The Role of Urban Wastewater in the Environmental Transmission of Antimicrobial Resistance: The Current Situation in Italy (2010-2019)

Comparative Genomics and Characterization of Shigella flexneri Isolated from Urban Wastewater

Shigella species are a group of highly transmissible Gram-negative pathogens. Increasing reports of infection with extensively drug-resistant varieties of this stomach bug has convinced the World Health Organization to prioritize Shigella for novel therapeutic interventions. We herein coupled the whole-genome sequencing of a natural isolate of Shigella flexneri with a pangenome ana-lysis to characterize pathogen genomics within this species, which will provide us with an insight into its existing genomic diversity and highlight the root causes behind the emergence of quick vaccine escape variants. The isolated novel strain of S. flexneri contained ~4,500 protein-coding genes, 57 of which imparted resistance to antibiotics. A comparative pan-genomic ana-lysis revealed genomic variability of ~64%, the shared conservation of core genes in central metabolic processes, and the enrichment of unique/accessory genes in virulence and defense mechanisms that contributed to much of the observed antimicrobial resistance (AMR). A pathway ana-lysis of the core genome mapped 22 genes to 2 antimicrobial resistance pathways, with the bulk coding for multidrug efflux pumps and two component regulatory systems that are considered to work synergistically towards the development of resistance phenotypes. The prospective evolvability of Shigella species as witnessed by the marked difference in genomic content, the strain-specific essentiality of unique/accessory genes, and the inclusion of a potent resistance mechanism within the core genome, strengthens the possibility of novel serotypes emerging in the near future and emphasizes the importance of tracking down genomic diversity in drug/vaccine design and AMR governance.

Antibiotic Resistance in Metal-Tolerant Microorganisms from Treatment Facilities

The study examines the antibiotic resistance of metal-tolerant bacteria isolated from the wastewater treatment plant of a large city to six antibiotics belonging to the β-lactam antibiotics, aminoglycosides and amphenicols. Resistance of bacteria from sewage sludge multitolerant to heavy metals to 18 antibiotics of the β-lactam antibiotics, tetracyclines, aminoglycosides, diaminopyrimidines, amphenicols and ansamycins was studied also. Out of 10, the metal-tolerant microorganisms isolated from wastewater treatment facilities only the Klebsiella pneumonia strain (tolerant to 3 mM Cu) from the sludge of a secondary settling tank did not show resistance to the studied antibiotics at the concentrations considered. Resistance to the maximum amount of antibiotics was typical for strains Serratia fonticola SS0-1, isolated from fresh sewage sludge and resistant to 5 mmol Cu and 3 mmol Pb, or Stenotrophomonas maltophilia SS0-5, also isolated from fresh sludge and resistant to 3 mmol Zn and Cu. It is possible that bacterial resistance to antibiotics develops not only as a result of the use of antibiotics themselves, but also as a result of environmental pollution with heavy metals, and vice versa.

Metagenomic insight into the prevalence and driving forces of antibiotic resistance genes in the whole process of three full-scale wastewater treatment plants

The spread of antibiotic resistance genes (ARGs) is an emerging global health concern, and wastewater treatment plants (WWTPs), as an essential carrier for the occurrence and transmission of ARGs, deserves more attention. Based on the Illumina NovaSeq high-throughput sequencing platform, this study conducted a metagenomic analysis of 18 samples from three full-scale WWTPs to explore the fate of ARGs in the whole process (influent, biochemical treatment, advanced treatment, and effluent) of wastewater treatment. Total 70 ARG subtypes were detected, among which multidrug, aminoglycoside, tetracycline, and macrolide ARGs were most abundant. The different treatment processes used for three WWTPs were capable of reducing ARG diversity, but did not significantly reduce ARG abundance. Compared to that by denitrification filters, the membrane bioreactor (MBR) process was advantageous in controlling the prevalence of multidrug ARGs in WWTPs. Linear discriminant analysis Effect Size (LEfSe) suggested g_Nitrospira, g_Curvibacter, and g_Mycobacterium as the key bacteria responsible for differential ARG prevalence among different WWTPs. Meanwhile, adeF, sul1, and mtrA were the persistent antibiotic resistance genes (PARGs) and played dominant roles in the prevalence of ARGs. Proteobacteria and Actinobacteria were the host bacteria of majority ARGs in WWTPs, while Pseudomonas and Nitrospira were the most crucial host bacteria influencing the dissemination of critical ARGs (e.g., adeF). In addition, microbial richness was determined to be the decisive factor affecting the diversity and abundance of ARGs in wastewater treatment processes. Overall, regulating the abundance of microorganisms and key host bacteria by selecting processes with microbial interception, such as MBR process, may be beneficial to control the prevalence of ARGs in WWTPs.

