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The ISME Journal Jan 2024Intestinal microbial disturbance is a direct cause of host disease. The bacterial Type VI secretion system (T6SS) often plays a crucial role in the fitness of pathogenic...
Intestinal microbial disturbance is a direct cause of host disease. The bacterial Type VI secretion system (T6SS) often plays a crucial role in the fitness of pathogenic bacteria by delivering toxic effectors into target cells. However, its impact on the gut microbiota and host pathogenesis is poorly understood. To address this question, we characterized a new T6SS in the pathogenic Aeromonas veronii C4. First, we validated the secretion function of the core machinery of A. veronii C4 T6SS. Second, we found that the pathogenesis and colonization of A. veronii C4 is largely dependent on its T6SS. The effector secretion activity of A. veronii C4 T6SS not only provides an advantage in competition among bacteria in vitro, but also contributes to occupation of an ecological niche in the nutritionally deficient and anaerobic environment of the host intestine. Metagenomic analysis showed that the T6SS directly inhibits or eliminates symbiotic strains from the intestine, resulting in dysregulated gut microbiome homeostasis. In addition, we identified three unknown effectors, Tse1, Tse2, and Tse3, in the T6SS, which contribute to T6SS-mediated bacterial competition and pathogenesis by impairing targeted cell integrity. Our findings highlight that T6SS can remodel the host gut microbiota by intricate interplay between T6SS-mediated bacterial competition and altered host immune responses, which synergistically promote pathogenesis of A. veronii C4. Therefore, this newly characterized T6SS could represent a general interaction mechanism between the host and pathogen, and may offer a potential therapeutic target for controlling bacterial pathogens.
Topics: Type VI Secretion Systems; Gastrointestinal Microbiome; Aeromonas veronii; Symbiosis; Ecosystem; Bacterial Proteins
PubMed: 38531781
DOI: 10.1093/ismejo/wrae053 -
Virus Research Oct 2023Aeromonas is one of the most serious pathogens in freshwater aquaculture. Overuse of antibiotics for the treatment of fish diseases has led to the frequent occurrence of...
Aeromonas is one of the most serious pathogens in freshwater aquaculture. Overuse of antibiotics for the treatment of fish diseases has led to the frequent occurrence of drug-resistant strains. Phage therapy is an alternative approach to overcoming the multi-drug resistance associated with antibiotics. In this study, a novel phage phiA034 targeting the host A. veronii A034 was isolated. The phage could infect 14 strains of 4 species Aeromonas. The phage phiA034 displayed head-tail structure with an icosahedral head in the TEM image. At the optimal MOI of 1, it had a latent period of nearly 20 minutes and a burst size of 286 PFU/cell. Besides, the phage phiA034 exhibited high tolerance to a wide range of temperature (30-70 °C) and acid-base (pH 6.0-10.0). The whole genome of phage phiA034 was sequenced with a size of 61,443 bp and annotated with 82 ORFs, mainly related to structure, DNA replication, and lysis. Based on the analysis and comparison of the genomes and proteomes, phage phiA034 could be classified as a novel species of an existing genus Duplodnaviria Heunggongvirae, Uroviricota, Caudoviricetes, Casjensviridae, Sharonstreetvirus. These findings have expanded the species bank and genomes library of bacterial virus and will promote the application of phage therapy in Aeromonas disease.
Topics: Animals; Bacteriophages; Aeromonas; DNA, Viral; Genome, Viral; Anti-Bacterial Agents
PubMed: 37579848
DOI: 10.1016/j.virusres.2023.199193 -
Frontiers in Immunology 2023As the primary natural barrier that protects against adverse environmental conditions, the skin plays a crucial role in the innate immune response of fish, particularly...
