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BioMed Research International 2021The main aim of this study was to develop a set of functions that can analyze the genomic data with less time consumption and memory. Epi-gene is presented as a solution...
The main aim of this study was to develop a set of functions that can analyze the genomic data with less time consumption and memory. Epi-gene is presented as a solution to large sequence file handling and computational time problems. It uses less time and less programming skills in order to work with a large number of genomes. In the current study, some features of the Epi-gene R-package were described and illustrated by using a dataset of the 14 genomes. The joining, relabeling, and conversion functions were also included in this package to handle the FASTA formatted sequences. To calculate the subsets of core genes, accessory genes, and unique genes, various Epi-gene functions have been used. Heat maps and phylogenetic genome trees were also constructed. This whole procedure was completed in less than 30 minutes. This package can only work on Windows operating systems. Different functions from other packages such as dplyr and ggtree were also used that were available in R computing environment.
Topics: Aeromonas hydrophila; Databases, Genetic; Genome, Bacterial; Genomics; Multigene Family; Phylogeny; Principal Component Analysis; Software
PubMed: 34595238
DOI: 10.1155/2021/5585586 -
Environmental Research Jan 2023The purpose of this research was to investigate the biodegradation of nitrofurantoin (NFT), a typical nitrofuran antibiotic of potential carcinogenic properties, by two...
The purpose of this research was to investigate the biodegradation of nitrofurantoin (NFT), a typical nitrofuran antibiotic of potential carcinogenic properties, by two microbial communities derived from distinct environmental niches - mountain stream (NW) and seaport water (SS). The collected environmental samples represent the reserve of the protected area with no human intervention and the contaminated area that concentrates intense human activities. The structure, composition, and diversity of the communities were analyzed at three timepoints during NFT biodegradation. Comamonadaceae (43.2%) and Pseudomonadaceae (19.6%) were the most abundant families in the initial NW sample. The top families in the initial SS sample included Aeromonadaceae (31.4%) and Vibrionaceae (25.3%). The proportion of the most abundant families in both consortia was remarkably reduced in all samples treated with NFT. The biodiversity significantly increased in both consortia treated with NFT suggesting that NFT significantly alters community structure in the aquatic systems. In this study, NFT removal efficiency and transformation products were also studied. The biodegradation rate decreased with the increasing initial NFT concentration. Biodegradation followed similar pathways for both consortia and led to the formation of transformation products: 1-aminohydantoin, semicarbazide (SEM), and hydrazine (HYD). SEM and HYD were detected for the first time as NFT biotransformation products. This study demonstrates that the structure of the microbial community may be directly correlated with the presence of NFT. Enchanced biodiversity of the microbial community does not have to be correlated with increase in functional capacity, such as the ability to biodegradation because higher biodiversity corresponded to lower biodegradation. Our findings provide new insights into the effect of NFT contamination on aquatic microbiomes. The study also increases our understanding of the environmental impact of nitrofuran residues and their biodegradation.
Topics: Humans; Nitrofurantoin; Biotransformation; Biodegradation, Environmental; Biodiversity; Microbiota; Microbial Consortia
PubMed: 36244438
DOI: 10.1016/j.envres.2022.114531 -
Drug Resistance Updates : Reviews and... Nov 2023Polymyxins are the last line of defense in infections caused by multidrug-resistant Gram-negative bacteria. The chromosomal EptA in Aeromonas genus was defined as a...
Polymyxins are the last line of defense in infections caused by multidrug-resistant Gram-negative bacteria. The chromosomal EptA in Aeromonas genus was defined as a nonmobile colistin resistance determinant 3 (NMCR-3). A total of 14 NMCR-3 genotypes were identified. The global prevalence of Aeromonas-borne NMCRs and MCRs indicates an increasing trend from 1968 to 2022. And an index of resistance risk, i.e, the ratio of η = MCR/NMCR, was proposed to evaluate the propagation potential of NMCR-3. The colistin resistance in North America and Europe faced a high risk of increasing incidence of MCR since large proportions of NMCR-3 variants disseminated from Aeromonas sources. We concluded that NMCR-3 variants act natural progenitors for MCR-3/5/7, and the future MCR variant(s) will most likely be MCR-5 or MCR-7, which is also an early warning of next MCR(s) emerging in Aeromonas.
