Characterization of Bacterial Communities and Their Antibiotic Resistance Profiles in Wastewaters Obtained from Pharmaceutical Facilities in Lagos and Ogun States, Nigeria

Antimicrobial resistance profiling of bacteria isolated from wastewater and environmental samples of pharmaceutical industries in South India

The study was aimed to determine the phenotypic and genotypic antimicrobial resistance in the isolated bacteria from the influent (25), effluent (15), surface and ground water samples (15) surrounding the pharmaceutical industries located in south India. From 55 samples, 48 isolates of 10 different bacteria were obtained. The identified bacterial isolates were viz. Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterobacter aerogenes, Corynebacterium sp., Acinetobacter sp., Aeromonas punctata, Ralstonia picketti, Staphylococcus aureus, Stenotrophomonas maltophillia, and Citrobacter freundii. The phenotypic profile of resistance through antibiotic susceptibility test was carried out against sixteen different antibiotics. Standard PCR technique was used for the detection of 12 resistance genes encoding carbapenems, quinoline, aminoglycoside, β-lactam belonging blaOXA-58,blaOXA-22,qnrA, qnrB, aac(6)-Ib-cr, aac (3)-XI, mec A, qepA, aadB, blaVIM, blaOXA-48 and blaNDM. Pseudomonas aeruginosa (1: TN/I/2020) showed presence of 3 resistance genes. qnrB (489 bp) gene was present in maximum of 7 isolates while blaVIM (196 bp) gene was present in 6 isolates. The resistance genes blaNDM (621 bp) was present in three different isolates; aac (X):6)-lb-cr (482 bp), qepA (495 bp), aadB (500 bp), blaOXA-58 (843 bp) resistant genes were present in two different isolates each among the bacterial isolates obtained in this study. In phenotypic resistance profiling by AST method, out of 16 antibiotics tested, 14 showed resistance. Similarly, in genotypic resistance profiling, among 12 resistance genes tested, a maximum of three resistance genes were noticed in Pseudomonas aeruginosa. There were positive and negative correlations observed between phenotypic and genotypic resistance among different antibiotics and their resistance genes indicating the variations in the resistance gene expression.

The two faces of antibiotics: an overview of the effects of antibiotic residues in foodstuffs

Antibiotics, which have been used for many years to treat infections, also play an important role in food contamination with antibiotic residues. There is also unnecessary use of antibiotics, particularly to increase production efficiency. Non-compliance with withdrawal periods and maximum residue limits (MRLs) for antibiotics used in food-producing animals results in undesirable events, such as allergic reactions, teratogenicity, carcinogenicity, changes in the microbiota and, in particular, antibiotic resistance. Therefore, it may be useful to avoid unnecessary use of antibiotics, to limit the use of antibiotics and to turn to alternatives that can be used instead of antibiotics. The aim of this review is to provide information on the undesirable effects of antibiotic residues in food-producing organisms and in the environment, their determination, and the precautions that can be taken.

Airborne antibiotic resistome and microbiome in pharmaceutical factories

Antimicrobial resistance is considered to be one of the biggest public health problems, and airborne transmission is an important but under-appreciated pathway for the spread of antibiotic resistance genes (ARGs) in the environment. Previous research has shown pharmaceutical factories to be a major source of ARGs and antibiotic resistant bacteria (ARB) in the surrounding receiving water and soil environments. Pharmaceutical factories are hotspots of antibiotic resistance, but the atmospheric transmission and its environmental risk remain more concerns. Here, we conducted a metagenomic investigation into the airborne microbiome and resistome in three pharmaceutical factories in China. Soil (average: 38.45%) and wastewater (average: 28.53%) were major contributors of airborne resistome. ARGs (vanR/vanS, blaOXA, and CfxA) conferring resistance to critically important clinically used antibiotics were identified in the air samples. The wastewater treatment area had significantly higher relative abundances of ARGs (average: 0.64 copies/16S rRNA). Approximately 28.2% of the detected airborne ARGs were found to be associated with plasmids, and this increased to about 50% in the wastewater treatment area. We have compiled a list of high-risk airborne ARGs found in pharmaceutical factories. Moreover, A total of 1,043 viral operational taxonomic units were identified and linked to 47 family-group taxa. Different CRISPR-Cas immune systems have been identified in bacterial hosts in response to phage infection. Similarly, higher phage abundance (average: 2451.70 PPM) was found in the air of the wastewater treatment area. Our data provide insights into the antibiotic resistance gene profiles and microbiome (bacterial and non-bacterial) in pharmaceutical factories and reveal the potential role of horizontal transfer in the spread of airborne ARGs, with implications for human and animal health.