As the primary natural barrier that protects against adverse environmental conditions, the skin plays a crucial role in the innate immune response of fish, particularly in relation to bacterial infections. However, due to the diverse functionality and intricate anatomical and cellular composition of the skin, deciphering the immune response of the host is a challenging task. In this study, single nuclei RNA-sequencing (snRNA-seq) was performed on skin biopsies obtained from Chinese longsnout catfish (), comparing -infected subjects to healthy control subjects. A total of 19,581 single nuclei cells were sequenced using 10x Genomics (10,400 in the control group and 9,181 in the treated group). Based on expressed unique transcriptional profiles, 33 cell clusters were identified and classified into 12 cell types including keratinocyte (KC), fibroblast (FB), endothelial cells (EC), secretory cells (SC), immune cells, smooth muscle cells (SMC), and other cells such as pericyte (PC), brush cell (BC), red blood cell (RBC), neuroendocrine cell (NDC), neuron cells (NC), and melanocyte (MC). Among these, three clusters of KCs, namely, KC1, KC2, and KC5 exhibited significant expansion after infection. Analysis of pathway enrichment revealed that KC1 was primarily involved in environmental signal transduction, KC2 was primarily involved in endocrine function, and KC5 was primarily involved in metabolism. Finally, our findings suggest that neutrophils may play a crucial role in combating infections. In summary, this study not only provides the first detailed comprehensive map of all cell types present in the skin of teleost fish but also sheds light on the immune response mechanism of the skin following infection in Chinese longsnout catfish.
Topics: Animals; Humans; Catfishes; Aeromonas hydrophila; RNA-Seq; Endothelial Cells; Immunity, Innate
PubMed: 37908355
DOI: 10.3389/fimmu.2023.1271466 -
MBio Feb 2024Many pathogenic Gram-negative bacteria use repeats-in-toxin adhesins for colonization and biofilm formation. In the cholera agent , flagellar-regulated hemagglutinin A...
Many pathogenic Gram-negative bacteria use repeats-in-toxin adhesins for colonization and biofilm formation. In the cholera agent , flagellar-regulated hemagglutinin A (FrhA) enables these functions. Using bioinformatic analysis, a sugar-binding domain was identified in FrhA adjacent to a domain of unknown function. AlphaFold2 indicated the boundaries of both domains to be slightly shorter than previously predicted and assisted in the recognition of the unknown domain as a split immunoglobulin-like fold that can assist in projecting the sugar-binding domain toward its target. The AlphaFold2-predicted structure is in excellent agreement with the molecular envelope obtained from small-angle X-ray scattering analysis of a recombinant construct spanning the sugar-binding and unknown domains. This two-domain construct was probed by glycan micro-array screening and showed binding to mammalian fucosylated glycans, some of which are characteristic erythrocyte markers and intestinal cell epitopes. Isothermal titration calorimetry further showed the construct-bound l-fucose with a of 21 µM. Strikingly, this recombinant protein construct bound and lysed erythrocytes in a concentration-dependent manner, and its hemolytic activity was blocked by the addition of l-fucose. A protein ortholog construct from was also produced and showed a similar glycan-binding pattern, binding affinity, erythrocyte-binding, and hemolytic activities. As demonstrated here with Hep-2 cells, fucose-based inhibitors of this sugar-binding domain can potentially be developed to block colonization by and other pathogenic bacteria that share this adhesin domain.IMPORTANCEThe bacterium, , which causes cholera, uses an adhesion protein to stick to human cells and begin the infection process. One part of this adhesin protein binds to a particular sugar, fucose, on the surface of the target cells. This binding can lead to colonization and killing of the cells by the bacteria. Adding l-fucose to the bacteria before they bind to the human cells can prevent attachment and has promise as a preventative drug to protect against cholera.
Topics: Animals; Humans; Vibrio cholerae; Cholera; Aeromonas veronii; Fucose; Adhesins, Bacterial; Polysaccharides; Toxins, Biological; Sugars; Mammals
PubMed: 38171003
DOI: 10.1128/mbio.02291-23 -
Environmental Research Dec 2023The overuse of antibiotics in aquaculture drives the emergence of multi-drug-resistant bacteria, and antibiotic-resistant genes (ARGs) can be disseminated to other...