Topics: Humans; Colistin; Aeromonas; Genotype
PubMed: 37703625
DOI: 10.1016/j.drup.2023.101006 -
The Science of the Total Environment Dec 2023Aquaculture environments can be hotspots for resistance genes through the surrounding environment. Our objective was to study the resistome, virulome and mobilome of...
Aquaculture environments can be hotspots for resistance genes through the surrounding environment. Our objective was to study the resistome, virulome and mobilome of Gram-negative bacteria isolated in seabream and bivalve molluscs, using a WGS approach. Sixty-six Gram-negative strains (Aeromonadaceae, Enterobacteriaceae, Hafniaceae, Morganellaceae, Pseudomonadaceae, Shewanellaceae, Vibrionaceae, and Yersiniaceae families) were selected for genomic characterization. The species and MLST were determined, and antibiotic/disinfectants/heavy metals resistance genes, virulence determinants, MGE, and pathogenicity to humans were investigated. Our study revealed new sequence-types (e.g. Aeromonas spp. ST879, ST880, ST881, ST882, ST883, ST887, ST888; Shewanella spp. ST40, ST57, ST58, ST60, ST61, ST62; Vibrio spp. ST206, ST205). >140 different genes were identified in the resistome of seabream and bivalve molluscs, encompassing genes associated with β-lactams, tetracyclines, aminoglycosides, quinolones, sulfonamides, trimethoprim, phenicols, macrolides and fosfomycin resistance. Disinfectant resistance genes qacE-type, sitABCD-type and formA-type were found. Heavy metals resistance genes mdt, acr and sil stood out as the most frequent. Most resistance genes were associated with antibiotics/disinfectants/heavy metals commonly used in aquaculture settings. We also identified 25 different genes related with increased virulence, namely associated with adherence, colonization, toxins production, red blood cell lysis, iron metabolism, escape from the immune system of the host. Furthermore, 74.2 % of the strains analysed were considered pathogenic to humans. We investigated the genetic environment of several antibiotic resistance genes, including bla, bla, aph(3″)-Ib, dfrA-type, aadA1, catA1-type, tet(A)/(E), qnrB19 and sul1/2. Our analysis also focused on identifying MGE in proximity to these genes (e.g. IntI1, plasmids and TnAs), which could potentially facilitate the spread of resistance among bacteria across different environments. This study provides a comprehensive examination of the diversity of resistance genes that can be transferred to both humans and the environment, with the recognition that aquaculture and the broader environment play crucial roles as intermediaries within this complex transmission network.
Topics: Humans; Multilocus Sequence Typing; Anti-Bacterial Agents; Aquaculture; Metals, Heavy; Disinfectants
PubMed: 37604365
DOI: 10.1016/j.scitotenv.2023.166351 -
Journal of Microbiology and... Oct 2020The emergence and spread of antimicrobial resistance in pathogenic bacteria of fish and shellfish have caused serious concerns in the aquaculture industry, owing to the... (Review)
Review
The emergence and spread of antimicrobial resistance in pathogenic bacteria of fish and shellfish have caused serious concerns in the aquaculture industry, owing to the potential health risks to humans and animals. Among these bacteria, , which is one of the most important primary pathogens in salmonids, is responsible for significant economic losses in the global aquaculture industry, especially in salmonid farming because of its severe infectivity and acquisition of antimicrobial resistance. Therefore, interest in the use of alternative approaches to prevent and control infections has increased in recent years, and several applications of bacteriophages (phages) have provided promising results. For several decades, and phages infecting this fish pathogen have been thoroughly investigated in various research areas including aquaculture. The general overview of phage usage to control bacterial diseases in aquaculture, including the general advantages of this strategy, has been clearly described in previous reviews. Therefore, this review specifically focuses on providing insights into the phages infecting , from basic research to biotechnological application in aquaculture, as well as recent advances in the study of .
Topics: Aeromonas salmonicida; Animals; Aquaculture; Bacterial Infections; Bacteriophages; Fish Diseases; Fishes
PubMed: 32807762
DOI: 10.4014/jmb.2005.05040 -
Fish & Shellfish Immunology Mar 2020Supplementing the diet with functional ingredients is a key strategy to improve fish performance and health in aquaculture. The amino acids of the urea and nitric oxide...
