Complete Sequences of Multidrug Resistance Plasmids Bearing rmtD1 and rmtD2 16S rRNA Methyltransferase Genes

Novel Insights into blaGES Mobilome Reveal Extensive Genetic Variation in Hospital Effluents

Mobile genetic elements contribute to the emergence and spread of multidrug-resistant bacteria by enabling the horizontal transfer of acquired antibiotic resistance among different bacterial species and genera. This study characterizes the genetic backbone of bla_GES in Aeromonas spp. and Klebsiella spp. isolated from untreated hospital effluents. Plasmids ranging in size from 9 to 244 kb, sequenced using Illumina and Nanopore platforms, revealed representatives of plasmid incompatibility groups IncP6, IncQ1, IncL/M1, IncFII, and IncFII-FIA. Different GES enzymes (GES-1, GES-7, and GES-16) were located in novel class 1 integrons in Aeromonas spp. and GES-5 in previously reported class 1 integrons in Klebsiella spp. Furthermore, in Klebsiella quasipneumoniae, bla_GES-5 was found in tandem as a coding sequence that disrupted the 3' conserved segment (CS). In Klebsiella grimontii, bla_GES-5 was observed in two different plasmids, and one of them carried multiple IncF replicons. Three Aeromonas caviae isolates presented bla_GES-1, one Aeromonas veronii isolate presented bla_GES-7, and another A. veronii isolate presented bla_GES-16. Multilocus sequence typing (MLST) analysis revealed novel sequence types for Aeromonas and Klebsiella species. The current findings highlight the large genetic diversity of these species, emphasizing their great adaptability to the environment. The results also indicate a public health risk because these antimicrobial-resistant genes have the potential to reach wastewater treatment plants and larger water bodies. Considering that they are major interfaces between humans and the environment, they could spread throughout the community to clinical settings. IMPORTANCE In the "One Health" approach, which encompasses human, animal, and environmental health, emerging issues of antimicrobial resistance are associated with hospital effluents that contain clinically relevant antibiotic-resistant bacteria along with a wide range of antibiotic concentrations, and lack regulatory status for mandatory prior and effective treatment. bla_GES genes have been reported in aquatic environments despite the low detection of these genes among clinical isolates within the studied hospitals. Carbapenemase enzymes, which are relatively unusual globally, such as GES type inserted into new integrons on plasmids, are worrisome. Notably, K. grimontii, a newly identified species, carried two plasmids with bla_GES-5, and K. quasipneumoniae carried two copies of bla_GES-5 at the same plasmid. These kinds of plasmids are primarily responsible for multidrug resistance among bacteria in both clinical and natural environments, and they harbor resistant genes against antibiotics of key importance in clinical therapy, possibly leading to a public health problem of large proportion.

Bacterial Hosts and Genetic Characteristics of Antibiotic Resistance Genes in Wastewater Treatment Plants of Xinjiang (China) Revealed by Metagenomics

Antibiotic resistance genes (ARGs) pose a widespread concern for human health and wastewater treatment plants (WWTPs) are considered to be a major source of ARG transmission. In this paper, the potential hosts and genetic characteristics of ARGs in the influent, activated sludge and effluent of WWTPs in Xinjiang were studied by metagenomics. Bacitracin resistance gene (bacA), beta-lactamase gene (class A beta-lactamase), multidrug resistance genes (mexD, qacEdelta1), and sulfonamide resistance genes (sul1, and sul2) are persistent antibiotic resistance genes (PARGs). The potential hosts of ARGs were mainly pathogens, with Escherichia coli (12.9%), Acinetobacter johnsonii (8.94%), and Klebsiella pneumoniae (5.30%) accounting for the highest proportions. Chromosomal sequences and plasmid sequences accounted for 42.0% and 22.6% of ARG-carrying contigs (ACCs) in the influent, respectively. Meanwhile, the effluent contained 58.3% of ACCs in plasmids and 8.30% in chromosomes. Bacitracin resistance genes and multidrug resistance genes were mainly carried by chromosomes, while resistance genes for macrolide–lincosamide–streptogramin (MLS), vancomycin, sulfonamide, beta-lactam, tetracycline, chloramphenicol, and aminoglycoside were mainly carried by plasmids. ICEPae690-sul1-qacEdelta1 and ICEPmiChn3-sul2 were stable coexistence structures and heighten the transfer potential of ARGs in the environment. This study provided a clearer picture of host bacterial sources and genetic context of ARGs in the environment.