Anthropogenic impact and antibiotic resistance among the indicator and pathogenic bacteria from several industrial and sewage discharge points along the coast from Pydibhimavaram to Tuni, East Coast of India

Increasing urbanisation and industrialisation of the Visakhapatnam region have brought domestic sewage and industrial wastewater discharge into the coastal ocean. This study examines the indicator and pathogenic bacteria's quantitative abundance and antibiotic susceptibility. This study collected surface and subsurface water samples from ten different regions (147 stations; 294 samples), including 12 industrial discharge points, surrounding stations and two harbours from the coast of Pydibheemavaram to Tuni. Physicochemical parameters like salinity, temperature, fluorescence, pH, total suspended matter, nutrients, chlorophyll-a and dissolved oxygen showed a difference between regions. We noticed the presence of indicator (Escherichia coli and Enterococcus faecalis) and pathogenic (Aeromonas hydrophila, Klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa, Salmonella and Shigella, Vibrio cholera and Vibrio parahaemolyticus) bacteria among the samples. Waters from the near harbour and Visakhapatnam steel plant showed lower bacterial load with no direct input from industries to the coastal water. Samples collected during the industrial discharge period had a higher bacterial load, including E. coli. Enteric bacteria were found in higher numbers at most stations. Some isolates were resistant to multiple antibiotics with higher antibiotic resistance and multiple antibiotic resistance indexes compared with the other coastal water habitats in the Bay of Bengal. The occurrence of these bacteria above the standard limits and with multiple antibiotic resistance in the study region may pose a potential threat to the local inhabitants. It can create an alarming situation in the coastal waters in the study region.

Temporal dynamic of antibiotic resistance genes in the Zaohe-Weihe hyporheic zone: driven by oxygen and bacterial community

The widespread spread of antibiotic resistance genes (ARGs) in hyporheic zone (HZ) has become an emerging environmental problem due to their potentially harmful nature. In this research, three different oxygen treatment systems were set up to study the effects of oxygen changes on the abundance of ARGs in the HZ. In addition, the effects of temperature and salinity on ARGs were investigated under aerobic and anaerobic systems, respectively. The bacterial community composition of sediment samples and the relationship with ARGs were analyzed. The explanation ratio and causality of the driving factors affecting ARGs were analyzed using variation partitioning analysis (VPA) and structural equation model (SEM). The relative abundance of ARGs and mobile genetic elements (MGEs) in the anaerobic system increased significantly, which was higher than that in the aerobic system and the aerobic-anaerobic interaction system. The experiment of salinity and temperature also further proved this result. There were many bacterial communities that affected tetracycline and sulfonamide ARGs in sediments, and these host bacteria are mainly concentrated in Proteobacteria, Firmicutes and Bacteroidetes. VPA and SEM further revealed that the abundance of ARGs was mainly influenced by changes in bacterial communities and oxygen conditions, and horizontal gene transfer (HGT) of MGEs also had a positive effect on the spread of ARGs. Those findings suggest that complex oxygen conditions in the HZ alter bacterial communities and promote MGEs-mediated horizontal transfer, which together lead to the spread of ARGs. This study has value as a reference for formulating effective strategies to minimize the propagation of ARGs in underground environment.

Antibiotic resistomes and their chemical residues in aquatic environments in Africa

The aquatic environment is a hotspot for the transfer of antibiotic resistance to humans and animals. Several reviews have put together research efforts on the presence and distribution of antibiotic resistant bacteria (ARB), antibiotic resistance genes (ARGs), and antibiotic chemical residue (ACRs) in food, hospital wastewater, and even in other aquatic environments. However, these reports are largely focused on data from developed countries, while data from developing countries and especially those in Africa, are only marginally discussed. This review is the first effort that distills information on the presence and distribution of ARGs and ACRs in the African aquatic environments (2012-2021). This review provides critical information on efforts put into the study of ARB, ARGs, and ACRs in aquatic environments in Africa through the lens of the different sub-regions in the continent. The picture provided is compared with those from some other continents in the world. It turns out that the large economies in Africa (South Africa, Nigeria, Tunisia, Kenya) all have a few reports of ARB and ARGs in their aquatic environment while smaller economies in the continent could barely provide reports of these in their aquatic environment (in most cases no report was found) even though they have some reports on resistomes from clinical studies. Interestingly, the frequency of these reports of ARB and ARGs in aquatic environments in Africa suggests that the continent is ahead of the South American continent but behind Europe and Asia in relation to providing information on these contaminants. Common ARGs found in African aquatic environment encode resistance to sulfonamide, tetracycline, β-lactam, and macrolide classes of antibiotics. The efforts and studies from African scientists in eliminating ARB and ARGs from the aquatic environment in Africa are also highlighted. Overall, this document is a ready source of credible information for scientists, policy makers, governments, and regional bodies on ARB, ARGs, and ACRs in aquatic environments in Africa. Hopefully, the information provided in this review will inspire some necessary responses from all stakeholders in the water quality sector in Africa to put in more effort into providing more scientific evidence of the presence of ARB, ARGs, and ACRs in their aquatic environment and seek more efficient ways to handle them to curtail the spread of antibiotic resistance among the population in the continent. This will in turn, put the continent on the right path to meeting the United Nations Sustainable Development Goals #3 and #6, which at the moment, appears to be largely missed by most countries in the continent.

