Fate and Persistence of a Pathogenic NDM-1-Positive Escherichia coli Strain in Anaerobic and Aerobic Sludge Microcosms

Aeromonas isolation reveals this genus's contribution to antimicrobial resistance fluxes across the wastewater-treated water-river interface

AIM

Aeromonas spp. are common members of water and wastewater microbiomes, but some are listed as opportunistic pathogens and are often reported to carry antimicrobial resistance (AMR) genes. We aimed to assess the performance of isolation media for capturing their distribution and their role in AMR dissemination into aquatic environments.

METHODS AND RESULTS

We investigated the abundance, diversity, and AMR profile of Aeromonas isolates from wastewater and receiving water bodies at five municipal wastewater treatment plants in Denmark using three isolation media. This was then compared with the diversity estimated from community-wide 16S rRNA gene amplicon sequencing and resistance patterns inferred from high-throughput qPCR of resistance genes. Isolates from ampicillin sheep blood agar were the most phylogenetically diverse, but the overall Aeromonas recovery on the three media was similarly good and matched the dominant amplicon sequence variants. While the dominant phylotypes were ubiquitous, some types were only detected in treated wastewater and the receiving rivers. The resistance prevalence was moderate and mostly to beta-lactams and tetracyclines. Isolates resistant to piperacilin-tazobactam, cefepime, and tetracycline downstream of the plants were linked to wastewater origin.

CONCLUSION

Overall, our work demonstrates Aeromonas and Aeromonas-mediated AMR fluxes at the wastewater/environment interfaces and provides methodological bases for monitoring aeromonads in wastewater and surface waters.

Assessing the additional health burden of antibiotic resistant Enterobacteriaceae in surface waters through an integrated QMRA and DALY approach

Antibiotic resistant Enterobacteriaceae pose a significant threat to public health. However, limited studies have evaluated the health risks associated with exposure to antibiotic-resistant bacteria (ARB), especially in natural environments. While quantitative microbial risk assessment (QMRA) assesses microbial risks in terms of the probability of infection, it does not account for the severity of health outcomes. In this study, a QMRA-DALY model was developed to integrate QMRA with health burden (disability-adjusted life years (DALY)) from infections caused by ARB. The model considers uncertainties in probability of infection and health burden assessment using Monte Carlo simulations. The study collected antimicrobial resistance (AMR) surveillance data from surface waters with different land uses. Results revealed water bodies with agricultural land use to be the main AMR hotspots, with the highest additional health burden observed in infections caused by meropenem-resistant E. coli (∆DALY = 0.0105 DALY/event) compared to antibiotic-susceptible E. coli. The estimated ∆DALY for antibiotic-resistant K. pneumoniae was lower than for antibiotic-resistant E. coli (highest ∆DALY = 0.00048 DALY/event). The study highlights the need for better evaluation of AMR associated health burden, and effective measures to mitigate the risks associated with antibiotic-resistant bacteria in natural environments.

Inactivation of a pathogenic NDM-1-positive Escherichia coli strain and the resistance gene blaNDM-1 by TiO2/UVA photocatalysis

Proliferation of bla_NDM-1 in water and wastewater is particularly concerning because of multidrug-resistance and horizontal transfer of the gene. In the present study, a pathogenic NDM-1-positive Escherichia coli strain (named E. coli NDM-1) and the bla_NDM-1 gene were treated with titanium dioxide (TiO₂)/ultraviolet A (UVA) photocatalysis. Effects of catalyst dose, UVA intensity, and phosphate on bacteria and intracellular and extracellular bla_NDM-1 genes were determined. With increases in TiO₂ dose and UVA intensity, the inactivation rate of E. coli NDM-1 increased greatly in saline solution. However, phosphate in water hindered adsorption of bacteria to TiO₂ and partly changed the TiO₂ photocatalytic pathway, resulting in low degradation efficiency. Although inactivation of E. coli NDM-1 was highly efficient, TiO₂/UVA photocatalysis had little effect on removal of the bla_NDM-1 gene. During the 2-h photocatalytic experiments, E. coli cells decreased by 4.7-log, while the bla_NDM-1 gene decreased by 0.7- ~ 1.5-log. Moreover, the degradation rate of extracellular bla_NDM-1 was ~2.7 times higher than that of intracellular genes. Abundance and transformation frequency of residual bla_NDM-1 genes remained high, even when bacteria were completely inactivated, indicating potential health risks. Increases in treatment time and UVA irradiation intensity are needed to remove the bla_NDM-1 gene to sufficiently low levels.

