Increased waterborne blaNDM-1 resistance gene abundances associated with seasonal human pilgrimages to the upper ganges river

Integrative genome-centric metagenomics for surface water surveillance: Elucidating microbiomes, antimicrobial resistance, and their associations

Surface water ecosystems are intimately intertwined with anthropogenic activities and have significant public health implications as primary sources of irrigation water in agricultural production. Our extensive metagenomic analysis examined 404 surface water samples from four different geological regions in Chile and Brazil, spanning irrigation canals (n = 135), rivers (n = 121), creeks (n = 74), reservoirs (n = 66), and ponds (n = 8). Overall, 50.25 % of the surface water samples contained at least one of the pathogenic or contaminant bacterial genera (Salmonella: 29.21 %; Listeria: 6.19 %; Escherichia: 35.64 %). Furthermore, a total of 1,582 antimicrobial resistance (AMR) gene clusters encoding resistance to 25 antimicrobial classes were identified, with samples from Brazil exhibiting an elevated AMR burden. Samples from stagnant water sources were characterized by dominant Cyanobacteriota populations, resulting in significantly reduced biodiversity and more uniform community compositions. A significant association between taxonomic composition and the resistome was supported by a Procrustes analysis (p < 0.001). Notably, regional signatures were observed regarding the taxonomic and resistome profiles, as samples from the same region clustered together on both ordinates. Additionally, network analysis illuminated the intricate links between taxonomy and AMR at the contig level. Our deep sequencing efforts not only mapped the microbial landscape but also expanded the genomic catalog with newly characterized metagenome-assembled genomes (MAGs), boosting the classification of reads by 12.85 %. In conclusion, this study underscores the value of metagenomic approaches in surveillance of surface waters, enhancing our understanding of microbial and AMR dynamics with far-reaching public health and ecological ramifications.

Exploring quinoxaline derivatives: An overview of a new approach to combat antimicrobial resistance

Antimicrobial resistance (AMR) has emerged as a long-standing global issue ever since the introduction of penicillin, the first antibiotic. Scientists are constantly working to develop innovative antibiotics that are more effective and superior. Unfortunately, the misuse of antibiotics has resulted in their declining effectiveness over the years. By 2050, it is projected that approximately 10 million lives could be lost annually due to antibiotic resistance. Gaining insight into the mechanisms behind the development and transmission of AMR in well-known bacteria including Escherichia coli, Bacillus pumilus, Enterobacter aerogenes, Salmonella typhimurium, and the gut microbiota is crucial for researchers. Environmental contamination in third world and developing countries also plays a significant role in the increase of AMR. Despite the availability of numerous recognized antibiotics to combat bacterial infections, their effectiveness is diminishing due to the growing problem of AMR. The overuse of antibiotics has led to an increase in resistance rates and negative impacts on global health. This highlights the importance of implementing strong antimicrobial stewardship and improving global monitoring, as emphasized by the World Health Organization (WHO) and other organizations. In the face of these obstacles, quinoxaline derivatives have emerged as promising candidates. They are characterized by their remarkable efficacy against a broad spectrum of harmful bacteria, including strains that are resistant to multiple drugs. These compounds are known for their strong structural stability and adaptability, making them a promising and creative solution to the AMR crisis. This review aims to assess the effectiveness of quinoxaline derivatives in treating drug-resistant infections, with the goal of making a meaningful contribution to the global fight against AMR.

Seasonal dynamics of antibiotic resistance genes and mobile genetic elements in a subtropical coastal ecosystem: Implications for environmental health risks

Antibiotic resistance poses a considerable global public health concern, leading to heightened rates of illness and mortality. However, the impact of seasonal variations and environmental factors on the health risks associated with antibiotic resistance genes (ARGs) and their assembly mechanisms is not fully understood. Based on metagenomic sequencing, this study investigated the antibiotic resistome, mobile genetic elements (MGEs), and microbiomes in a subtropical coastal ecosystem of the Beibu Gulf, China, over autumn and winter, and explored the factors influencing seasonal changes in ARG and MGE abundance and diversity. Results indicated that ARG abundance and diversity were higher in winter than in autumn, with beta-lactam and multidrug resistance genes being the most diverse and abundant, respectively. Similarly, MGE abundance and diversity increased in winter and were strongly correlated with ARGs. In contrast, more pronounced associations between microbial communities, especially archaea, and the antibiotic resistome were observed in autumn than in winter. The co-occurrence network identified multiple interactions between MGEs and various multidrug efflux pumps in winter, suggesting a potential for ARG dissemination. Multivariate correlation analyses and path modeling indicated that environmental factors driving microbial community changes predominantly influenced antibiotic resistome assembly in autumn, while the relative importance of MGEs increased significantly in winter. These findings suggest an elevated health risk associated with antimicrobial resistance in the Beibu Gulf during winter, attributed to the dissemination of ARGs by horizontal gene transfer. The observed seasonal variations highlight the dynamic nature of antibiotic resistance dissemination in coastal ecosystems, emphasizing the need for comprehensive surveillance and management measures to address the growing threat of antimicrobial resistance in vulnerable environments.

Metallo-beta-lactamases: mechanisms, treatment challenges, and future prospects

INTRODUCTION

Metallo-beta-lactamases (MBLs) are responsible for resistance to almost all beta-lactam antibiotics. Found predominantly in Gram-negative bacteria, they severely limit treatment options. Understanding the epidemiology, risk factors, treatment, and prevention of infections caused by MBL-producing organisms is essential to reduce their burden.

AREAS COVERED

The origins and structure of MBLs are discussed. We describe the mechanisms of action that differentiate MBLs from other beta-lactamases. We discuss the global epidemiology of MBL-producing organisms and their impact on patients' outcomes. By exposing the mechanisms of transmission of MBLs among bacterial populations, we emphasize the importance of infection prevention and control.

EXPERT OPINION

MBLs are spreading globally and challenging the majority of available antibacterial agents. Genotypic tests play an important role in the identification of MBL production. Phenotypic tests are less specific but may be used in low-resource settings, where MBLs are more predominant. Infection prevention and control are critical to reduce the spread of organisms producing MBL in healthcare systems. New combinations such as avibactam-aztreonam and new agents such as cefiderocol have shown promising results for the treatment of infections caused by MBL-producing organisms. New antibiotic and non-antibiotic agents are being developed and may improve the management of infections caused by MBL-producing organisms.

Affecting factors and mechanism of removing antibiotics and antibiotic resistance genes by nano zero-valent iron (nZVI) and modified nZVI: A critical review

Antibiotics and antibiotic resistance genetic pollution have become a global environmental and health concern recently, with frequent detection in various environmental media. Therefore, finding ways to control antibiotics and antibiotic resistance genes (ARGs) is urgently needed. Nano zero-valent iron (nZVI) has shown a positive effect on antibiotics degradation and restraining ARGs, making it a promising solution for controlling antibiotics and ARGs. However, given the current increasingly fragmented research focus and results, a comprehensive review is still lacking. In this work, we first introduce the origin and transmission of antibiotics and ARGs in various environmental media, and then discuss the affecting factors during the degradation of antibiotics and the control of ARGs by nZVI and modified nZVI, including pH, nZVI dose, and oxidant concentration, etc. Then, the mechanisms of antibiotic and ARGs removal promoted by nZVI are also summarized. In general, the mechanism of antibiotic degradation by nZVI mainly includes adsorption and reduction, while promoting the biodegradation of antibiotics by affecting the microbial community. nZVI can also be combined with persulfates to degrade antibiotics through advanced oxidation processes. For the control of ARGs, nZVI not only changes the microbial community structure, but also affects the proliferation of ARGs through affecting the fate of mobile genetic elements (MGEs). Finally, some new ideas on the application of nZVI in the treatment of antibiotic resistance are proposed. This paper provides a reference for research and application in this field.

Mobile genetic elements affect the dissemination of antibiotic resistance genes (ARGs) of clinical importance in the environment

The prevalence of antibiotic resistance genes (ARGs) in the environment is a quintessential One Health issue that threats both human and ecosystem health; however, the source and transmission of ARGs, especially clinically important ARGs (CLIARGs), in the environment have not yet been well studied. In the present study, shotgun metagenomic approaches were used to characterize the microbiome, resistome, and mobilome composition in human feces and six different environment sample types in South China. Overall, the resistome harbored 157 CLIARGs, with specific ARG hotspots (e.g., human feces, wastewater treatment plants, livestock manure and wastewater) excreting significantly higher abundance of CLIARGs compared with the natural environment. A redundancy analysis (RDA) was performed and revealed that the bacterial community compositions and mobile genetic elements (MGEs) explained 55.08% and 34.68% of the variations in ARG abundance, respectively, indicating that both bacterial community and MGEs are key contributors to the maintenance and dissemination of CLIARGs in the environment. The network analysis revealed non-random co-occurrence patterns between 200 bacterial genera and 147 CLIARGs, as well as between 135 MGEs and 123 CLIARGs. In addition to numerous co-shared CLIARGs among different sample types, the source tracking program based on the FEAST probabilistic model was used to estimate the relative contributions of the CLIARGs from potential sources to the natural environment. The source tracking analysis results delineated that mobilome, more than microbiome, contributed CLIARG transmission from those ARG hotspots into natural environment, and the MGEs in WWTPs seem to play the most significant role in the spread of CLIARGs to the natural environment (average contribution 32.9%-46.4%). Overall, this study demonstrated the distribution and dissemination of CLIARGs in the environment, and aimed to better inform strategies to control the spread of CLIARGs into the natural environment.

