A global multinational survey of cefotaxime-resistant coliforms in urban wastewater treatment plants

Changes of composition and antibiotic resistance of fecal coliform bacteria in municipal wastewater treatment plant

The dynamics of the composition and antibiotic resistance of the fecal coliform bacteria (FCB) in a typical wastewater treatment plant (WWTP) were investigated concerning the seasonal changes. Results showed that WWTP could remove the FCB concentration by 3∼5 logs within the effluent of 104∼105 CFU/L, but the antibiotic resistant rate of FCB species increased significantly after WWTP. The dominant FCB changed from Escherichia coli in the influent (∼73.0%) to Klebsiella pneumoniae in the effluent (∼53.3%) after WWTP, where the Escherichia coli was removed the most, while Klebsiella pneumoniae was the most persistent. The secondary tank removed the most of FCB (by 3∼4 logs) compared to other processes, but increased all the concerned antibiotic resistant rate. The potential super bugs of FCB community showing resistance to all the target antibiotics were selected in the biological treatment unit of WWTP. The FCB showed the highest multiple antibiotic resistance (92.9%) in total which even increased to 100% in the effluent. Klebsiella has the highest antibiotic resistant rate in FCB, with a multiple antibiotic resistance rate of 98.4%. These indicated that the Klebsiella pneumoniae not just Escherichia coli should be specially emphasized after WWTP concerning the health risk associated with FCB community.

Temporal and spatial changes in the abundance of antibiotic resistance gene markers in a wastewater treatment plant

In this study, we investigated the temporal and spatial quantitative changes in the concentration of antibiotic resistance gene (ARG) markers in a municipal wastewater treatment plant (WWTP). Four ARGs conferring resistance to different classes of antibiotics (ermB, sul1, tet[W], and blaCTXM) and a gene used as a proxy for ARG pollution (intl1) were quantified in two separate sampling campaigns covering two and half years of operation of the WWTP. First, a systematic monthly monitoring of multiple points in the inlet and the outlet revealed an absolute decrease in the concentration of all analyzed ARGs. However, the relative abundance of sul1 and intl1 genes relative to the total bacterial load (estimated using the universal marker 16S rDNA) increased in the outlet samples as compared to the inlet. To pinpoint the exact stage of removal and/or enrichment within the WWTP, a second sampling including the stages of the biological treatment was performed bimonthly. This revealed a distinct enrichment of sul1 and intl1 genes during the biological treatment phase. Moreover, the temporal and spatial variations in ARG abundance patterns within the WWTP underscored the complexity of the dynamics associated with the removal of ARGs during wastewater treatment. Understanding these dynamics is pivotal for developing efficient strategies to mitigate the dissemination of ARGs in aquatic environments. PRACTITIONER POINTS: Regular monitoring of ARG markers in WWTPs is essential to assess temporal and spatial changes, aiding in the development of effective mitigation strategies. Understanding the dynamics of ARG abundance during biological treatment is crucial for optimizing processes and minimizing dissemination in aquatic environments. Increased relative abundance of certain ARGs highlights potential enrichment during wastewater treatment, necessitating targeted interventions. Systematic monitoring of multiple points within WWTPs can provide valuable insights into the efficacy of treatment processes in reducing ARG levels over time. The complexity of ARG abundance patterns underscores the need to develop holistic approaches to tackle antibiotic resistance in wastewater systems.

Extended-spectrum β-lactamase-producing bacteria and their resistance determinants in different wastewaters and rivers in Nepal

Wastewaters serve as significant reservoirs of antibiotic resistant bacteria. Despite the evidence of antimicrobial resistance in wastewaters and river water in Kathmandu, direct linkage between them is not discussed yet. This study investigated the prevalence of extended-spectrum β-lactamase (ESBL)-producing bacteria and associated resistance genes in wastewaters and river water. Out of 246 bacteria from wastewaters, 57.72% were ESBL producers and 77.64% of them were multidrug resistant (MDR). ESBL producing E. coli was dominant in municipal and hospital wastewaters (HWW) as well as in river water while K. pneumoniae was common in pharmaceutical wastewater. The blaSHV and blaTEM genes were prevalent and commonly co-occurred with aac(6')-Ib-cr in K. pneumoniae isolated pharmaceutical wastewater. blaCTX-M carrying E. coli from hospital co-harbored aac(6')-Ib-cr while that from municipal influent and river water co-harbored qnrS. Whole genome sequencing data revealed the presence of diverse ARGs in bacterial isolates against multiple antibiotics. In average, an E. coli and a K. pneumoniae isolate contained 55.75 ± 0.96 and 40.2 ± 5.36 ARGs, respectively. Multi-locus sequence typing showed the presence of globally high-risk clones with wider host range such as E. coli ST10, and K. pneumoniae ST15 and ST307 in HWW and river indicating frequent dissemination of antimicrobial resistance in wastewater of Kathmandu. Whole genome sequence data aligned with phenotypic antibiograms and resistance genes detected by PCR in selected isolates. The presence of significant plasmid replicons (IncF, IncY) and mobile genetic elements (IS903, IS26) indicate high frequency of spreading antibiotic resistance. These findings indicate burden and dissemination of antimicrobial resistance in the environment and highlight the need for effective strategies to mitigate the antibiotic resistance.

The IncC and IncX1 resistance plasmids present in multi-drug resistant Escherichia coli strains isolated from poultry manure in Poland

The study describes the whole-genome sequencing of two antibiotic-resistant representative Escherichia coli strains, isolated from poultry manure in 2020. The samples were obtained from a commercial chicken meat production facility in Poland. The antibiotic resistance profile was characterized by co-resistance to β-lactam antibiotics, aminoglycosides, and fluoroquinolones. The three identified resistance plasmids (R-plasmids), pECmdr13.2, pECmdr13.3, and pECmdr14.1, harbored various genes conferring resistance to tetracyclines (tetR[A]) for, aminoglycoside (aph, aac, and aad families), β-lactam (blaCMY-2, blaTEM-176), sulfonamide (sul1, sul2), fluoroquinolone (qnrS1), and phenicol (floR). These plasmids, which have not been previously reported in Poland, were found to carry IS26 insertion elements, the intI1-integrase gene, and conjugal transfer genes, facilitating horizontal gene transfer. Plasmids pECmdr13.2 and pECmdr14.1 also possessed a mercury resistance gene operon related to transposon Tn6196; this promotes plasmid persistence even without antibiotic selection pressure due to co-selection mechanisms such as co-resistance. The chicken manure-derived plasmids belonged to the IncX1 (narrow host range) and IncC (broad host range) incompatibility groups. Similar plasmids have been identified in various environments, clinical isolates, and farm animals, including cattle, swine, and poultry. This study holds significant importance for the One Health approach, as it highlights the potential for antibiotic-resistant bacteria from livestock and food sources, particularly E. coli, to transfer through the food chain to humans and vice versa.

Hidden threats in the plastisphere: Carbapenemase-producing Enterobacterales colonizing microplastics in river water

Carbapenem resistance poses a significant burden on healthcare systems worldwide. Microplastics (MPs) have emerged as potential contributors to antibiotic resistance spread in the environment. However, the link between MPs and carbapenem resistance remains unexplored. We investigated the prevalence of carbapenem-resistant bacteria colonizing MPs placed in a river. Three replicates of a mixture of polypropylene (PP), polyethylene (PE) and polyethylene terephthalate (PET) and of PET alone were placed both upstream and downstream a wastewater treatment plant (WWTP) discharge. Carbapenem-resistant Enterobacterales (CRE) were further characterized by phenotypic tests and whole-genome sequencing. The abundance of carbapenem-resistant bacteria on MPs increased significantly downstream the WWTP. Their prevalence was higher in the MPs mixture compared to PET alone. CRE strains colonizing MPs included Klebsiella pneumoniae (n = 3), Klebsiella quasipneumoniae (n = 3), Raoultella ornithinolytica (n = 2), Enterobacter kobei (n = 1) and Citrobacter freundii (n = 1), most (n = 8) recovered after the WWTP discharge. All strains exhibited at least one of the tested virulence traits (biofilm formation at 37 °C, haemolytic activity and siderophore production), were multi-drug resistant and carried carbapenemase-encoding genes [blaKPC-3 (n = 5), blaGES-5 (n = 2) or blaKPC-3 + blaGES-5 (n = 3)]. Uncommon phenotypes of resistance to imipenem/relebactam (n = 3) and ceftazidime/avibactam (n = 2) were observed. Two blaKPC-3-positive K. pneumoniae successfully transfer this gene trough conjugation. Genome analysis predicted all strains as human pathogens. The blaKPC-3 was associated with the Tn4401d transposon on a pBK30683-like plasmid in most of the isolates (n = 7). The blaGES-5 was mostly linked to class 3 integrons. A K. pneumoniae strain belonging to the outbreak-causing high-risk clone ST15 carried both blaKPC-3 and blaCTX-M-15. Two K. quasipneumoniae isolates carried the plasmid-mediated colistin resistance gene mcr-9. Our results underscore the role of MPs as vectors for CRE dissemination, particularly following WWTPs discharges. MPs may act as carriers, facilitating the dissemination of carbapenemase-encoding genes and potentially contributing to increased CRE incidence in the environment.

