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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 -
Antibiotics (Basel, Switzerland) Mar 2022The emergence of antimicrobial-resistant bacteria is an enormous challenge to public health. and are opportunistic pathogens in fish. They exert tremendous adverse...
The emergence of antimicrobial-resistant bacteria is an enormous challenge to public health. and are opportunistic pathogens in fish. They exert tremendous adverse effects on aquaculture production, owing to their acquired antibiotic resistance. A few Clinical and Laboratory Standards Institute (CLSI) epidemiological cut-off values (ECVs) against spp. are available. We evaluated antimicrobial susceptibility by establishing 8 ECVs using two analytical methods, normalized resistance interpretation and ECOFFinder. We detected antimicrobial resistance genes in two motile spp. isolated from aquatic animals. Results showed that 89.2% of and 75.8% of isolates were non-wild types according to the oxytetracycline ECV and ECV, respectively. The antimicrobial resistance genes included , , , , , , , , , , and . The most common gene in spp. isolates was , followed by . Some strains carried more than one gene, with - and - found in ; however, was not detected in any of the strains. Furthermore, 18.6% of and 24.2% of isolates showed presumptive multidrug-resistant phenotypes. The emergence of multidrug resistance among aquatic aeromonads suggests the spread of drug resistance and difficult to treat bacterial infections.
PubMed: 35326806
DOI: 10.3390/antibiotics11030343 -
BMC Microbiology Jan 2021Hypervirulent Aeromonas hydrophila (vAh) is an emerging pathogen in freshwater aquaculture that results in the loss of over 3 million pounds of marketable channel...
BACKGROUND
Hypervirulent Aeromonas hydrophila (vAh) is an emerging pathogen in freshwater aquaculture that results in the loss of over 3 million pounds of marketable channel catfish, Ictalurus punctatus, and channel catfish hybrids (I. punctatus, ♀ x blue catfish, I. furcatus, ♂) each year from freshwater catfish production systems in Alabama, U.S.A. vAh isolates are clonal in nature and are genetically unique from, and significantly more virulent than, traditional A. hydrophila isolates from fish. Even with the increased virulence, natural infections cannot be reproduced in aquaria challenges making it difficult to determine modes of infection and the pathophysiology behind the devastating mortalities that are commonly observed. Despite the intimate connection between environmental adaptation and plastic response, the role of environmental adaption on vAh pathogenicity and virulence has not been previously explored. In this study, secreted proteins of vAh cultured as free-living planktonic cells and within a biofilm were compared to elucidate the role of biofilm growth on virulence.
RESULTS
Functional proteolytic assays found significantly increased degradative activity in biofilm secretomes; in contrast, planktonic secretomes had significantly increased hemolytic activity, suggesting higher toxigenic potential. Intramuscular injection challenges in a channel catfish model showed that in vitro degradative activity translated into in vivo tissue destruction. Identification of secreted proteins by HPLC-MS/MS revealed the presence of many putative virulence proteins under both growth conditions. Biofilm grown vAh produced higher levels of proteolytic enzymes and adhesins, whereas planktonically grown cells secreted higher levels of toxins, porins, and fimbrial proteins.
CONCLUSIONS
This study is the first comparison of the secreted proteomes of vAh when grown in two distinct ecological niches. These data on the adaptive physiological response of vAh based on growth condition increase our understanding of how environmental niche partitioning could affect vAh pathogenicity and virulence. Increased secretion of colonization factors and degradative enzymes during biofilm growth and residency may increase bacterial attachment and host invasiveness, while increased secretion of hemolysins, porins, and other potential toxins under planktonic growth (or after host invasion) could result in increased host mortality. The results of this research underscore the need to use culture methods that more closely mimic natural ecological habitat growth to improve our understanding of vAh pathogenesis.
Topics: Aeromonas hydrophila; Alabama; Animals; Aquaculture; Bacterial Proteins; Bacteriological Techniques; Biofilms; Chromatography, High Pressure Liquid; Fish Diseases; Gram-Negative Bacterial Infections; Ictaluridae; Plankton; Proteomics; Tandem Mass Spectrometry; Virulence; Whole Genome Sequencing
PubMed: 33407117
DOI: 10.1186/s12866-020-02065-2 -
Heliyon Apr 2020Agricultural drainage ditches represent a major source of nutrient pollution. Shifts in nitrogen source and use of animal manures have changed the bacterial composition...