Antibiotic occurrence, environmental risks, and their removal from aquatic environments using microalgae: Advances and future perspectives

Antibiotic pollution has caused a continuous increase in the development of antibiotic-resistant bacteria and antibiotic-resistant genes (ARGs) in aquatic environments worldwide. Algae-based bioremediation technology is a promising eco-friendly means to remove antibiotics and highly resistant ARGs, and the generated biomass can be utilized to produce value-added products of industrial significance. This review discussed the prevalence of antibiotics and ARGs in aquatic environments and their environmental risks to non-target organisms. The potential of various microalgal species for antibiotic and ARG removal, their mechanisms, strategies for enhanced removal, and future directions were reviewed. Antibiotics can be degraded into non-toxic compounds in microalgal cells through the action of extracellular polymeric substances, glutathione-S-transferase, and cytochrome P450; however, antibiotic stress can alter microalgal gene expression and growth. This review also deciphered the effect of antibiotic stress on microalgal physiology, biomass production, and biochemical composition that can impact their commercial applications.

High throughput qPCR unveils shared antibiotic resistance genes in tropical wastewater and river water

The global challenge posed by rising antimicrobial resistance, and the adoption of a One Health approach, has led to the prioritisation of surveillance for antibiotic resistance genes (ARGs) in various environments. Herein lies an information gap, particularly in the context of Thailand, where there is scarce data on ARG prevalence across diverse environmental matrices and throughout different seasons. This study aimed to fill this void, analysing ARG prevalence by high-throughput qPCR in influent (n = 12) and effluent wastewater (n = 12) and river water (n = 12). The study reveals a substantial and largely uniform presence of ARGs across all water sample types (87 % similarity). Intriguingly, no ARGs were exclusive to specific water types, indicating an extensive circulation of resistance determinants across the aquatic environment. The genes intI1, tnpA, and intI3, part of the integrons and mobile genetic elements group, were detected in high relative abundance in both wastewater and river water samples, suggesting widespread pollution of rivers with wastewater. Additional high-prevalence ARGs across all water types included qepA, aadA2, merA, sul1, qacF/H, sul2, aadB, and ereA. More alarmingly, several ARGs (e.g., blaVIM, intI3, mcr-1, mexB, qepA, vanA, and vanB) showed higher relative abundance in effluent and river water than in influents, which suggests malfunctioning or inadequate wastewater treatment works and implicates this as a possible mechanism for environmental contamination. Nine genes (i.e., blaCTX-M, blaVIM, emrD, ermX, intI1, mphA, qepA, vanA, and vanB) were recovered in greater relative abundance during the dry season in river water samples as compared to the wet season, suggesting there are seasonal impacts on the efficacy of wastewater treatment practices and pollution patterns into receiving waters. This study highlights the urgency for more effective measures to reduce antibiotic resistance dissemination in water systems.

Genomic investigation unveils high-risk ESBL producing Enterobacteriaceae within a rural environmental water body

Antimicrobial resistance is regarded as a global threat to public health, animals, and the environment, emerging in response to extensive utilization of antimicrobials. The determinants of antimicrobial resistance are transported to susceptible bacterial populations through genetic recombination or through gene transfer, mediated by bacteriophages, plasmids, transposons, and insertion sequences. To determine the penetration of antimicrobial resistance into the bacterial population of the Thiruvandarkoil Lake, a water body located in the rural settings of Puducherry, India, culture-based microbiological and genomic approaches were used. Resistant bacterial isolates obtained from microbiological screening were subjected to whole genome sequencing and the genetic determinants of antimicrobial resistance were identified using in silico genomic tools. Cephalosporin-resistant isolates were found to produce extended spectrum beta lactamases, encoded by blaVEB-6 (in Proteus mirabilis PS01), blaSHV-12 and ompK36 mutation (in Klebsiella quasipneumoniae PS02) and blaSHV-12, blaACT-16, blaCTX-M and blaNDM-1 in (Enterobacter hormaechei PS03). Genes encoding heavy metal resistance, virulence and resistance to detergents were also detected in these resistant isolates. Among ESBL-producing organisms, one mcr-9-positive Enterobacter hormaechei was also identified in this study. To our knowledge, this is the first report of mcr-9 carrying bacterium in the environment in India. This study seeks the immediate attention of policy makers, researchers, government officials and environmental activists in India, to develop surveillance programs to monitor the dissemination of antimicrobial resistance in the environment.

Development of a national antibiotic multimetric index for identifying watersheds vulnerable to antibiotic pollution

Improved surveillance of antibiotics and antibiotic resistance (AR) throughout the environment is an important aspect of the prevention and control of threats posed to human and ecological health. In response to field investigations often limited by resources and time, this study aims to develop a systematic approach to assess watershed vulnerability to antibiotic pollution and AR by integrating modeling and field studies. The national antibiotic pollution vulnerability index was developed to identify watersheds most impacted by antibiotic sources. The index incorporates multiple metrics representing antibiotic pollution driven by both agricultural activities and municipal wastewater (i.e. outpatient antibiotic prescriptions, wastewater treatment plant effluent flow, stream order and dilution factor of effluent-receiving streams, manure application, and animal facilities), alongside climate change indicators (i.e., temperature, precipitation, and runoff). The pollution index was applied at a state level in North Carolina to identify the most-impacted watersheds and inform site selection for targeted field study quantifying azithromycin, ciprofloxacin, sulfamethoxazole, and trimethoprim concentrations. Modeled-informed sites in NC demonstrated the highest reported concentrations of azithromycin, trimethoprim, and sulfamethoxazole compared to previous NC studies, confirming the index effectiveness in identifying watersheds with higher antibiotic concentrations. At the national scale, watersheds relatively more vulnerable to antibiotic pollution are predominantly located in the Midwest, South, and Northeast regions of the U.S., with Iowa and Indiana being the most impacted states. Climate change is expected to exacerbate watershed vulnerability to agriculture-driven AR in the Midwest and Northeast due to an increase in precipitation and mean temperature coupled with intense agricultural activities. In addition, due to climate change-induced reductions in precipitation and runoff, watersheds in the Midwest, Mid-Atlantic, and South Central are dominantly at higher risk of effluent-driven AR occurrences. We have disseminated the developed indices as open-source online tools to aid in prioritizing strategies to mitigate AR occurrence across the U.S.

Water, Water Everywhere, but Every Drop Unique: Challenges in the Science to Understand the Role of Contaminants of Emerging Concern in the Management of Drinking Water Supplies

The protection and management of water resources continues to be challenged by multiple and ongoing factors such as shifts in demographic, social, economic, and public health requirements. Physical limitations placed on access to potable supplies include natural and human-caused factors such as aquifer depletion, aging infrastructure, saltwater intrusion, floods, and drought. These factors, although varying in magnitude, spatial extent, and timing, can exacerbate the potential for contaminants of concern (CECs) to be present in sources of drinking water, infrastructure, premise plumbing and associated tap water. This monograph examines how current and emerging scientific efforts and technologies increase our understanding of the range of CECs and drinking water issues facing current and future populations. It is not intended to be read in one sitting, but is instead a starting point for scientists wanting to learn more about the issues surrounding CECs. This text discusses the topical evolution CECs over time (Section 1), improvements in measuring chemical and microbial CECs, through both analysis of concentration and toxicity (Section 2) and modeling CEC exposure and fate (Section 3), forms of treatment effective at removing chemical and microbial CECs (Section 4), and potential for human health impacts from exposure to CECs (Section 5). The paper concludes with how changes to water quantity, both scarcity and surpluses, could affect water quality (Section 6). Taken together, these sections document the past 25 years of CEC research and the regulatory response to these contaminants, the current work to identify and monitor CECs and mitigate exposure, and the challenges facing the future.

Comparative bacteriome and antibiotic resistome analysis of water and sediment of the Ganga River of India

A comparative analysis between water and sediment can provide better information to understand the dynamics of the inhabitant microbiome and their respective antibiotic resistance genes of a river. Therefore, the present investigation was carried to explore the limited information available on bacterial microbiome and their predictive antibiotic resistance genes (ARGs) from water and sediment of the Ganga River. The study utilized the NGS-based sequences previously submitted under the accession number (PRJNA847424 and PRJNA892876). Overall analysis revealed that twenty phyla and fifty-four genera were shared between the water and sediment of the Ganga River. Of them, nine phyla and nineteen genera were observed as significantly different (p-value < 0.05). Where the majority of the genera were associated with the sediment samples over the water that identify the sediment samples as more diverse for species richness. Similarly, seventy-six ARGs were shared between water and sediment samples. Of the ten abundant antibiotic resistance pathways, seven were relatively abundant in sediment samples as compared to the water. Vancomycin resistance genes were significantly more abundant among sediment samples, whereas β-lactam resistance genes were equally distributed in water and sediment samples. The network analysis further revealed that five genera (Flavobacterium, Pseudomonas, Acinetobacter, Candidatus_divison CL5003, and Candidatus_division SWB02) showed a significantly positive correlation with six antibiotic resistance pathways (β-lactam, vancomycin, multidrug resistance, tetracycline, aminoglycoside, and macrolide resistance pathways). The study comes out with several findings where sediment may be considered as a more atrocious habitat for evolving the resistance mechanisms against threatful antibiotics over the water samples of the Ganga River.