Molecular epidemiology and mechanisms of carbapenem and colistin resistance in Klebsiella and other Enterobacterales from treated wastewater in Croatia

Among the most problematic bacteria with clinical relevance are the carbapenem-resistant Enterobacterales (CRE), as there are very limited options for their treatment. Treated wastewater can be a route for the release of these bacteria into the environment and the population. The aim of this study was to isolate CRE from treated wastewater from the Zagreb wastewater treatment plant and to determine their phenotypic and genomic characteristics. A total of 200 suspected CRE were isolated, 148 of which were confirmed as Enterobacterales by MALDI-TOF MS. The predominant species was Klebsiella spp. (n = 47), followed by Citrobacter spp. (n = 40) and Enterobacter cloacae complex (cplx.) (n = 35). All 148 isolates were carbapenemase producers with a multidrug-resistant phenotype. Using multi-locus sequence typing and whole-genome sequencing (WGS), 18 different sequence types were identified among these isolates, 14 of which were associated with human-associated clones. The virulence gene analysis of the sequenced Klebsiella isolates (n = 7) revealed their potential pathogenicity. PCR and WGS showed that the most frequent carbapenemase genes in K. pneumoniae were blaOXA-48 and blaNDM-1, which frequently occurred together, while blaKPC-2 together with blaNDM-1 was mainly detected in K. oxytoca, E. cloacae cplx. and Citrobacter spp. Colistin resistance was observed in 40% of Klebsiella and 57% of Enterobacter isolates. Underlying mechanisms identified by WGS include known and potentially novel intrinsic mechanisms (point mutations in the pmrA/B, phoP/Q, mgrB and crrB genes) and acquired mechanisms (mcr-4.3 gene). The mcr-4.3 gene was identified for the first time in K. pneumoniae and is probably located on the conjugative IncHI1B plasmid. In addition, WGS analysis of 13 isolates revealed various virulence genes and resistance genes to other clinically relevant antibiotics as well as different plasmids possibly associated with carbapenemase genes. Our study demonstrates the important role that treated municipal wastewater plays in harboring and spreading enterobacterial pathogens that are resistant to last-resort antibiotics.

Emergence and dissemination of epidemic-causing OXA-244 carbapenemase-producing Escherichia coli ST38 through hospital sewage in Norway, 2020-2022

BACKGROUND

Population-based sewage surveillance has emerged as a promising approach for studying the prevalence of antibiotic resistance in pathogens.

AIM

To determine the temporal prevalence of cefotaxime-resistant Escherichia coli in sewage from five sewage treatment plants located in Bergen city, to determine whether ESBL- and carbapenemase-producing E. coli are consistently disseminated in the receiving environment through sewage.

METHOD

A total of 569 cefotaxime-resistant E. coli were isolated over a period of 19 months (August 2020 to February 2022) using ECC CHROMagar™ plates from 82 samples, antibiotic sensitivity profiles were determined, using Sensititre™ plates. The draft genome sequences were determined, using Illumina MiSeq-based sequencing. Complete genome sequences were determined, using Oxford Nanopore-based sequencing.

FINDINGS

All 569 strains obtained from influent (N=461) and effluent (N=108) were multi-drug resistant. Most of the sequenced strains (52 of 61) carried blaCTX-M-15 (38.5%) and blaCTX-M-27 (34.6%). The most prevalent sequence types (STs) for ESBL-carrying strains were ST131 (32.8%) and ST38 (21.3%). All CTX-M-27-carrying ST131 strains belonged to clade A or C1, while CTX-M-15-harbouring strains were present in all the clades. Five OXA-244-producing ST38 strains, genetically similar to epidemic-causing strains from Western Norway, France and the Netherlands, were isolated only from raw and treated sewage of the treatment plant receiving hospital sewage.

CONCLUSION

This is the first study showing persistent dissemination of OXA-244-producing ST38 clones through sewage in Norway, demonstrating that hospital sewage is the likely source of OXA-244-producing ST38 clones reaching the receiving environment.

Environmental stress increases the invasion success of antimicrobial resistant bacteria in river microbial communities

Environmental microbiomes are constantly exposed to invasion events through foreign, antibiotic resistant bacteria that were enriched in the anthropic sphere. However, the biotic and abiotic factors, as well as the natural barriers that determine the invasion success of these invader bacteria into the environmental microbiomes are poorly understood. A great example of such invasion events are river microbial communities constantly exposed to resistant bacteria originating from wastewater effluents. Here, we aim at gaining comprehensive insights into the key factors that determine their invasion success with a particular focus on the effects of environmental stressors, regularly co-released in wastewater effluents. Understanding invasion dynamics of resistant bacteria is crucial for limiting the environmental spread of antibiotic resistance. To achieve this, we grew natural microbial biofilms on glass slides in rivers for one month. The biofilms were then transferred to laboratory, recirculating flume systems and exposed to a single pulse of a model resistant invader bacterium (Escherichia coli) either in presence or absence of stress induced by Cu2+. The invasion dynamics of E. coli into the biofilms were then monitored for 14 days. Despite an initially successful introduction of E. coli into the biofilms, independent of the imposed stress, over time the invader perished in absence of stress. However, under stress the invading strain successfully established and proliferated in the biofilms. Noteworthy, the increased establishment success of the invader coincided with a loss in microbial community diversity under stress conditions, likely due to additional niche space becoming available for the invader.

Mitigating risks and maximizing sustainability of treated wastewater reuse for irrigation

Scarcity of freshwater for agriculture has led to increased utilization of treated wastewater (TWW), establishing it as a significant and reliable source of irrigation water. However, years of research indicate that if not managed adequately, TWW may deleteriously affect soil functioning and plant productivity, and pose a hazard to human and environmental health. This review leverages the experience of researchers, stakeholders, and policymakers from Israel, the United-States, and Europe to present a holistic, multidisciplinary perspective on maximizing the benefits from municipal TWW use for irrigation. We specifically draw on the extensive knowledge gained in Israel, a world leader in agricultural TWW implementation. The first two sections of the work set the foundation for understanding current challenges involved with the use of TWW, detailing known and emerging agronomic and environmental issues (such as salinity and phytotoxicity) and public health risks (such as contaminants of emerging concern and pathogens). The work then presents solutions to address these challenges, including technological and agronomic management-based solutions as well as source control policies. The concluding section presents suggestions for the path forward, emphasizing the importance of improving links between research and policy, and better outreach to the public and agricultural practitioners. We use this platform as a call for action, to form a global harmonized data system that will centralize scientific findings on agronomic, environmental and public health effects of TWW irrigation. Insights from such global collaboration will help to mitigate risks, and facilitate more sustainable use of TWW for food production in the future.

