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Computers in Biology and Medicine Jul 2024Ovarian cancer (OC) is found to be the third most common gynecologic malignancy over the world, having the highest mortality rate among such tumors. Emerging studies...
BACKGROUND
Ovarian cancer (OC) is found to be the third most common gynecologic malignancy over the world, having the highest mortality rate among such tumors. Emerging studies underscore the presence of microorganisms within tumor tissues, with certain pathogens intricately linked to disease onset and progression. Disruption of the microbiome frequently precipitates disturbances in host metabolic and immune pathways, thereby fostering the development of cancer.
METHODS
In this study, we initiated the investigation by conducting microbial reannotation on the RNA sequencing data derived from ovarian cancer tissues. Subsequently, a comprehensive array of analyses on tissue microbes was executed. These analyses encompassed the assessment of intergroup variations in microbial diversity, differential microbiological analysis, exploration of the association between host gene expression and microbial abundance, as well as an enrichment analysis of functional pathways linked to host genes associated with microbes.
RESULTS
The analysis results revealed that Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes were the main components at phylum level in ovarian tissue. Notably, the microbial composition of ovarian cancer tissue significantly diverged from that of normal ovarian tissue e, exhibiting markedly lower alpha diversity and distinct beta diversity. Besides, pathogenic microorganisms Achromobacter xylosoxidans and Enterobacter hormaechei were enriched in cancer tissue. Host genes associated with these pathogens were enriched in key pathways including "JAK-STAT signaling pathway", "Transcriptional misregulation in cancer", and "Th1 and Th2 cell differentiation", suggesting their role in ovarian cancer progression through microbial dysbiosis and immune response interaction.
CONCLUSION
Abundance of pathogenic microorganisms in ovarian cancer tissue could modulate the expression of host genes, consequently impacting cancer-related signaling pathways and fostering cancer progression.
Topics: Humans; Female; Ovarian Neoplasms; Microbiota; Disease Progression
PubMed: 38833797
DOI: 10.1016/j.compbiomed.2024.108641 -
The American Journal of Case Reports Jun 2024BACKGROUND Peritoneal dialysis (PD) serves as a critical renal replacement therapy for individuals with end-stage renal disease (ESRD), leveraging the peritoneum for... (Review)
Review
BACKGROUND Peritoneal dialysis (PD) serves as a critical renal replacement therapy for individuals with end-stage renal disease (ESRD), leveraging the peritoneum for fluid and substance exchange. Despite its effectiveness, PD is marred by complications such as peritonitis, which significantly impacts patient outcomes. The novelty of our report lies in the presentation of a rare case of PD-associated peritonitis caused by 2 unusual pathogens, emphasizing the importance of rigorous infection control measures. CASE REPORT We report on an 80-year-old African-American female patient with ESRD undergoing PD, who was admitted twice within 8 months for non-recurring episodes of peritonitis. These episodes were attributed to the rare pathogens Achromobacter denitrificans/xylosoxidans and Carbapenem-resistant Acinetobacter baumannii. Despite presenting with similar symptoms during each episode, such as abdominal pain and turbid dialysis effluent, the presence of these uncommon bacteria highlights the intricate challenges in managing infections associated with PD. The treatment strategy encompassed targeted antibiotic therapy, determined through susceptibility testing. Notably, the decision to remove the PD catheter followed extensive patient education, ensuring the patient comprehended the rationale behind this approach. This crucial step, along with the subsequent shift to hemodialysis, was pivotal in resolving the infection, illustrating the importance of patient involvement in the management of complex PD-related infections. CONCLUSIONS This case underscores the complexities of managing PD-associated peritonitis, particularly with uncommon and resistant bacteria. It emphasizes the importance of rigorous infection control measures, the need to consider atypical pathogens, and the critical role of patient involvement in treatment decisions. Our insights advocate for a more informed approach to handling such infections, aiming to reduce morbidity and improve patient outcomes. The examination of the literature on recurrent peritonitis and treatment strategies provides key perspectives for navigating these challenging cases effectively.
Topics: Humans; Peritonitis; Female; Aged, 80 and over; Peritoneal Dialysis; Kidney Failure, Chronic; Acinetobacter baumannii; Achromobacter denitrificans; Anti-Bacterial Agents; Gram-Negative Bacterial Infections; Acinetobacter Infections; Practice Guidelines as Topic
PubMed: 38831580
DOI: 10.12659/AJCR.943953 -
International Journal of Antimicrobial... May 2024
PubMed: 38815701
DOI: 10.1016/j.ijantimicag.2024.107218 -
Saudi Journal of Biological Sciences Jul 2024Phytate content in feed ingredients can negatively impact digestibility and palatability. To address this issue, it is necessary to study microbes capable of breaking...
Phytate content in feed ingredients can negatively impact digestibility and palatability. To address this issue, it is necessary to study microbes capable of breaking down phytate content. This study aimed to isolate and characterize phytase-producing bacteria from decaying materials rich in phytic acid. The research was conducted in several stages. The first stage involved isolating phytase-producing bacteria from the acidification of using growth media containing Na-phytate. Bacterial isolates that produced clear zones were then tested for their activity and ability to produce several enzymes, specifically phytase, cellulase, and protease. The next step was to test the morphological characteristics of the bacterial isolate. The final stage of bacterial identification consisted of DNA isolation, followed by PCR amplification of the 16S rRNA gene, DNA sequence homology analysis, and construction of a phylogenetic tree. Based on research, three isolates were found to produce clear phytase zones: isolates R5 (20.3 mm), R7 (16.1 mm) and R8 (31.7 mm). All isolates were able to produce the enzymes phytase (5.45-6.54 U/ml), cellulase (2.60-2.92 U/ml), and protease (22.2-23.4 U/ml). Metagenomic testing identified isolate R7 and R8 as and isolate R5 as . The isolation and characterization of phytase-producing bacteria from acidification resulted in the identification of two promising candidates that can be applied as sources of phytase producers. Phytase-producing bacteria can be utilized to improve digestibility and palatability in animal feed.
