Antibiotic Resistance Genes Associated with Marine Surface Sediments: A Baseline from the Shores of Kuwait

A review of spatial distribution of typical antibiotic resistance genes in marine environment surrounding China

Antibiotic resistance genes (ARGs) have been steadily increasing due to the extensive overuse of antibiotics in the marine environment. Currently, the research considering ARGs distribution in marine ecosystems gains more interest. As the coastal sea has been regarded as one of the most polluted areas by antibiotic contaminants in China. However, no comprehensive review of the spatial distribution of ARGs in marine environment surrounding China. The main objective of this review is to investigate the level, characteristic, and spatial distribution of ARGs in the marine environment (seawater and sediments) surrounding China. Key sea areas, such as Bohai Sea, Yellow Sea, East China Sea, and South China Sea were selected in this review. The marine environment was the reservoir of ARGs, and ARGs in seawater were generally 1 to 2 orders of magnitude higher than that in sediments. Total ARGs were more abundant in the Yellow Sea, followed by the Bohai Sea, the East China Sea, and the South China Sea. This study raises questions regarding the spread and distribution for antibiotic resistance in marine environments.

Determining the spatiotemporal variation, sources, and ecological processes of antibiotic resistance genes in a typical lake of the middle reaches of the Yangtze River

Antibiotic resistance genes (ARGs) are emerging environmental pollutants, influenced by complex regulatory factors. River-lake systems act as natural reservoirs for ARGs and provide an ideal model for studying their regulatory mechanisms. This study employed high-throughput quantitative PCR, high-throughput sequencing, correlation analyses, and model predictions to investigate the dynamics of ARGs and their influencing factors in Liangzi Lake, located in the mid-reaches of the Yangtze River. The research specifically centered on three environmental components: lake water, sediment, and river water. Results indicated that the ARGs from eight major antibiotic classes, displaying distinct seasonal distribution patterns. In comparison to the sediment, the water phase demonstrated a higher diversity of ARGs, with the highest level of ARGs sharing observed between lake and river waters (approximately 83.7 %). Furthermore, seasonal variations significantly influenced the distributions of both ARGs and bacterial communities. The diversity of ARGs was highest during the summer and autumn, and specific bacterial species exhibited robust correlations with ARGs (including matA/mel, aac (6')-Ib-03, and blaROB). It is worth noting that environmental attributes and bacterial diversity had the most substantial impact on the dynamic changes in ARGs. Lastly, source tracking analysis pinpointed that sediment as the primary source of ARGs in lake water, constituting 45 % to 48 % of the total ARGs. Our study provides a comprehensive analysis of ARGs and their influencing factors in the river-lake system of the middle reaches of the Yangtze River, with Liangzi Lake as a representative case.

K. Habeebullah S, Ali AK, Al-Zakri WM. Diversity and spatiotemporal variations in bacterial and archaeal communities within Kuwaiti territorial waters of the Northwest Arabian Gulf