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

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

Comparison of Cefotaxime-Resistant Escherichia coli and sul1 and intI1 by qPCR for Monitoring of Antibiotic Resistance of Wastewater, Surface Water, and Recycled Water

Awareness of the need for surveillance of antimicrobial resistance (AMR) in water environments is growing, but there is uncertainty regarding appropriate monitoring targets. Adapting culture-based fecal indicator monitoring to include antibiotics in the media provides a potentially low-tech and accessible option, while quantitative polymerase chain reaction (qPCR) targeting key genes of interest provides a broad, quantitative measure across the microbial community. The purpose of this study was to compare findings obtained from the culture of cefotaxime-resistant (cefR) Escherichia coli with two qPCR methods for quantification of antibiotic resistance genes across wastewater, recycled water, and surface waters. The culture method was a modification of US EPA Method 1603 for E. coli, in which cefotaxime is included in the medium to capture cefR strains, while qPCR methods quantified sul1 and intI1. A common standard operating procedure for each target was applied to samples collected by six water utilities across the United States and processed by two laboratories. The methods performed consistently, and all three measures reflected the same overarching trends across water types. The qPCR detection of sul1 yielded the widest dynamic range of measurement as an AMR indicator (7-log versus 3.5-log for cefR E. coli), while intI1 was the most frequently detected target (99% versus 96.5% and 50.8% for sul1 and cefR E. coli, respectively). All methods produced comparable measurements between labs (p < 0.05, Kruskal-Wallis). Further study is needed to consider how relevant each measure is to capturing hot spots for the evolution and dissemination of AMR in the environment and as indicators of AMR-associated human health risk.

Microbiome and Resistome Profiles along a Sewage-Effluent-Reservoir Trajectory Underline the Role of Natural Attenuation in Wastewater Stabilization Reservoirs

Antibiotic-resistant bacteria and antibiotic resistance gene (ARGs) loads dissipate through sewage treatment plants to receiving aquatic environments, but the mechanisms that mitigate the spread of these ARGs are not well understood due to the complexity of full-scale systems and the difficulty of source tracking in downstream environments. To overcome this problem, we targeted a controlled experimental system comprising a semicommercial membrane-aerated bioreactor (MABR), whose effluents fed a 4,500-L polypropylene basin that mimicked effluent stabilization reservoirs and receiving aquatic ecosystems. We analyzed a large set of physicochemical measurements, concomitant with the cultivation of total and cefotaxime-resistant Escherichia coli, microbial community analyses, and quantitative PCR (qPCR)/digital droplet PCR (ddPCR) quantification of selected ARGs and mobile genetic elements (MGEs). The MABR removed most of the sewage-derived organic carbon and nitrogen, and simultaneously, E. coli, ARG, and MGE levels dropped by approximately 1.5- and 1.0-log unit mL-1, respectively. Similar levels of E. coli, ARGs, and MGEs were removed in the reservoir, but interestingly, unlike in the MABR, the relative abundance (normalized to 16S rRNA gene-inferred total bacterial abundance) of these genes also decreased. Microbial community analyses revealed the substantial shifts in bacterial and eukaryotic community composition in the reservoir relative to the MABR. Collectively, our observations lead us to conclude that the removal of ARGs in the MABR is mainly a consequence of treatment-facilitated biomass removal, whereas in the stabilization reservoir, mitigation is linked to natural attenuation associated with ecosystem functioning, which includes abiotic parameters, and the development of native microbiomes that prevent the establishment of wastewater-derived bacteria and associated ARGs. IMPORTANCE Wastewater treatment plants are sources of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs), which can contaminate receiving aquatic environments and contribute to antibiotic resistance. We focused on a controlled experimental system comprising a semicommercial membrane-aerated bioreactor (MABR) that treated raw sewage, whose effluents fed a 4,500-L polypropylene basin that mimicked effluent stabilization reservoirs. We evaluated ARB and ARG dynamics across the raw-sewage-MABR-effluent trajectory, concomitant with evaluation of microbial community composition and physicochemical parameters, in an attempt to identify mechanisms associated with ARB and ARG dissipation. We found that removal of ARB and ARGs in the MABR was primarily associated with bacterial death or sludge removal, whereas in the reservoir it was attributed to the inability of ARBs and associated ARGs to colonize the reservoir due to a dynamic and persistent microbial community. The study demonstrates the importance of ecosystem functioning in removing microbial contaminants from wastewater.

Selection of indicator contaminants of emerging concern when reusing reclaimed water for irrigation - A proposed methodology

Organic and microbial contaminants of emerging concern (CECs), even though not yet regulated, are of great concern in reclaimed water reuse projects. Due to the large number of CECs and their different characteristics, it is useful to include only a limited number of them in monitoring programs. The selection of the most representative CECs is still a current and open question. This study presents a new methodology for this scope, in particular for the evaluation of the performance of a polishing treatment and the assessment of the risk for the environment and the irrigated crops. As to organic CECs, the methodology is based on four criteria (occurrence, persistence, bioaccumulation and toxicity) expressed in terms of surrogates (respectively, concentrations in the secondary effluent, removal achieved in conventional activated sludge systems, Log K_ow and predicted-no-effect concentration). It consists of: (i) development of a dataset including the CECs found in the secondary effluent, together with the corresponding values of surrogates found in the literature or by in-field investigations; (ii) normalization step with the assignment of a score between 1 (low environmental impact) and 5 (high environmental impact) to the different criteria based on threshold values set according to the literature and experts' judgement; (iii) CEC ranking according to their final score obtained as the sum of the specific scores; and (iv) selection of the representative CECs for the different needs. Regarding microbial CECs, the selection is based on their occurrence and their highest detection frequency in the secondary effluent and in the receiving water, the antibiotic consumption patterns, and recommendations by national and international organisations. The methodology was applied within the ongoing reuse project SERPIC resulting in a list of 30 indicator CECs, including amoxicillin, bisphenol A, ciprofloxacin, diclofenac, erythromycin, ibuprofen, iopromide, perfluorooctane sulfonate (PFOS), sulfamethoxazole, tetracycline, Escherichia coli, faecal coliform, 16S rRNA, sul1, and sul2.

The African Wastewater Resistome: Identifying Knowledge Gaps to Inform Future Research Directions

Antimicrobial resistance (AMR) is a growing global public health threat. Furthermore, wastewater is increasingly recognized as a significant environmental reservoir for AMR. Wastewater is a complex mixture of organic and inorganic compounds, including antibiotics and other antimicrobial agents, discharged from hospitals, pharmaceutical industries, and households. Therefore, wastewater treatment plants (WWTPs) are critical components of urban infrastructure that play a vital role in protecting public health and the environment. However, they can also be a source of AMR. WWTPs serve as a point of convergence for antibiotics and resistant bacteria from various sources, creating an environment that favours the selection and spread of AMR. The effluent from WWTPs can also contaminate surface freshwater and groundwater resources, which can subsequently spread resistant bacteria to the wider environment. In Africa, the prevalence of AMR in wastewater is of particular concern due to the inadequate sanitation and wastewater treatment facilities, coupled with the overuse and misuse of antibiotics in healthcare and agriculture. Therefore, the present review evaluated studies that reported on wastewater in Africa between 2012 and 2022 to identify knowledge gaps and propose future perspectives, informing the use of wastewater-based epidemiology as a proxy for determining the resistome circulating within the continent. The study found that although wastewater resistome studies have increased over time in Africa, this is not the case in every country, with most studies conducted in South Africa. Furthermore, the study identified, among others, methodology and reporting gaps, driven by a lack of skills. Finally, the review suggests solutions including standardisation of protocols in wastewater resistome works and an urgent need to build genomic skills within the continent to handle the big data generated from these studies.