Antimicrobial Susceptibility of Commensal E. coli Isolated from Wild Birds in Umbria (Central Italy)

The role of wildlife, including birds, in antimicrobial resistance is nowadays a speculative topic for the scientific community as they could be spreaders/sources of antimicrobial resistance genes. In this respect, we aimed to investigate the antimicrobial susceptibility of 100 commensal Escherichia coli strains, isolated from wild birds from an Umbrian rescue centre and admitted to the Veterinary Teaching Hospital of Perugia (Central Italy) mainly for traumatic injuries. The possible presence of Salmonella spp. and ESBL-producing E. coli was also estimated. The highest prevalence of resistance was observed for ampicillin (85%) and amoxicillin/clavulanic acid (47%), probably due to their extensive use in human and veterinary medicine. Seventeen out of the one hundred E. coli isolates (17%) displayed a multidrug-resistance profile, including the beta-lactam category, with the most common resistance patterns to three or four classes of antibiotics. Resistance to ciprofloxacin, cefotaxime and ceftazidime exhibited values of 18%, 17% and 15%, respectively. Eight out of the hundred E. coli isolates (8%) were ESBL and seven showed multidrug resistance profiles. Salmonella spp. was not isolated. Resistance to third-generation cephalosporins, also detected in long-distance migratory birds, suggests the need for monitoring studies to define the role of wild birds in antimicrobial resistance circuits.

Antimicrobial Peptides Therapy: An Emerging Alternative for Treating Drug-Resistant Bacteria

Microbial resistance to antibiotics is an ancient and dynamic issue that has brought a situation reminiscent of the pre-antibiotic era to the limelight. Currently, antibiotic resistance and the associated infections are widespread and pose significant global health and economic burden. Thus, the misuse of antibiotics, which has increased resistance, has necessitated the search for alternative therapeutic agents for combating resistant pathogens. Antimicrobial peptides (AMPs) hold promise as a viable therapeutic approach against drug-resistant pathogens. AMPs are oligopeptides with low molecular weight. They have broad-spectrum antimicrobial activities against pathogenic microorganisms. AMPs are nonspecific and target components of microbes that facilitate immune response by acting as the first-line defense mechanisms against invading pathogenic microbes. The diversity and potency of AMPs make them good candidates for alternative use. They could be used alone or in combination with several other biomaterials for improved therapeutic activity. They can also be employed in vaccine production targeting drug-resistant pathogens. This review covers the opportunities and advances in AMP discovery and development targeting antimicrobial resistance (AMR) bacteria. Briefly, it presents an overview of the global burden of the antimicrobial resistance crisis, portraying the global magnitude, challenges, and consequences. After that, it critically and comprehensively evaluates the potential roles of AMPs in addressing the AMR crisis, highlighting the major potentials and prospects.

Exploring the microbiome, antibiotic resistance genes, mobile genetic element, and potential resistant pathogens in municipal wastewater treatment plants in Brazil

Wastewater treatment plants (WWTPs) have been widely investigated in Europe, Asia and North America regarding the occurrence and fate of antibiotic resistance (AR) elements, such as antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and antibiotic resistant bacteria and pathogens. However, monitoring data about AR elements in municipal WWTPs in Brazil are scarce. This study investigated the abundance of intI1, five ARGs (sul1, tetA, blaTEM, ermB and qnrB) and 16S rRNA in raw and treated wastewater of three WWTPs, using different sewage treatments named CAS (Conventional activated sludge), UASB/BTF (UASB followed by biological trickling filter) and MAS/UV (modified activated sludge with UV disinfection stage). Bacterial diversity and the presence of potentially pathogenic groups were also evaluated, and associations between genetic markers and the bacterial populations were presented. All WWTPs decreased the loads of genetic markers finally discharged to receiving water bodies and showed no evidence of being hotspots for antimicrobial resistance amplification in wastewater, since the abundances of intI1 and ARGs within the bacterial population were not increased in the treated effluents. UASB/BTF showed a similar performance to that of the CAS and MAS/UV, reinforcing the sanitary and environmental advantages of this biological treatment, widely applied for wastewater treatment in warm climate regions. Bacterial diversity and richness increased after treatments, and bacterial communities in wastewater samples differed due to catchment areas and treatment typologies. Potential pathogenic population underwent considerable decrease after the treatments; however, strong significant correlations with intI1 and ARGs revealed potential multidrug-resistant pathogenic bacteria (Aeromonas, Arcobacter, Enterobacter, Escherichia-Shigella, Stenotrophomonas and Streptococcus) in the treated effluents, although in reduced relative abundances. These are contributive results for understanding the fate of ARGs, MGEs and potential pathogenic bacteria after wastewater treatments, which might support actions to mitigate their release into Brazilian aquatic environments in the near future.

