to determine the gene copies. The results were modeled as a logarithmic regression (N = mlnt + b) to explore the fate of target genes. Genes sul1, Intl1, sul2, and tetM had the highest abundance following the application of the two manure types. The logarithmic regression model fitted the results well (R ² values up to 0.99). The reduction rate of all genes (except for the genes fexA and cfr) in manure-pond microcosms was faster than those in manure-soil microcosms. Importantly, sul1, intl1, sul2, and tetM had the lowest reduction rates in all the samples and the low reduction rates of tetM was the first time to be reported. These results indicated that ARG management should focus on using technologies for the ARG elimination before the manure applications rather than waiting for subsequent attenuation in soil or water, particularly the ARGs (such as sul1, intl1, sul2, and tetM investigated in this study) that had high abundance and low reduction rate in the soil and water after application of manure.

Occurrence of the mcr-1 Colistin Resistance Gene and other Clinically Relevant Antibiotic Resistance Genes in Microbial Populations at Different Municipal Wastewater Treatment Plants in Germany

Seven wastewater treatment plants (WWTPs) with different population equivalents and catchment areas were screened for the prevalence of the colistin resistance gene mcr-1 mediating resistance against last resort antibiotic polymyxin E. The abundance of the plasmid-associated mcr-1 gene in total microbial populations during water treatment processes was quantitatively analyzed by qPCR analyses. The presence of the colistin resistance gene was documented for all of the influent wastewater samples of the seven WWTPs. In some cases the mcr-1 resistance gene was also detected in effluent samples of the WWTPs after conventional treatment reaching the aquatic environment. In addition to the occurrence of mcr-1 gene, CTX-M-32, blaTEM, CTX-M, tetM, CMY-2, and ermB genes coding for clinically relevant antibiotic resistances were quantified in higher abundances in all WWTPs effluents. In parallel, the abundances of Acinetobacter baumannii, Klebsiella pneumoniae, and Escherichia coli were quantified via qPCR using specific taxonomic gene markers which were detected in all influent and effluent wastewaters in significant densities. Hence, opportunistic pathogens and clinically relevant antibiotic resistance genes in wastewaters of the analyzed WWTPs bear a risk of dissemination to the aquatic environment. Since many of the antibiotic resistance gene are associated with mobile genetic elements horizontal gene transfer during wastewater treatment can't be excluded.

Association study of multiple antibiotic resistance and virulence: a strategy to assess the extent of risk posed by bacterial population in aquatic environment

The present study explored the association between multiple antibiotic resistance (MAR) index and virulence index to determine what percent of environmental antibiotic-resistant (eARB) bacteria could pose threat as potential pathogen. 16srRNA-based sequencing of 113 non-duplicate isolates identified majority of them to be gram negative belonging to Enterobacter, Pseudomonas, Aeromonas, Proteus, Acinetobacter, and Klebsiella. Statistical comparison of MAR indices of the abovementioned genera indicated differences in the median values among the groups (p < 0.001). Pair-wise multiple comparison by Dunn's method indicated significant difference in MAR indices (p < 0.05), based on which multiple antibiotic resistance phenotype could be ranked in the order Pseudomonas > Klebsiella = Acinetobacter > Proteus > Aeromonas > Enterobacter. Association between MAR index and virulence index revealed that 25% of isolates in the population under study posed high threat to human/animal or both; out of which 75% isolates belonged to genus Pseudomonas. Based on observations of comparative analysis of the six gram-negative genera, it could be concluded that Pseudomonas isolates from environment pose significantly high threat as potential pathogens while Enterobacter isolates posed no threat.

Integrated Evaluation Concept to Assess the Efficacy of Advanced Wastewater Treatment Processes for the Elimination of Micropollutants and Pathogens

A multidisciplinary concept has been developed to compare advanced wastewater treatment processes for their efficacy of eliminating micropollutants and pathogens. The concept is based on (i) the removal/formation of selected indicator substances and their transformation products (TPs), (ii) the assessment of ecotoxicity via in vitro tests, and (iii) the removal of pathogens and antibiotic resistant bacteria. It includes substances passing biological wastewater treatment plants regulated or proposed to be regulated in the European Water Framework Directive, TPs formed in biological processes or during ozonation, agonistic/antagonistic endocrine activities, mutagenic/genotoxic activities, cytotoxic activities, further activities like neurotoxicity as well as antibiotics resistance genes, and taxonomic gene markers for pathogens. At a pilot plant, ozonation of conventionally treated wastewater resulted in the removal of micropollutants and pathogens and the reduction of estrogenic effects, whereas the in vitro mutagenicity increased. Subsequent post-treatment of the ozonated water by granular activated carbon (GAC) significantly reduced the mutagenic effects as well as the concentrations of remaining micropollutants, whereas this was not the case for biofiltration. The results demonstrate the suitability of the evaluation concept to assess processes of advanced wastewater treatment including ozonation and GAC by considering chemical, ecotoxicological, and microbiological parameters.