Sewage-based surveillance shows presence of Klebsiella pneumoniae resistant against last resort antibiotics in the population in Bergen, Norway

The aim of this study was to understand the prevalence of antibiotic resistance in Klebsiella pneumoniae present in the population in Bergen city, Norway using city-scale sewage-based surveillance, as well as the potential spread of K. pneumoniae into the marine environment through treated sewage. From a total of 30 sewage samples collected from five different sewage treatment plants (STPs), 563 presumptive K. pneumoniae isolates were obtained on Simmons Citrate Agar with myo-Inositol (SCAI) plates, and 44 presumptive K. pneumoniae isolates on SCAI plates with cefotaxime. Colistin resistance was observed in 35 isolates, while cefotaxime resistance and tigecycline resistance was observed in only five isolates each, out of 563 presumptive K. pneumoniae isolates. All 44 isolates obtained on cefotaxime-containing plates were multidrug-resistant, with 25% (n = 11) showing resistance against tigecycline. Clinically important acquired antibiotic resistance genes (ARGs), like bla_CTX-M-14, bla_CTX-M-15, qnrS1, aac(3)-IIe, tet(A), and sul1, were detected in several sequenced Klebsiella spp. isolates (n = 53). All sequenced colistin-resistant isolates (n = 13) had a mutation in the mgrB gene with nucleotide substitution at position C88T creating a premature stop codon. All sequenced tigecycline-resistant isolates (n = 4) harbored a Tet(A) variant with 22 amino acid (aa) substitutions compared to the reference protein. The sequenced K. pneumoniae isolates (n = 44) belonged to 22 different sequence types (STs) with ST730 (29.5%) as most prevalent, followed by pathogenic ST307 (11.4%). Virulence factors, including aerobactin (iutA), enterobactin (entABCDEFS and fepABCDG), salmochelin (iro), and yersiniabactin (ybt) were detected in several sequenced K. pneumoniae isolates, suggesting pathogenicity potential. Heavy metal resistance genes were common in sequenced K. pneumoniae isolates (n = 44) with silver (silABCEFPRS) and copper (pcoABDRS) resistance genes present in 79.5% of the isolates. Sewage-based surveillance can be a useful tool for understanding antibiotic resistance in pathogens present within a population and to provide up-to date information on the current resistance situation. Our study presents a framework for population-based surveillance of resistance in K. pneumoniae.

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

PURPOSE OF REVIEW

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

RECENT FINDINGS

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

A set of antibiotic-resistance mechanisms and virulence factors in GES-16-producing Klebsiella quasipneumoniae subsp. similipneumoniae from hospital wastewater revealed by whole-genome sequencing

Klebsiella quasipneumoniae subsp. similipneumoniae has emerged as a human pathogen and sporadic isolates from non-clinical sources were reported. Here, we described the phenotypic- and genomic-characteristics of a multidrug-resistant (MDR) and potentially hypervirulent (MDR-hv) Klebsiella quasipneumoniae subsp. similipneumoniae (KqA1) isolated from hospital wastewater. The antibiotic susceptibility profile of KqA1 was investigated using disk-diffusion method, broth microdilution method, and agar dilution method, and the genetic characteristics of antimicrobial resistance, mobile genetics elements, and virulence were evaluated by genomic DNA sequencing on the Illumina® NovaSeq6000 platform as well as by bioinformatic analysis. Resistome analyses revealed the presence of genes related to resistance to β-lactams, aminoglycosides, quinolones, tetracyclines, sulfonamides, trimethoprim, chloramphenicol, macrolides, and fosfomycin. New genetic contexts to bla_GES-16 (carbapenemase gene) and to fosA (fosfomycin resistance gene) were described. A set of mechanisms that can contribute to antibiotic resistance, commonly detected in Klebsiella spp., was also found including chromosomal mutations, efflux systems, proteins, and regulators. Moreover, KqA1 presented genes related to tolerance to metals (arsenic, copper, nickel, cobalt, magnesium, cadmium, zinc, tellurium, selenium) and to biocides (quaternary-ammonium compounds). The isolate was classified as potentially hypervirulent due to a wide range of virulence factors found associated to regulation, motility, biofilm, effector delivery systems, immune modulation, nutritional/metabolic factors, adherence, invasion, and competitive advantage. The occurrence of MDR-hv KqA1 in hospital wastewater points out how this environment matrix plays a crucial role in the maintenance and selection of critical bacterial pathogens. Regarding One Health perspective, it is evident the need for multidisciplinary implementation of control measures for antibiotic-resistant bacteria, not only in hospital settings but also in a general environmental context to mitigate the dissemination of MDR and hv bacteria.

A systematic review and meta-analysis on antimicrobial resistance in marine bivalves

Bivalves are filter-feeding animals able to accumulate contaminants and microorganisms, either of marine or terrestrial origin. The aim of this study was to describe the prevalence of antimicrobial resistance (AMR) in bacterial isolates from bivalves using a systematic review of the literature. Comprehensive searches of MEDLINE, EMBASE, and Web of Science were carried out, based upon a registered protocol (PROSPERO), and following the preferred Reporting Items for Systematic reviews and Meta-Analysis (PRISMA) guidelines. The methodological quality of the included studies was assessed using a modified Hoy checklist. Meta-analyses of prevalence were carried out using random-effects models. In total, 103 articles were selected from 1,280 records and were included in the final analysis. The studies were from Asia (n = 54), Europe (n = 27), South and North America (n = 10 and n = 6, respectively), Africa (n = 2), Oceania (n = 1), and multicentre and intercontinental (n = 3). The meta-analysis of multiple antibiotic resistance (MAR) index revealed Aeromonas spp. as the genus with the highest prevalence of AMR (37%), followed by Vibrio spp. (34%), Salmonella spp. (18%), and Escherichia coli (15%). Resistance to third/fourth/fifth generation cephalosporins and fluoroquinolones, two highest priority, critically important antimicrobials (HPCIA), was recorded in approximately 10% of E. coli isolates. Resistance to carbapenems was very low (<2%) in Salmonella spp. and in E. coli, but was found in 5% of Vibrio spp. and in more than a third of Aeromonas spp. isolates. In aquatic bacteria, resistance to carbapenems was higher in Asian than in European isolates. Our study shows the presence of antibiotic resistant bacteria (ARB), including bacteria resistant to HPCIA, in marine bivalves, posing a risk for consumers.

Towards the standardization of Enterococcus culture methods for waterborne antibiotic resistance monitoring: A critical review of trends across studies

Antibiotic resistance is a major 21^st century One Health (humans, animals, environment) challenge whose spread limits options to treat bacterial infections. There is growing interest in monitoring water environments, including surface water and wastewater, which have been identified as key recipients, pathways, and sources of antibiotic resistant bacteria (ARB). Aquatic environments also facilitate the transmission and amplification of ARB. Enterococcus spp. often carry clinically-important antibiotic resistance genes and are of interest as environmental monitoring targets. Enterococcus spp. are Gram-positive bacteria that are typically of fecal origin; however, they are also found in relevant environmental niches, with various species and strains that are opportunistic human pathogens. Although the value of environmental monitoring of antibiotic-resistant Enterococcus has been recognized by both national and international organizations, lack of procedural standardization has hindered generation of comparable data needed to implement integrated surveillance programs. Here we provide a comprehensive methodological review to assess the techniques used for the culturing and characterization of antibiotic-resistant Enterococcus across water matrices for the purpose of environmental monitoring. We analyzed 117 peer-reviewed articles from 33 countries across six continents. The goal of this review is to provide a critical analysis of (i) the various methods applied globally for isolation, confirmation, and speciation of Enterococcus isolates, (ii) the different methods for profiling antibiotic resistance among enterococci, and (iii) the current prevalence of resistance to clinically-relevant antibiotics among Enterococcus spp. isolated from various environments. Finally, we provide advice regarding a path forward for standardizing culturing of Enterococcus spp. for the purpose of antibiotic resistance monitoring in wastewater and wastewater-influenced waters within a global surveillance framework.