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

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

Review of Antimicrobial Resistance in Wastewater in Japan: Current Challenges and Future Perspectives

Antimicrobial resistance (AMR) circulates through humans, animals, and the environments, requiring a One Health approach. Recently, urban sewage has increasingly been suggested as a hotspot for AMR even in high-income countries (HICs), where the water sanitation and hygiene infrastructure are well-developed. To understand the current status of AMR in wastewater in a HIC, we reviewed the epidemiological studies on AMR in the sewage environment in Japan from the published literature. Our review showed that a wide variety of clinically important antibiotic-resistant bacteria (ARB), antibiotic resistance genes (ARGs), and antimicrobial residues are present in human wastewater in Japan. Their concentrations are lower than in low- and middle-income countries (LMICs) and are further reduced by sewage treatment plants (STPs) before discharge. Nevertheless, the remaining ARB and ARGs could be an important source of AMR contamination in river water. Furthermore, hospital effluence may be an important reservoir of clinically important ARB. The high concentration of antimicrobial agents commonly prescribed in Japan may contribute to the selection and dissemination of AMR within wastewater. Our review shows the importance of both monitoring for AMR and antimicrobials in human wastewater and efforts to reduce their contamination load in wastewater.

The Geological Characteristics of the Vadose Zone Influence the Impact of Treated Wastewater on the Groundwater Quality (SCA.Re.S. Project 2019-2020)

This study evaluated whether some chemical and microbial contaminants in treated sewage effluents from two wastewater treatment plants (WWTP) reached the groundwater when they drained through a fractured karst vadose zone (WWTP-K) and a porous vadose zone (WWTP-P). Forty-five samples of sewage water (SW), treated water (TW), and monitoring well (MW), collected from WWTP-P (24) and WWTP-K (21), were analyzed for a range of microbiological and chemical properties. The E. coli and Salmonella counts were below the limits outlined in the Legislative Decree 152/06 in effluents from both types of WWTP. Enteric viruses were found in 37.5% and 12.5% of the SW and TW from WWTP-P, respectively. The percentages of Pepper mild mottle virus isolated were higher in TW (62.5% in WWTP-P, 85.7% in WWTP-K) than in SW and MW. The residual concentrations of contaminants of emerging concern (CEC) of each drug category were higher in the MW downstream of WWTP-K than of WWTP-P. Our results showed that the porous vadose zone was more effective at reducing the contaminant loads than the fractured karst one, especially the CEC, in the effluent. The legislation should include other parameters to minimize the risks from treated effluent that is discharged to soil.

Degradation of Bacterial Antibiotic Resistance Genes during Exposure to Non-Thermal Atmospheric Pressure Plasma

Bacterial resistance to antibiotics has become a major public health problem in recent years. The occurrence of antibiotics in the environment, especially in wastewater treatment plants, has contributed to the development of antibiotic-resistant bacteria (ARB) and the spread of antibiotic resistance genes (ARGs). Despite the potential of some conventional processes used in wastewater treatment plants, the removal of ARB and ARGs remains a challenge that requires further research and development of new technologies to avoid the release of emerging contaminants into aquatic environments. Non-thermal atmospheric pressure plasmas (NTAPPs) have gained a significant amount of interest for wastewater treatment due to their oxidizing potential. They have shown their effectiveness in the inactivation of a wide range of bacteria in several fields. In this review, we discuss the application of NTAPPs for the degradation of antibiotic resistance genes in wastewater treatment.

A comprehensive review on current technologies for removal of endocrine disrupting chemicals from wastewaters

In the recent years, endocrine disrupting compounds (EDCs) has received increasing attention due to their significant toxic effects on human beings and wildlife by affecting their endocrine systems. As an important group of emerging pollutant, EDCs have been detected in various aquatic environments, including surface waters, groundwater, wastewater, runoff, and landfill leachates. Their removal from water resources has also been an emerging concern considering growing population as well as reducing access to fresh water resources. EDC removal from wastewaters is highly dependent on physicochemical properties of the given EDCs present in each wastewater types as well as various aquatic environments. Due to chemical, physical and physicochemical diversities in these parameters, variety of technologies consisting of physical, biological, electrochemical, and chemical processes have been developed for their removal. This review highlights that the effectiveness of EDC removal is highly dependent of selecting the appropriate technology; which decision is made upon a full wastewater chemical characterization. This review aims to provide a comprehensive perspective about all the current technologies used for EDCs removal from various aquatic matrices along with rising challenges such as the antimicrobial resistance gene transfer during EDC treatment.