The overuse of antibiotics in aquaculture drives the emergence of multi-drug-resistant bacteria, and antibiotic-resistant genes (ARGs) can be disseminated to other bacteria through vertical- and horizontal gene transfer (VGT and HGT) under selective pressure. Profiling the antibiotic resistome and understanding the global distribution of ARGs constitutes the first step in developing a control strategy. Hence, this study utilized extensive genomic data from hundreds of Aeromonas strains in aquaculture to profile resistome patterns and explores their association with isolation year, country, and species characteristics. Overall, ∼400 Aeromonas genomes were used to predict the ARGs from A. salmonicida, A. hydrophila, A. veronii, A. media, and A. sobria. ARGs such as sul1, tet(A), and tet(D), which display a similar proportion of positive strains among species, were subjected to phylodynamic and phylogeographic analyses. More than a hundred ARGs were identified, some of which exhibited either species-specific or non-species-specific patterns. A. salmonicida and A. media were found to have a higher proportion of species-specific ARGs than other strains, which might lead to more distinct patterns of ARG acquisition. Overall, ∼25% of strains have either sul1, tet(A), or tet(D) gene(s), but no significant difference was observed in the proportion of positive strains by species. Phylogeographic analysis revealed that the abundant numbers of sul1, tet(A), and/or tet(D) introduced in a few East Asian and North American countries could spread to both adjacent and faraway countries. In recent years, the proportions of these ARGs have dramatically increased, particularly in strains sourced from aquatic environments, suggesting control is required of the overuse of antibiotics in aquaculture. The findings of this research offer significant insights into the global dissemination of ARGs.
Topics: Aeromonas; Anti-Bacterial Agents; Drug Resistance, Multiple, Bacterial; Aquaculture; North America; Genes, Bacterial
PubMed: 37805184
DOI: 10.1016/j.envres.2023.117273 -
Frontiers in Immunology 2024, a gram-negative coccobacillus bacterium, can cause various infections in humans, including septic arthritis, diarrhea (traveler's diarrhea), gastroenteritis, skin and...
, a gram-negative coccobacillus bacterium, can cause various infections in humans, including septic arthritis, diarrhea (traveler's diarrhea), gastroenteritis, skin and wound infections, meningitis, fulminating septicemia, enterocolitis, peritonitis, and endocarditis. It frequently occurs in aquatic environments and readily contacts humans, leading to high infection rates. This bacterium has exhibited resistance to numerous commercial antibiotics, and no vaccine has yet been developed. Aiming to combat the alarmingly high infection rate, this study utilizes techniques to design a multi-epitope vaccine (MEV) candidate against this bacterium based on its aerolysin toxin, which is the most toxic and highly conserved virulence factor among the species. After retrieval, aerolysin was processed for B-cell and T-cell epitope mapping. Once filtered for toxicity, antigenicity, allergenicity, and solubility, the chosen epitopes were combined with an adjuvant and specific linkers to create a vaccine construct. These linkers and the adjuvant enhance the MEV's ability to elicit robust immune responses. Analyses of the predicted and improved vaccine structure revealed that 75.5%, 19.8%, and 1.3% of its amino acids occupy the most favored, additional allowed, and generously allowed regions, respectively, while its ERRAT score reached nearly 70%. Docking simulations showed the MEV exhibiting the highest interaction and binding energies (-1,023.4 kcal/mol, -923.2 kcal/mol, and -988.3 kcal/mol) with TLR-4, MHC-I, and MHC-II receptors. Further molecular dynamics simulations demonstrated the docked complexes' remarkable stability and maximum interactions, i.e., uniform RMSD, fluctuated RMSF, and lowest binding net energy. models also predict the vaccine will stimulate a variety of immunological pathways following administration. These analyses suggest the vaccine's efficacy in inducing robust immune responses against . With high solubility and no predicted allergic responses or toxicity, it appears safe for administration in both healthy and -infected individuals.
Topics: Humans; Artificial Intelligence; Aeromonas hydrophila; Diarrhea; Travel; Machine Learning; Vaccines; Epitopes, T-Lymphocyte; Adjuvants, Immunologic; Adjuvants, Pharmaceutic; Bacterial Toxins; Pore Forming Cytotoxic Proteins
PubMed: 38495891
DOI: 10.3389/fimmu.2024.1369890 -
Microbiology Spectrum May 2024Hospital sewage serves as a crucial reservoir for antibiotic resistance genes. As colistin and carbapenems are the last-resort antibiotics, the emergence of their...