Supplementing the diet with functional ingredients is a key strategy to improve fish performance and health in aquaculture. The amino acids of the urea and nitric oxide (NO) cycles - arginine, ornithine and citrulline - perform crucial roles in the immune response through the generation of NO and the synthesis of polyamine used for tissue repair. We previously found that citrulline supplementation improves and maintains circulating free arginine levels in rainbow trout more effectively than arginine supplementation. Here, to test whether supplementation of urea cycle amino acids modulates the immune response in rainbow trout (Oncorhynchus mykiss), we supplemented a commercial diet with high levels (2% of total diet) of either arginine, ornithine or citrulline during a 7-week feeding trial, before challenging fish with the bacterium Aeromonas salmonicida. We carried out two separate experiments to investigate fish survival and 24 h post-infection to investigate the immediate response of free amino acid levels, and transcriptional changes in genes encoding urea cycle, NO cycle and polyamine synthesis enzymes. There were no differences in percentage fish mortality between diets, however there were numerous highly significant changes in free amino acid levels and gene expression to both dietary supplementation and infection. Out of 26 amino acids detected in blood plasma, 8 were significantly changed by infection and 9 by dietary supplementation of either arginine, ornithine or citrulline. Taurine, glycine and aspartic acid displayed the largest decreases in circulating levels in infected fish, while ornithine and isoleucine were the only amino acids that increased in concentration. We investigated transcriptional responses of the enzymes involved in arginine metabolism in liver and head kidney; transcripts for polyamine synthesis enzymes showed highly significant increases in both tissues across all diets following infection. The paralogous arginase-encoding genes, Arg1a, Arg1b, Arg2a and Arg2b, displayed complex responses across tissues and also due to diet and infection. Overall, these findings improve our understanding of amino acid metabolism following infection and suggests new potential amino acid targets for improving the immune response in salmonids.
Topics: Aeromonas salmonicida; Animal Feed; Animal Nutritional Physiological Phenomena; Animals; Arginine; Citrulline; Diet; Dietary Supplements; Gene Expression Regulation; Gram-Negative Bacterial Infections; Oncorhynchus mykiss; Ornithine
PubMed: 31968266
DOI: 10.1016/j.fsi.2020.01.026 -
International Journal of Antimicrobial... Aug 2023Antimicrobial resistance (AMR) is one of the most pressing public health concerns; therefore, it is imperative to advance our understanding of the factors influencing... (Meta-Analysis)
Meta-Analysis Review
Antimicrobial resistance (AMR) is one of the most pressing public health concerns; therefore, it is imperative to advance our understanding of the factors influencing AMR from Global and One Health perspectives. To address this, Aeromonas populations were identified using 16S rRNA gene libraries among human, agriculture, aquaculture, drinking water, surface water, and wastewater samples, supporting its use as indicator bacteria to study AMR. A systematic review and meta-analysis was then performed from Global and One Health perspectives, including data from 221 articles describing 15 891 isolates from 57 countries. The interconnectedness of different environments was evident as minimal differences were identified between sectors among 21 different antimicrobials. However, resistance to critically important antibiotics (aztreonam and cefepime) was significantly higher among wastewater populations compared with clinical isolates. Additionally, isolates from untreated wastewater typically exhibited increased AMR compared with those from treated wastewater. Furthermore, aquaculture was associated with increased AMR to ciprofloxacin and tetracycline compared with wild-caught seafood. Using the World Health Organization AWaRe classifications, countries with lower consumption of "Access" compared to "Watch" drugs from 2000 to 2015 demonstrated higher AMR levels. The current analysis revealed negative correlations between AMR and anthropogenic factors, such as environmental performance indices and socioeconomic standing. Environmental health and sanitation were two of the environmental factors most strongly correlated with AMR. The current analysis highlights the negative impacts of "Watch" drug overconsumption, anthropogenic activity, absence of wastewater infrastructure, and aquaculture on AMR, thus stressing the need for proper infrastructure and global regulations to combat this growing problem.