The physiological and ecological properties of bacterial persisters discovered from municipal sewage sludge and the potential risk

Bacterial persisters are a special microbial population and are considered to be the bacterial reservoir of antibiotic-resistant bacteria. They can survive antibiotic treatment even in high concentrations of antibiotics and revive in the appropriate conditions. However, the characteristics of bacterial persisters in the municipal sewage sludge and their potential environmental risks have not yet been paid much attention to. In this study, bacterial persisters were discovered from the sludge of wastewater treatment plants in four different regions (Jilin, Lhasa, Shenzhen, and Yili), and the metagenomic analysis confirmed that bacterial persisters were ubiquitous in all four municipal sewage sludge and positively related to the protobacterium populations. At the taxonomic genus level, a total of 57 genera of bacterial persisters were shared by the four sewage sludge, and the genera with abundance exceeding 2% were Acinetobacter, Lysinibacillus, Aeromonas, Brevundimonas, Pseudomonas, and Alcaligenes, among which Acinetobacter accounted for 57.24%. Genus Lysinibacillus and Aeromonas were significant in Jilin and Lhasa, respectively. The persistence mechanism of bacterial persisters derived from sludge was also clarified, among which, Aeromonas, Brevundimonas, and Alcaligenes rely on the hipBA toxin-antitoxin system, while Acinetobacter enters the persistence state mainly through the stringent response system based on (p)ppGpp. Moreover, it was found that a typical bacterial persister originated from Acinetobacter, named T9-9, could tolerate a variety of antibiotics, such as 1000 μg/mL of kanamycin, 160 μg/mL of tetracycline, and 30 μg/mL of ciprofloxacin. Even if the ultraviolet intensity was 6-36 times the usual dosage of ultraviolet disinfection in wastewater treatment plants, it could not completely kill T9-9, but the killing efficiency by chlorine disinfection technology could reach 100%. This study pointed out an environmental risk of bacterial persisters that existed in sewage sludge that had been neglected and strongly recommended to improve the disinfection process in the wastewater treatment plant.

Escherichia coli Capacity to Repopulate Microcosms Under Osmotic/U.V. Synergic Stress in Tropical Waters

In both Brazilian and European regulations, the impact assessment of sewage discharges into coastal waters is based on microbiological analyses of fecal indicators such as Escherichia coli, frequently used in prevision hydrodynamic models. However, the decay rates of E. coli vary depending on environmental conditions, and analysis may lead to inaccurate conclusions. This study aimed to analyze the decay of culturable and viable (but not culturable) E. coli in outdoor conditions, by creating microcosms inoculated with pre-treated sewage. The microcosms were filled with 9.88 L of filtered water (0.22 μm membrane), 3.5% salt, 0.1-0.2% BHI, and 1% bacterial suspension obtained by reverse filtration. PMA-qPCR of E. coli uidA gene and Colilert measurements were applied to evaluate population counts after 2 h, 4 h, and 26 h. After nine hours of exposure to solar radiation, the viable cells decreased to 2.76% (interpolated value) of the initial population, and the cultivable fraction of the viable population accounted for 0.50%. In the dark period, the bacteria grew again, and viable cells reached 8.54%, while cultivable cells grew to 48.14% of initial population. This behavior is possibly due to the use of nutrients recycled from dead cells. Likewise, populations of E. coli in sewage outfalls remain viable in the sediments, where resuspension can renew blooming.