Genomic Analysis of Carbapenem-Resistant Pseudomonas aeruginosa Isolated From Urban Rivers Confirms Spread of Clone Sequence Type 277 Carrying Broad Resistome and Virulome Beyond the Hospital

The dissemination of antibiotic-resistant priority pathogens beyond hospital settings is both a public health and an environmental problem. In this regard, high-risk clones exhibiting a multidrug-resistant (MDR) or extensively drug-resistant (XDR) phenotype have shown rapid adaptation at the human-animal-environment interface. In this study, we report genomic data and the virulence potential of the carbapenemase, São Paulo metallo-β-lactamase (SPM-1)-producing Pseudomonas aeruginosa strains (Pa19 and Pa151) isolated from polluted urban rivers, in Brazil. Bioinformatic analysis revealed a wide resistome to clinically relevant antibiotics (carbapenems, aminoglycosides, fosfomycin, sulfonamides, phenicols, and fluoroquinolones), biocides (quaternary ammonium compounds) and heavy metals (copper), whereas the presence of exotoxin A, alginate, quorum sensing, types II, III, and IV secretion systems, colicin, and pyocin encoding virulence genes was associated with a highly virulent behavior in the Galleria mellonella infection model. These results confirm the spread of healthcare-associated critical-priority P. aeruginosa belonging to the MDR sequence type 277 (ST277) clone beyond the hospital, highlighting that the presence of these pathogens in environmental water samples can have clinical implications for humans and other animals.

Essential Oils: An Impending Substitute of Synthetic Antimicrobial Agents to Overcome Antimicrobial Resistance

Antimicrobial resistance (AMR) is an emerging problem in the world that has a significant impact on our society. AMR made conventional drugs futile against microorganisms and diseases untreatable. Plant-derived medicines are considered to be safe alternatives as compared to synthetic drugs. Active ingredients and the mixtures of these natural medicines have been used for centuries, due to their easy availability, low cost, and negligible side effects. Essential oils (EOs) are the secondary metabolites that are produced by aromatic plants to protect them from microorganisms. However, these EOs and their constituents have shown good fighting potential against drug-resistant pathogens. These oils have been proved extremely effective antimicrobial agents in comparison to antibiotics. Also, the combination of synthetic drugs with EOs or their components improve their efficacy. So, EOs can be established as an alternative to synthetic antimicrobial agents to eradicate tough form of infectious microorganisms. EO's can interact with multiple target sites, like the destruction of cytoplasm membrane or inhibition of protein synthesis and efflux pump, etc. The purpose of this review is to provide information about the antimicrobial activity of EOs attained from different plants, their combination with synthetic antimicrobials. In addition, mechanism of antimicrobial activity of several EOs and their constituents was reported.

Complete Genome Sequence of Multidrug-Resistant Edwardsiella ictaluri Strain MS-17-156

Edwardsiella ictaluri is a significant pathogen of cultured fish, particularly channel catfish. Here, we present the complete genome sequence of a multidrug-resistant E. ictaluri strain, MS-17-156, isolated from diseased channel catfish. The genome sequence of this multidrug-resistant strain is expected to help us understand the molecular mechanism of antibiotic resistance in this important pathogen.

Antibiotic resistome in landfill leachate from different cities of China deciphered by metagenomic analysis

High throughput sequencing-based metagenomic analysis and network analysis were applied to investigate the broad-spectrum profiles of ARGs in landfill leachate from 12 cities in China. In total, 526 ARG subtypes belonging to 21 ARG types were detected with abundances ranging from 1.1 × 10^-6 to 2.09 × 10^-1 copy of ARG/copy of 16S rRNA gene. 68 ARG subtypes that accounted for 73.4%-93.4% of the total ARG abundances were shared by all leachate samples. The four most abundant ARGs, sul1, sul2, aadA and bacA can be served as ARG indicators to quantitatively predict the total abundances by linear functions (r² = 0.577-0.819, P < 0.001). No distinct regional distribution pattern of the ARGs was observed among different cities in China, while the ARG compositions of the leachate were clearly distinct from those of other environmental sample types. Nearly 90% ARG subtypes in the anaerobic digestion sludge from sewage treatment plants (STPADS) were shared by the leachate and the abundances of leachate and STPADS ARGs generalists accounted for 84.5% and 87.7% of total abundances in these two types of anaerobic samples, respectively. Furthermore, Procrustes analysis suggested that microbial community composition might be the determining factor of ARG compositions in landfill leachate. ARGs within the same type or among the different types showed higher incidences of non-random co-occurrence and 17 genera might be potential hosts of multiple ARGs. This study highlighted that landfill leachate is an important reservoir of various ARGs and provided a useful reference for the surveillance and risk management of ARGs in landfill environments.