Water scarcity is one of the main challenges in sustainable agricultural development particularly in developing countries therefore, irrigation of food crops with wastewater effluent has become a ...common practice in order to meet the growing food demand. The aim of this study was to determine the impact of wastewater irrigation on bacterial community and antibiotic resistance dynamics in soil and vegetables in an agricultural setting. To determine bacterial diversity, occurrence and overall dynamics of antibiotic resistant genes (ARGs) in effluent irrigated soil and vegetables, 16S rRNA gene metagenomics, shotgun metagenomics and molecular PCR technique were utilized. A shift in bacterial community profile was observed as notable reduction in proteobacteria and increase in firmicutes phyla from the microcosm soil following wastewater effluent irrigation. Shotgun metagenomics revealed diverse ARGs belonging to at least nine different classes of antibiotics in the effluent wastewater. However, only blaTEM (beta-lactamase) and aadA (aminoglycoside) resistance gene sequences were identified in microcosm soil following irrigation and only blaTEM was detected on effluent irrigated vegetable surfaces (spinach and beetroots). From the study, only blaTEM gene was identified across all samples; effluent wastewater, effluent-treated soil, and vegetables. The data suggests a possible dissemination and persistence of the beta-lactamase blaTEM gene from effluent wastewater into agricultural soil and vegetables. This study enhances our understanding of antibiotic resistance spread and highlights the importance of monitoring antibiotic resistance in agro-systems, which is critical for informing policies aimed at sustainable use of wastewater effluent in water-stressed countries.
•Wastewater effluent potentially introduces antibiotic resistance genes into the soil and vegetables.•The beta-lactamase (blaTEM) gene from effluent wastewater is potentially introduced into agricultural soil and vegetables.•Monitoring antibiotic resistance in agro-systems is critical for informing policies aimed at sustainable use of wastewater.•Irrigation with wastewater effluent remains unregulated in most developing countries.
Wastewater effluent, Antibiotic resistant genes, Agriculture, Metagenomics, Microcosm.
The consumption of crops fertilized with human waste represents a potential route of exposure to antibiotic-resistant fecal bacteria. The present study evaluated the abundance of bacteria and ...antibiotic resistance genes by using both culture-dependent and molecular methods. Various vegetables (lettuce, carrots, radish, and tomatoes) were sown into field plots fertilized inorganically or with class B biosolids or untreated municipal sewage sludge and harvested when of marketable quality. Analysis of viable pathogenic bacteria or antibiotic-resistant coliform bacteria by plate counts did not reveal significant treatment effects of fertilization with class B biosolids or untreated sewage sludge on the vegetables. Numerous targeted genes associated with antibiotic resistance and mobile genetic elements were detected by PCR in soil and on vegetables at harvest from plots that received no organic amendment. However, in the season of application, vegetables harvested from plots treated with either material carried gene targets not detected in the absence of amendment. Several gene targets evaluated by using quantitative PCR (qPCR) were considerably more abundant on vegetables harvested from sewage sludge-treated plots than on vegetables from control plots in the season of application, whereas vegetables harvested the following year revealed no treatment effect. Overall, the results of the present study suggest that producing vegetable crops in ground fertilized with human waste without appropriate delay or pretreatment will result in an additional burden of antibiotic resistance genes on harvested crops. Managing human exposure to antibiotic resistance genes carried in human waste must be undertaken through judicious agricultural practice.
Bacterial diversity is known to be a driver of soil ecosystem services and it is influenced by the natural integrity of the environments. Samples from garden soil, saline soil and sludge-impacted ...soil were studied to evaluate the influence of soil properties on bacterial abundance and diversity for improved management. Soil samples were collected from 0 to 15 cm depth and analyzed for selected physico-chemical properties using routine laboratory procedures. 16S rRNA gene-based metagenomics analysis was used to identify and quantify bacteria from the samples. Garden soil had pH (H2O) of 5.8, electrical conductivity (EC) of 0.3 dS m−1, organic matter (OM) content of 0.66%, total phosphorus (P) and cation exchange capacity (CEC) of 132 ppm and 2.40 Cmol kg−1, respectively, and 8.39% clay; sludge impacted soil had a pH (H2O) of 5.8, EC of 5.7 dS m−1, OM content of 57.5%, 2641 ppm P, CEC content of 8.62 Cmol kg−1 and 18.23% clay; while salt affected (saline) soil had a pH (H2O) of 7.6, EC of 4.4 dS m−1, OM of 0.5%, P content of 24.9 ppm, CEC of 4.05 Cmol kg−1 and 13.07% of clay contents. The distribution of bacteria phyla identified in the soils is as follows: sludge-impacted soil (15), garden (13) and bare saline (10). Next generation sequencing shows that five of the phyla in the order Proteobacteria > Actinobacteria > Firmicutes > Bacteroidetes > Acidobacteria were present and dominant in all the soils. Soils under the different land uses significantly varied in their properties. It is concluded that bacterial diversity was influenced by the degree of habitat disturbance caused by variation in land-use management practices which affected properties of the soils. This study opens up new frontiers in expanding metagenomics studies in the semi-arid environments of Botswana and contributes to the identification of soil bacteria which are useful to ecosystem functions.