Irrigation of Olives with Reclaimed Wastewaters and Deficit Strategies Affect Pathogenic Bacteria Contamination of Water and Soil

This study aimed to evaluate pathogenic bacterial contamination of the water-soil-plant system in potted olive trees irrigated with reclaimed wastewater. Desalinated water (DW) obtained by treating municipal wastewater (SW) and reclaimed water (RW) obtained by mixing SW with the brine (BR) produced by DESERT technology (tertiary treatment by ultrafiltration, active carbon and reverse osmosis) were used. Two different irrigation regimes were compared: full irrigation (FI) and regulated deficit irrigation (RDI). During two irrigation seasons the concentrations of Escherichia coli, enterococci, spores of sulfite-reducing Clostridia (SRC) and Salmonella spp. were monitored in water, soil and fruit samples. Microbial concentrations in DW were always below the threshold for reuse in agriculture, while RW showed the highest level of contamination for all observed parameters. RDI management appeared to increase the soil content of SRC spores with respect to FI. Sporadically low SRC spore contamination was recorded in some fruits only in 2018, regardless of the irrigation source, probably because of accidental contamination during sampling or post-harvest handling. This study encourages the creation of a better regulatory framework reference, with specific guidelines for the use of RW as part of integrated environmental systems for the management of sustainable agriculture.

What is the effect on antibiotic resistant genes of chlorine disinfection in drinking water supply systems? A systematic review protocol

BACKGROUND

Antibiotic-resistant bacteria (ARB) usually enter water sources in different ways, such as via municipal and hospital wastewaters. Because conventional technologies used to treat water inefficient in removing these contaminants (especially antibiotic-resistant genes; ARGs), these contaminants easily enter drinking water distribution networks and pose serious threats to consumers' health. This study's main purpose is to systematically investigate the effect of chlorine disinfection on ARGs in drinking water supply systems. This study could play an important role in elucidating the effect of chlorine disinfection on ARGs.

METHODS

The systematic review outlining this protocol will be performed according to the Collaboration for Environmental Evidence (CEE) guidelines. The main question is, "what is the effect of chlorine disinfection on ARGs in drinking water supply systems?" For this purpose, the articles will be considered, in which chlorine's effect on ARGs is investigated. The search includes electronic resources, grey literature, and related websites. Electronic resources include Scopus, PubMed, Embase, Web of Science Core Collection, and Science Direct. After the final search, the obtained articles will be collected in the reference management software (Endnote X8). Upon removing the duplicate articles, the first stage of article screening will be performed based on the title and abstract the articles. In the second stage, the articles obtained from the first screening stage will be screened based on the full text of the articles based on the eligibility criteria. Then, two members of the expert team extract the data. To assess the validity of the articles, bias sources will be determined by an expert team. Biases will be defined according to the criteria designed by Bilotta et al. Finally, a narrative synthesis will be performed for the extracted data; if appropriate data are available, quantitative analysis will also be performed.

Resistome Diversity and Dissemination of WHO Priority Antibiotic Resistant Pathogens in Lebanese Estuaries

Anthropogenic pressure is known to be a key driver of antimicrobial resistance (AMR) dissemination in the environment. Especially in lower income countries, with poor infrastructure, the level of AMR dissemination is high. Therefore, we assessed the levels and diversity of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in Lebanese rivers at estuaries’ sites (n = 72) of the Mediterranean Sea in spring 2017 and winter 2018. Methods: A combined approach using culture techniques and high throughput qPCR were applied to identify ARB and ARGs in rivers along the Lebanese coast. Results: Multidrug-resistant Gram-negative (Enterobacterales and Pseudomonas spp.) and Gram-positive bacterial pathogens were isolated. Levels of ARGs were highest in the winter campaign and areas with high anthropogenic activities and population growth with an influx of refugees. Conclusion: Qualitative analysis of ARB and the analysis of the Lebanese estuaries’ resistome revealed critical levels of contamination with pathogenic bacteria and provided significant information about the spread of ARGs in anthropogenically impacted estuaries.