Profile of Bacterial Community and Antibiotic Resistance Genes in Typical Vegetable Greenhouse Soil

The use of vegetable greenhouse production systems has increased rapidly because of the increasing demand for food materials. The vegetable greenhouse production industry is confronted with serious environmental problems, due to their high agrochemical inputs and intensive utilization. Besides this, antibiotic-resistant bacteria, carrying antibiotic-resistance genes (ARGs), may enter into a vegetable greenhouse with the application of animal manure. Bacterial communities and ARGs were investigated in two typical vegetable-greenhouse-using counties with long histories of vegetable cultivation. The results showed that Proteobacteria, Firmicutes, Acidobacteria, Chloroflexi, and Gemmatimonadetes were the dominant phyla, while aadA, tetL, sul1, and sul2 were the most common ARGs in greenhouse vegetable soil. Heatmap and principal coordinate analysis (PCoA) demonstrated that the differences between two counties were more significant than those among soils with different cultivation histories in the same county, suggesting that more effects on bacterial communities and ARGs were caused by soil type and manure type than by the accumulation of cultivation years. The positive correlation between the abundance of the intI gene with specific ARGs highlights the horizontal transfer potential of these ARGs. A total of 11 phyla were identified as the potential hosts of specific ARGs. Based on redundancy analysis (RDA), Ni and pH were the most potent factors determining the bacterial communities, and Cr was the top factor affecting the relative abundance of the ARGs. These results might be helpful in drawing more attention to the risk of manure recycling in the vegetable greenhouse, and further developing a strategy for practical manure application and sustainable production of vegetable greenhouses.

Development of novel effective agents from 1H-indolylammonium trifluoroacetates effective against conditionally pathogenic microorganisms

Introduction: The problem of antibiotic resistance of microorganisms is becoming more urgent in the twenty-first century. More and more pathogenic microbes are becoming resistant to two or more antibiotics. This problem has become worse into the COVID-19 pandemic. The search for new compounds with antimicrobial activity is one of the principles for overcoming the antibiotic resistance of microorganisms.

Materials and methods: Methods for the preparation, isolation, and identification of salts of 2,3,5-trimethyl-, 1,2,3,5-tetramethyl-, 2,3-dimethyl-5-methoxy-, 5-methoxy-1,2,3-trimethyl-1H-indole-6-amines and trifluoroacetic acid were developed and laboratory microbiological studies of them for antimicrobial activity were carried out. Sensitivity of the test-strains of microorganisms to the new compounds was studied. A method of serial dilutions to determine the minimal inhibitory concentration (MIC) of the compounds under study was used in the study.

Results and discussion: The compounds 5–8 showed a pronounced antibacterial activity against the test strains of microorganisms in vitro with MIC from 0.98 µg/mL to 125.0 µg/mL. The prospects for targeted synthesis of biologically active compounds which are derivatives of 1H-indolylamines with a trifluoromethyl group in the molecule were determined, and after additional studies, the compounds 5–8 may find application as water-soluble synthetic antimicrobial agents.

Conclusion: The laboratory microbiological screening of showed that they have an antimicrobial effect that exceeds the activity of the reference drug, dioxidine. The presence of molecular mechanisms predicted in silico in the spectrum of biological activity of the studied compounds, such as Pseudolysin inhibitor, Omptin inhibitor, Undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase inhibitor, UDP-epimerase inhibitor, Bacterial efflux pump inhibitor, suggests the presence of antimicrobial activity against gram-positive and gram-negative microorganisms. Trifluoroacetates 2,3,5-trimethyl-1H-indole-6-ammonium (5), 1,2,3,5-tetramethyl-1H-indole-6-ammonium (6), 2,3-dimethyl-5-methoxy-1H-indole-6-ammonium (7), 1,2,3-trimethyl-5-methoxy-1H-indole-6-ammonium (8), after additional studies, may find application as water-soluble synthetic antimicrobial agents.

Resistant Genes and Multidrug-Resistant Bacteria in Wastewater: A Study of Their Transfer to the Water Reservoir in the Czech Republic

Wastewater is considered the most serious source of the spread of antibiotic resistance in the environment. This work, therefore, focuses on the fate and spread of antibiotic resistance genes (ARGs) in wastewater and the monitoring of multidrug-resistant strains. ARGs were monitored in the nitrification and sedimentation tanks of the wastewater treatment plant (WWTP) and in the dam into which this WWTP flows, at various times. The highest relative abundance was found for the blaTEM > tetW > blaNDM-1 > vanA resistance genes, respectively. An increased concentration of tetracycline (up to 96.00 ng/L) and ampicillin (up to 19.00 ng/L) was found in water samples compared to other antibiotics detected. The increased incidence of seven ARGs and four antibiotics was observed in the November and December sampling times. Isolated ampicillin-resistant strains showed a high degree of resistance to ampicillin (61.2% of the total isolates had a minimum inhibitory concentration (MIC) ≥ 20 mg/mL). In 87.8% of isolates, out of the total number, the occurrence of two or more ARGs was confirmed. These multidrug-resistant strains were most often identified as Aeromonas sp. This strain could represent a significant role in the spread of multidrug resistance through wastewater in the environment.