A Quantitative Survey of Bacterial Persistence in the Presence of Antibiotics: Towards Antipersister Antimicrobial Discovery

Background: Bacterial persistence to antibiotics relates to the phenotypic ability to survive lethal concentrations of otherwise bactericidal antibiotics. The quantitative nature of the time-kill assay, which is the sector's standard for the study of antibiotic bacterial persistence, is an invaluable asset for global, unbiased, and cross-species analyses. Methods: We compiled the results of antibiotic persistence from antibiotic-sensitive bacteria during planktonic growth. The data were extracted from a sample of 187 publications over the last 50 years. The antibiotics used in this compilation were also compared in terms of structural similarity to fluorescent molecules known to accumulate in Escherichia coli. Results: We reviewed in detail data from 54 antibiotics and 36 bacterial species. Persistence varies widely as a function of the type of antibiotic (membrane-active antibiotics admit the fewest), the nature of the growth phase and medium (persistence is less common in exponential phase and rich media), and the Gram staining of the target organism (persistence is more common in Gram positives). Some antibiotics bear strong structural similarity to fluorophores known to be taken up by E. coli, potentially allowing competitive assays. Some antibiotics also, paradoxically, seem to allow more persisters at higher antibiotic concentrations. Conclusions: We consolidated an actionable knowledge base to support a rational development of antipersister antimicrobials. Persistence is seen as a step on the pathway to antimicrobial resistance, and we found no organisms that failed to exhibit it. Novel antibiotics need to have antipersister activity. Discovery strategies should include persister-specific approaches that could find antibiotics that preferably target the membrane structure and permeability of slow-growing cells.

Prevalence of Potentially Pathogenic Antibiotic-Resistant Aeromonas spp. in Treated Urban Wastewater Effluents versus Recipient Riverine Populations: a 3-Year Comparative Study

Antibiotic resistance continues to be an emerging threat both in clinical and environmental settings. Among the many causes, the impact of postchlorinated human wastewater on antibiotic resistance has not been well studied. Our study compared antibiotic susceptibility among Aeromonas spp. in postchlorinated effluents to that of the recipient riverine populations for three consecutive years against 12 antibiotics. Aeromonas veronii and Aeromonas hydrophila predominated among both aquatic environments, although greater species diversity was evident in treated wastewater. Overall, treated wastewater contained a higher prevalence of nalidixic acid-, trimethoprim-sulfamethoxazole (SXT)-, and tetracycline-resistant isolates, as well as multidrug-resistant (MDR) isolates compared to upstream surface water. After selecting for tetracycline-resistant strains, 34.8% of wastewater isolates compared to 8.3% of surface water isolates were multidrug resistant, with nalidixic acid, streptomycin, and SXT being the most common. Among tetracycline-resistant isolates, efflux pump genes tetE and tetA were the most prevalent, though stronger resistance correlated with tetA. Over 50% of river and treated wastewater isolates exhibited cytotoxicity that was significantly correlated with serine protease activity, suggesting many MDR strains from effluent have the potential to be pathogenic. These findings highlight that conventionally treated wastewater remains a reservoir of resistant, potentially pathogenic bacterial populations being introduced into aquatic systems that could pose a threat to both the environment and public health.IMPORTANCE Aeromonads are Gram-negative, asporogenous rod-shaped bacteria that are autochthonous in fresh and brackish waters. Their pathogenic nature in poikilotherms and mammals, including humans, pose serious environmental and public health concerns especially with rising levels of antibiotic resistance. Wastewater treatment facilities serve as major reservoirs for the dissemination of antibiotic resistance genes (ARGs) and resistant bacterial populations and are, thus, a potential major contributor to resistant populations in aquatic ecosystems. However, few longitudinal studies exist analyzing resistance among human wastewater effluents and their recipient aquatic environments. In this study, considering their ubiquitous nature in aquatic environments, we used Aeromonas spp. as bacterial indicators of environmental antimicrobial resistance, comparing it to that in postchlorinated wastewater effluents over 3 years. Furthermore, we assessed the potential of these resistant populations to be pathogenic, thus elaborating on their potential public health threat.