Performance Efficiency of Conventional Treatment Plants and Constructed Wetlands towards Reduction of Antibiotic Resistance

Domestic and industrial wastewater discharges harbor rich bacterial communities, including both pathogenic and commensal organisms that are antibiotic-resistant (AR). AR pathogens pose a potential threat to human and animal health. In wastewater treatment plants (WWTP), bacteria encounter environments suitable for horizontal gene transfer, providing an opportunity for bacterial cells to acquire new antibiotic-resistant genes. With many entry points to environmental components, especially water and soil, WWTPs are considered a critical control point for antibiotic resistance. The primary and secondary units of conventional WWTPs are not designed for the reduction of resistant microbes. Constructed wetlands (CWs) are viable wastewater treatment options with the potential for mitigating AR bacteria, their genes, pathogens, and general pollutants. Encouraging performance for the removal of AR (2-4 logs) has highlighted the applicability of CW on fields. Their low cost of construction, operation and maintenance makes them well suited for applications across the globe, especially in developing and low-income countries. The present review highlights a better understanding of the performance efficiency of conventional treatment plants and CWs for the elimination/reduction of AR from wastewater. They are viable alternatives that can be used for secondary/tertiary treatment or effluent polishing in combination with WWTP or in a decentralized manner.

Potential Use of Untreated Wastewater for Assessing COVID-19 Trends in Southern Italy

As a complement to clinical disease surveillance, the monitoring of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in wastewater can be used as an early warning system for impending epidemics. This study investigated the dynamics of SARS-CoV-2 in untreated wastewater with respect to the trend of coronavirus disease 2019 (COVID-19) prevalence in Southern Italy. A total of 210 wastewater samples were collected between May and November 2020 from 15 Apulian wastewater treatment plants (WWTP). The samples were concentrated in accordance with the standard of World Health Organization (WHO, Geneva, Switzerland) procedure for Poliovirus sewage surveillance, and molecular analysis was undertaken with real-time reverse-transcription quantitative PCR (RT-(q) PCR). Viral ribonucleic acid (RNA) was found in 12.4% (26/210) of the samples. The virus concentration in the positive samples ranged from 8.8 × 102 to 6.5 × 104 genome copies/L. The receiver operating characteristic (ROC) curve modeling showed that at least 11 cases/100,000 inhabitants would occur after a wastewater sample was found to be positive for SARS-CoV-2 (sensitivity = 80%, specificity = 80.9%). To our knowledge, this is the first study in Italy that has applied wastewater-based epidemiology to predict COVID-19 prevalence. Further studies regarding methods that include all variables (meteorological phenomena, characteristics of the WWTP, etc.) affecting this type of wastewater surveillance data would be useful to improve data interpretation.

Emergence of Metallo-β-Lactamases and OXA-48 Carbapenemase Producing Gram-Negative Bacteria in Hospital Wastewater in Algeria: A Potential Dissemination Pathway Into the Environment

Antibiotic-resistant bacteria can leave hospitals and therefore contaminate the environment and, most likely, humans and animals, through different routes, among which wastewater discharge is of great importance. This study aims to assess the possible role of hospital sewage as reservoir and dissemination pathway of carbapenem-resistant Gram-negative bacilli (GNB). Carbapenem-resistant GNB were selectively isolated from wastewater collected from a public hospital in Batna, Algeria. Species identification was carried out using matrix-assisted laser desorption and ionization time-of-flight mass spectrometry, and antibiotic susceptibility was evaluated by the disc diffusion method. β-Lactamase production was investigated phenotypically using the double-disk synergy assay and the modified CarbaNP test, then the molecular mechanisms of β-lactam-resistance were studied by PCR and sequencing. Ten Enterobacteriaceae and 14 glucose-nonfermenting GNB isolates were obtained. All Enterobacteriaceae isolates were positive for OXA-48 and TEM-1D β-lactamases, where seven of them coproduced an extended-spectrum β-lactamase. VIM-2 carbapenemase was detected in six glucose-nonfermenting GNB isolates. However, three Pseudomonas aeruginosa, one Comamonas jiangduensis and one Acinetobacter baumannii isolates were positive for VIM-4 variant. In addition, NDM-1 enzyme was detected in four A. baumannii isolates. Our findings highlight the potential impact of hospital wastewater in the spread of drug resistance mechanisms outside of hospitals.

Sortase A (SrtA) inhibitors as an alternative treatment for superbug infections

Virulence factor, sortase A (SrtA), has crucial roles in the pathogenesis of Gram-positive superbugs. SrtA is a bacterial cell membrane enzyme that anchors crucial virulence factors to the cell wall surface of Gram-positive bacteria. SrtA is not necessary for bacterial growth and viability and is conveniently accessible in the cell membrane; therefore, it is an ideal target for antivirulence drug development. In this review, we focus on antimicrobial resistance (AMR)-expressing bacteria and SrtA as a potential target for overcoming AMR. The mechanism of action of SrtA and its inhibition by various types of inhibitors, such as synthetic small molecules, peptides, and natural products, are provided. Future SrtA research perspectives for alternative drug development to antibiotics are also proposed.