Treatment of simulated industrial pharmaceutical wastewater containing amoxicillin antibiotic via advanced oxidation processes

The treatment of pharmaceutical industrial wastewaters, containing the antibiotic amoxicillin (218.29 mg L^-1), via some advanced oxidation processes (POA), was studied. The H₂O₂ photolysis process presented the highest percentage of mineralization (97%), after the total reaction time (180 min). However, the photo-Fenton process showed the highest organic carbon removal rate, mineralizing 65% of the initial concentration, in 30 min. Because of this fact, this process was studied in more detail. The initial concentration of ferrous ions (0.03-1.00 mmol L^-1) did not affect the performance of the photo-Fenton process, possibly operating using concentrations of below 15 mg L^-1 (0.27 mmol L^-1), that is the iron content limit for discharging wastewaters established in the Brazilian environmental legislation. Furthermore, experiments were performed according to the composite experimental design technique (Doehlert matrix), analyzing the following variables: (i) the inlet molar flow rate of H₂O₂ (F_H2O2 ) and (ii) the initial concentration of ferrous ions ([Fe²⁺]). Besides that, the initial mineralization rate and the total organic carbon removal percentages, measured at 5, 10, 15 and 30 min of reaction, were chosen as the response variables. It was observed that F_H2O2 was the most important variable in relation to the initial degradation rate. In the optimal conditions (F_H2O2  = 3.27 mmol min^-1 and [Fe²⁺] = 0.27 mmol L^-1), the photo-Fenton process achieved a percentage of organic carbon removal of 84%, in only 30 min of reaction, presenting an interesting potential for real industrial applications, combined, or not, with conventional technologies (as biological treatments, for example).

Prevalence of Antibiotic Resistance Genes in Pharmaceutical Wastewaters

Pharmaceutical wastewaters are recognized as reservoirs of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB), and also as hotspots for their horizontal gene transfer (HGT) using mobile genetic elements. Our study employed the use of PCR analysis of metagenomic DNA samples obtained from four pharmaceutical wastewaters using known primers to study the prevalence of thirty-six ARGs and four MGEs active against the commonly used antibiotics in Nigeria. The ARGs most frequently detected from the metagenomic DNA samples in each of the antibiotic classes under study include tetracycline [tet(G)], aminoglycoside [aadA, strA and strB], chloramphenicol [catA1], sulphonamides [sulI and sulII], and β-lactams and penicillins [blaOXA]. The ARGs showed a 100% prevalence in their various environmental sources. The pharmaceutical facility PFIV showed the highest concentration of ARGs in this study. The highest concentration for MGEs was shown by pharmaceutical facility PFIII, positive for intl1, intl2, and IFS genes. This study highlights the wide distribution of ARGs to the antibiotics tested in the wastewater, making pharmaceutical wastewater reservoirs of ARGs which could potentially be transferred from commensal microorganisms to human pathogens.

Impact factors of the accumulation, migration and spread of antibiotic resistance in the environment

Antibiotic resistance is a great concern, which leads to global public health risks and ecological and environmental risks. The presence of antibiotic-resistant genes and antibiotic-resistant bacteria in the environment exacerbates the risk of spreading antibiotic resistance. Among them, horizontal gene transfer is an important mode in the spread of antibiotic resistance genes, and it is one of the reasons that the antibiotic resistance pollution has become increasingly serious. At the same time, free antibiotic resistance genes and resistance gene host bacterial also exist in the natural environment. They can not only affect horizontal gene transfer, but can also migrate and aggregate among environmental media in many ways and then continue to affect the proliferate and transfer of antibiotic resistance genes. All this shows the seriousness of antibiotic resistance pollution. Therefore, in this review, we reveal the sensitive factors affecting the distribution and spread of antibiotic resistance through three aspects: the influencing factors of horizontal gene transfer, the host bacteria of resistance genes and the migration of antibiotic resistance between environmental media. This review reveals the huge role of environmental migration in the spread of antibiotic resistance, and the environmental behavior of antibiotic resistance deserves wider attention. Meanwhile, extracellular antibiotic resistance genes and intracellular antibiotic resistance genes play different roles, so they should be studied separately.

Structure of Bacterial Community with Resistance to Antibiotics in Aquatic Environments. A Systematic Review

Aquatic environments have been affected by the increase in bacterial resistant to antibiotics. The aim of this review is to describe the studies carried out in relation to the bacterial population structure and antibiotic resistance genes in natural and artificial water systems. We performed a systematic review based on the PRISMA guideline (preferred reporting items for systematic reviews and meta-analyzes). Articles were collected from scientific databases between January 2010 and December 2020. Sixty-eight papers meeting the inclusion criteria, i.e., "reporting the water bacterial community composition", "resistance to antibiotics", and "antibiotic resistance genes (ARG)", were evaluated according to pre-defined validity criteria. The results indicate that the predominant phyla were Firmicutes and Bacteroidetes in natural and artificial water systems. Gram-negative bacteria of the family Enterobacteraceae with resistance to antibiotics are commonly reported in drinking water and in natural water systems. The ARGs mainly reported were those that confer resistance to β-lactam antibiotics, aminoglycosides, fluoroquinolones, macrolides and tetracycline. The high influence of anthropogenic activity in the environment is evidenced. The antibiotic resistance genes that are mainly reported in the urban areas of the world are those that confer resistance to the antibiotics that are most used in clinical practice, which constitutes a problem for human and animal health.