Antimicrobial resistance remains a significant global and One Health threat, owing to the diminishing effectiveness of antibiotics against rapidly evolving multidrug-resistant bacteria, and the ...limited innovative research towards the development of new antibiotic therapeutics. In this article, we present the whole-genome sequence data of Proteus mirabilis-MN029 obtained from highly accurate long-read PacBioⓇ HiFi technology. The antibacterial activities of the selected African native plant species were also evaluated using the disk diffusion method. Acquired antibiotic resistance genes and chromosomal mutations corresponding to antibiotics of clinical importance were identified from genomic data. Using ethlyl acetate as solvent, Pterocarpus angolensis leaf extracts showed the most promising antibacterial effects against Proteus mirabilis-MN029. These datasets will be useful for future experimental research aimed at designing new antibacterial drugs from plant extracts that are effective alone or in combination with existing antibiotics to overcome multidrug-resistance mechanisms.
A wastewater treatment plant (WWTP) is an environment high in nutrient concentration with diverse bacterial populations and can provide an ideal environment for the proliferation of mobile elements ...such as plasmids. WWTPs have also been identified as reservoirs for antibiotic resistance genes that are associated with human pathogens. The objectives of this study were to isolate and characterize self-transmissible or mobilizable resistance plasmids associated with effluent from WWTP. An enrichment culture approach designed to capture plasmids conferring resistance to high concentrations of erythromycin was used to capture plasmids from an urban WWTP servicing a population of ca. 210,000. DNA sequencing of the plasmids revealed diversity of plasmids represented by incompatibility groups IncU, col-E, IncFII and IncP-1β. Genes coding resistance to clinically relevant antibiotics (macrolide, tetracycline, beta-lactam, trimethoprim, chloramphenicol, sulphonamide), quaternary ammonium compounds and heavy metals were co-located on these plasmids, often within transposable and integrative mobile elements. Several of the plasmids were self-transmissible or mobilizable and could be maintained in the absence of antibiotic selection. The IncFII plasmid pEFC36a showed the highest degree of sequence identity to plasmid R1 which has been isolated in England more than 50 years ago from a patient suffering from a Salmonella infection. Functional conservation of key regulatory features of this F-like conjugation module were demonstrated by the finding that the conjugation frequency of pEFC36a could be stimulated by the positive regulator of plasmid R1 DNA transfer genes, TraJ.
Wastewater treatment plants (WWTPs) are useful environments for investigating the occurrence, diversity, and evolution of plasmids encoding clinically relevant antibiotic resistance genes (ARGs). Our ...objective was to isolate and sequence plasmids encoding meropenem resistance from bacterial hosts within Canadian WWTPs. We used two enrichment culture approaches for primary plasmid isolation, followed by screening for antibiotic resistance, conjugative mobility, and stability in enteric bacteria. Isolated plasmids were sequenced using Illumina MiSeq and Sanger sequencing methods. Bioinformatics analyses resolved a multi-resistance IncF/MOB
F12
plasmid, pFEMG (209 357 bp), harbouring resistance genes to β-lactam (bla
CMY-42
, bla
TEM-1β
, and bla
NDM-5
), macrolide (mphA-mrx-mphR), tetracycline (tetR-tetB-tetC-tetD), trimethoprim (dfrA12), aminoglycoside (aadA2), and sulfonamide (sul1) antibiotic classes. We also isolated an IncI1/MOB
P12
plasmid pPIMR (172 280 bp) carrying similar β-lactamase and a small multi-drug efflux resistance gene cluster (bla
CMY-42
-blc-sugE) to pFEMG. The co-occurrence of different ARGs within a single 24 552 bp cluster in pFEMG — interspersed with transposons, insertion sequence elements, and a class 1 integron — may be of significant interest to human and veterinary medicine. Additionally, the presence of conjugative and plasmid maintenance genes in the studied plasmids corresponded to observed high conjugative transfer frequencies and stable maintenance. Extensive investigation is required to further understand the fitness trade-offs of plasmids with different types of conjugative transfer and maintenance modules.