Hospital sewage serves as a crucial reservoir for antibiotic resistance genes. As colistin and carbapenems are the last-resort antibiotics, the emergence of their resistance genes has become a significant concern in clinical settings. In this study, we found that two novel alleles (.43 and .2) with two carbapenemase genes ( and ) were encoded in a single strain isolated from hospital sewage. Our phylogenetic analysis revealed that the gene clustered with (with 95.55% amino acid identity), while the gene clustered with (with 68.68% amino acid identity). BLAST search against GenBank showed that was exclusively detected in spp. Mobile genetic elements were not found in the genetic context of , suggesting that the dissemination of in spp. may be dependent on vertical transfer or recombination. The was adjacent to a recombinase gene and flanked by two IS elements, indicating a potential mobilization mechanism mediated by recombination and/or ISs. The gene was located on an IncU plasmid and adjacent to an IS. In summary, our study provides evidence for spp. as one of the potential reservoirs of colistin and carbapenem resistance genes.IMPORTANCEThe study discovered two novel genes ( and ) and two carbapenemase genes ( and ) in a single strain retrieved from hospital sewage. Using phylogenetic analysis and comparative data evaluation, the study revealed the genetic relatedness and dissemination potential of the detected resistance genes. With the exclusive discovery that is only present in spp. and the lack of mobile genetic elements in its genetic context, there is a strong indication of limited dissemination. The identification of these four resistance genes in a single strain of provided valuable insights into their potential presence in this genus. This study revealed that hospital sewage functions as a significant reservoir for antibiotic resistance genes, including colistin and carbapenem resistance genes.
Topics: beta-Lactamases; Bacterial Proteins; Anti-Bacterial Agents; Drug Resistance, Multiple, Bacterial; Phylogeny; Aeromonas caviae; Microbial Sensitivity Tests; Sewage; Colistin; Carbapenems; Humans; Plasmids
PubMed: 38511954
DOI: 10.1128/spectrum.03685-23 -
Microbial Genomics May 2024spp. are commonly found in the aquatic environment and have been responsible for motile septicemia (MAS) in striped catfish, resulting in significant economic loss....
spp. are commonly found in the aquatic environment and have been responsible for motile septicemia (MAS) in striped catfish, resulting in significant economic loss. These organisms also cause a range of opportunistic infections in humans with compromised immune systems. Here, we conducted a genomic investigation of 87 isolates derived from diseased catfish, healthy catfish and environmental water in catfish farms affected by MAS outbreaks in eight provinces in Mekong Delta (years: 2012-2022), together with 25 isolates from humans with bloodstream infections (years: 2010-2020). Genomics-based typing method precisely delineated species while traditional methods such as PCR and MALDI-TOF were unable identify was found to be more prevalent than in both diseased catfish and human infections. sequence type (ST) 656 followed by ST251 were the predominant virulent species-lineages in diseased catfish (43.7 and 20.7 %, respectively), while diverse STs were found in humans with bloodstream infections. There was evidence of widespread transmission of ST656 and ST251 on striped catfish in the Mekong Delta region. ST656 and ST251 isolates carried a significantly higher number of acquired antimicrobial resistance (AMR) genes and virulence factors in comparison to other STs. They, however, exhibited several distinctions in key virulence factors (i.e. lack of type IV pili and enterotoxin in ), AMR genes (i.e. presence of carbapenemase in ), and accessory gene content. To uncover potential conserved proteins of spp. for vaccine development, pangenome analysis has unveiled 2202 core genes between ST656 and ST251, of which 78 proteins were in either outer membrane or extracellular proteins. Our study represents one of the first genomic investigations of the species distribution, genetic landscape, and epidemiology of in diseased catfish and human infections in Vietnam. The emergence of antimicrobial resistant and virulent strains underscores the needs of enhanced genomic surveillance and strengthening vaccine research and development in preventing diseases in catfish and humans, and the search for potential vaccine candidates could focus on core genes encoded for membrane and secreted proteins.
Topics: Animals; Catfishes; Vietnam; Aeromonas; Gram-Negative Bacterial Infections; Humans; Sepsis; Fish Diseases; Phylogeny; Genomics; Genome, Bacterial; Virulence Factors; Anti-Bacterial Agents
PubMed: 38739115
DOI: 10.1099/mgen.0.001248 -
Annals of Clinical Microbiology and... May 2024The population structure and the correlation between antimicrobial resistance (AMR) phenotypes and genotypes in Aeromonas species isolated from patients with...
BACKGROUND
The population structure and the correlation between antimicrobial resistance (AMR) phenotypes and genotypes in Aeromonas species isolated from patients with gastroenteritis are not well understood. The aims of the study were to: (1) investigate the antimicrobial susceptibility profiles of Aeromonas species isolated from patients with gastroenteritis; (2) explore the relationship between AMR genes and resistance phenotypes; and (3) describe the population structure of these isolates and provide evidence of transmission events among them.