Occurrence of emerging sulfonamide resistance (sul1 and sul2) associated with mobile integrons-integrase (intI1 and intI2) in riverine systems

Global use of antibiotics has exceedingly enhanced in agricultural, veterinary and prophylactic human use in recent days. Hence, these antibiotics can easily be found in the environment. This study revealed the occurrence of emerging MDR and ESBL producing strains, pollution profile, and factors integrons (intI1 and intI2) and environmental factors associated, in the riverine systems under different ecological and geo-climatic zones were investigated. The samples were collected based on anthropogenic intervention such as discharge of domestic wastes, industrial wastes, hospital, and municipal wastes. Among 160bacterial morphotypes, 121 (75.62%) exhibited MDR trait with maximum resistance towards lincosamide (CD = 71.3%), beta-lactams (P = 70.6%; AMX = 66.3%), cephalosporin (CZ = 60.6%; CXM = 34.4%), sulfonamide (COT = 50.6%; TR = 43.8%) followed by macrolide (E = 29.4%), tetracycline (TET = 18.8%), aminoglycosides (S = 18.8%; GEN = 6.3%), fluoroquinolones (NX = 18.1%; OF = 4.4%) and carbapenem (IPM = 5.0%). IntI1 gene was detected in 73 (60.3%) of isolates, whereas intI2 was found in 11 (9.09%) isolates. Eight (6.61%) isolates carried both integron genes (intI1 and intI2). sul1 and dfrA1 genes were detected in 53 (72.6%) and 63 (86.3%) isolates, respectively. A total of 103 (85.1%) were found ESBL positive with the presence of ESBL genes in 100 (97.08%) isolates. In riverine systems most prevalent ESBL gene blaTEM (93.0%) was detected alone as well as in combination with bla genes. The data can be utilized for public awareness and regulation of guidelines by local governing bodies as an alarming threat to look-out against the prevalent resistance in environment thereby assisting in risk management during epidemics. This study is a comprehensive investigation of emerging antibiotic pollutants and its resistance in bacteria associated with factors integrons-integrase responsible for its dissemination. It may also assist in global surveillance of antibiotic resistance and policies to curtail unnecessary antibiotic use.

Co-occurrence of multidrug resistance, β-lactamase and plasmid mediated AmpC genes in bacteria isolated from river Ganga, northern India

Wastewater effluents released in surface water provides suitable nutrient rich environment for the growth and proliferation of antibiotic resistant bacteria (ARB) and genes (ARG). Consequently, bacterial resistance has highly evolved over the recent years and diversified that each antibiotic class is inhibited by a distinct mechanism. In the present study, the prevalence of Multidrug resistant (MDR), extended spectrum β-lactamases (ESBL) and plasmid mediated Amp-C producing strains was analyzed in 28 surface water samples collected near domestic effluent discharge sites in river Ganga located across 11 different geographical indices of Uttar Pradesh, India. A total of 243 bacterial strains with different phenotypes were isolated. Among 243 isolates, 206 (84.77%) exhibited MDR trait displaying maximum resistance towards β-lactams (P = 78.19%; AMX = 72.84%), glycopeptides (VAN = 32.92%; TEI = 79.42%), cephalosporins (CF = 67.90%; CFX = 38.27%), and lincosamides (CD = 78.18%) followed by sulfonamide, macrolide and tetracycline. ESBL production was confirmed in 126 (51.85%) isolates that harbored the genes: blaTEM (95.24%), blaSHV (22.22%), blaOXA (11.90%) and blaCTX-M group (14.28%). The presence of plasmid mediated AmpC was detected only in 6.17% of isolates. The existence of such pathogenic strains in the open environment generates an urgent need for incorporating stringent measures to reduce the antibiotic consumption and hence its release.

A comprehensive review of water quality monitoring and assessment in Nigeria

Nigeria is the most populated black nation in the world with about 199 million people. About 66.3 million Nigerians do not have access to safe drinking water. In this study, research findings on water quality monitoring and assessment in Nigeria over the past two decades were systematically reviewed. There are still grave enforcement issues in Nigeria as quality guidelines are still being contravened at no cost to the infringer due to the corrupt socio-political circumstances of the country. The quality of surface water, groundwater, rainwater and commercially available water was discussed in line with their pollution sources. The quality of surface water was generally poor. Groundwater pollution has come due to landfill leachate, oil and gas exploration and production, sewage and hydrogeological interactions of the groundwater with the base rock. The hydrogeological effect has led to the observation of lead and barium in groundwater in many locations across the country. The main issue with rainwater in Nigeria is the low pH but it was observed to be fairly clean. Commercially available water (bottled or sachet) is currently the best source of drinking water for the Nigerian populace. Bottled water quality is higher than for sachet water and the latter largely influenced by microbe contamination. Future perspectives in water quality monitoring and assessment are suggested in the evaluation of emerging contaminants and micro-pollutants and the utilisation of internet-enabled technologies.