An overview on the prevalence and potential impact of antimicrobials and antimicrobial resistance in the aquatic environment of India

India at present is one of the leading countries in antimicrobial drug production and use, leading to increasing antimicrobial resistance (AMR) and public health problems. Attention has mainly been focused on the human and food animals' contribution to AMR neglecting the potential contribution of the perceptibly degraded aquatic environment in India. The paper reviews the available published literature in India on the prevalence of antimicrobial residues and their dissemination pathways in wastewater of pharmaceutical industries, sewage treatment plants, hospitals, riverine, community pond water, and groundwater. The prevalence of antimicrobial residue concentration, pathogenic and non-pathogenic bacteria antimicrobial resistant bacteria (ARB), their drug resistance levels, and their specific antimicrobial resistant genes (ARGs) occurring in various water matrices of India have been comprehensively depicted from existing literature. The concentration of some widely used antimicrobials recorded from the sewage treatment plants and hospital wastewater and rivers in India has been compared with other countries. The ecotoxicological risk posed by these antimicrobials in the various water matrices in India indicated high hazard quotient (HQ) values for pharmaceutical effluents, hospital effluents, and river water. The degraded aquatic environment exhibited the selection of a wide array of co-existent resistant genes for antibiotics and metals. The review revealed improper use of antibiotics and inadequate wastewater treatment as major drivers of AMR contaminating water bodies in India and suggestion for containing the challenges posed by AMR in India has been proposed.

A holistic review on trend, occurrence, factors affecting pesticide concentration, and ecological risk assessment

Demographic outbursts and increased food demands invoke excessive use of pesticides in the agricultural field for increasing productivity which leads to the relentless decline of riverine health and its tributaries. These tributaries are connected to a plethora of point and non-point sources that transport pollutants including pesticides into the Ganga river's mainstream. Simultaneous climate change and lack of rainfall significantly increase pesticide concentration in the soil and water matrix of the river basin. This paper is intended to review the paradigm shift of pesticide pollution in the last few decades in the river Ganga and its tributaries. Along with this, a comprehensive review suggests the ecological risk assessment method which facilitates policy development, sustainable riverine ecosystem management, and decision-making. Before 2011, the total mixture of Hexachlorocyclohexane was found at 0.004-0.026 ng/mL in Hooghly, but now, the concentration has increased up to 0.465-4.132 ng/mL. Aftermath of critical review, we observed maximum residual commodities and pesticide contamination reported in Uttar Pradesh > West Bengal > Bihar > Uttara Khand possibly because of agricultural load, increasing settlement, and incompetency of sewage treatment plant in the reclamation of pesticide contamination.

Profile and actual transmissibility of Carbapenem resistance genes: Intracellular and extracellular DNA in hospital wastewater

The current worldwide spread of carbapenem resistance genes (CRGs) has posed a major public health threat, which continues to grow in severity. Hospital wastewaters (HWWs) are major reservoirs for antibiotic resistance genes, while resistomes in HWWs are still poorly characterized when it comes to CRGs. We comprehensively characterized the profile and actual transmissibility of extracellular CRGs (eCRGs) and intracellular CRGs (iCRGs) in HWWs for the first time. In this study, CRGs showed similar relative abundance in treated and untreated HWWs. Meanwhile, HWWs treatments led to the enrichment of bla_IMP-8, probably attributed to the promotion of Novosphingobium and Prosthecobacter after treatment. To evaluate the transmission potential of CRGs, extracellular and intracellular carbapenem-resistant plasmids were captured from HWWs by transformation and conjugation, respectively. We found an interesting phenomenon regarding the transmission characteristics of CRGs: bla_KPC-carrying plasmids could only be captured by transformation, while bla_NDM-carrying plasmids were captured by conjugation. Further experiments showed that HWW treatments increased the conjugation ability of bla_NDM. In conclusion, our study demonstrated that HWWs are significant reservoirs of CRGs and various CRGs exhibit different modes of transmission in HWWs. CRGs cannot be removed by membrane bioreactor and chlorine disinfection. An urgent need is to develop more efficient wastewater treatments to limit CRG dissemination.

Evolution and implementation of One Health to control the dissemination of antibiotic-resistant bacteria and resistance genes: A review

Antibiotic resistance is a serious threat to humanity and its environment. Aberrant usage of antibiotics in the human, animal, and environmental sectors, as well as the dissemination of resistant bacteria and resistance genes among these sectors and globally, are all contributing factors. In humans, antibiotics are generally used to treat infections and prevent illnesses. Antibiotic usage in food-producing animals has lately emerged as a major public health concern. These medicines are currently being utilized to prevent and treat infectious diseases and also for its growth-promoting qualities. These methods have resulted in the induction and spread of antibiotic resistant infections from animals to humans. Antibiotics can be introduced into the environment from a variety of sources, including human wastes, veterinary wastes, and livestock husbandry waste. The soil has been recognized as a reservoir of ABR genes, not only because of the presence of a wide and varied range of bacteria capable of producing natural antibiotics but also for the usage of natural manure on crop fields, which may contain ABR genes or antibiotics. Fears about the human health hazards of ABR related to environmental antibiotic residues include the possible threat of modifying the human microbiota and promoting the rise and selection of resistant bacteria, and the possible danger of generating a selection pressure on the environmental microflora resulting in environmental antibiotic resistance. Because of the connectivity of these sectors, antibiotic use, antibiotic residue persistence, and the existence of antibiotic-resistant bacteria in human-animal-environment habitats are all linked to the One Health triangle. The pillars of support including rigorous ABR surveillance among different sectors individually and in combination, and at national and international level, overcoming laboratory resource challenges, and core plan and action execution should be strictly implemented to combat and contain ABR under one health approach. Implementing One Health could help to avoid the emergence and dissemination of antibiotic resistance while also promoting a healthier One World. This review aims to emphasize antibiotic resistance and its regulatory approaches from the perspective of One Health by highlighting the interconnectedness and multi-sectoral nature of the human, animal, and environmental health or ill-health facets.

Global groundwater vulnerability for Pharmaceutical and Personal care products (PPCPs): The scenario of second decade of 21st century

The global production of PPCPs have increased by multiple folds promoting excessive exposure of its metabolites to humans via different aquatic systems. The higher residence time of toxic precursors of these metabolites pose direct human health risk. Among the different aquatic systems, the contamination of groundwater by PPCPs is the most concerning threat. This threat is especially critical considering the lesser oxidizing potential of the groundwater as compared to freshwater/river water. A major challenge also arises due to excessive dependency of the world's population on groundwater, which is exponentially increasing with time. This makes the identification and characterization of spatial contamination hotspots highly probabilistic as compared to other freshwater systems. The situation is more vulnerable in developing countries where there is a reported inadequacy of wastewater treatment facilities, thereby forcing the groundwater to behave as the only available sequestrating sink for all these contaminants. With increased consumption of antibiotics and other pharmaceuticals compounds, these wastes have proven capability in terms of enhancing the resistance among the biotic community of the soil systems, which ultimately can become catastrophic and carcinogenic in near future. Recent studies are supporting the aforementioned concern where compounds like diclofenac (analgesic) have attained a concentration of 1.3 mgL^-1 in the aquifer systems of Delhi, India. The situation is far worse for developed nations where prolonged and indiscriminate usage of antidepressants and antibiotics have life threating consequences. It has been confirmed that certain compounds like ofloxacin (antibiotics) and bis-(2-ethylhexyl)phthalate are present in some of the most sensitive wells/springs of the United States and Mexico. The current trend of the situation has been demonstrated by integrating a comparative approach of the published literatures in last three years. This review provides first-hand information report for formulating a directive policy framework for tackling PPCPs issues in the groundwater system.

The source, fate and prospect of antibiotic resistance genes in soil: A review

Antibiotic resistance genes (ARGs), environmental pollutants of emerging concern, have posed a potential threat to the public health. Soil is one of the huge reservoirs and propagation hotspot of ARGs. To alleviate the potential risk of ARGs, it is necessary to figure out the source and fate of ARGs in the soil. This paper mainly reviewed recent studies on the association of ARGs with the microbiome and the transmission mechanism of ARGs in soil. The compositions and abundance of ARGs can be changed by modulating microbiome, soil physicochemical properties, such as pH and moisture. The relationships of ARGs with antibiotics, heavy metals, polycyclic aromatic hydrocarbons and pesticides were discussed in this review. Among the various factors mentioned above, microbial community structure, mobile genetic elements, pH and heavy metals have a relatively more important impact on ARGs profiles. Moreover, human health could be impacted by soil ARGs through plants and animals. Understanding the dynamic changes of ARGs with influencing factors promotes us to develop strategies for mitigating the occurrence and dissemination of ARGs to reduce health risks.