Viability-based quantification of antibiotic resistance genes and human fecal markers in wastewater effluent and receiving waters

Antibiotic resistance is a public health issue with links to environmental sources of antibiotic resistance genes (ARGs). ARGs from nonviable sources may pose a hazard given the potential for transformation whereas ARGs in viable sources may proliferate during host growth or conjugation. In this study, ARGs in the effluent from three municipal wastewater treatment plants (WWTPs) and the receiving surface waters were investigated using a viability-based qPCR technique (vPCR) with propidium monoazide (PMA). ARGs sul1, tet(G), and bla_TEM, fecal indicator marker BacHum, and 16S rRNA gene copies/mL were found to be significantly lower in viable-cells than in total concentrations for WWTP effluent. Viable-cell and total gene copy concentrations were similar in downstream samples except for tet(G). Differences with respect to season in the prevalence of nonviable ARGs in surface water or WWTP effluent were not observed. The results of this study indicate that qPCR may overestimate viable-cell ARGs and fecal indicator genes in WWTP effluent but not necessarily in the surface water >1.8 km downstream.

Fate of Antibiotic Resistant Pseudomonas putida and Broad Host Range Plasmid in Natural Soil Microcosms

Plasmid conjugation is one of the dominant mechanisms of horizontal gene transfer, playing a noticeable role in the rapid spread of antibiotic resistance genes (ARGs). Broad host range plasmids are known to transfer to diverse bacteria in extracted soil bacterial communities when evaluated by filter mating incubation. However, the persistence and dissemination of broad range plasmid in natural soil has not been well studied. In this study, Pseudomonas putida with a conjugative antibiotic resistance plasmid RP4 was inoculated into a soil microcosm, the fate and persistence of P. putida and RP4 were monitored by quantitative PCR. The concentrations of P. putida and RP4 both rapidly decreased within 15-day incubation. P. putida then decayed at a significantly lower rate during subsequent incubation, however, no further decay of RP4 was observed, resulting in an elevated RP4/P. putida ratio (up to 10) after 75-day incubation, which implied potential transfer of RP4 to soil microbiota. We further sorted RP4 recipient bacteria from the soil microcosms by fluorescence-activated cell sorting. Spread of RP4 increased during 75-day microcosm operation and was estimated at around 10^-4 transconjugants per recipient at the end of incubation. Analysis of 16S rRNA gene sequences of transconjugants showed that host bacteria of RP4 were affiliated to more than 15 phyla, with increased diversity and shift in the composition of host bacteria. Proteobacteria was the most dominant phylum in the transconjugant pools. Transient transfer of RP4 to some host bacteria was observed. These results emphasize the prolonged persistence of P. putida and RP4 in natural soil microcosms, and highlight the potential risks of increased spread potential of plasmid and broader range of host bacteria in disseminating ARGs in soil.

Bacteriophages To Sensitize a Pathogenic New Delhi Metallo β-Lactamase-Positive Escherichia coli to Solar Disinfection

Bacteriophages active against a New Delhi metallo beta lactamase (NDM)-positive E. coli PI-7 were isolated from municipal wastewater and tested for their lytic effect against the bacterial host. Bacteriophages were highly specific to E. coli PI-7 when tested for host-range. After determining host-specificity, bacteriophages were tested for their ability to sensitize E. coli PI-7 to solar irradiation. Solar irradiation coupled with bacteriophages successfully reduced the length of the lag-phase for E. coli PI-7 from 4 h to 2 h in buffer solution. The reduction of lag-phase length was also observed in filtered wastewater effluent and chlorinated effluent. Previously, we found through gene expression analysis that cell wall, oxidative stress, and DNA repair functions played a large role in protecting E. coli PI-7 against solar damage. Here, gene expression analysis of bacteriophage-supplemented solar-irradiated E. coli PI-7 revealed downregulation of cell wall functions. Downregulation of functions implicated in scavenging and detoxifying reactive oxygen species, as well as DNA repair genes, was also observed in bacteriophage-supplemented solar-irradiated E. coli PI-7. Moreover, solar irradiation activates recA, which can induce lytic activity of bacteriophages. Overall, the combined treatment led to gene responses that appeared to make E. coli PI-7 more susceptible to solar disinfection and bacteriophage infection. Our findings suggest that bacteriophages show good potential to be used as a biocontrol tool to complement solar irradiation in mitigating the persistence of antibiotic-resistant bacteria in reuse waters.