Distribution of Antibiotic-Resistant Enterobacteriaceae Pathogens in Potable Spring Water of Eastern Indian Himalayas: Emphasis on Virulence Gene and Antibiotic Resistance Genes in Escherichia coli

Every year millions of people die due to fatal waterborne diseases around the world especially in developing countries like India. Sikkim, a northeastern state of India, greatly depends on natural water sources. About 80% of the population of Sikkim depends on natural spring water for domestic as well as agricultural use. Recent waterborne disease outbreaks in the state raises a concerning question on water quality. In this study, we analyzed water quality especially for the detection of Enterobacteriaceae members from four districts of the state. Isolation with selective culture media techniques and taxonomic characterization of Enterobacteriaceae bacteria with 16S rRNA gene showed the prevalence of Escherichia coli (37.50%), Escherichia fergusonii (29.41%), Klebsiella oxytoca (36.93%), Citrobacter freundii (37.92%), Citrobacter amalonaticus (43.82%), Enterobacter sp. (43.82%), Morganella morganii (43.82%), Hafnia alvei (32.42%), Hafnia paralvei (38.74%), and Shigella flexneri (30.47%) in the spring water of Sikkim. Antibiotic susceptibility test (AST) showed resistance of the isolates to common antibiotics like ampicillin, amoxicillin as well as to third generation antibiotics like ceftazidime and carbapenem. None of the isolates showed resistance to chloramphenicol. E. coli isolated from spring water of Sikkim showed presence of different virulence genes such as stx1 (81.81%), elt (86.66%), and eae (66.66%) along with resistance gene for ampicillin (CITM) (80%), quinolones (qnrB) (44.44%), tetracycline (tetO) (66.66%), and streptomycin (aadA1) (66.66%). The data indicates a high incidence rate of multiple antibiotic resistant enteric bacteria in the spring water of Sikkim. Additionally, the presence of enteric bacteria in the water samples indicates widespread fecal contamination of the spring water.

Tetracycline Induces the Formation of Biofilm of Bacteria from Different Phases of Wastewater Treatment

The study monitored the effect of tetracycline on bacterial biofilm formation and compared biofilm formation by resistant bacterial strains in different phases of the wastewater treatment process in wastewater treatment plant (WWTP). The crystal violet staining method was used to evaluate the biofilm formation. Biofilm-related bacterial properties were characterized by hydrophobicity, autoaggregation and motility tests. The relative abundance of tetracycline resistance genes (tetW, tetM, tetO, tetA and tetB) in wastewaters were subsequently quantified using qPCR. The results show that the isolates from the nitrification tank produce biofilm with up to 10 times greater intensity relative to the isolates from the sedimentation tank. In isolates of Aeromonas sp. from the nitrification tank, increased biofilm production in the occurrence of tetracycline from a concentration of 0.03125 µg/mL was observed. The tetW gene showed the highest relative abundance out of all the tested genes. From the sampling points, its abundance was the highest in the sedimentation tank of the WWTP. Based on these results, it can be assumed that resistant bacteria are able to form a biofilm and sub-inhibitory tetracycline concentrations induce biofilm formation. WWTPs thus represent a reservoir of antibiotic resistance genes and contribute to the spread of resistance in the natural environment.

Antibiotic Resistance Genes Occurrence in Wastewaters from Selected Pharmaceutical Facilities in Nigeria

The proliferation of antibiotic-resistant bacteria (ARB) and the prevalence of antibiotic resistance genes (ARGs) in wastewaters are well-established factors that contribute to the reduced potency of antibiotics used in healthcare worldwide. The human health risk associated with the proliferation of ARB and ARGs need to be understood in order to design mitigation measures to combat their dissemination. Using the PCR analysis of genomic DNA, the prevalence of 41 ARGs active against the commonly used six classes of antibiotics was evaluated in 60 bacterial isolates obtained from pharmaceutical wastewaters in Nigeria. The ARGs most frequently detected from the bacterial isolates in each of the antibiotic classes under study include catA1 (58.3%); sulI (31.7%); tet(E) (30%); aac(3)-IV (28.3%); ermC (20%); blaTEM, blaCTX-M, blaNDM-1 at 18.3% each; which encode for resistance to chloramphenicol, sulfonamides, tetracycline, aminoglycoside, macrolide-lincosamide-streptogramin and β-lactams and penicillins, respectively. Acinetobacter spp., accession number MH396735 expressed the highest number of ARGs of all the bacterial isolates, having at least one gene that encodes for resistance to all the classes of antibiotics in the study. This study highlights wide distribution of ARB and ARGs to the antibiotics tested in the wastewater, making pharmaceutical wastewater reservoirs of ARGs which could potentially be transferred from commensal microorganisms to human pathogens.