Agricultural drainage ditches represent a major source of nutrient pollution. Shifts in nitrogen source and use of animal manures have changed the bacterial composition both in species of bacteria and their abundance in agricultural ditches. This change affects how nitrogen is being cycled and potentially the final forms of available nutrients. In particular, animal manures often have bacteria such as present, increasing the abundance of a bacterial species in ditches. Research has shown that the effect of different nitrogen sources is to change bacterial community composition (class, family). How this influences the role of an individual bacterial species is poorly understood. Thus, our question was how individual species would respond to different sources of nitrogen. We used , and that are common in agricultural ditches and exposed them to different concentrations of nitrogen in cultures of 1 × 10 and 1 × 10 dilutions from a stock solution of bacteria. Nitrogen sources were ammonium chloride, sodium nitrate and urea. The results showed and have strong similarities particularly with nitrate-N and urea-N utilization and the response was often correlated with the amount of nutrient added. while similar did not show any strong correlation with amount of nutrient added. was different from the other three bacteria in utilization or production. Research has provided insight into the role of some bacteria in nitrogen cycling and may be valuable in the future to developing management strategies to reduce nutrients.
PubMed: 32322713
DOI: 10.1016/j.heliyon.2020.e03711 -
PeerJ 2023Tilapia is a primary aquaculture fish in Thailand, but little is known about the occurrence of antimicrobial resistance (AMR) in , spp., and colonizing healthy tilapia...
BACKGROUND
Tilapia is a primary aquaculture fish in Thailand, but little is known about the occurrence of antimicrobial resistance (AMR) in , spp., and colonizing healthy tilapia intended for human consumption and the co-occurrence of these AMR bacteria in the cultivation water.
METHODS
This study determined the phenotype and genotype of AMR, extended-spectrum -lactamase (ESBL) production, and virulence factors of , spp., and isolated from hybrid red tilapia and cultivation water in Thailand. Standard culture methods such as USFDA's BAM or ISO procedures were used for the original isolation, with all isolates confirmed by biochemical tests, serotyping, and species-specific gene detection based on PCR.
RESULTS
A total of 278 isolates consisting of 15 , 188 spp., and 75 isolates were retrieved from a previous study. All isolates of and isolates were resistance to at least one antimicrobial, with 26.7% and 72.3% of the isolates being multidrug resistant (MDR), respectively. All isolates were resistant to ampicillin (100%), followed by oxytetracycline (26.7%), tetracycline (26.7%), trimethoprim (26.7%), and oxolinic acid (20.0%). The predominant resistance genes in were (20.0%), followed by 13.3% of isolates having , , , , and isolates also exhibited a high prevalence of resistance to ampicillin (79.3%), oxolinic acid (75.5%), oxytetracycline (71.8%), chloramphenicol (62.8%), and florfenicol (55.3%). The most common resistance genes in these isolates were (65.4%), (64.9%), (63.8%), and (55.9%). All isolates were susceptible to all antimicrobials tested, while the most common resistance gene was (12.0%). One isolate of was positive for , while all isolates of and isolates were negative for integrons and . None of the bacterial isolates in this study were producing ESBL. The occurrence of (20.0%) in these isolates from tilapia aquaculture may signify a serious occupational and consumer health risk given that colistin is a last resort antimicrobial for treatment of Gram-negative bacteria infections.
CONCLUSIONS
Findings from this study on AMR bacteria in hybrid red tilapia suggest that aquaculture as practiced in Thailand can select for ubiquitous AMR pathogens, mobile genetic elements, and an emerging reservoir of and colistin-resistant bacteria. Resistant and pathogenic bacteria, such as resistance to ampicillin and tetracycline, or MDR circulating in aquaculture, together highlight the public health concerns and foodborne risks of zoonotic pathogens in humans from cultured freshwater fish.
Topics: Animals; Aeromonas hydrophila; Ampicillin; Anti-Bacterial Agents; Colistin; Drug Resistance, Bacterial; Oxolinic Acid; Oxytetracycline; Tetracycline; Tilapia; Virulence Factors
PubMed: 36855429
DOI: 10.7717/peerj.14896 -
The Brazilian Journal of Infectious... 2019Aeromonas species are renowned enteric pathogens with virulence determinants linked to human diseases, such as gastroenteritis, skin, soft-tissue and muscle infections,...