Estuarine Aquacultures at the Crossroads of Animal Production and Antibacterial Resistance: A Metagenomic Approach to the Resistome

It is recognized that the spread of antibiotic resistance (AR) genes among aquatic environments, including aquaculture and the human environment, can have detrimental effects on human and animal health and the ecosystem. Thus, when transmitted to the human microbiome or pathogens, resistance genes risk human health by compromising the eventual treatment of infections with antibiotic therapy. This study aimed to define the resistance profile of aquaculture farms and their potential risk for spreading. Twenty-four sediments from oyster and gilthead sea bream aquaculture farms located in three Portuguese river estuaries (17 sediments from Sado, 4 from Aveiro, and 3 from Lima) were studied by comparative metagenomic analysis. The computation of the diversity of genes conferring resistance per antibiotic class revealed a significant increase in aminoglycosides, beta-lactams, disinfectants, quinolones, and tetracyclines counts. In all geographic locations under study, the most diverse AR genes confer resistance to the macrolides, tetracyclines and oxazolidinones classes, all of which are medically important for human and animal therapies, as well as resistance to disinfectants. The diversity of mobile genetic elements correlated with the number of AR genes such as tetracyclines, suggesting that AR could be easily mobilized among bacterial genomes and microbiomes.

(Antibiotic-Resistant) E. coli in the Dutch-German Vecht Catchment─Monitoring and Modeling

Fecally contaminated waters can be a source for human infections. We investigated the occurrence of fecal indicator bacteria (E. coli) and antibiotic-resistant E. coli, namely, extended spectrum beta-lactamase (ESBL)-producing E. coli (ESBL-EC) and carbapenemase-producing E. coli (CP-EC) in the Dutch-German transboundary catchment of the Vecht River. Over the course of one year, bacterial concentrations were monitored in wastewater treatment plant (WWTP) influents and effluents and in surface waters with and without WWTP influence. Subsequently, the GREAT-ER model was adopted for the prediction of (antibiotic-resistant) E. coli concentrations. The model was parametrized and evaluated for two distinct scenarios (average flow scenario, dry summer scenario). Statistical analysis of WWTP monitoring data revealed a significantly higher (factor 2) proportion of ESBL-EC among E. coli in German compared to Dutch WWTPs. CP-EC were present in 43% of influent samples. The modeling approach yielded spatially accurate descriptions of microbial concentrations for the average flow scenario. Predicted E. coli concentrations exceed the threshold value of the Bathing Water Directive for a good bathing water quality at less than 10% of potential swimming sites in both scenarios. During a single swimming event up to 61 CFU of ESBL-EC and less than 1 CFU of CP-EC could be taken up by ingestion.

Clinically Relevant β-Lactam Resistance Genes in Wastewater Treatment Plants

Antimicrobial resistance (AMR) is one of the largest global concerns due to its influence in multiple areas, which is consistent with One Health's concept of close interconnections between people, animals, plants, and their shared environments. Antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) circulate constantly in various niches, sediments, water sources, soil, and wastes of the animal and plant sectors, and is linked to human activities. Sewage of different origins gets to the wastewater treatment plants (WWTPs), where ARB and ARG removal efficiency is still insufficient, leading to their transmission to discharge points and further dissemination. Thus, WWTPs are believed to be reservoirs of ARGs and the source of spreading AMR. According to a World Health Organization report, the most critical pathogens for public health include Gram-negative bacteria resistant to third-generation cephalosporins and carbapenems (last-choice drugs), which represent β-lactams, the most widely used antibiotics. Therefore, this paper aimed to present the available research data for ARGs in WWTPs that confer resistance to β-lactam antibiotics, with a particular emphasis on clinically important life-threatening mechanisms of resistance, including extended-spectrum β-lactamases (ESBLs) and carbapenemases (KPC, NDM).

Escherichia coli Isolated from Vegans, Vegetarians and Omnivores: Antibiotic Resistance, Virulence Factors, Pathogenicity Islands and Phylogenetic Classification

Pathogenic strains of Escherichia coli have acquired virulence factors, which confer an increased ability to cause a broad spectrum of enteric diseases and extraintestinal infections. The aim of this study was to analyze the antimicrobial resistance profile of and the presence of virulence-associated genes (VAGs) in E. coli fecal isolates from omnivores, vegetarians and vegans. A control group of 60 isolates from omnivores, as well as a study group with 41 isolates from vegetarians and 17 from vegans, were analyzed. Isolates from both groups showed a high rate of resistance to ampicillin, amoxicillin-clavulanic acid and nalidixic acid, and some of them were positive for the ESBL test (12% of isolates from vegetarians/vegans and 5% of isolates from omnivores). The most predominant VAGs detected in isolates from omnivores were fimH (70%), iutA (32%), fyuA (32%) and traT (32%), while among isolates from vegetarians or vegans, the most predominant were traT (62%), kpsMT k1 (28%) and iutA (22%). Most isolates from omnivores (55%) were positive for PAI I536, while most of those from vegetarians/vegans (59%) were positive for PAI IV536. Phylogenetic group A, composed of commensal non-pathogenic isolates that survive in the intestinal tract, was the most prevalent in both control and study groups. Some VAGs were found in only one of the groups, such as the pathogenicity island PAI III536, found in 12% of the isolates from omnivores, while the kpsMT III gene (15%) was detected only among isolates from vegetarians/vegans. Interestingly, this gene codes for a polysaccharide capsule found mainly in E. coli isolates causing intestinal infections, including EPEC, ETEC and EHEC. Finally, our results show that there were no advantages in vegetarian or vegan diets compared to the omnivorous diet, as in both groups we detected isolates harboring VAGs and displaying resistance to antibiotics, especially those most commonly used to treat urinary tract infections.

Establishing a marine monitoring programme to assess antibiotic resistance: A case study from the Gulf Cooperation Council (GCC) region

The World Health Organization considers antimicrobial resistance as one of the most pressing global issues which poses a fundamental threat to human health, development, and security. Due to demographic and environmental factors, the marine environment of the Gulf Cooperation Council (GCC) region may be particularly susceptible to the threat of antimicrobial resistance. However, there is currently little information on the presence of AMR in the GCC marine environment to inform the design of appropriate targeted surveillance activities. The objective of this study was to develop, implement and conduct a rapid regional baseline monitoring survey of the presence of AMR in the GCC marine environment, through the analysis of seawater collected from high-risk areas across four GCC states: (Bahrain, Oman, Kuwait, and the United Arab Emirates). 560 Escherichia coli strains were analysed as part of this monitoring programme between December 2018 and May 2019. Multi-drug resistance (resistance to three or more structural classes of antimicrobials) was observed in 32.5% of tested isolates. High levels of reduced susceptibility to ampicillin (29.6%), nalidixic acid (27.9%), tetracycline (27.5%), sulfamethoxazole (22.5%) and trimethoprim (22.5%) were observed. Reduced susceptibility to the high priority critically important antimicrobials: azithromycin (9.3%), ceftazidime (12.7%), cefotaxime (12.7%), ciprofloxacin (44.6%), gentamicin (2.7%) and tigecycline (0.5%), was also noted. A subset of 173 isolates was whole genome sequenced, and high carriage rates of qnrS1 (60/173) and bla _CTX-M-15 (45/173) were observed, correlating with reduced susceptibility to the fluoroquinolones and third generation cephalosporins, respectively. This study is important because of the resistance patterns observed, the demonstrated utility in applying genomic-based approaches to routine microbiological monitoring, and the overall establishment of a transnational AMR surveillance framework focussed on coastal and marine environments.

Research needs for optimising wastewater-based epidemiology monitoring for public health protection

Wastewater-based epidemiology (WBE) is an unobtrusive method used to observe patterns in illicit drug use, poliovirus, and severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The pandemic and need for surveillance measures have led to the rapid acceleration of WBE research and development globally. With the infrastructure available to monitor SARS-CoV-2 from wastewater in 58 countries globally, there is potential to expand targets and applications for public health protection, such as other viral pathogens, antimicrobial resistance (AMR), pharmaceutical consumption, or exposure to chemical pollutants. Some applications have been explored in academic research but are not used to inform public health decision-making. We reflect on the current knowledge of WBE for these applications and identify barriers and opportunities for expanding beyond SARS-CoV-2. This paper critically reviews the applications of WBE for public health and identifies the important research gaps for WBE to be a useful tool in public health. It considers possible uses for pathogenic viruses, AMR, and chemicals. It summarises the current evidence on the following: (1) the presence of markers in stool and urine; (2) environmental factors influencing persistence of markers in wastewater; (3) methods for sample collection and storage; (4) prospective methods for detection and quantification; (5) reducing uncertainties; and (6) further considerations for public health use.