Prevalence of Waterborne blaNDM-1 Gene Producing Carbapenem-resistant Klebsiella pneumoniae from Al-Hillah River Water, Babylon Province, Iraq

The current work suggested the occurrence of blaNDM-1 gene among Klebsiella pneumoniae recovered from surface waters of the Al-Hillah River. Between January and April 2015, water samples (101) were taken from seven different area of the Al-Hillah River, Babylon province, Iraq. K.pneumoniae was reported in percentage of 35 (34.6%). The antibiotics susceptibility profile of K.pneumoniae was determined with disk diffusion assay. The most common resistance was detected for penicillins agents (ampicillin and cloxacillin) with 20(57.14%) and 17(48.57%) resistance rate, respectively. Two isolates of K.pneumoniae were carbapenem-resistant. Phenotypic screening of metallo β-lactamase detection was carried out using imipenem–EDTA double disk synergy test for carbapenem resistant isolates, 2(100%) isolates with positive result. Conventional Polymerase Chain Reaction (PCR) test was used for detection NDM-1 beta-lactamase, 1 (50%) K.pneumoniae isolate harboring this gene.

Spatiotemporal distribution of antimicrobial resistant organisms in different water environments in urban and rural settings of Bangladesh

The spatial distribution of clinically important antibiotic resistant bacteria (ARB) and associated genes is important to identify the environmental distribution of contamination and 'hotspots' of antimicrobial resistance (AMR). We conducted an integrated survey of AMR in drinking water, wastewater and surface water (rivers and ponds) in three settings in Bangladesh: rural households, rural poultry farms, and urban food markets. Spatial mapping was conducted via geographic information system (GIS) using ArcGIS software. Samples (n = 397) were analyzed for the presence of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec), carbapenem-resistant E. coli (CR-Ec) and resistance genes (bla_CTX-M-1,bla_NDM-1). In rural households, 5% of drinking water supply samples tested positive for ESBL-Ec, and a high proportion of wastewater, pond and river water samples were positive for ESBL-Ec (90%, 76%, and 85%, respectively). In poultry farms, 10% of drinking water samples tested positive for ESBL-Ec compared to a high prevalence in wastewater, pond and river water (90%, 68%, and 85%, respectively). CR-Ec prevalence in household wastewater and pond water was relatively low (8% and 5%, respectively) compared to river water (33%). In urban areas, 38% of drinking water samples and 98% of wastewater samples from food markets tested positive for ESBL-Ec while 30% of wastewater samples tested positive for CR-Ec. Wastewaters had the highest concentrations of ESBL-Ec, CR-Ec, bla_CTXM-1 and bla_NDM-1 and these were significantly higher in urban compared to rural samples (p < 0.05). ESBL-Ec is ubiquitous in drinking water, wastewater and surface water bodies in both rural and urban areas of Bangladesh. CR-Ec is less widespread but found at a high prevalence in wastewater discharged from urban food markets and in rural river samples. Surveillance and monitoring of antibiotic resistant organisms and genes in waterbodies is an important first step in addressing environmental dimensions of AMR.

Antibiotic resistance in the environment

Antibiotic resistance is a global health challenge, involving the transfer of bacteria and genes between humans, animals and the environment. Although multiple barriers restrict the flow of both bacteria and genes, pathogens recurrently acquire new resistance factors from other species, thereby reducing our ability to prevent and treat bacterial infections. Evolutionary events that lead to the emergence of new resistance factors in pathogens are rare and challenging to predict, but may be associated with vast ramifications. Transmission events of already widespread resistant strains are, on the other hand, common, quantifiable and more predictable, but the consequences of each event are limited. Quantifying the pathways and identifying the drivers of and bottlenecks for environmental evolution and transmission of antibiotic resistance are key components to understand and manage the resistance crisis as a whole. In this Review, we present our current understanding of the roles of the environment, including antibiotic pollution, in resistance evolution, in transmission and as a mere reflection of the regional antibiotic resistance situation in the clinic. We provide a perspective on current evidence, describe risk scenarios, discuss methods for surveillance and the assessment of potential drivers, and finally identify some actions to mitigate risks.

Quantitative Risk Assessment for the Introduction of Carbapenem-Resistant Enterobacteriaceae (CPE) into Dutch Livestock Farms

Early detection of emerging carbapenem-resistant Enterobacteriaceae (CPE) in food-producing animals is essential to control the spread of CPE. We assessed the risk of CPE introduction from imported livestock, livestock feed, companion animals, hospital patients, and returning travelers into livestock farms in The Netherlands, including (1) broiler, (2) broiler breeder, (3) fattening pig, (4) breeding pig, (5) farrow-to-finish pig, and (6) veal calf farms. The expected annual number of introductions was calculated from the number of farms exposed to each CPE source and the probability that at least one animal in an exposed farm is colonized. The total number of farms with CPE colonization was estimated to be the highest for fattening pig farms, whereas the probability of introduction for an individual farm was the highest for broiler farms. Livestock feed and imported livestock are the most likely sources of CPE introduction into Dutch livestock farms. Sensitivity analysis indicated that the number of fattening pig farms determined the number of high introductions in fattening pigs from feed, and that uncertainty on CPE prevalence impacted the absolute risk estimate for all farm types. The results of this study can be used to inform risk-based surveillance for CPE in livestock farms.

Surveillance and prevalence of antimicrobial resistant bacteria from public settings within urban built environments: Challenges and opportunities for hygiene and infection control

Antimicrobial resistant (AMR) bacteria present one of the biggest threats to public health; this must not be forgotten while global attention is focussed on the COVID-19 pandemic. Resistant bacteria have been demonstrated to be transmittable to humans in many different environments, including public settings in urban built environments where high-density human activity can be found, including public transport, sports arenas and schools. However, in comparison to healthcare settings and agriculture, there is very little surveillance of AMR in the built environment outside of healthcare settings and wastewater. In this review, we analyse the existing literature to aid our understanding of what surveillance has been conducted within different public settings and identify what this tells us about the prevalence of AMR. We highlight the challenges that have been reported; and make recommendations for future studies that will help to fill knowledge gaps present in the literature.

Metagenomic exploration reveals a differential patterning of antibiotic resistance genes in urban and peri-urban stretches of a riverine system

Antimicrobial resistance in the riverine ecosystem of urban areas is an alarming concern worldwide, indicating the importance of molecular monitoring to understand their patterning in urban and peri-urban areas. In the present study, we evaluated the influence of urban rivers on the connected peri-urban rivers of a riverine system of India in the context of antibiotic resistance genes. The rivers traversing through urban (Mula, Mutha, Pawana, and Ramnadi) and peri-urban stretches (Bhima and Indrayani) form the riverine system of Pune district in Maharashtra, India. The MinION-based shotgun metagenomic analysis revealed the resistome against 26 classes of antibiotics, including the last line of antibiotics. In total, we observed 278 ARG subtypes conferring resistance against multiple drugs (40%), bacitracin (10%), aminoglycoside (7.5%), tetracycline (7%), and glycopeptide (5%). Further, the alpha diversity analysis suggested relatively higher ARG diversity in the urban stretches than peri-urban stretches of the riverine system. The NMDS (non-metric multidimensional scaling) analysis revealed significant differences with overlapping similarities (stress value = 0.14, p-value = 0.004, ANOSIM statistic R: 0.2328). These similarities were reasoned by assessing the influence of downstream sites (sites at the outskirts of Pune city; however, directly impacted), which revealed significant differences in the ARG contents of urban and peri-urban stretches (stress value = 0.14, p-value = 0.001, ANOSIM statistic R: 0.6137). Overall, we detected the dissemination of antibiotic resistance genes from the polluted urban rivers into the peri-urban rivers located downstream in the connected riverine system potentially driven by anthropogenic activities.

Persisting antibiotic resistance gene pollution and its association with human sewage sources in tropical marine beach waters

Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are pollutants of worldwide concern that threaten human health and ecosystems. Anthropogenic activities and wastewater could be ARB and ARG pollution sources; however, research on ARG abundance and microbial source tracking (MST) of contamination in tropical marine waters is limited. This study examined spatiotemporal variations of six ARGs (bla_NDM, bla_TEM, bla_VIM, mcr-1, sul1, and tetQ) against the widely used antibiotic groups and a class 1 integron-integrase gene (intI1) at two Thai tropical recreational beaches (n = 41). Correlations between ARGs and sewage-specific MST markers (i.e., crAssphage and human polyomaviruses [HPyVs]) and fecal indicator bacteria (i.e., total coliforms, fecal coliforms, and enterococci) were also investigated. Bla_TEM, intI1, sul1, and tetQ were ubiquitous at both beaches (85.4-100% detection rate); intI1 was the most abundant (3-6 orders in log₁₀ copies/100 mL), followed by bla_TEM (2-4 orders), sul1 (2-3 orders), and tetQ (2-4 orders). Bla_NDM was found in 7.3% (up to 4 orders), and no mcr-1 was detected. Interestingly, bla_VIM was prevalent at one beach (2-5 orders; n = 17), but found in only one sample at the other (4 orders). Temporal, but not spatial, differences were noticed; bla_TEM was at higher levels in the wet season. IntI1 correlated with sul1 and tetQ (Spearman's rho = 0.47-0.97), suggesting potential horizontal gene transfer. CrAssphage, but not HPyVs, correlated with intI1, sul1, and tetQ (Spearman's rho = 0.50-0.74). Higher numbers of ARGs tended to co-occur in samples with higher crAssphage concentrations, implying sewage contribution to the marine water, with a persisting ARG background. This study provides insight into the ARG pollution status of tropical coastal waters and suggests crAssphage as a proxy for ARG pollution, which could facilitate effective management policies to minimize ARG dissemination in marine environments.