METHODS
This microbiological survey was performed at the Microbiology Laboratory of the Emek Medical Center in Afula, Israel. Cultivation of Aeromonas was attempted from stool samples that tested positive by PCR. Antimicrobial susceptibility testing (AST) was performed using the Sensititre GN3F microdilution panel. Whole genome sequencing (WGS) was done using the Illumina NextSeq500/550 system. Phylogenetic studies involved multi-locus sequence typing (MLST) and core genome (cg) MLST. Resistance mechanisms were identified using the Comprehensive Antibiotic Resistance Database and compared with the AST results.
RESULTS
The study included 67 patient-unique isolates. The species that were identified included A. caviae (n = 58), A. dhakensis (n = 3), A. media (n = 2), A. veronii (n = 2) and A. hydrophila (n = 2). Isolates were almost uniformly susceptible to amikacin, gentamicin, aztreonam, cefepime, ceftazidime, ciprofloxacin and meropenem. All isolates with the exception of 1-2 isolates were resistant to ampicillin, cefazolin and ampicillin-sulbactam which was compatible with the presence of the bla genes. Variable resistance rates were observed to cefuroxime, cefoxitin, ceftriaxone, piperacillin-tazobactam that were not correlated with the presence of other β-lactamase genes. Resistance to tetracycline and trimethoprim-sulfamethoxazole correlated with the presence of tetA and sul1, respectively. The population structure of A. caviae was highly diverse with the minority of the isolates (16/57) clustering into six defined sequence types. A cgMLST-based distance of four genes was found in one pair of isolates, suggesting common source transmission.
CONCLUSIONS
A. caviae is the dominant species related to gastroenteritis and is characterized by a diverse population structure, with almost no evidence for common-source transmission. Resistance rates to most antimicrobial agents were low and partially matched with the presence of resistance genes.
Topics: Humans; Gastroenteritis; Aeromonas; Microbial Sensitivity Tests; Anti-Bacterial Agents; Genotype; Phylogeny; Gram-Negative Bacterial Infections; Whole Genome Sequencing; Multilocus Sequence Typing; Child; Phenotype; Adult; Feces; Child, Preschool; Female; Male; Middle Aged; Drug Resistance, Bacterial; Israel; Aged; Infant; Adolescent; Young Adult; Drug Resistance, Multiple, Bacterial
PubMed: 38783344
DOI: 10.1186/s12941-024-00706-2 -
Frontiers in Microbiology 2024Strawberry ( × ) fruits are vulnerable to bacterial contamination; some species are pathogenic and can affect human health. Comprehending the bacterial composition and...
BACKGROUND
Strawberry ( × ) fruits are vulnerable to bacterial contamination; some species are pathogenic and can affect human health. Comprehending the bacterial composition and diversity at different ripe stages is a key determinant of the fruit health, productivity, and quality.
METHODOLOGY
An amplicon metagenomic approach on the 16S rRNA region was used to identify the bacterial diversity in exocarp of fruits collected from a farm field at two ripe stages: breaking (white, phase two) and ripe (red, phase four) and purchased from different retail market stands at ripe (red, phase four, ready-to-eat) stage. Besides, the fruit quality was assessed.
RESULTS
Strawberries carries a high microorganisms diversity, with , and being the most abundant families across the samples. Among the groups, and were the most abundant families at breaking (phase two) and ripe (phase four), whereas , and were the most abundant families in the market group. Although samples from group four-field and market were at the same ripe stage, the bacterial species composition was divergent. spp. were prevalent (above 60%) in samples collected from the market group, and (above 70%) species were mostly found in the samples collected from the field settings regardless of the phase. Besides, and were detected in the ready-to-eat samples from both the field and the market, while was detected in the samples that originated from the market. Interestingly, and , two human opportunistic pathogens, were detected in the fruits from the market only. According to alpha and beta diversity analyses, strawberry fruits displayed significant differences ( < 0.05) in bacterial communities within the ripe group, with the samples from the market showing the most bacterial diversity. Although we do not directly correlate the quality attributes with bacterial diversity, the results indicated a clear separation between groups according with their ripe stage and origin.
CONCLUSION
This study provides a comprehensive framework of the bacterial diversity throughout the transition from unripe to ripe strawberries which may aid in the development of preventative measures to manage the postharvest contamination.
PubMed: 38435684
DOI: 10.3389/fmicb.2024.1348316