The Resistome of ESKAPEE Pathogens in Untreated and Treated Wastewater: A Polish Case Study

The aim of this study was to quantify ESKAPEE bacteria, genes encoding resistance to antibiotics targeting this group of pathogens, as well as integrase genes in municipal wastewater and river water. Environmental DNA was extracted from the collected samples and used in deep sequencing with the Illumina TruSeq kit. The abundance of bacterial genera and species belonging to the ESKAPEE group, 400 ARGs associated with this microbial group, and three classes of integrase genes were determined. A taxonomic analysis revealed that Acinetobacter was the dominant bacterial genus, whereas Acinetobacter baumannii and Escherichia coli were the dominant bacterial species. The analyzed samples were characterized by the highest concentrations of the following ARGs: bla_GES, bla_OXA-58, bla_TEM, qnrB, and qnrS. Acinetobacter baumannii, E. coli, and genes encoding resistance to β-lactams (bla_VEB-1, bla_IMP-1, bla_GES, bla_OXA-58, bla_CTX-M, and bla_TEM) and fluoroquinolones (qnrS) were detected in samples of river water collected downstream from the wastewater discharge point. The correlation analysis revealed a strong relationship between A. baumannii (bacterial species regarded as an emerging human pathogen) and genes encoding resistance to all tested groups of antimicrobials. The transmission of the studied bacteria (in particular A. baumannii) and ARGs to the aquatic environment poses a public health risk.

A Comprehensive Study of the Microbiome, Resistome, and Physical and Chemical Characteristics of Chicken Waste from Intensive Farms

The application of chicken waste to farmland could be detrimental to public health. It may contribute to the dissemination of antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) from feces and their subsequent entry into the food chain. The present study analyzes the metagenome and resistome of chicken manure and litter obtained from a commercial chicken farm in Poland. ARB were isolated, identified, and screened for antibiogram fingerprints using standard microbiological and molecular methods. The physicochemical properties of the chicken waste were also determined. ARGs, integrons, and mobile genetic elements (MGE) in chicken waste were analyzed using high-throughput SmartChip qPCR. The results confirm the presence of many ARGs, probably located in MGE, which can be transferred to other bacteria. Potentially pathogenic or opportunistic microorganisms and phytopathogens were isolated. More than 50% of the isolated strains were classified as being multi-drug resistant, and the remainder were resistant to at least one antibiotic class; these pose a real risk of entering the groundwater and contaminating the surrounding environment. Our results indicate that while chicken manure can be sufficient sources of the nutrients essential for plant growth, its microbiological aspects make this material highly dangerous to the environment.

Insights into the microbial community of treated wastewater, its year-round variability and impact on the receiver, using cultivation, microscopy and amplicon-based methods

Apart from chemical constituents, wastewater treatment plant (WWTP) effluents also release microorganisms that can be important to the receiving water bodies either from a sanitary point of view, or taking to the account the biogeochemical potential of the recipients. However, little is known about the treated wastewater microbial community, its composition, seasonal changes, functions and fate in the waters of the receiver. Thus, this study presents a synergistic approach coupling new and traditional methods: analytical chemistry, classical microbiology (cultivation- and microscopy-based methods), as well as Next Generation Sequencing and a quantitative real-time polymerase chain reaction (qPCR). The results show that in terms of bacterial community composition, treated wastewater differed from the environmental samples, irrespectively if they were related or unrelated to the WWTP effluent discharge. The canonical correspondence analysis (CCA) taking into account chemical parameters and taxonomical biodiversity indirectly confirmed the seasonal deterioration of the treated wastewater quality as a result of temperature-driven change of activated sludge community structure and biomass washout (observed also by DAPI staining). Despite seasonal fluctuations of total suspended solids and inter-related parameters (such as COD, BOD, TN, TP), the treated wastewater quality remained within current discharge limits. It was due to treatment processes intensively adjusted by WWTP operators, particularly those necessary to maintain an appropriate rate of autotrophic processes of nitrification and to support biological phosphorus removal. This can explain the observed microbiome composition similarity among WWTP effluents at high taxonomic levels. Obtained data also suggest that besides wastewater treatment efficiency, WWTP effluents are still sources of both human-related microorganisms as well as bacteria equipped in genes involved in N-cycling. Their potential of participation in nutrients cycling in the receivers is widely unknown and require critical attention and better understanding.

Prevalence of enteric opportunistic pathogens and extended-spectrum cephalosporin- and carbapenem-resistant coliforms and genes in wastewater from municipal wastewater treatment plants in Croatia

Extended-spectrum β-lactamase (ESBL)- and carbapenemase-producing Enterobacterales are a critical global health problem and wastewater treatment plants (WWTPs) can promote their spread into the environment; yet their efficacy is not well characterized. Here, we have used conventional culturing to monitor coliform bacteria and quantitative PCR to monitor 2 ESBL and 5 carbapenemase (CP) genes and 4 enteric opportunistic pathogens (EOPs) in the influent and effluent of 7 Croatian WWTPs in two seasons. In general, levels of total, cefotaxime- and carbapenem-resistant coliforms were significantly reduced but not eliminated by conventional treatment in most WWTPs. Most WWTPs efficiently removed EOPs such as K. pneumoniae and A. baumannii, while E. coli and Enterococcus spp. were reduced but still present in relatively high concentrations in the effluent. ESBL genes (bla_TEM and bla_CTX-M-32) were only slightly reduced or enriched after treatment. CP genes, bla_KPC-3, bla_NDM and bla_OXA-48-like, were sporadically detected, while bla_IMP and bla_VIM were frequently enriched during treatment and correlated with plant size, number or size of hospitals in the catchment area, and COD effluent concentration. Our results suggest that improvements in wastewater treatment technologies are needed to minimize the risk of environmental contamination with top priority EOPs and ARGs and the resulting public health.

Similarities in Virulence and Extended Spectrum Beta-Lactamase Gene Profiles among Cefotaxime-Resistant Escherichia coli Wastewater and Clinical Isolates

The World Health Organization has identified antibiotic resistance as one of the largest threats to human health and food security. In this study, we compared antibiotic resistance patterns between ESBL-producing Escherichia coli from human clinical diseases and cefotaxime-resistant environmental strains, as well as their potential to be pathogenic. Antibiotic susceptibility was tested amongst clinical isolates (n = 11), hospital wastewater (n = 22), and urban wastewater (n = 36, both influent and treated effluents). Multi-drug resistance predominated (>70%) among hospitalwastewater and urban wastewater influent isolates. Interestingly, isolates from clinical and urban treated effluents showed similar multi-drug resistance rates (~50%). Most hospital wastewater isolates were Phylogroup A, while clinical isolates were predominately B2, with a more diverse phylogroup population in urban wastewater. ESBL characterization of cefotaxime-resistant populations identified blaCTX-M-1 subgroup as the most common, whereby blaKPC was more associated with ceftazidime and ertapenem resistance. Whole-genome sequencing of a carbapenemase-producing hospital wastewater E. coli strain revealed plasmid-mediated blaKPC-2. Among cefotaxime-resistant populations, over 60% of clinical and 30% of treated effluent E. coli encoded three or more virulence genes exhibiting a pathogenic potential. Together, the similarity among treated effluent E. coli populations and clinical strains suggest effluents could serve as a reservoir for future multi-drug resistant E. coli clinical infections.

Natural recreational waters and the risk that exposure to antibiotic resistant bacteria poses to human health

Antimicrobial resistance (AMR) is widely recognised as a considerable threat to human health, wellbeing and prosperity. Many clinically important antibiotic resistance genes are understood to have originated in the natural environment. However, the complex interactions between humans, animals and the environment makes the health implications of environmental AMR difficult to quantify. This narrative review focuses on the current state of knowledge regarding antibiotic resistant bacteria (ARB) in natural bathing waters and implications for human health. It considers the latest research focusing on the transmission of ARB from bathing waters to humans. The limitations of existing evidence are discussed, as well as research priorities. The authors are of the opinion that future studies should include faecally contaminated bathing waters and people exposed to these environments to accurately parameterise environment-to-human transmission.