Growth Behavior of E. coli, Enterococcus and Staphylococcus Species in the Presence and Absence of Sub-inhibitory Antibiotic Concentrations: Consequences for Interpretation of Culture-Based Data

Culture-based approaches are used to monitor, e.g., drinking water or bathing water quality and to investigate species diversity and antibiotic resistance levels in environmental samples. For health risk assessment, it is important to know whether the growing cultures display the actual abundance of, e.g., clinically relevant antibiotic resistance phenotypes such as vancomycin-resistant Enterococcus faecium/Enterococcus faecalis (VRE) or methicillin-resistant Staphylococcus aureus. In addition, it is important to know whether sub-inhibitory antibiotic concentrations, which are present in surface waters, favor the growth of antibiotic-resistant strains. Therefore, clinically relevant bacteria were isolated from different water sources and the growth behavior of 58 Escherichia coli, 71 Enterococcus, and 120 Staphylococcus isolates, belonging to different species and revealing different antibiotic resistance patterns, was studied with respect to "environmental" antibiotic concentrations. The finding that VRE could only be detected after specific enrichment can be explained by their slow growth compared to non-resistant strains. Interpreting their absence in standardized culture-based methods as nonexistent might be a fallacy. Sub-inhibitory antibiotic concentrations that were detected in sewage and receiving river water did not specifically promote antibiotic-resistant strains. Generally, those antibiotics that influenced cell metabolism directly led to slightly reduced growth rates and less than maximal optical densities after 48 h of incubation.

Presence and distribution of Macrolides-Lincosamide-Streptogramin resistance genes and potential indicator ARGs in the university ponds in Guangzhou, China

This study aimed to determine the occurrence, abundance, and variation of seven Macrolides-Lincosamide-Streptogramin (MLS) resistance genes (ereB, ermA, ermB, ermF, mefA, vatB, mphA) and six potential indicator ARGs (tet (B), sul1, qnrS, fexA, IntI1, ermB) from three ponds at university by quantitative PCR and assess the impacts on the surroundings. Solid samples (fish feces, soil and sediment) and water samples were tested. All the genes were found at low levels in soil samples. For the MLS resistance genes, only two MLS genes (ermB, ermF) were detected in all samples and significant correlations between ermB and Σ MLS (R = 0.91 in solid samples; R = 0.86 in water samples, p < 0.01) were found. For the potential indicators, intl1 and sul1 were present at high levels in the three different ponds while the other genes showed varying levels. These findings show that the ermB gene can probably be served as an indicator to evaluate the overall level of MLS resistance genes. The fairly low abundance of all the tested resistance genes in soil samples and the moderate levels in other samples suggests that the university ponds kept a good state and did not have a significant impact on their surroundings.

One step forwards for the routine use of high-throughput DNA sequencing in environmental monitoring. An efficient and standardizable method to maximize the detection of environmental bacteria

We propose an innovative, repeatable, and reliable experimental workflow to concentrate and detect environmental bacteria in drinking water using molecular techniques. We first concentrated bacteria in water samples using tangential flow filtration and then we evaluated two methods of environmental DNA extraction. We performed tests on both artificially contaminated water samples and real drinking water samples. The efficiency of the experimental workflow was measured through qPCR. The successful applicability of the high‐throughput DNA sequencing (HTS) approach was demonstrated on drinking water samples. Our results demonstrate the feasibility of our approach in high‐throughput‐based studies, and we suggest incorporating it in monitoring strategies to have a better representation of the microbial community. In the recent years, HTS techniques have become key tools in the study of microbial communities. To make the leap from academic laboratories to the routine monitoring (e.g., water treatment plants laboratories), we here propose an experimental workflow suitable for the introduction of HTS as a standard method for detecting environmental bacteria.