Kuwaiti territorial waters of the northwest Arabian Gulf represent a unique aquatic ecosystem prone to various environmental and anthropogenic stressors that pose significant constraints on the resident biota which must withstand extreme temperatures, salinity levels, and reducing conditions, among other factors to survive. Such conditions create the ideal environment for investigations into novel functional genetic adaptations of resident organisms. Firstly, however, it is essential to identify said organisms and understand the dynamic nature of their existence. Thus, this study provides the first comprehensive analysis of bacterial and archaeal community structures in the unique waters of Kuwait located in the Northwest Arabian Gulf and analyzes their variations with respect to depth, season, and location, as well as their susceptibility to changes in abundance with respect to various physicochemical parameters. Importantly, this study is the first of its kind to utilize a shotgun metagenomics approach with sequencing performed at an average depth of 15 million paired end reads per sample, which allows for species-level community profiling and sets the framework for future functional genomic investigations. Results showed an approximately even abundance of both archaeal (42.9%) and bacterial (57.1%) communities, but significantly greater diversity among the bacterial population, which predominantly consisted of members of the Proteobacteria, Cyanobacteria, and Bacteroidetes phyla in decreasing order of abundance. Little to no significant variations as assessed by various metrics including alpha and beta diversity analyses were observed in the abundance of archaeal and bacterial populations with respect to depth down the water column. Furthermore, although variations in differential abundance of key genera were detected at each of the three sampling locations, measurements of species richness and evenness revealed negligible variation (ANOVA p<0.05) and only a moderately defined community structure (ANOSIM r2 = 0.243; p>0.001) between the various locations. Interestingly, abundance of archaeal community members showed a significant increase (log2 median ratio of RA = 2.6) while the bacterial population showed a significant decrease (log2 median ratio = -1.29) in the winter season. These findings were supported by alpha and beta diversity analyses as well (ANOSIM r2 = 0.253; p>0.01). Overall, this study provides the first in-depth analysis of both bacterial and archaeal community structures developed using a shotgun metagenomic approach in the waters of the Northwest Arabian Gulf thus providing a framework for future investigations of functional genetic adaptations developed by resident biota attempting to survive in the uniquely extreme conditions to which they are exposed.

Development of pharmacophore model to identify potential DNA gyrase inhibitors

There is great concern in the medical community due to rapid increase in antibiotic resistance, causing 700,000 deaths annually worldwide. Therefore, there is paramount need to develop novel and innovative antibacterial agents active against resistant bacterial strains. DNA gyrase is a crucial enzyme in bacterial replication that is absent in eukaryotes, making it effective curative target for antibacterials. To identify potential DNA gyrase inhibitors by virtual screening of NCI database using a 3-step approach. A total of 271 compounds with known IC50 values against Escherichia coli DNA GyrA were selected to develop a pharmacophore model for dual screening approach to identify new potential hits from the NCI database. In the second step, the NCI database was also screened using in-house built NN-QSAR model. Molecular docking of common 5298 compounds screened from both methods were performed against E. coli DNA GyrA (PDB id- 6RKU), and 3004 compounds are reported to exhibit lower binding energies than ciprofloxacin (-6.77 Kcal/mol). The top three compounds (NCI371878, NCI371876 and NCI142159) reported with binding energy of -13.5, -13.19 and -13.03 Kcal/mol were further subjected to MD simulation studies for 100 ns supporting the stability of the docked complexes.

Antibiotic Resistance Mediated by Escherichia coli in Kuwait Marine Environment as Revealed through Genomic Analysis

Antibiotic-resistance gene elements (ARGEs) such as antibiotic-resistance genes (ARGs), integrons, and plasmids are key to the spread of antimicrobial resistance (AMR) in marine environments. Kuwait's marine area is vulnerable to sewage contaminants introduced by numerous storm outlets and indiscriminate waste disposal near recreational beaches. Therefore, it has become a significant public health issue and warrants immediate investigation. Coliforms, especially Gram-negative Escherichia coli, have been regarded as significant indicators of recent fecal pollution and carriers of ARGEs. In this study, we applied a genome-based approach to identify ARGs' prevalence in E. coli isolated from mollusks and coastal water samples collected in a previous study. In addition, we investigated the plasmids and intl1 (class 1 integron) genes coupled with the ARGs, mediating their spread within the Kuwait marine area. Whole-genome sequencing (WGS) identified genes resistant to the drug classes of beta-lactams (blaCMY-150, blaCMY-42, blaCTX-M-15, blaDHA-1, blaMIR-1, blaOKP-B-15, blaOXA-1, blaOXA-48, blaTEM-1B, blaTEM-35), trimethoprim (dfrA14, dfrA15, dfrA16, dfrA1, dfrA5, dfrA7), fluroquinolone (oqxA, oqxB, qnrB38, qnrB4, qnrS1), aminoglycoside (aadA2, ant(3'')-Ia, aph(3'')-Ib, aph(3')-Ia, aph(6)-Id), fosfomycin (fosA7, fosA_6, fosA, fosB1), sulfonamide (sul1, sul2, sul3), tetracycline (tet-A, tet-B), and macrolide (mph-A). The MFS-type drug efflux gene mdf-A is also quite common in E. coli isolates (80%). The plasmid ColRNAI was also found to be prevalent in E. coli. The integron gene intI1 and gene cassettes (GC) were reported to be in 36% and 33%, respectively, of total E. coli isolates. A positive and significant (p < 0.001) correlation was observed between phenotypic AMR-intl1 (r = 0.311) and phenotypic AMR-GC (r = 0.188). These findings are useful for the surveillance of horizontal gene transfer of AMR in the marine environments of Kuwait.