Wastewater bypass is a major temporary point-source of antibiotic resistance genes and multi-resistance risk factors in a Swiss river

Untreated combined sewage (bypass) is often discharged by wastewater treatment plants to receiving rivers during stormwater events, where it may contribute to increased levels of antibiotic resistance genes (ARGs) and multi-resistance risk factors (multi-resistant bacteria and multi-resistance genomic determinants (MGDs)) in the receiving water. Other contamination sources, such as soil runoff and resuspended river sediment could also play a role during stormwater events. Here we report on stormwater event-based sampling campaigns to determine temporal dynamics of ARGs and multi-resistance risk factors in bypass, treated effluent, and the receiving river, as well as complimentary data on catchment soils and surface sediments. Both indicator ARGs (qPCR) and resistome (ARG profiles revealed by metagenomics) indicated bypass as the main contributor to the increased levels of ARGs in the river during stormwater events. Furthermore, we showed for the first time that the risk of exposure to bypass-borne multi-resistance risk factors increase under stormwater events and that many of these MGDs were plasmid associated and thus potentially mobile. In addition, elevated resistance risk factors persisted for some time (up to 22 h) in the receiving water after stormwater events, likely due to inputs from distributed overflows in the catchment. This indicates temporal dynamics should be considered when interpreting the risks of exposure to resistance from event-based contamination. We propose that reducing bypass from wastewater treatment plants may be an important intervention option for reducing dissemination of antibiotic resistance.

Resistance profiles and diversity of β-lactamases in Escherichia coli strains isolated from city-scale sewage surveillance in Bergen, Norway mimic clinical prevalence

The aim of this study was to examine antibiotic resistance profiles and diversity of β-lactamases in Escherichia coli present within the population and the potential spread of resistant E. coli into the receiving environment using city-scale sewage surveillance. In E. coli isolates from ECC plates without antibiotics from ten influent samples (n = 300), highest resistance was observed against ampicillin (16.6%), sulfamethoxazole (9.7%) and trimethoprim (9.0%), while in effluent samples (n = 262) it was against sulfamethoxazole (11.8%), ampicillin (11.5%) and tetracycline (8.8%). All isolates (n = 123) obtained on cefotaxime-containing plates were multidrug-resistant. Several clinically important antibiotic resistance genes (ARGs) were detected in 46 E. coli isolates subjected to whole-genome sequencing, including carbapenemases like NDM-6, VIM-1 and OXA-48-variant, as well as tigecycline resistance gene tet(X4). CTX-M-15 was the most prevalent (42.9%) extended-spectrum β-lactamase among cefotaxime-resistant isolates, followed by CTX-M-27 (31.4%) and CTX-M-14 (17.1%), resembling clinical prevalence in Norway. Most of the sequenced isolates carried other clinically relevant ARGs, such as dfrA17, sul1, sul2, tet(A), aph(6)-Id, aph(3'')-Ib and aadA5. Sixteen different sequence types (STs) were identified, including ST131 (39.1%), ST38 (10.9%) and ST69 (8.7%). One E. coli isolate belonging to novel ST (ST11874) carried multiple virulence factors including genotoxin, salmochelin, aerobactin and yersiniabactin, suggesting that this isolate has potential to cause health concerns in future. Our study reveals presence of clinically relevant ARGs like bla_NDM-6 and tet(X4) in pathogenic strains, which have so far not been reported from the clinics in Norway. Our study may thus, provide a framework for population-based surveillance of antibiotic resistance.

Making waves: How does the emergence of antimicrobial resistance affect policymaking?

This article considers current trends in antimicrobial resistance (AMR) research and knowledge gaps relevant to policymaking in the water sector. Specifically, biological indicators of AMR (antibiotic-resistant bacteria and their resistance genes) and detection methods that have been used so far are identified and discussed, as well as the problems with and solutions to the collection of AMR data, sewage surveillance lessons from the COVID-19 pandemic, and the financial burden caused by AMR, which could be synergically used to improve advocacy on AMR issues in the water sector. Finally, this article proposes solutions to overcoming existing hurdles and shortening the time it will take to have an impact on policymaking and regulation in the sector.

Seizing the moment: now is the time for integrated global surveillance of antimicrobial resistance in wastewater environments

Antimicrobial resistance (AMR) is a growing global health threat that requires coordinated action across One Health sectors (humans, animals, environment) to stem its spread. Environmental surveillance of AMR is largely behind the curve in current One Health surveillance programs, but recent momentum in the establishment of infrastructure for monitoring of the SARS-CoV-2 virus in sewage provides an impetus for analogous AMR monitoring. Simultaneous advances in research have identified striking trends in various AMR measures in wastewater and other impacted environments across global transects. Methodologies for tracking AMR, including metagenomics, are rapidly advancing, but need to be standardized and made modular for access by LMICs, while also developing systems for sample archiving and data sharing. Such efforts will help optimize effective global AMR policy.

Towards risk assessment for antibiotic resistant pathogens in recycled water: a systematic review and summary of research needs

Risk assessment is critical for identifying target concentrations of antibiotic resistant pathogens necessary for mitigating potential harmful exposures associated with water reuse. However, there is currently limited available data characterizing the concentrations of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in recycled water to support robust efforts at risk assessment. The objective of this systematic review was to identify and synthesize the existing literature documenting the presence and abundance of ARB and ARGs in recycled water. In addition, this review identifies best practices and explores monitoring targets for studying ARB and ARGs in recycled water to guide future work and identifies key research needs aimed at better supporting quantitative microbial risk assessment focused on recycled water and antibiotic resistance. Future efforts to collect data about ARB and ARG prevalence in recycled water should report concentration data per unit volume. Sample metadata should also be provided, including a description of treatment approach, a description of planned water uses (e.g., potable, irrigation), methods for conveyance to the point of use, and available physicochemical water quality data. Additional research is needed aimed at identifying recommended ARB and ARG monitoring targets and for developing approaches to incorporate metagenomic data into risk assessment.

On-site chlorination responsible for effective disinfection of wastewater from hospital

Both hospital effluent and a model sewage treatment plant (STP) wastewater prepared by mixing STP influent and STP secondary effluent at a volume ratio of 1:9 were directly treated with chlorine for investigation of their effects on disinfection of antimicrobial-resistant bacteria (AMRB) and antimicrobial-susceptible bacteria (AMSB). The overall results indicate that the chlorine disinfection effectively inactivated the majority of AMRB and AMSB, expect for MRSA and Staphylococcus aureus in both wastewaters. No significant differences could further be observed in the taxonomic diversity of micro-organisms after the treatment. The degrees of disinfection given by the direct chlorination were comparable to those attained by combination of conventional activated sludge process and additional chlorine treatment at the STP. The results of this study evoked a recommendation to operate local chlorination treatment directly for the wastewater from medicinal facilities prior to its flow into the STP as sewage. Although additional disinfection treatment at the STP seems necessary to remove the recalcitrant MRSA and Staphylococcus aureus, the present study desirably contributes to a great reduction of the loads of STP and urgent prevention of spreading of infectious diseases in the present state.

Antibiotic susceptibility of human gut-derived facultative anaerobic bacteria is different under aerobic versus anaerobic test conditions

Facultative anaerobes are the most common cause of infections in anoxic parts of the human body, including deep wound, vagina, periodontal pockets, gastrointestinal tract, genitourinary tract and lungs. Generally, antibiotic susceptibility tests (AST) for facultative anaerobes are performed under aerobic conditions due to ease of handling and rapid growth. However, variation in susceptibility of facultative anaerobes to antibiotics under aerobic and anaerobic conditions can lead to failure of antibiotic treatment. Our study evaluated the susceptibility of facultative anaerobic microorganisms to antibiotics during growth under anaerobic or aerobic conditions. We compared the resistance patterns of representatives from 15 bacterial genera isolated from the human-gastrointestinal tract against 22 different antibiotics from six classes under aerobic and anaerobic conditions. Preliminary results obtained by a disc diffusion method were verified using minimum inhibitory concentration (MIC) testing. The results demonstrated that 7-strains had a similar pattern of drug resistance under both conditions, while the remaining ten strains had significant differences in resistance patterns between aerobic and anaerobic conditions for at least one antibiotic. We conclude that successful antibiotic therapy for host-associated pathogens requires proper assessment of the oxygen condition of the growth environment and MIC testing of each pathogen under anaerobic and aerobic conditions.