Easy Access to Antibiotics; Spread of Antimicrobial Resistance and Implementation of One Health Approach in India

Antimicrobial resistance (AMR) is a global public health concern because of its fast spread. India, one of the world's top consumer of antibiotics and second most populated country has its unique constraints of social, cultural and economic strata. The continual self-medication, use of antibiotics for the growth promotion in animals, and accumulation of residual antibiotics in the environment challenge the implementation of AMR containment policy. Hence, the present review attempts to delineate the influence of antibiotics abuse on the human, animal and environmental health under the realm of one health. It was based on the literature search using public databases to highlight the rapid surge in the burden of AMR in India affecting various sectors and/or ecosystems in India. It was found that the irrational and overuse of antibiotics in different sectors have led to the emergence of extended antimicrobial resistance wherein the environment acts as a reservoir of antibiotic resistance genes (ARGs); completing the cycle of contamination and recontamination. There are efforts by government policy makers to reduce the burden of AMR in the country to reduce the health risks, through the One Health approach. Parallel efforts in educating healthcare professionals, strict legislation for pharmacies and pharmaceutical companies should be prioritize. At the same time surveillance of newly emerged AMR pathogens, prioritising research focusing on AMR, and awareness camps or programs among the local population is critical while addressing the consequences of spared of AMR in India.

β-Lactam Resistance Gene NDM-1 in the Aquatic Environment: A Review

New Delhi Metallo-β-lactamase-1 (NDM-1) offers carbapenem antibiotics resistance that creates an evolving challenge in treating bacterial infections. NDM-1-bearing strains were observed in surface waters around New Delhi in 2010 and after then identified globally. The usage of antibiotics may hasten the growth of the NDM-1-producing bacteria, which pose severe hazards to human and animal health. The emergence of the NDM-1 in the aquatic environment is turning out to be a growing concern worldwide. NDM-1 gene conferring resistance to a widespread class of antibiotics has been observed in bacteria disseminated in animal production wastewaters, hospital sewage, domestic sewage, industrial effluents, wastewater treatment plants, drinking water, surface water, and even in groundwater. This review recapitulates the currently published research studies on the prevalence and geographical distribution of the NDM-1 gene in the aquatic environment, its habitats, and healthcare risk associated with NDM-1-producing bacteria, in addition to molecular techniques employed to reveal the occurrence of the NDM-1 in the aquatic environment, including conventional polymerase chain reaction, real-time qPCR, DNA hybridization, and microarray-based methods.

Occurrence of emerging contaminants in highly anthropogenically influenced river Yamuna in India

River Yamuna is one of the major lifelines of Northern India. The study quantified 16 target compounds including pharmaceuticals, personal care products, and hormones in the Yamuna river. Surface water samples were collected from 13 locations spanning 575 km along the river, and from two of its tributaries, Hindon river and Hindon canal. Spatiotemporal variations in the occurrence of the target compounds at the 13 sites during summer and post-monsoon season were investigated. Caffeine, estrone, gemfibrozil, sulfamethoxazole, testosterone and trimethoprim were found in all the samples, indicating substantial usage and/or persistence in the environment. The mean concentration of the target compounds ranged from 25.5 to 2187.5 ng/L. Higher concentrations were detected during the post monsoon, compared to the summer season. The highest concentration detected was of trimethoprim (8807.6 ng/L) during summer sampling, followed by caffeine (6489.9 ng/L) and gemfibrozil (2991 ng/L), during the post-monsoon sampling. The lowest concentration detected was of estrone (10.7 ng/L), during the summer sampling. The runoff from the catchment areas is one of the contributing factors for the increased concentration of the compounds during post monsoon. During summer, the river bed goes dry, facilitating the adsorption of the compounds onto the river bed sediments. The three sampling locations Okhla barrage (ponding of water from drains traversing Delhi), confluence of Yamuna with Shahadara drain (industrial and poultry cluster, and Ghazipur dumping yard) and Agra city (industrial clusters) were the hotspots in terms of total concentration of the target compounds. The study also reported the presence of PPCPs and hormones in the finished drinking water of two DWTPs at Mathura and Agra.

Extended Ecological Restoration of Bacterial Communities in the Godavari River During the COVID-19 Lockdown Period: a Spatiotemporal Meta-analysis

The unprecedented COVID-19 pandemic has had major impact on human health worldwide. Whilst national and international COVID-19 lockdown and travel restriction measures have had widespread negative impact on economies and mental health, they may have beneficial effect on the environment, reducing air and water pollution. Mass bathing events (MBE) also known as Kumbh Mela are known to cause perturbations of the ecosystem affecting resilient bacterial populations within water of rivers in India. Lockdowns and travel restrictions provide a unique opportunity to evaluate the impact of minimum anthropogenic activity on the river water ecosystem and changes in bacterial populations including antibiotic-resistant strains. We performed a spatiotemporal meta-analysis of bacterial communities of the Godavari River, India. Targeted metagenomics revealed a 0.87-fold increase in the bacterial diversity during the restricted activity of lockdown. A significant increase in the resilient phyla, viz. Proteobacteria (70.6%), Bacteroidetes (22.5%), Verrucomicrobia (1.8%), Actinobacteria (1.2%) and Cyanobacteria (1.1%), was observed. There was minimal incorporation of allochthonous bacterial communities of human origin. Functional profiling using imputed metagenomics showed reduction in infection and drug resistance genes by - 0.71-fold and - 0.64-fold, respectively. These observations may collectively indicate the positive implications of COVID-19 lockdown measures which restrict MBE, allowing restoration of the river ecosystem and minimise the associated public health risk.

Antibiotic resistance genes and mobile genetic elements in a rural river in Southeast China: Occurrence, seasonal variation and association with the antibiotics

Human activities in rural areas, such as livestock farming, aquaculture, and rural domestic sewage discharge, may result in antibiotic resistance genes (ARGs) pollution in rural rivers. A systematic monitoring in different seasons was conducted in a typical agriculture-polluted river with Real-Time Quantitative PCR. A total of 11 ARGs and 2 related mobile genetic elements (MGEs) were detected at all sites with relative abundances of 6.9 × 10^-10-0.2 copies/16S rRNA copies. Among them, sul1, sul2 and int1 were the dominant target genes in water samples. tetW, ermB, and floR were more abundant in November (the dry season), while other ARGs, MGEs and 16s rRNA were at a higher absolute abundance in warm seasons. There was less spatial variation of ARGs in the dry season than in the other two seasons. Furthermore, the relative abundance of ARGs was higher at sampling sites adjoining pollution sources. In addition, cluster analysis implied that ARGs in upstream sediments may be released into surface water and migrate downstream in the direction of river flow. There was no significant correlation between ARGs and their corresponding antibiotics. However, the total concentration of tetracycline was significantly correlated with the non-paired ARGs, including sul3, floR, and ermB. At the same time, heavy metals (Zn, Pb, Cd, Cr⁶⁺, As) and other environmental parameters (permanganate index, pH, DO) may apply selective pressure on the spread of ARGs, according to redundancy and Pearson's correlation analysis.

Removal of antibiotic-resistant genes during drinking water treatment: A review

Once contaminate the drinking water source, antibiotic resistance genes (ARGs) will propagate in drinking water systems and pose a serious risk to human health. Therefore, the drinking water treatment processes (DWTPs) are critical to manage the risks posed by ARGs. This study summarizes the prevalence of ARGs in raw water sources and treated drinking water worldwide. In addition, the removal efficiency of ARGs and related mechanisms by different DWTPs are reviewed. Abiotic and biotic factors that affect ARGs elimination are also discussed. The data on presence of ARGs in drinking water help come to the conclusion that ARGs pollution is prevalent and deserves a high priority. Generally, DWTPs indeed achieve ARGs removal, but some biological treatment processes such as biological activated carbon filtration may promote antibiotic resistance due to the enrichment of ARGs in the biofilm. The finding that disinfection and membrane filtration are superior to other DWTPs adds weight to the advice that DWTPs should adopt multiple disinfection barriers, as well as keep sufficient chlorine residuals to inhibit re-growth of ARGs during subsequent distribution. Mechanistically, DWTPs obtain direct and inderect ARGs reduction through DNA damage and interception of host bacterias of ARGs. Thus, escaping of intracellular ARGs to extracellular environment, induced by DWTPs, should be advoided. This review provides the theoretical support for developping efficient reduction technologies of ARGs. Future study should focus on ARGs controlling in terms of transmissibility or persistence through DWTPs due to their biological related nature and ubiquitous presence of biofilm in the treatment unit.