Topics: Humans; Aeromonas; Wastewater; Global Health; One Health; RNA, Ribosomal, 16S; Drug Resistance, Bacterial; Anti-Bacterial Agents; Anti-Infective Agents
PubMed: 37201798
DOI: 10.1016/j.ijantimicag.2023.106848 -
Archives of Razi Institute Dec 2023The genus is a widespread pathogen that includes more than 30 Gram-negative species, many of which are opportunistic bacteria. Aeromonas species are naturally... (Review)
Review
The genus is a widespread pathogen that includes more than 30 Gram-negative species, many of which are opportunistic bacteria. Aeromonas species are naturally distributed in various aquatic sources. Infectious processes in marine animals such as fish usually develop under stressful conditions, and when their immune systems are weakened. MicroRNAs (miRNAs/miRs) are short, non-coding RNAs that post-transcriptionally regulate gene expression. Their diverse biological functions, such as influencing cell development, proliferation, differentiation, tumorigenesis, metabolism, and apoptosis have been studied in various animals. Fish is the most important source of aquatic nutrients throughout the world, and its market is constantly growing. Overpopulation in aquaculture brings infectious diseases that threaten the development of aquaculture around the world. There is extensive evidence that microRNAs are involved in modulating infectious processes and regulating the inflammatory response to major bacterial fish infections, including . Here, we review the current literature on the fish microRNA repertoire and outline the physiological roles assigned to microRNAs to provide a foundation for future research during infection. Understanding the interaction between microRNAs and may provide clues to a remarkable strategy for preventing infections in fish.
Topics: MicroRNAs; Animals; Aeromonas; Gram-Negative Bacterial Infections; Fish Diseases; Fishes
PubMed: 38828176
DOI: 10.32592/ARI.2023.78.6.1668 -
BMC Microbiology Dec 2019Gut microbes can contribute to their hosts in food digestion, nutrient absorption, and inhibiting the growth of pathogens. However, only limited studies have focused on...
BACKGROUND
Gut microbes can contribute to their hosts in food digestion, nutrient absorption, and inhibiting the growth of pathogens. However, only limited studies have focused on the gut microbiota of freshwater snails. Pomacea canaliculata is considered one of the worst invasive alien species in the world. Elucidating the diversity and composition of the microbiota in the gut of P. canaliculata snails may be helpful for better understanding the widespread invasion of this snail species. In this study, the buccal masses, stomachs, and intestines were isolated from seven P. canaliculata snails. The diversity and composition of the microbiota in the three gut sections were then investigated based on high-throughput Illumina sequencing targeting the V3-V4 regions of the 16S rRNA gene.
RESULTS
The diversity of the microbiota was highest in the intestine but lowest in the buccal mass. A total of 29 phyla and 111 genera of bacteria were identified in all of the samples. In general, Ochrobactrum, a genus of putative cellulose-degrading bacteria, was the most abundant (overall relative abundance: 13.6%), followed by Sediminibacterium (9.7%), Desulfovibrio (7.8%), an unclassified genus in the family Aeromonadaceae (5.4%), and Cloacibacterium (5.4%). The composition of the microbiota was diverse among the different gut sections. Ochrobactrum (relative abundance: 23.15% ± 7.92%) and Sediminibacterium (16.95 ± 5.70%) were most abundant in the stomach, an unclassified genus in the family Porphyromonadaceae (14.28 ± 7.29%) and Leptotrichia (8.70 ± 4.46%) were highest in the buccal mass, and two genera in the families Aeromonadaceae (7.55 ± 4.53%) and Mollicutes (13.47 ± 13.03%) were highest in the intestine.
CONCLUSIONS
The diversity and composition of the microbiome vary among different gut sections of P. canaliculata snails. Putative cellulose-degrading bacteria are enriched in the gut of P. canaliculata.
Topics: Animals; Bacteria; Female; Gastrointestinal Microbiome; Gastrointestinal Tract; Genetic Variation; High-Throughput Nucleotide Sequencing; Intestines; RNA, Ribosomal, 16S; Snails; Stomach
PubMed: 31805864
DOI: 10.1186/s12866-019-1661-x -
Microbiology Spectrum Dec 2023The has been reported in Central Asia and Europe countries like Afghanistan and France in and strains from animals and patients, respectively. However, there is no...
The has been reported in Central Asia and Europe countries like Afghanistan and France in and strains from animals and patients, respectively. However, there is no record of -carrying strain from the natural environment, and -carrying has not been reported in the Asia Pacific. Here, we report the first known enviromental -carrying in the world from reservoir water in Singapore. We have performed a comprehensive genetic environment alignment and comparison of between our strain and other strains from different countries and sources and found the located on a highly conserved gene cluster. We suggest that environmental strains may act as a hidden reservoir involved in the circulating of . The finding of conserved cluster also suggested the existence of multiple transmission pathways of in the Asia-Pacific region, involving multiple sources and different species.
Topics: Animals; Humans; beta-Lactamases; Aeromonas; Asia; France; Anti-Bacterial Agents; Microbial Sensitivity Tests
PubMed: 37909756
DOI: 10.1128/spectrum.01391-23