Production of medium chain fatty acids from fermentation of antibiotic residuals: Fate of antibiotic resistance genes

The potential of antibiotic resistance genes (ARGs) amplification restricts the biological recovery of antibiotic fermentation residues (AFRs) through two-stage anaerobic fermentation. This study explored the fate of ARGs during the fermentation of AFRs that comprising of acidification and chain elongation (CE). Results showed that with the alteration of fermentation process from acidification to CE, microbial richness was significantly increased, total abundance of ARGs was slightly decreased by 1.84%, and the significant negative correlations between ARGs and microbes were increased, implied the inhibitory effect of CE microbes to ARGs amplification. However, the total abundance of mobile genetic elements (MGEs) was increased by 24.5%, indicating that the potential of gene horizontal transfer of ARGs increased. This work suggested that two-stage anaerobic fermentation could effectively restrict the ARGs amplification, but more concerns are needed for the long-term dissemination of ARGs.

Production of medium chain fatty acids from antibiotic fermentation residuals pretreated by ionizing radiation: Elimination of antibiotic resistance genes

The propagation of antibiotic resistance genes (ARGs) restricts the application of antibiotic fermentation residues (AFRs). This study investigated medium chain fatty acids (MCFA) production from AFRs, focusing on the effect of ionizing radiation pretreatment on the fates of ARGs. The results indicated that ionizing radiation pretreatment not only stimulated the MCFA production, but also inhibited the proliferation of ARGs. Radiation at 10-50 kGy decreased ARGs abundances by 0.6-21.1% at the end of fermentation process. Mobile genetic elements (MGEs) exhibited higher resistance to ionizing radiation, radiation over 30 kGy was required to suppress the proliferation of MGEs. Radiation at 50 kGy achieved an adequate inhibition to MGEs, and the degradation efficiency was 17.8-74.5% for different kinds of MGEs. This work suggested that ionizing radiation pretreatment could be a good option to ensure the safer application of AFRs by eliminating the ARGs and preventing the horizontal gene transfer of ARGs.

Screening of marine sediment-derived microorganisms and their bioactive metabolites: a review

Marine sediments are one of the largest habitats on Earth, and their unique ecology, such as high salinity, high pressure, and hypoxia, may activate certain silent genes in marine microbes, resulting in microbes, enzymes, active products, and specific metabolic pathways that can adapt to these specific ecological environments. Marine sediment-derived microorganisms and their bioactive metabolites are of great significance and have potential commercial development prospects for food, pharmaceutical, chemical industries, agriculture, environmental protection and human nutrition and health. In recent years, although there have been numerous scientific reports surrounding marine sediment-derived microorganisms and their bioactive metabolites, a comprehensive review of their research progress is lacking. This paper presents the development and renewal of traditional culture-dependent and omics analysis techniques and their application to the screening of marine sediment-derived microorganisms producing bioactive substances. It also highlights recent research advances in the last five years surrounding the types, functional properties and potential applications of bioactive metabolites produced by marine sediment-derived microorganisms. These bioactive metabolites mainly include antibiotics, enzymes, enzyme inhibitors, sugars, proteins, peptides, and some other small molecule metabolites. In addition, the review ends with concluding remarks on the challenges and future directions for marine sediment-derived microorganisms and their bioactive metabolites. The review report not only helps to deepen the understanding of marine sediment-derived microorganisms and their bioactive metabolites, but also provides some useful information for the exploitation and utilization of marine microbial resources and the mining of new compounds with potential functional properties.