Abundance and Diversity of Phages, Microbial Taxa, and Antibiotic Resistance Genes in the Sediments of the River Ganges Through Metagenomic Approach

In this study, we have analyzed the metagenomic DNA from the pooled sediment sample of the river Ganges to explore the abundance and diversity of phages, microbial community, and antibiotic resistance genes (ARGs). Utilizing data from Illumina platform, 4,174 (∼0.0013%) reads were classified for the 285 different DNA viruses largely dominated by the group of 260 distinctive phages (3,602 reads, ∼86.3%). Among all, Microcystis (782 hits), Haemophilus (403), Synechococcus (386), Pseudomonas (279), Enterococcus (232), Bacillus (196), Rhodococcus (166), Caulobacter (163), Salmonella (146), Enterobacteria (143), Mycobacterium and (128) phages show the highest abundance and account for ∼90% of the total identified phages. In addition, we have also identified corresponding host pertaining to these phages. Mainly, Proteobacteria (∼69.3%) dominates the microbial population structure. Primarily, orders such as Caulobacterales (∼28%), Burkholderiales (∼13.9%), Actinomycetales (∼13.7%), and Pseudomonadales (∼7.5%) signify the core section. Furthermore, 21,869 (∼0.00695%) reads were classified in 20 ARG types (classes) and 240 ARGs (subtypes), among which 4 ARG types, namely multidrug resistance (12,041 reads, ∼55%), bacitracin (3,202 reads, ∼15%), macrolide-lincosamide-streptogramin (1,744 reads, ∼7.98%), and fosmidomycin (990 reads, ∼4.53%), have the highest abundance. Simultaneously, six resistance mechanisms were also recognized with the dominance of antibiotic efflux (72.8%, 15,919 reads). The results unveil the distribution of (pro)-phages; microbial community; and various ARGs in the Ganges river sediments.

Carbapenemase-producing Gram-negative bacteria in aquatic environments: a review

Antibiotic resistance is one of the greatest public-health challenges worldwide, especially with regard to Gram-negative bacteria (GNB). Carbapenems are the β-lactam antibiotics of choice with the broadest spectrum of activity and, in many cases, are the last-resort treatment for several bacterial infections. Carbapenemase-encoding genes, mainly carried by mobile genetic elements, are the main mechanism of resistance against carbapenems in GNB. These enzymes exhibit a versatile hydrolytic capacity and confer resistance to most β-lactam antibiotics. After being considered a clinical issue, increasing attention is being giving to the dissemination of such resistance mechanisms in the environment and especially through water. Aquatic environments are among the most significant microbial habitats on our planet, known as a favourable medium for antibiotic gene transfer, and they play a crucial role in the huge spread of drug resistance in the environment and the community. In this review, we present current knowledge regarding the spread of carbapenemase-producing isolates in different aquatic environments, which may help the implementation of control and prevention strategies against the spread of such dangerous resistant agents in the environment.

β-Lactam antibiotics and antibiotic resistance in Asian lakes and rivers: An overview of contamination, sources and detection methods

Lakes and rivers are sources of livelihood, food and water in many parts of the world. Lakes provide natural resources and valuable ecosystem services. These aquatic ecosystems are also vulnerable to known and new environmental pollutants. Emerging water contaminants are now being studied including antibiotics because of the global phenomenon on antibiotic resistance. β-Lactam antibiotics are widely used in human and animal disease prevention or treatment. The emergence of antibiotic resistance is a public health threat when bacteria become more resistant and infections consequently increase requiring treatment using last resort drugs that are more expensive. This review summarizes the key findings on the occurrence, contamination sources, and determination of β-lactam antibiotics and β-lactam antibiotic resistant bacteria and genes in the Asian lake and river waters. The current methods in the analytical measurements of β-lactam antibiotics in water involving solid-phase extraction and liquid chromatography-mass spectrometry are discussed. Also described is the determination of antibiotic resistance genes which is primarily based on a polymerase chain reaction method. To date, β-lactam antibiotics in the Asian aquatic environments are reported in the ng/L concentrations. Studies on β-lactam resistant bacteria and resistance genes were mostly conducted in China. The occurrence of these emerging contaminants is largely uncharted because many aquatic systems in the Asian region remain to be studied. Comprehensive investigations encompassing the environmental behavior of β-lactam antibiotics, emergence of resistant bacteria, transfer of resistance genes to non-resistant bacteria, multiple antibiotic resistance, and effects on aquatic biota are needed particularly in rivers and lakes that are eventual sinks of these water contaminants.

A Novel N4-Like Bacteriophage Isolated from a Wastewater Source in South India with Activity against Several Multidrug-Resistant Clinical Pseudomonas aeruginosa Isolates

In India, multidrug resistance determinants are much more abundant in community-associated bacterial pathogens due to the improper treatment of domestic and industrial effluents. In particular, a high bacterial load of the opportunistic pathogen P. aeruginosa in sewage and water bodies in India is well documented.

Multidrug-resistant community-acquired infections caused by the opportunistic human pathogen Pseudomonas aeruginosa are increasingly reported in India and other locations globally. Since this organism is ubiquitous in the environment, samples such as sewage and wastewater are rich reservoirs of P. aeruginosa bacteriophages. In this study, we report the isolation and characterization of a novel P. aeruginosa N4-like lytic bacteriophage, vB_Pae_AM.P2 (AM.P2), from wastewater in Kerala, India. AM.P2 is a double-stranded DNA podovirus that efficiently lyses the model strain, PAO1, at a multiplicity of infection as low as 0.1 phage per bacterium and resistance frequency of 6.59 × 10⁻⁴. Synergy in bactericidal activity was observed between AM.P2 and subinhibitory concentrations of the antibiotic ciprofloxacin. Genome sequencing of AM.P2 revealed features similar to those of the N4-like P. aeruginosa phages LUZ7 and KPP21. As judged by two independent assay methods, spot tests and growth inhibition, AM.P2 successfully inhibited the growth of almost 30% of strains from a contemporary collection of multidrug-resistant P. aeruginosa clinical isolates from South India. Thus, AM.P2 may represent an intriguing candidate for inclusion in bacteriophage cocktails developed for various applications, including water decontamination and clinical bacteriophage therapy.

IMPORTANCE In India, multidrug resistance determinants are much more abundant in community-associated bacterial pathogens due to the improper treatment of domestic and industrial effluents. In particular, a high bacterial load of the opportunistic pathogen P. aeruginosa in sewage and water bodies in India is well documented. The isolation and characterization of bacteriophages that could target emerging P. aeruginosa strains, representing possible epicenters for community-acquired infections, could serve as a useful alternative tool for various applications, such as phage therapy and environmental treatment. Continuing to supplement the repertoire of broad-spectrum bacteriophages is an essential tool in confronting this problem.

DNA phosphorothioate modification facilitates the dissemination of mcr-1 and blaNDM-1 in drinking water supply systems

The mechanism driving the dissemination of antibiotic resistance genes (ARGs) in drinking water supply systems (DWSSs) with multiple barriers remains poorly understood despite several recent efforts. Phosphorothioate (PT) modifications, governed by dndABCDE genes, occur naturally in various bacteria and involve the incorporation of sulfur into the DNA backbone. PT is regarded as a mild antioxidant in vivo and is known to provide protection against bacterial genomes. We combined quantitative polymerase chain reaction, metagenomic, and network analyses for the water treatment process and laboratory-scale experiments for chlorine treatment using model strains to determine if DNA PT modification occurred in DWSS and facilitated the dissemination of mobilized colistin resistance-1 (mcr-1) and New Delhi metallo-β-lactamase-1 (bla_NDM-1) in DWSS. Our results indicated that the relative abundance of dndB increased in the effluent, compared with the influent, in the water treatment plants. Presence of dndB copies had a positive correlation with the concentration of chloramine disinfectant. Network analysis revealed Bdellovibrio as a potential host for MCR genes, NDM genes, and dndB in the DWSS. E. coli DH10B (Wild-type with the dndABCDE gene cluster and ΔdndB) model strains were used to investigate resistance to chlorine treatment at the concentration range of 0.5-3 mg/L. The resistance of the wild-type strain increased with increasing concentration of chlorine. DNA PT modification protected MCR- and NDM-carrying bacteria from chloramine disinfection during the water treatment process. The higher relative abundance of ARGs in the effluent of the water treatment plants may be due to the resistance of DNA PT modification to chloramine disinfection, thereby causing the enrichment of genera carrying MCR, NDM, and dndB. This study provides a new understanding on the mechanism of ARG dissemination in DWSS, which will help to improve the performance of drinking water treatment to control the risk associated with antibiotic-resistant bacteria.