INTRODUCTION
Aeromonas species are renowned enteric pathogens with virulence determinants linked to human diseases, such as gastroenteritis, skin, soft-tissue and muscle infections, and septicemia. A recent concern of resistance in this organism has emerged, especially the presence carbapenemases. Herein we describe a case series of emerging carbapenem-resistant Aeromonas species infection in our hospital in Cali, Colombia.
MATERIALS AND METHODS
Cases from 2012 to 2018 are reported. Clinical data was abstracted from the clinical charts and laboratory information. Phenotypic detection of resistance was identified using the VITEK®2 system (BioMérieux) and broth microdilution MicroScan WalkAway plus System (Beckman Coulter). CARBA NP-test and multiplex qPCR assay was performed in 11 isolates to identify genes encoding carbapenemases (bla bla bla and bla).
RESULTS
21 cases of Aeromonas infection in hospitalized patients with phenotypic resistance to carbapenems were studied. The median age was 50 years, 55% (12/21) were male, and 67% (14/21) were healthcare-associated infections (HAI). Aeromonas hydrophila was the most common species (19/21). Forty-three percent (9/21) of the patients were immunocompromised. The mortality was 33% (7/21), and in patients with bacteremia was 100%. Most patients received empirical treatment with meropenem and failed to this treatment. PCR amplification tests showed negative results for the carbapenemases analyzed.
CONCLUSION
Emerging phenotypic carbapenem-resistant infection has been seen in our hospital, most as HAI. High mortality was found, especially in immunocompromised patients and in those who failled empirical treatment with carbapenems. As the main carbapenemases tested were negative, carbapenem-resistant could be attributed to an intrinsic metallo-β-lactamase, CphA encoded by the cphA gene, possible hyperproduction of ampC β-lactamase and/or porins expression.
Topics: Adult; Aeromonas; Aged; Anti-Bacterial Agents; Carbapenems; Colombia; Cross-Sectional Studies; Female; Gram-Negative Bacterial Infections; Humans; Male; Microbial Sensitivity Tests; Middle Aged; Phenotype; beta-Lactam Resistance; beta-Lactamases
PubMed: 31541615
DOI: 10.1016/j.bjid.2019.08.005 -
BMC Genomics Sep 2018Aeromonas hydrophila is a potential zoonotic pathogen and primary fish pathogen. With overlapping characteristics, multiple isolates are often mislabelled and... (Comparative Study)
Comparative Study
BACKGROUND
Aeromonas hydrophila is a potential zoonotic pathogen and primary fish pathogen. With overlapping characteristics, multiple isolates are often mislabelled and misclassified. Moreover, the potential pathogenic factors among the publicly available genomes in A. hydrophila strains of different origins have not yet been investigated.
RESULTS
To identify the valid strains of A. hydrophila and their pathogenic factors, we performed a pan-genomic study. It revealed that there were 13 mislabelled strains and 49 valid strains that were further verified by Average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH) and in silico multiple locus strain typing (MLST). Multiple numbers of phages were detected among the strains and among them Aeromonas phi 018 was frequently present. The diversity in type III secretion system (T3SS) and conservation of type II and type VI secretion systems (T2SS and T6SS, respectively) among all the strains are important to study for designing future strategies. The most prevalent antibiotic resistances were found to be beta-lactamase, polymyxin and colistin resistances. The comparative analyses of sequence type (ST) 251 and other ST groups revealed that there were higher numbers of virulence factors in ST-251 than in other STs group.
CONCLUSION
Publicly available genomes have 13 mislabelled organisms, and there are only 49 valid A. hydrophila strains. This valid pan-genome identifies multiple prophages that can be further utilized. Different A. hydrophila strains harbour multiple virulence factors and antibiotic resistance genes. Identification of such factors is important for designing future treatment regimes.
Topics: Aeromonas hydrophila; Bacterial Proteins; Computational Biology; Computer Simulation; Drug Resistance, Bacterial; Genome, Bacterial; Molecular Typing; Phylogeny; Sequence Analysis, DNA; Virulence Factors
PubMed: 30257645
DOI: 10.1186/s12864-018-5100-4 -
BMC Research Notes Nov 2023Eel (Anguilla bicolor bicolor) is an Indonesian export commodity. However, it is facing a problem related to Aeromonas hydrophila, which can cause motile aeromonas...