Resistome in Lake Bolonha, Brazilian Amazon: Identification of Genes Related to Resistance to Broad-Spectrum Antibiotics

Resistance to antibiotics is one of the most relevant public health concerns in the world. Aquatic environments play an important role because they are reservoirs for antibiotic resistance genes and antibiotic-resistant strains, contributing to the spread of resistance. The present study investigated the resistome in Lake Bolonha (three sampling sites) in the Amazon region using a metagenomics approach and culture-dependent methods. Whole-metagenome-based results showed that the most abundant phyla were Protobacteria, Actinobacteria, Firmicutes, Bacteroidetes and Cyanobacteria. The composition of the resistome demonstrated that the genes that confer resistance to β-lactams were prevalent at all sampling sites, followed by genes conferring resistance to aminoglycosides and tetracycline. Acquired genes encoding extended-spectrum β-lactamases (e.g., bla_CTX–M) and resistance to carbapenems (e.g., bla_IMP and bla_VIM) were detected through metagenome analysis. Bacteria were isolated from culture medium supplemented with cefotaxime or imipenem, and isolates were identified and analyzed for their antibiotic susceptibility profiles and resistance genes. In total, 98 bacterial isolates belonging to the genera Pseudomonas (37), Acinetobacter (32), Klebsiella (13), Enterobacter (9), Pantoe (3), Stenotrophomonas (3), and Methylobacterium (1) were obtained. Among isolates, the most abundant genes were bla_CTX–M (28.3%), bla_SHV (22.6%) and bla_TEM (18.8%) in isolates from cefotaxime-supplemented medium and bla_VIM (28.8%) and bla_IMP (22.2%) in isolates recovered from imipenem-supplemented medium. The genes intl1 and intl2 were detected in 19.3% and 7.1% of isolates. Antibiograms showed that 94.9% (from cefotaxime-supplemented medium) and 85.7% (from imipenem-supplemented medium) of the isolates were multidrug resistant. Besides cefotaxime and imipenem, isolates were mostly resistant to aztreonam (91.8%), amoxicillin (98.8%), ampicillin (82.6%), and nalidixic acid (77.5%). Hence, the present study demonstrates that Lake Bolonha is a reservoir of bacteria resistant to antibiotics and resistance genes, some of which are of critical importance to human health.

Urbanization and Waterborne Pathogen Emergence in Low-Income Countries: Where and How to Conduct Surveys?

A major forthcoming sanitary issue concerns the apparition and spreading of drug-resistant microorganisms, potentially threatening millions of humans. In low-income countries, polluted urban runoff and open sewage channels are major sources of microbes. These microbes join natural microbial communities in aquatic ecosystems already impacted by various chemicals, including antibiotics. These composite microbial communities must adapt to survive in such hostile conditions, sometimes promoting the selection of antibiotic-resistant microbial strains by gene transfer. The low probability of exchanges between planktonic microorganisms within the water column may be significantly improved if their contact was facilitated by particular meeting places. This could be specifically the case within biofilms that develop on the surface of the myriads of floating macroplastics increasingly polluting urban tropical surface waters. Moreover, as uncultivable bacterial strains could be involved, analyses of the microbial communities in their whole have to be performed. This means that new-omic technologies must be routinely implemented in low- and middle-income countries to detect the appearance of resistance genes in microbial ecosystems, especially when considering the new ‘plastic context.’ We summarize the related current knowledge in this short review paper to anticipate new strategies for monitoring and surveying microbial communities.

Fate of environmental pollutants

This annual review covers the literature published in 2018 on topics related to the occurrence and fate of environmental pollutants in wastewater. Due to the vast amount of literature published on this topic, we have discussed only a portion of the quality research publications, due to the limitation of space. The abstract search was carried out using Web of Science, and the abstracts were selected based on their relevance. In a few cases, full-text articles were referred to understand new findings better. This review is divided into the following sections: antibiotic-resistant bacteria (ARBs) and antibiotic-resistant genes (ARGs), disinfection by-products (DBPs), drugs of abuse (DoAs), estrogens, heavy metals, microplastics, per- and polyfluoroalkyl compounds (PFAS), pesticides, and pharmaceuticals and personal care products (PPCPs), with the addition of two new classes of pollutants to previous years (DoAs and PFAS).

Genetic characterization of a novel sequence type of multidrug-resistant Citrobacter freundii strain recovered from wastewater treatment plant

A multidrug-resistant Citrobacter freundii strain R17 was isolated from a wastewater treatment plant in China. Whole-genome sequencing of strain R17 revealed a new sequence type (ST412) chromosome (length 5,124,258 bp) and an Inc FII (Yp) group plasmid pCFR17_1 (length 206,820 bp). A total of 13 antibiotic-resistance genes (ARGs) that confer resistance to eight different antibiotic groups were encoded by strain R17 and 12 of them were carried by plasmid pCFR17_1. These data and analysis suggest that the environment-derived C. freundii strains may serve as potential sources of ARGs and highlight the need of further surveillance of this bacteria in the future.

Whole Genome Sequencing of Extended-Spectrum Beta-Lactamase (ESBL)-Producing Escherichia coli Isolated From a Wastewater Treatment Plant in China

Background and Objectives

Wastewater treatment plants (WWTPs) are one of the major reservoirs for antimicrobial resistant bacteria (ARB) and antimicrobial resistance genes (ARGs) in the environment. Thus, the investigation on ARB and ARGs from WWTPs has attracted increasing attention in recent years. In order to uncover the resistome in a WWTP treating effluents from a pharmaceutical industry in China, the extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli strains were isolated and their whole genome sequences were obtained and analyzed. Moreover, metagenomic sequencing was applied to give a comprehensive view of antibiotic resistance in this WWTP.