Screening of natural compounds for identification of novel inhibitors against β-lactamase CTX-M-152 reported among Kluyvera georgiana isolates: An in vitro and in silico study

Multidrug resistance due to the expression of extended spectrum β-lactamases (ESBLs) by bacterial pathogens is an alarming health concern with huge socio-economic burden. Here, 102 bacterial isolates from Wastewater treatment plants (WTPs) were screened for resistance to different antibiotics. Kirby-Bauer method and phenotypic disc confirmatory test confirmed the prevalence of 20 ESBLs. Polymerase chain reaction-based detection confirmed 11 bla_CTX-M positive bacterial isolates. Genotyping of bacterial isolates by 16S rRNA gene sequencing showed the dissemination of bla_CTX-M in Escherichia fergusonii, Escherichia coli, Shigella sp., Kluyvera georgiana and Enterobacter sp. Amongst Kluyvera georgiana isolates, two were harboring bla_CTX-M-152. The 3D model of CTX-M-152 protein was generated using SwissProt and characterized by Ramachandran plot and SAVES. A library of natural compounds was screened to identify novel CTX-M-152 inhibitor(s). High-throughput virtual screening (HTVS), standard precision (SP) and extra precision (XP) docking led to the identification of five natural compounds (Naringin dihydrochalcone, Salvianolic acid B, Inositol, Guanosine and Ellagic acid) capable of binding to active site of CTX-M-152. Futher, characterization by MM-GBSA (Molecular Mechanism General Born Surface Area), and ADMET (Adsorption, Distribution, Metabolism, Excretion and Toxicity) showed that Ellagic acid was the most potent inhibitor of CTX-M-152. Molecular dynamics simulation also confirmed that Ellagic acid form a stable complex with CTX-M-152. The ability of Ellagic acid to inhibit growth of bacteria harboring CTX-M-152 was confirmed by MIC (Minimum Inhibitory Concentration; broth dilution method) and Zone of Inhibition (ZOI) studies with respect to Cefotaxime. The identification of a novel inhibitor of CTX-M-152 from a natural source holds promise for employment in the control of bacterial infections.

Source tracking of antibiotic resistance genes in the environment - Challenges, progress, and prospects

Antibiotic resistance has become a global public health concern, rendering common infections untreatable. Given the widespread occurrence, increasing attention is being turned toward environmental pathways that potentially contribute to antibiotic resistance gene (ARG) dissemination outside the clinical realm. Studies during the past decade have clearly proved the increased ARG pollution trend along with gradient of anthropogenic interference, mainly through marker-ARG detection by PCR-based approaches. However, accurate source-tracking has been always confounded by various factors in previous studies, such as autochthonous ARG level, spatiotemporal variability and environmental resistome complexity, as well as inherent method limitation. The rapidly developed metagenomics profiles ARG occurrence within the sample-wide genomic context, opening a new avenue for source tracking of environmental ARG pollution. Coupling with machine-learning classification, it has been demonstrated the potential of metagenomic ARG profiles in unambiguously assigning source contribution. Through identifying indicator ARG and recovering ARG-host genomes, metagenomics-based analysis will further increase the resolution and accuracy of source tracking. In this review, challenges and progresses in source-tracking studies on environmental ARG pollution will be discussed, with specific focus on recent metagenomics-guide approaches. We propose an integrative metagenomics-based framework, in which coordinated efforts on experimental design and metagenomic analysis will assist in realizing the ultimate goal of robust source-tracking in environmental ARG pollution.

Metallo-β-Lactamases: Structure, Function, Epidemiology, Treatment Options, and the Development Pipeline

Modern medicine is threatened by the global rise of antibiotic resistance, especially among Gram-negative bacteria. Metallo-β-lactamase (MBL) enzymes are a particular concern and are increasingly disseminated worldwide, though particularly in Asia. Many MBL producers have multiple further drug resistances, leaving few obvious treatment options. Nonetheless, and more encouragingly, MBLs may be less effective agents of carbapenem resistance in vivo, under zinc limitation, than in vitro Owing to their unique structure and function and their diversity, MBLs pose a particular challenge for drug development. They evade all recently licensed β-lactam-β-lactamase inhibitor combinations, although several stable agents and inhibitor combinations are at various stages in the development pipeline. These potential therapies, along with the epidemiology of producers and current treatment options, are the focus of this review.

Prevalence of antibiotic resistance in the tropical rivers of Sri Lanka and India

We evaluate the imprints of urbanization, landuse and lifestyle on the prevalence and provenance of antibiotic resistance in the tropical rivers of Sri Lanka (Kelani and Gin) and India (Sabarmati, and Brahmaputra River). The prevalence of E. coli in the Kelani, Sabarmati, and Brahmaputra Rivers was in the range of 10-27, 267-76,600, and <50 CFU ml^-1 respectively. Isolated E. coli colonies were subjected to six antibiotics to assess their resistance. We found higher resistance to old generation antibiotics like tetracycline (TC), and sulfamethoxazole (ST) transcends the resistance for fluoroquinolones like norfloxacin (NFX), ciprofloxacin (CIP), and levofloxacin (LVX). Interestingly, both Indian rivers had exhibited relatively higher resistance to TC and ST than the Kelani river or Gin River, implying that the Sri Lankan situation is relatively less critical. At genetic level the resistance for β-lactams, fluoroquinolones and sulphonamides, were detected in many samples, as reported globally. While the resistance genes for aac-(6')-1b-cr, qnrS and sul1 were detected in both Sri Lankan and Indian Rivers, bla_TEM and ampC were specific to the Indian Rivers only. Decoupling of the prevalence of metal contamination and antibiotic resistance has been noticed in India and Sri Lanka. Study implies that urbanization, landuse, and lifestyle (ULL) are the three most critical factors governing multidrug resistance (MDR) and fecal contamination.

Soil types influence the characteristic of antibiotic resistance genes in greenhouse soil with long-term manure application

Composted livestock and poultry manure, which may contain antibiotic resistance genes (ARGs), is widely used as natural fertilizer in China. But the influence of soil types on ARGs is not well characterized, particularly at greenhouse sites with long-term manure application. We investigated the distribution of ARGs in the cinnamon, fluvo-aquic and saline-alkali soils in greenhouse of Yellow River Delta region, China. A total of 193 ARGs subtypes were detected, with multidrug and aminoglycoside resistance genes as the most universal ARGs subtypes. Soil types influenced the ARGs distribution, where higher levels of diversity and relative abundance of ARGs in the fluvo-aquic and saline-alkali soils compared with those in the cinnamon soils. Among abiotic factors, sand, pH and Zn contributed more to the pattern of ARGs in the cinnamon soils, whereas sand and Cd, clay and Pb contributed the most in the fluvo-aquic and saline-alkali soils respectively. Furthermore, positive correlations between the relative abundances of ARGs and mobile genetic elements (MGEs) in the fluvo-aquic soils, suggesting higher dissemination potential of ARGs in this type of soil. Overall, MGEs played a positive primary role in the ARGs distribution in greenhouse soil than heavy metal co-selection and soil physicochemical properties.

Surveillance of antibiotic resistant Escherichia coli in human populations through urban wastewater in ten European countries

Antibiotic resistance surveillance data is lacking in many parts of the world, limiting effective therapy and management of resistance development. Analysis of urban wastewater, which contains bacteria from thousands of individuals, opens up possibilities to generate informative surveillance data in a standardized and resource-efficient way. Here, we evaluate the relationship between antibiotic resistance prevalence in E. coli from wastewater and clinical samples by studying countries with different resistance situations as assessed by traditional clinical surveillance. Composite, influent wastewater samples were collected over 24 h from treatment plants serving major cities in ten European countries. Using a broth screening method, resistance to six antibiotic classes was analyzed for 2507 E. coli isolates (n = 247-252 per country). Resistance prevalence in wastewater E. coli was compared to that in clinical E. coli reported by the European Antibiotic Resistance Surveillance Network. Resistance prevalence was lower in wastewater than clinical E. coli but followed similar geographic trends. Significant relationships were found for resistance to aminopenicillins (R² = 0.72, p = 0.0019) and fluoroquinolones (R² = 0.62, p = 0.0072), but not for aminoglycosides (R² = 0.13, p = 0.31) and third-generation cephalosporins (R² = 0.00, p = 0.99) where regression analyses were based on considerably fewer resistant isolates. When all four antibiotic classes were taken into account, the relationship was strong (R² = 0.85, p < 0.0001). Carbapenem resistance was rare in both wastewater and clinical isolates. Wastewater monitoring shows promise as method for generating surveillance data reflecting the clinical prevalence of antibiotic resistant bacteria. Such data may become especially valuable in regions where clinical surveillance is currently limited.

Factors associated with elevated levels of antibiotic resistance genes in sewer sediments and wastewater

The sewer environment is a potential hotspot for the proliferation of antibiotic resistance genes (ARGs) and other hazardous microbial agents. Understanding the potential for ARG proliferation and retardation and/or accumulation in sewer sediments is of interest for protecting the health of sewage workers and the broader community in the event of sewer overflows as well as for interpreting sewage epidemiology data. To better understand this understudied environment for antibiotic resistance, a field survey was conducted to identify the factors that may control ARGs in sewer sediments and sewage. qPCR was performed for select ARGs and amplicon sequencing was performed for paired samples from combined and separate sanitary sewer systems. Metagenomic sequencing was performed on combined sewer sediments. The relative abundances of sul1, tet(O), tet(W), ermF, and vanA were higher in wastewater compared to sewer sediments, while NDM-1 was greater in sewer sediment and ermF was similar between the two matrices. NDM-1 was observed in sewer sediment but rarely above detection in wastewater in this study. This may indicate that larger/more frequent wastewater samples are needed for detection and/or that retardation and/or accumulation in sewage sediment may need to be considered when interpreting wastewater-based epidemiology data for ARGs. Random forest analyses indicated that season and conductivity were important variables and to a lesser extent so were pH, TSS, heavy metals, and sewer type for explaining the variance of the ARGs. These variables explained the 19-61% of the variance of sul1, tet(O), tet(G), and tet(W) quantified in wastewater. These variables performed less well for explaining the variance in sewer sediments (0.2-24%). Sewer sediment and wastewater had distinct microbial community structures and biomarkers for each are described. Metagenomics indicated that a high diversity of ARGs, including several of medical importance, were observed in the combined sewer sediment. This work provides insight into the complex sewer microbiome and the potential hazard posed by different sewer matrices.