Dissemination of antibiotic resistance genes from the Pearl River Estuary to adjacent coastal areas

The spread of antibiotic resistance genes (ARGs) is a growing concern over the world's various environments. Coastal environments may receive pollutants from land runoffs via estuaries. However, the impact of ARG contamination from estuarine regions to coastal areas is rarely reported. This study used high-throughput quantitative PCR to examine the diversity and abundance of ARGs in Pearl River Estuary (PRE) and adjacent coastal areas. We found that the distribution of ARGs in seawater exhibited the distance-decay phenomenon from the estuary to coastal areas, while the sediment samples did not exhibit an obvious distribution pattern. The estuarine water was found to be the hotspot of ARGs, with 74 ARG species detected and absolute abundance being 5.93 × 10⁵ copies per mL, on average, while less species and lower abundance of ARGs were detected in coastal waters. Ordination analysis showed that estuarine ARG communities were significantly different from coastal ARG communities for water samples. SourceTracker analysis revealed that ARGs from the estuarine environment contributed only a minor fraction of ARG contamination to downstream coastal areas (1.5%-7.4% for water samples, and 0.7-1.8% for sediment samples), indicating the strong dilution effect of seawater. Mantel tests, redundancy analysis and random forest model analysis identified salinity, nutrients, microbial community structure and mobile genetic elements (MGEs) as important factors influencing ARG distribution. Partial least squares-path model revealed that, among all environmental factors, MGEs directly affected the distribution of ARGs, while other factors indirectly contributed by affecting the MGEs assemblage. Our study provides insight into the dissemination of ARGs from the PRE to adjacent coastal areas.

Antibiotic Resistance Genes in Aerosols: Baseline from Kuwait

Antimicrobial resistance (AMR) is one of the biggest threats to human health worldwide. The World Health Organization (WHO, Geneva, Switzerland) has launched the "One-Health" approach, which encourages assessment of antibiotic-resistant genes (ARGs) within environments shared by human-animals-plants-microbes to constrain and alleviate the development of AMR. Aerosols as a medium to disseminate ARGs, have received minimal attention. In the present study, we investigated the distribution and abundance of ARGs in indoor and outdoor aerosols collected from an urban location in Kuwait and the interior of three hospitals. The high throughput quantitative polymerase chain reaction (HT-qPCR) approach was used for this purpose. The results demonstrate the presence of aminoglycoside, beta-lactam, fluoroquinolone, tetracycline, macrolide-lincosamide-streptogramin B (MLSB), multidrug-resistant (MDR) and vancomycin-resistant genes in the aerosols. The most dominant drug class was beta-lactam and the genes were IMP-2-group (0.85), Per-2 group (0.65), OXA-54 (0.57), QnrS (0.50) and OXA-55 (0.55) in the urban non-clinical settings. The indoor aerosols possessed a richer diversity (Observed, Chao1, Shannon's and Pielou's evenness) of ARGs compared to the outdoors. Seasonal variations (autumn vs. winter) in relative abundances and types of ARGs were also recorded (R² of 0.132 at p < 0.08). The presence of ARGs was found in both the inhalable (2.1 µm, 1.1 µm, 0.7 µm and < 0.3 µm) and respirable (>9.0 µm, 5.8 µm, 4.7 µm and 3.3 µm) size fractions within hospital aerosols. All the ARGs are of pathogenic bacterial origin and are hosted by pathogenic forms. The findings present baseline data and underpin the need for detailed investigations looking at aerosol as a vehicle for ARG dissemination among human and non-human terrestrial biota.