Diversity of species and antimicrobial resistance determinants of staphylococci in superficial waters in Spain

The objectives were to determine the presence and diversity of staphylococcal species in surface waters in La Rioja region (Spain), and to characterize recovered isolates. Staphylococci were detected in 42 of 47 evaluable samples, and 72 isolates were obtained, of which 13 were coagulase-positive (CoPS) and 59 were coagulase-negative (CoNS). Twelve CoPS were identified as S. aureus and typed as follows (number of strains): t002/t502/ST5 (four), t10668/ST425 (one), t10712//ST1643 (one), t843/ST130 (one), t10855/ST2461 (one), t3369/ST2657 (one), t1166/ST133 (one), t8083/ST2049 (one) and t045/ST2460 (one); and one as S. pseudintermedius ST147. Virulence genes tst, cna and lukS/F-I were detected, and one strain showed the immune evasion cluster type F. Regarding CoNS, 12 different species were recovered (number of strains): S. epidermidis (11), S. vitulinus (10), S. sciuri (nine), S. fleurettii (seven), S. lentus (six), S. simulans (five), S. xylosus (four), S. chromogenes (two), S. hominis (two), and S. equorum, S. succinus and S. warneri (one each). Fourteen CoNS isolates presented a multidrug resistance phenotype, with the following resistance genes: blaZ, mecA, fusB, fusC, erm(C), mph(C), erm(A), msr(A)/(B), mph(C), ant(4')-Ia, tet(K), tet(L), cat_pc194 and str The high diversity of staphylococcal species, as well as multiple resistance and virulence genes, highlights the importance of surface waters as a temporary reservoir and source of transmission.

Concentration of facultative pathogenic bacteria and antibiotic resistance genes during sewage treatment and in receiving rivers

Whereas the hygienic condition of drinking and bathing water by law must be monitored by culture-based methods, for quantification of microbes and antibiotic resistance in soil or the aquatic environment, often molecular genetic assays are used. For comparison of both methods, knowledge of their correlation is necessary. Therefore the population of total bacteria, Escherichia coli, enterococci and staphylococci during sewage treatment and in receiving river water was compared by agar plating and quantitative polymerase chain reaction (qPCR) assays. In parallel, all samples were investigated for clinically relevant antibiotic resistance genes. Whereas plating and qPCR data for total bacteria correlated well in sewage after primary treatment, qPCR data of river water indicated higher cell numbers for E. coli. It is unknown if these cells are 'only' not growing under standard conditions or if they are dead. Corresponding to the amount of non-culturable cells, the 'breakpoints' for monitoring water quality should be adapted. The abundances of clinically relevant antibiotic resistance genes in river water were in the same order of magnitude or even higher than in treated sewage. For estimation of the health risk it is important to investigate which species carry respective genes and whether these genes are disseminated via gene transfer.

Vancomycin-Resistant Enterococci and Bacterial Community Structure following a Sewage Spill into an Aquatic Environment

Sewage spills can release antibiotic-resistant bacteria into surface waters, contributing to environmental reservoirs and potentially impacting human health. Vancomycin-resistant enterococci (VRE) are nosocomial pathogens that have been detected in environmental habitats, including soil, water, and beach sands, as well as wildlife feces. However, VRE harboring vanA genes that confer high-level resistance have infrequently been found outside clinical settings in the United States. This study found culturable Enterococcus faecium harboring the vanA gene in water and sediment for up to 3 days after a sewage spill, and the quantitative PCR (qPCR) signal for vanA persisted for an additional week. Culturable levels of enterococci in water exceeded recreational water guidelines for 2 weeks following the spill, declining about five orders of magnitude in sediments and two orders of magnitude in the water column over 6 weeks. Analysis of bacterial taxa via 16S rRNA gene sequencing showed changes in community structure through time following the sewage spill in sediment and water. The spread of opportunistic pathogens harboring high-level vancomycin resistance genes beyond hospitals and into the broader community and associated habitats is a potential threat to public health, requiring further studies that examine the persistence, occurrence, and survival of VRE in different environmental matrices.

IMPORTANCE

Vancomycin-resistant enterococci (VRE) are harmful bacteria that are resistant to the powerful antibiotic vancomycin, which is used as a last resort against many infections. This study followed the release of VRE in a major sewage spill and their persistence over time. Such events can act as a means of spreading vancomycin-resistant bacteria in the environment, which can eventually impact human health.