Role played by the environment in the emergence and spread of antimicrobial resistance (AMR) through the food chain

The role of food-producing environments in the emergence and spread of antimicrobial resistance (AMR) in EU plant-based food production, terrestrial animals (poultry, cattle and pigs) and aquaculture was assessed. Among the various sources and transmission routes identified, fertilisers of faecal origin, irrigation and surface water for plant-based food and water for aquaculture were considered of major importance. For terrestrial animal production, potential sources consist of feed, humans, water, air/dust, soil, wildlife, rodents, arthropods and equipment. Among those, evidence was found for introduction with feed and humans, for the other sources, the importance could not be assessed. Several ARB of highest priority for public health, such as carbapenem or extended-spectrum cephalosporin and/or fluoroquinolone-resistant Enterobacterales (including Salmonella enterica), fluoroquinolone-resistant Campylobacter spp., methicillin-resistant Staphylococcus aureus and glycopeptide-resistant Enterococcus faecium and E. faecalis were identified. Among highest priority ARGs bla CTX -M, bla VIM, bla NDM, bla OXA -48-like, bla OXA -23, mcr, armA, vanA, cfr and optrA were reported. These highest priority bacteria and genes were identified in different sources, at primary and post-harvest level, particularly faeces/manure, soil and water. For all sectors, reducing the occurrence of faecal microbial contamination of fertilisers, water, feed and the production environment and minimising persistence/recycling of ARB within animal production facilities is a priority. Proper implementation of good hygiene practices, biosecurity and food safety management systems is very important. Potential AMR-specific interventions are in the early stages of development. Many data gaps relating to sources and relevance of transmission routes, diversity of ARB and ARGs, effectiveness of mitigation measures were identified. Representative epidemiological and attribution studies on AMR and its effective control in food production environments at EU level, linked to One Health and environmental initiatives, are urgently required.

Hidden Resistome: Enrichment Reveals the Presence of Clinically Relevant Antibiotic Resistance Determinants in Treated Wastewater-Irrigated Soils

Treated-wastewater (TW) irrigation transfers antibiotic-resistant bacteria (ARB) to soil, but persistence of these bacteria is generally low due to resilience of the soil microbiome. Nonetheless, wastewater-derived bacteria and associated antibiotic resistance genes (ARGs) may persist below detection levels and potentially proliferate under copiotrophic conditions. To test this hypothesis, we exposed soils from microcosm, lysimeter, and field experiments to short-term enrichment in copiotroph-stimulating media. In microcosms, enrichment stimulated growth of multidrug-resistant Escherichia coli up to 2 weeks after falling below detection limits. Lysimeter and orchard soils irrigated in-tandem with either freshwater or TW were subjected to culture-based, qPCR and shotgun metagenomic analyses prior, and subsequent, to enrichment. Although native TW- and freshwater-irrigated soil microbiomes and resistomes were similar to each other, enrichment resulted in higher abundances of cephalosporin- and carbapenem-resistant Enterobacteriaceae and in substantial differences in the composition of microbial communities and ARGs. Enrichment stimulated ARG-harboring Bacillaceae in the freshwater-irrigated soils, whereas in TWW-irrigated soils, ARG-harboring γ-proteobacterial families Enterobacteriaceae and Moraxellaceae were more profuse. We demonstrate that TW-derived ARB and associated ARGs can persist at below detection levels in irrigated soils and believe that similar short-term enrichment strategies can be applied for environmental antimicrobial risk assessment in the future.

Evaluation of Metagenomic-Enabled Antibiotic Resistance Surveillance at a Conventional Wastewater Treatment Plant

Wastewater treatment plants (WWTPs) receive a confluence of sewage containing antimicrobials, antibiotic resistant bacteria, antibiotic resistance genes (ARGs), and pathogens and thus are a key point of interest for antibiotic resistance surveillance. WWTP monitoring has the potential to inform with respect to the antibiotic resistance status of the community served as well as the potential for ARGs to escape treatment. However, there is lack of agreement regarding suitable sampling frequencies and monitoring targets to facilitate comparison within and among individual WWTPs. The objective of this study was to comprehensively evaluate patterns in metagenomic-derived indicators of antibiotic resistance through various stages of treatment at a conventional WWTP for the purpose of informing local monitoring approaches that are also informative for global comparison. Relative abundance of total ARGs decreased by ∼50% from the influent to the effluent, with each sampling location defined by a unique resistome (i.e., total ARG) composition. However, 90% of the ARGs found in the effluent were also detected in the influent, while the effluent ARG-pathogen taxonomic linkage patterns identified in assembled metagenomes were more similar to patterns in regional clinical surveillance data than the patterns identified in the influent. Analysis of core and discriminatory resistomes and general ARG trends across the eight sampling events (i.e., tendency to be removed, increase, decrease, or be found in the effluent only), along with quantification of ARGs of clinical concern, aided in identifying candidate ARGs for surveillance. Relative resistome risk characterization further provided a comprehensive metric for predicting the relative mobility of ARGs and likelihood of being carried in pathogens and can help to prioritize where to focus future monitoring and mitigation. Most antibiotics that were subject to regional resistance testing were also found in the WWTP, with the total antibiotic load decreasing by ∼40–50%, but no strong correlations were found between antibiotics and corresponding ARGs. Overall, this study provides insight into how metagenomic data can be collected and analyzed for surveillance of antibiotic resistance at WWTPs, suggesting that effluent is a beneficial monitoring point with relevance both to the local clinical condition and for assessing efficacy of wastewater treatment in reducing risk of disseminating antibiotic resistance.

Antimicrobial Resistance in Escherichia coli Strains Isolated from Humans and Pet Animals

Throughout scientific literature, we can find evidence that antimicrobial resistance has become a big problem in the recent years on a global scale. Public healthcare systems all over the world are faced with a great challenge in this respect. Obviously, there are many bacteria that can cause infections in humans and animals alike, but somehow it seems that the greatest threat nowadays comes from the Enterobacteriaceae members, especially Escherichia coli. Namely, we are witnesses to the fact that the systems that these bacteria developed to fight off antibiotics are the strongest and most diverse in Enterobacteriaceae. Our great advantage is in understanding the systems that bacteria developed to fight off antibiotics, so these can help us understand the connection between these microorganisms and the occurrence of antibiotic-resistance both in humans and their pets. Furthermore, unfavorable conditions related to the ease of E. coli transmission via the fecal-oral route among humans, environmental sources, and animals only add to the problem. For all the above stated reasons, it is evident that the epidemiology of E. coli strains and resistance mechanisms they have developed over time are extremely significant topics and all scientific findings in this area will be of vital importance in the fight against infections caused by these bacteria.

Predicting clinical resistance prevalence using sewage metagenomic data

Antibiotic resistance surveillance through regional and up-to-date testing of clinical isolates is a foundation for implementing effective empirical treatment. Surveillance data also provides an overview of geographical and temporal changes that are invaluable for guiding interventions. Still, due to limited infrastructure and resources, clinical surveillance data is lacking in many parts of the world. Given that sewage is largely made up of human fecal bacteria from many people, sewage epidemiology could provide a cost-efficient strategy to partly fill the current gap in clinical surveillance of antibiotic resistance. Here we explored the potential of sewage metagenomic data to assess clinical antibiotic resistance prevalence using environmental and clinical surveillance data from across the world. The sewage resistome correlated to clinical surveillance data of invasive Escherichia coli isolates, but none of several tested approaches provided a sufficient resolution for clear discrimination between resistance towards different classes of antibiotics. However, in combination with socioeconomic data, the overall clinical resistance situation could be predicted with good precision. We conclude that analyses of bacterial genes in sewage could contribute to informing management of antibiotic resistance.