Responses and successions of sulfonamides, tetracyclines and fluoroquinolones resistance genes and bacterial community during the short-term storage of biogas residue and organic manure under the incubator and natural conditions

Biogas residue and organic manure are frequently used for crop planting. However, the evaluation of antibiotic resistant bacteria (ARB), antibiotic resistance genes (ARGs) and bacterial community before their applications to fields is still lacking. This study monitored the variations of bacteria resistant to sulfadiazine, tetracycline and norfloxacin, 57 resistance genes for sulfonamides, tetracyclines and fluoroquinolones as well as the bacterial community during the 28-day aerobic storage of biogas residue and organic manure by using viable plate counts, high-throughput qPCR and Illumina MiSeq sequencing methods. Then two storage conditions, incubator (25 °C) and natural environment, were used to assess the responses of ARB and ARGs to the environmental factors. Results showed that a total of 35 and 21 ARGs were detected in biogas residue and organic manure, respectively. ARB and ARGs were enriched up to 8.01-fold in biogas residue after the 28-day storage, but varied in a narrow range during the storage of organic manure. Compared with the incubator condition, the proliferation of ARB and ARGs in biogas residue under the natural condition was relatively inhibited by the varied and complicated environmental factors. However, we found that there was no significant difference of ARB and ARGs in organic manure between the incubator and natural conditions. Bacterial community was also shifted during the storage of biogas residue, especially Bacteroidetes_VC2.1_Bac22, Aequorivita, Luteimonas and Arenimonas. Network analysis revealed that the relationship in biogas residue was much more complicated than that in organic manure, which ultimately resulted in large successions of ARB and ARGs during the short-term storage of biogas residue. Therefore, we suggest that further measures should be taken before the application of biogas residue to fields.

Removal of Antibiotic-Resistant Bacteria and Antibiotic Resistance Genes Affected by Varying Degrees of Fouling on Anaerobic Microfiltration Membranes

An anaerobic membrane bioreactor was retrofitted with polyvinylidene fluoride (PVDF) microfiltration membrane units, each of which was fouled to a different extent. The membranes with different degrees of fouling were evaluated for their efficiencies in removing three antibiotic-resistant bacteria (ARB), namely, bla_NDM-1-positive Escherichia coli PI-7, bla_CTX-M-15-positive Klebsiella pneumoniae L7, and bla_OXA-48-positive E. coli UPEC-RIY-4, as well as their associated plasmid-borne antibiotic resistance genes (ARGs). The results showed that the log removal values (LRVs) of ARGs correlated positively with the extent of membrane fouling and ranged from 1.9 to 3.9. New membranes with a minimal foulant layer could remove more than 5 log units of ARB. However, as the membranes progressed to subcritical fouling, the LRVs of ARB decreased at increasing operating transmembrane pressures (TMPs). The LRV recovered back to 5 when the membrane was critically fouled, and the achieved LRV remained stable at different operating TMPs. Furthermore, characterization of the surface attributed the removal of both the ARB and ARGs to adsorption, which was facilitated by an increasing hydrophobicity and a decreasing surface ζ potential as the membranes fouled. Our results indicate that both the TMP and the foulant layer synergistically affected ARB removal, but the foulant layer was the main factor that contributed to ARG removal.

Anaerobic Membrane Bioreactor Effluent Reuse: A Review of Microbial Safety Concerns

Broad and increasing interest in sustainable wastewater treatment has led a paradigm shift towards more efficient means of treatment system operation. A key aspect of improving overall sustainability is the potential for direct wastewater effluent reuse. Anaerobic membrane bioreactors (AnMBRs) have been identified as an attractive option for producing high quality and nutrient-rich effluents during the treatment of municipal wastewaters. The introduction of direct effluent reuse does, however, raise several safety concerns related to its application. Among those concerns are the microbial threats associated with pathogenic bacteria as well as the emerging issues associated with antibiotic-resistant bacteria and the potential for proliferation of antibiotic resistance genes. Although there is substantial research evaluating these topics from the perspectives of anaerobic digestion and membrane bioreactors separately, little is known regarding how AnMBR systems can contribute to pathogen and antibiotic resistance removal and propagation in wastewater effluents. The aim of this review is to provide a current assessment of existing literature on anaerobic and membrane-based treatment systems as they relate to these microbial safety issues and utilize this assessment to identify areas of potential future research to evaluate the suitability of AnMBRs for direct effluent reuse.