Methods

18 ESBL-producing E. coli strains were isolated from a WWTP located in Taizhou, China on April, 2017. All strains were sequenced using Illumina HiSeq 2000 sequencer. The whole genome sequences were assembled using SPAdes software and annotated with RAST server. Sequence types (STs), plasmids, ARGs and virulence genes were predicted from the genomes using MLST, Plasmid Finder, ResFinder and Virulence Finder, respectively. Metagenomic DNA of the same sample was extracted and sequenced using Illumina Hiseq X Ten platform. Metagenomic sequences were assembled using SOAPdenovo software.

Results

All 18 ESBL-producing E. coli strains were resistant to ampicillin, cefazolin, and ceftriaxone. Analysis of their genomes revealed that all strains carried beta-lactamase encoding genes and the most prevalent type was bla _CTX-M . Various virulence genes and ARGs confronting resistance to other types of antimicrobial agents were also predicted. Further investigation on the metagenomics data indicated 11 ARGs with high amino acid identities to the known ARGs. Five of these ARGs, aadA1, aac(6')-lb-cr, flo(R), sul2 and sul1, were also present in the genomes of the ESBL-producing E. coli isolated from the same sample.

Conclusion

Our study revealed the resistome of a pharmaceutical WWTP by both culture-dependent and metegenomic methods. The existence of ESBL-producing E. coli strains, indicating that pharmaceutical WWTP can play a significant role in the emergence of ARB. The occurrence of ARGs annotated from the metagenomic data suggests that pharmaceutical WWTP can play a significant role in the emergence of ARGs. Our findings highlight the need for strengthening the active surveillance of ARB and ARGs from pharmaceutical industry.

A study of the type of antimicrobial action of novel compounds synthesized from substituted benzaminoindoles

The antimicrobial activity of novel compounds is tested by determining the minimum inhibitory concentration of the agent in question and investigating a few other parameters, including the type of antimicrobial action the drug exhibits. The aim of this study was to determine the type of antimicrobial action of the compounds synthesized from the substituted benzaminoindoles. The strain of Staphylococcus aureus АТСС 6538-Р was briefly exposed to the compounds with laboratory codes 5D, 7D, HD, and S3. Bacterial growth was evaluated macroscopically under transmitted light. Additionally, photoelectric colorimetry was applied to monitor changes in the optical density of the culture medium. The minimum inhibitory concentrations of the studied compounds delayed bacterial growth for 2–3 days and had a bacteriostatic effect on S. aureus.

Delineating the origins of the multidrug-resistant pathogens in ornamental fish farms by multilocus sequence typing and identification of a novel multidrug-resistant plasmid

To evaluate the overuse of antibiotics and to identify the origin of pathogens in the ornamental fish industry, we conducted a field investigation of three representative fish farms in Liaoning province, China. Drug-resistant pathogens in the fishponds and groundwater were isolated and subtyped by multilocus sequence typing (MLST). In total, 33 pathogenic strains, including Aeromonas veronii and five other pathogens, were isolated from diseased fish and from groundwater. MLST revealed that A. veronii obtained from diseased fish in three fish farms can be subtyped into four sequence types, which were also identified in the corresponding groundwater. All of the isolates obtained from diseased fish showed resistance to at least four antibiotics. Notably, Citrobacter freundii JY-17 exhibited resistance to the majority of the antibiotics and was a carrier of a megaplasmid with 15 drug resistance genes. PCR assays targeting β-lactam, kanamycin, macrolide, phenicol, sulfonamide, and trimethoprim resistance genes in the pathogens from the diseased fish and groundwater were also conducted. The results revealed strong correlations between antibiotic treatment and increased antimicrobial resistance in fish pathogens. The results suggested that groundwater is the origin of the pathogens in ornamental fish. Antibiotic treatment of ornamental fish promoted the emergence of resistant pathogens.

Antibiotics bioremediation: Perspectives on its ecotoxicity and resistance

Antibiotic is one of the most significant discoveries and have brought a revolution in the field of medicine for human therapy. In addition to the medical uses, antibiotics have broad applications in agriculture and animal husbandry. In developing nations, antibiotics use have helped to increase the life expectancy by lowering the deaths due to bacterial infections, but the risks associated with antibiotics pollution is largely affecting people. Since antibiotics are released partially degraded and undegraded into environment creating antibiotic pollution, and its bioremediation is a challenging task. In the present review, we have discussed the primary antibiotic sources like hospitals, dairy, and agriculture causing antibiotic pollution and their innovative detection methods. The strong commitment towards the resistance prevention and participation, nations through strict policies and their implementations now come to fight against the antibiotic resistance under WHO. The review also deciphers the bacterial evolution based strategies to overcome the effects of antibiotics, so the antibiotic degradation and elimination from the environment and its health benefits. The present review focuses on the environmental sources of antibiotics, it's possible degradation mechanisms, health effects, and bacterial antibiotics resistance mechanisms.