The potential of shallot skin powder and actinomycetes metabolites as antimicrobe and antibiofilm in the treatment of eel (Anguilla bicolor bicolor) infected with Aeromonas hydrophila.
BACKGROUND
Eel (Anguilla bicolor bicolor) is an Indonesian export commodity. However, it is facing a problem related to Aeromonas hydrophila, which can cause motile aeromonas septicemia (MAS) and produce biofilm formation. Problem with antibiotic resistance challenges the need of an alternative treatment. Therefore, it is important to explore a solution to treat infection and the biofilm formed by A. hydrophila.
OBJECTIVES
In this study, we used shallot skin powder and actinomycetes metabolite 20 PM as antimicrobe and antibiofilm to treated eels infected with A. hydrophila.
RESULTS
Shallot skin powder (6.25 g 100 g feed) and Actinomycetes 20 PM metabolite (2 mL 100 g feed) were found to be effective as antimicrobe and antibiofilm agent in treating eels infected with A. hydrophila. Eel treated with antibiotic, shallot skin powder, and actinomycetes metabolite had 80%, 66%, and 73% survival rates, respectively. Other indicators such as red blood cell count, hemoglobin, and hematocrit were increased, but white blood cell count and phagocytic activity were dropped. Biofilm destruction were analyzed using scanning electron microscopy to determined antibiofilm activity of actinomycetes metabolite against biofilm of A. Hydrophila.
CONCLUSIONS
Shallot skin powder and actinomycetes metabolite were potential to treat infection of A. hydrophila in eel as an alternative treatment to antibiotics.
Topics: Animals; Anguilla; Aeromonas hydrophila; Powders; Shallots; Actinobacteria; Actinomyces; Biofilms; Gram-Negative Bacterial Infections
PubMed: 37946241
DOI: 10.1186/s13104-023-06611-9 -
Frontiers in Microbiology 2022is an emerging waterborne and foodborne pathogen with pathogenicity to humans and warm water fishes, which severely threatens human health, food safety and aquaculture....
is an emerging waterborne and foodborne pathogen with pathogenicity to humans and warm water fishes, which severely threatens human health, food safety and aquaculture. A novel method for the rapid, accurate, and sensitive detection of pathogenic is still needed to reduce the impact on human health and aquaculture. In this work, we developed a rapid, accurate, sensitive, and visual detection method (dRAA-CRISPR/Cas12a), without elaborate instruments, integrating the dualplex recombinase-assisted amplification (dRAA) assay and CRISPR/Cas12a system to detect pathogenic expressing and/or virulence genes. The dRAA-CRISPR/Cas12a method has high sensitivity, which can rapidly detect (about 45 min) with the limit of detection in 2 copies of genomic DNA per reaction, and has high specificity for three pathogenic strains ( , , and ). Moreover, dRAA-CRISPR/Cas12a method shows satisfactory practicability in the analysis of the spiked human blood and stool and fish samples. These results demonstrate that our developed pathogenic detection method, dRAA-CRISPR/Cas12a, is a promising potential method for the early diagnosis of human infection and on-site detection of in food and aquaculture.
PubMed: 36274718
DOI: 10.3389/fmicb.2022.973996 -
Frontiers in Microbiology 2022, a ubiquitous bacterium in aquatic habitats with broad host ranges, has earned the nickname of a 'Jack-of-all-trades'. However, there is still a limited understanding...
, a ubiquitous bacterium in aquatic habitats with broad host ranges, has earned the nickname of a 'Jack-of-all-trades'. However, there is still a limited understanding of the mechanism of how this bacterium fit the competition with other species in dynamic surroundings. The type VI secretion system (T6SS) is macromolecular machinery found in Gram-negative bacteria's cell envelope that is responsible for bacterial killing and/or pathogenicity toward different host cells. In this study, the depression of T6SS under iron-limiting conditions was detected. The ferric uptake regulator (Fur) was then found to act as an activator of T6SS by directly binding to the Fur box region in A promoter in the T6SS gene cluster. The transcription of A was repressed in Δ. Moreover, the inactivation of Fur resulted in considerable defects in the interbacterial competition activity and pathogenicity of and . These findings provide the first direct evidence that Fur positively regulates the expression and functional activity of T6SS in Gram-negative bacteria and will help to understand the fascinating mechanism of competitive advantage for in different ecological niches.
PubMed: 36845974
DOI: 10.3389/fmicb.2022.1099611