Antimicrobial resistance is considered a “One-Health” problem, impacting humans, animals, and the environment. The problem of the rapid development and spread of bacteria resistant to multiple ...antibiotics is a rising global health threat affecting both rich and poor nations. Low- and middle-income countries are at highest risk, in part due to the lack of innovative research on the surveillance and discovery of novel therapeutic options. Fast and effective drug discovery is crucial towards combatting antimicrobial resistance and reducing the burden of infectious diseases. African medicinal plants have been used for millennia in folk medicine to cure many diseases and ailments. Over 10% of the Southern African vegetation is applied in traditional medicine, with over 15 species being partially or fully commercialized. These include the genera Euclea, Ficus, Aloe, Lippia. And Artemisia, amongst many others. Bioactive compounds from indigenous medicinal plants, alone or in combination with existing antimicrobials, offer promising solutions towards overcoming multi-drug resistance. Secondary metabolites have different mechanisms and modes of action against bacteria, such as the inhibition and disruption of cell wall synthesis; inhibition of DNA replication and ATP synthesis; inhibition of quorum sensing; inhibition of AHL or oligopeptide signal generation, broadcasting, and reception; inhibition of the formation of biofilm; disruption of pathogenicity activities; and generation of reactive oxygen species. The aim of this review is to highlight some promising traditional medicinal plants found in Africa and provide insights into their secondary metabolites as alternative options in antibiotic therapy against multi-drug-resistant bacteria. Additionally, synergism between plant secondary metabolites and antibiotics has been discussed.
Sewage sludge recovered from wastewater treatment plants contains antibiotic residues and is rich in antibiotic resistance genes, selected for and enriched in the digestive tracts of human using ...antibiotics. The use of sewage sludge as a crop fertilizer constitutes a potential route of human exposure to antibiotic resistance genes through consumption of contaminated crops. Several gene targets associated with antibiotic resistance (catA1, catB3, ereA, ereB, erm(B), str(A), str(B), qnrD, sul1, and mphA), mobile genetic elements (int1, mobA, IncW repA, IncP1 groups -α, -β, -δ, -γ, -ε), and bacterial 16S rRNA (rrnS) were quantified by qPCR from soil and vegetable samples obtained from unamended and sludge-amended plots at an experimental field in London, Ontario. The qPCR data reveals an increase in abundance of gene targets in the soil and vegetables samples, indicating that there is potential for additional crop exposure to antibiotic resistance genes carried within sewage sludge following field application. It is therefore advisable to allow an appropriate delay period before harvesting of vegetables for human consumption.
•Wastewater storage tank potentially reduces bacterial abundance.•Wastewater irrigation influences abundance and diversity of ARB.•Animal feces may contribute to ARGs dissemination.•High diversity of ...bla genes from a pond in rural community.•NGS approaches ideal for One health AMR surveillance.
Antimicrobial resistance poses serious socioeconomic and ecological threat globally, warranting innovative approaches for surveillance and monitoring. One Health concept was considered in the analysis of soil, animal feces, pond water, wastewater and vegetable samples from a rural community and the environment in Palapye, Botswana. Culture-dependent and next-generation sequencing approaches were used for characterization of bacteria and antibiotic resistance genes. Viable potentially pathogenic bacteria exhibiting multi-drug resistance profiles corresponding to various clinically relevant antibiotics were observed. Next-generation sequence analysis also reveals occurrence and diversity of bacterial communities and acquired antibiotic resistance genes corresponding to clinically important classes of antibiotics (beta-lactam, aminoglycoside, tetracycline, fosfomycin, trimethoprim, sulfonamide, quinolone, macrolide, and phenicol). High diversity was observed for beta-lactamase encoding (bla) genes from pond water in a rural community. Phylum gammaproteobacteria was revealed as the most abundant from metagenomics sequences of both community and environment samples. Multi-drug and heavy metal resistance encoding Serratia mercensens DM6 was identified from whole genome sequence data. This study serves as proof-of-concept for the application of next-generation sequencing in low- and middle-income countries and supports the One Health surveillance of antimicrobial resistance. The data generated can contribute towards antimicrobial stewardship programs and implementation of National Action Plan on antimicrobial resistance.
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