Metagenomes from Coastal Sediments of Kuwait: Insights into the Microbiome, Metabolic Functions and Resistome

Coastal sediments in the proximity of wastewater and emergency outfalls are often sinks of pharmaceutical compounds and other organic and inorganic contaminants that are likely to affect the microbial community. The metabolites of these contaminants affect microbial diversity and their metabolic processes, resulting in undesirable effects on ecosystem functioning, thus necessitating the need to understand their composition and functions. In the present investigation, we studied the metagenomes of 12 coastal surface sediments through whole genome shot-gun sequencing. Taxonomic binning of the genes predicted about 86% as bacteria, 1% as archaea, >0.001% as viruses and Eukaryota, and 12% as other communities. The dominant bacterial, archaeal, and fungal genera were Woeseia, Nitrosopumilus, and Rhizophagus, respectively. The most prevalent viral families were Myoviridae and Siphoviridae, and the T4 virus was the most dominant bacteriophage. The unigenes further aligned to 26 clusters of orthologous genes (COGs) and five carbohydrate-active enzymes (CAZy) classes. Glycoside hydrolases (GH) and glycoside transferase (GT) were the highest-recorded CAzymes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) level 3 functions were subjugated by purine metabolism > ABC transporters > oxidative phosphorylation > two-component system > pyrimidine metabolism > pyruvate metabolism > quorum sensing > carbon fixation pathways > ribosomes > and glyoxalate and dicarboxylate metabolism. Sequences allying with plasmids, integrons, insertion sequences and antibiotic-resistance genes were also observed. Both the taxonomies and functional abundances exhibited variation in relative abundances, with limited spatial variability (ANOVA p > 0.05; ANOSIM-0.05, p > 0.05). This study underlines the dominant microbial communities and functional genes in the marine sediments of Kuwait as a baseline for future biomonitoring programs.

Evolution and Emergence of Antibiotic Resistance in Given Ecosystems: Possible Strategies for Addressing the Challenge of Antibiotic Resistance

Antibiotics were once considered the magic bullet for all human infections. However, their success was short-lived, and today, microorganisms have become resistant to almost all known antimicrobials. The most recent decade of the 20th and the beginning of the 21st century have witnessed the emergence and spread of antibiotic resistance (ABR) in different pathogenic microorganisms worldwide. Therefore, this narrative review examined the history of antibiotics and the ecological roles of antibiotics, and their resistance. The evolution of bacterial antibiotic resistance in different environments, including aquatic and terrestrial ecosystems, and modern tools used for the identification were addressed. Finally, the review addressed the ecotoxicological impact of antibiotic-resistant bacteria and public health concerns and concluded with possible strategies for addressing the ABR challenge. The information provided in this review will enhance our understanding of ABR and its implications for human, animal, and environmental health. Understanding the environmental dimension will also strengthen the need to prevent pollution as the factors influencing ABR in this setting are more than just antibiotics but involve others like heavy metals and biocides, usually not considered when studying ABR.

Non-corresponding contaminants in marine surface sediments as a factor of ARGs spread in the Sea of Azov

The present study aims to analyze the level and total toxicity of the most common pollutants in surface sediments and assess their impact on the occurrence of antibiotic resistance genes (ARGs) in the Sea of Azov. Biotesting using the whole-cell bacterial lux-biosensors showed high integral toxicity of surface sediments and the presence of genotoxicants and substances that cause oxidative stress and protein damage. Using cluster analysis, it was shown that the distribution of pollutants in the Sea of Azov depends on the type of surface sediments. The relative abundance and distribution of 14 ARGs in surface sediments were shown. Principle component analyses results suggest that non-corresponding contaminants do not exert direct influence on the ARGs abundance in the surface sediments of the Sea of Azov. Thus, the need to investigate the significance of non-corresponding pollutants in the selection and distribution of ARGs in the aquatic environment remains a pressing problem.