Selective Adsorption and Photocatalytic Degradation of Extracellular Antibiotic Resistance Genes by Molecularly-Imprinted Graphitic Carbon Nitride

There is a growing need to mitigate the discharge of extracellular antibiotic resistance genes (ARGs) from municipal wastewater treatment systems. Here, molecularly-imprinted graphitic carbon nitride (MIP-C₃N₄) nanosheets were synthesized for selective photocatalytic degradation of a plasmid-encoded ARG (bla_NDM-1, coding for multidrug resistance New Delhi metallo-β-lactamase-1) in secondary effluent. Molecular imprinting with guanine enhanced ARG adsorption, which improved the utilization of photogenerated oxidizing species to degrade bla_NDM-1 rather than being scavenged by background nontarget constituents. Consequently, photocatalytic removal of bla_NDM-1 in secondary effluent with MIP-C₃N₄ (k = 0.111 ± 0.028 min^-1) was 37 times faster than with bare graphitic carbon nitride (k = 0.003 ± 0.001 min^-1) under UVA irradiation (365 nm, 3.64 × 10^-6 Einstein/L·s). MIP-C₃N₄ can efficiently catalyze the fragmentation of bla_NDM-1, which decreased the potential for ARG repair by transformed bacteria. Molecular imprinting also changed the primary degradation pathway; electron holes (h⁺) were the predominant oxidizing species responsible for bla_NDM-1 removal with MIP-C₃N₄ versus free radicals (i.e., ·OH and O₂^-) for coated but nonimprinted C₃N₄. Overall, MIP-C₃N₄ efficiently removed bla_NDM-1 from secondary effluent, demonstrating the potential for molecular imprinting to enhance the selectivity and efficacy of photocatalytic processes to mitigate dissemination of antibiotic resistance from sewage treatment systems.

Behavior of last resort antibiotic resistance genes (mcr-1 and blaNDM-1) in a drinking water supply system and their possible acquisition by the mouse gut flora

Mcr-1 and bla_NDM-1 antibiotic resistance genes (ARGs) confer resistance to colistins and carbapenems, which are often antibiotics used as a last resort in tertiary care hospitals. Dissemination of these two ARGs in drinking water supply systems and their effect on healthy gut bacteria are poorly studied. In this study, the dissemination of mcr-1 and bla_NDM-1 in a drinking water supply system, and their effect on the antibiotic resistance of mouse gut bacteria are explored. Metagenome analysis revealed that source water (Taipu river and Jinze reservoir) was polluted with ARGs. Mcr-1 and bla_NDM-1 can be disseminated through the water distribution system. Even advanced water treatments (ozone and biological activated carbon (BAC)) could not effectively remove mcr-1 and bla_NDM-1. Low concentrations of chloramine disinfectants in the water distribution system were not effective at limiting ARG abundance. Mobile genetic elements were also found to play a major role in the dissemination of ARGs via horizontal gene transfer (HGT) throughout the water supply system. Statistical analysis revealed that there was no effect of temperature on the abundance of mcr-1 and bla_NDM-1 throughout the water supply system. A last resort ARG, mcr-1 can disseminate from drinking water to the healthy mouse gut. The presence of mcr-1 in a strain belonging to Enterococcus hirae, which is different from the strain belonging to the Bacillus cereus group isolated from drinking water, strongly supports the phenomena of HGT inside the gut. This research provides novel insights into the role of drinking water in disseminating ARGs to the gut and strongly suggests that drinking water may also play a major role apart from other factors known to be involved in the prevalence of last resort ARGs in the gut.

Mass bathing events in River Kshipra, Central India- influence on the water quality and the antibiotic susceptibility pattern of commensal E.coli

BACKGROUND

Antibiotic resistance is one of the major global health emergencies. One potential source of dissemination of resistant bacteria is mass gatherings, e.g. mass bathing events. We evaluated the physicochemical parameters of water quality and the antibiotic resistance pattern in commensal Escherichia coli from river-water and river-sediment in pre-, during- and post-mass bathing events in river Kshipra, Central India.

METHOD/DESIGN

Water and sediment samples were collected from three selected points during eight mass bathing events during 2014-2016. Water quality parameters (physical, chemical and microbiological) were analyzed using standard methods. In river water and sediment samples, antibiotic susceptibility patterns of isolated E. coli to 17 antibiotics were tested.

RESULTS

pH, turbidity and dissolved oxygen were significantly lower and total dissolved solid, free carbon dioxide were higher during mass bathing, whilst TSS, BOD and COD were lowest in pre-bathing and highest in post-bathing period. E.coli with multi drug resistance (MDR) or extended spectrum beta-lactamase (ESBL) production were between 9-44% and 6-24%, respectively in river-water as well as river-sediment. Total coliform count/ml and E. coli count were higher during-and post-bathing in river water than in pre-bathing period. Thus, the percentage of resistance was significantly higher during and post-bathing period (p<.05) than in pre-bathing. Colony forming unit (CFU)/ml in river-sediment was much higher than in river-water. Percentage of resistance was significantly higher in river-water (p<.05) than in river-sediment.

CONCLUSIONS

Antibiotic resistance in E.coli isolated from the Kshipra River showed significant variation during mass bathing events. Guidelines and regulatory standards are needed to control environmental dissemination of resistant bacteria.

A Capability Perspective on Antibiotic Resistance, Inequality, and Child Development

Nussbaum’s capability theory by drawing attention to multiple determinants of wellbeing provides a rich and relevant evaluative space for framing antibiotic resistance. I consider the implications of antibiotic resistance for child development and adult capabilities. There are common risk factors for childhood growth stunting and the spread of infectious diseases in both antibiotic sensitive and resistant forms. The interaction between infectious diseases, antibiotic resistance and growth stunting illustrates a clustering of disadvantage. The control of antibiotic resistance requires wide-ranging cooperative action. Cooperation is predicated on an expectation of equitable access to effective antibiotics. This expectation is confounded by inequality both in access to antibiotics, and in the risk that available antibiotics will be ineffective. Securing child development (and adult capabilities) requires that inequalities both in access to antibiotics and in risk factors for the dissemination and transmission of antibiotic resistance are addressed. Inequality undermines the cooperative activity that is control of infectious diseases and compounds the threat to the securing of capabilities that arises from antibiotic resistance.

Antimicrobial resistance in the environment: The Indian scenario

Antimicrobial resistance (AMR) continues to pose a significant public health problem in terms of mortality and economic loss. Health authorities of several countries including India have formulated action plans for its containment. In this fight against AMR, it is important to realize the contribution by all the following four spheres: humans, animals, food and environment. This review incorporates all the spheres of One Health concept from the Indian perspective. India has one of the highest rates of resistance to antimicrobial agents used both in humans and food animals. The environment, especially the water bodies, have also reported the presence of resistant organisms or their genes. Specific socio-economic and cultural factors prevalent in India make the containment of resistance more challenging. Injudicious use of antimicrobials and inadequate treatment of waste waters are important drivers of AMR in India. Use of sludge in agriculture, improper discard of livestock animals and aquaculture industry are considered AMR contributors in other countries but Indian data regarding these are lacking. Efforts to combat AMR have been initiated by the Indian health authorities but are still at preliminary stages. Keeping in view the challenges unique to India, future directions are proposed.

Environmental Prevalence of Carbapenem Resistance Enterobacteriaceae (CRE) in a Tropical Ecosystem in India: Human Health Perspectives and Future Directives

In the past few decades, infectious diseases have become increasingly challenging to treat, which is explained by the growing number of antibiotic-resistant bacteria. Notably, carbapenem-resistant Enterobacteriaceae (CRE) infections at global level attribute a vast, dangerous clinical threat. In most cases, there are enormous difficulties for CRE infection except a few last resort toxic drugs such as tigecycline and colistin (polymyxin E). Due to this, CRE has now been categorized as one among the three most dangerous multidrug resistance (MDR) pathogens by the US Centres for Disease Control and Prevention (CDC). Considering this, the study of the frequency of CRE infections and the characterization of CRE is an important area of research in clinical settings. However, MDR bacteria are not only present in hospitals but are spreading more and more into the environment, thereby increasing the risk of infection with resistant bacteria outside the hospital. In this context, developing countries are a global concern where environmental regulations are often insufficient. It seems likely that overcrowding, poor sanitation, socioeconomic status, and limited infrastructures contribute to the rapid spread of MDR bacteria, becoming their reservoirs in the environment. Thus, in this review, we present the occurrence of CRE and their resistance determinants in different environmental compartments in India.