Detection of Antibiotic Resistance Genes in Source and Drinking Water Samples from a First Nations Community in Canada

Access to safe drinking water is now recognized as a human right by the United Nations. In developed countries like Canada, access to clean water is generally not a matter of concern. However, one in every five First Nations reserves is under a drinking water advisory, often due to unacceptable microbiological quality. In this study, we analyzed source and potable water from a First Nations community for the presence of coliform bacteria as well as various antibiotic resistance genes. Samples, including those from drinking water sources, were found to be positive for various antibiotic resistance genes, namely, ampC, tet(A), mecA, β-lactamase genes (SHV-type, TEM-type, CTX-M-type, OXA-1, and CMY-2-type), and carbapenemase genes (KPC, IMP, VIM, NDM, GES, and OXA-48 genes). Not surprisingly, substantial numbers of total coliforms, including Escherichia coli, were recovered from these samples, and this result was also confirmed using Illumina sequencing of the 16S rRNA gene. These findings deserve further attention, as the presence of coliforms and antibiotic resistance genes potentially puts the health of the community members at risk.

IMPORTANCE

In this study, we highlight the poor microbiological quality of drinking water in a First Nations community in Canada. We examined the coliform load as well as the presence of antibiotic resistance genes in these samples. This study examined the presence of antibiotic-resistant genes in drinking water samples from a First Nations Community in Canada. We believe that our findings are of considerable significance, since the issue of poor water quality in First Nations communities in Canada is often ignored, and our findings will help shed some light on this important issue.

Ozone treatment of conditioned wastewater selects antibiotic resistance genes, opportunistic bacteria, and induce strong population shifts

An ozone treatment system was investigated to analyze its impact on clinically relevant antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs). A concentration of 0.9±0.1g ozone per 1g DOC was used to treat conventional clarified wastewater. PCR, qPCR analyses, Illumina 16S Amplicon Sequencing, and PCR-DGGE revealed diverse patterns of resistances and susceptibilities of opportunistic bacteria and accumulations of some ARGs after ozone treatment. Molecular marker genes for enterococci indicated a high susceptibility to ozone. Although they were reduced by almost 99%, they were still present in the bacterial population after ozone treatment. In contrast to this, Pseudomonas aeruginosa displayed only minor changes in abundance after ozone treatment. This indicated different mechanisms of microorganisms to cope with the bactericidal effects of ozone. The investigated ARGs demonstrated an even more diverse pattern. After ozone treatment, the erythromycin resistance gene (ermB) was reduced by 2 orders of magnitude, but simultaneously, the abundance of two other clinically relevant ARGs increased within the surviving wastewater population (vanA, blaVIM). PCR-DGGE analysis and 16S-Amplicon-Sequencing confirmed a selection-like process in combination with a substantial diversity loss within the vital wastewater population after ozone treatment. Especially the PCR-DGGE results demonstrated the survival of GC-rich bacteria after ozone treatment.

Seasonality of antibiotic prescriptions for outpatients and resistance genes in sewers and wastewater treatment plant outflow

To test the hypothesis of a seasonal relationship of antibiotic prescriptions for outpatients and the abundance of antibiotic resistance genes (ARGs) in the wastewater, we investigated the distribution of prescriptions and different ARGs in the Dresden sewer system and wastewater treatment plant during a two-year sampling campaign. Based on quantitative PCR (qPCR), our results show a clear seasonal pattern for relative ARGs abundances. The higher ARGs levels in autumn and winter coincide with the higher rates of overall antibiotic prescriptions. While no significant differences of relative abundances were observed before and after the wastewater treatment for most of the relative ARGs, the treatment clearly influenced the microbial community composition and abundance. This indicates that the ARGs are probably not part of the dominant bacterial taxa, which are mainly influenced by the wastewater treatment processes, or that plasmid carrying bacteria remain constant, while plasmid free bacteria decrease. An exception was vancomycin (vanA), showing higher relative abundance in treated wastewater. It is likely that a positive selection or community changes during wastewater treatment lead to an enrichment of vanA. Our results demonstrate that in a medium-term study the combination of qPCR and next generation sequencing corroborated by drug-related health data is a suitable approach to characterize seasonal changes of ARGs in wastewater and treated wastewater.