PubMed: 38813263
DOI: 10.1016/j.sjbs.2024.104006 -
Cureus Apr 2024Vertebral fractures remain a diagnostic challenge nowadays. The first and most common diagnosis needed to be ruled out is osteoporosis. Other diagnoses to rule out...
Vertebral fractures remain a diagnostic challenge nowadays. The first and most common diagnosis needed to be ruled out is osteoporosis. Other diagnoses to rule out involve pathological fractures. Pathological fractures are a group of pathologies that result in a spine fracture as part of an underlying disease process that affects the spine. This group includes Paget's disease, tumors, osteomyelitis, and vertebral compression fractures. Fractures secondary to vertebral osteomyelitis are presented as collapsed vertebral bodies secondary to bone destruction and the formation of lytic lesions. Clinical presentation includes severe back pain refractory to analgesic therapy, persistent unexplained fever, and leukocytosis without any other obvious focus of infection. In cases like the one presented here, early biopsy and culture should be performed on every patient that fits these criteria. However, as it presents unspecific symptoms most of the time, it is not suspected, and therefore it is associated with high morbidity and mortality.
PubMed: 38803779
DOI: 10.7759/cureus.59141 -
Microbiome May 2024Antibiotics and microplastics are two major aquatic pollutants that have been associated to antibiotic resistance selection in the environment and are considered a risk...
BACKGROUND
Antibiotics and microplastics are two major aquatic pollutants that have been associated to antibiotic resistance selection in the environment and are considered a risk to human health. However, little is known about the interaction of these pollutants at environmental concentrations and the response of the microbial communities in the plastisphere to sub-lethal antibiotic pollution. Here, we describe the bacterial dynamics underlying this response in surface water bacteria at the community, resistome and mobilome level using a combination of methods (next-generation sequencing and qPCR), sequencing targets (16S rRNA gene, pre-clinical and clinical class 1 integron cassettes and metagenomes), technologies (short and long read sequencing), and assembly approaches (non-assembled reads, genome assembly, bacteriophage and plasmid assembly).
RESULTS
Our results show a shift in the microbial community response to antibiotics in the plastisphere microbiome compared to surface water communities and describe the bacterial subpopulations that respond differently to antibiotic and microplastic pollution. The plastisphere showed an increased tolerance to antibiotics and selected different antibiotic resistance bacteria (ARB) and antibiotic resistance genes (ARGs). Several metagenome assembled genomes (MAGs) derived from the antibiotic-exposed plastisphere contained ARGs, virulence factors, and genes involved in plasmid conjugation. These include Comamonas, Chryseobacterium, the opportunistic pathogen Stenotrophomonas maltophilia, and other MAGs belonging to genera that have been associated to human infections, such as Achromobacter. The abundance of the integron-associated ciprofloxacin resistance gene aac(6')-Ib-cr increased under ciprofloxacin exposure in both freshwater microbial communities and in the plastisphere. Regarding the antibiotic mobilome, although no significant changes in ARG load in class 1 integrons and plasmids were observed in polluted samples, we identified three ARG-containing viral contigs that were integrated into MAGs as prophages.
CONCLUSIONS
This study illustrates how the selective nature of the plastisphere influences bacterial response to antibiotics at sub-lethal selective pressure. The microbial changes identified here help define the selective role of the plastisphere and its impact on the maintenance of environmental antibiotic resistance in combination with other anthropogenic pollutants. This research highlights the need to evaluate the impact of aquatic pollutants in environmental microbial communities using complex scenarios with combined stresses. Video Abstract.
Topics: Anti-Bacterial Agents; Bacteria; Microbiota; RNA, Ribosomal, 16S; Integrons; Drug Resistance, Bacterial; Water Pollutants, Chemical; Microplastics; High-Throughput Nucleotide Sequencing; Metagenome; Plasmids; Water Microbiology; Drug Resistance, Microbial
PubMed: 38790062
DOI: 10.1186/s40168-024-01803-2 -
Journal of Orthopaedic Case Reports May 2024Achromobacter xylosoxidans is an uncommon opportunistic organism, mainly causing infection in immune-compromised hosts. A. xylosoxidans is a non-fermenting Gram-negative...
INTRODUCTION
Achromobacter xylosoxidans is an uncommon opportunistic organism, mainly causing infection in immune-compromised hosts. A. xylosoxidans is a non-fermenting Gram-negative bacillus. Being closely associated with Alcaligenes species was also called A. xylosoxidans.
CASE REPORT
A few cases of periprosthetic infection by A. xylosoxidans have been reported outside India. A periprosthetic infection with A. xylosoxidans following a total knee arthroplasty is reported in a female.
CONCLUSION
A. xylosoxidans is a pathogen capable of causing prosthetic joint infection even in immunocompetent patients. Thorough debridement and appropriate antibiotic treatment is essential for the success of revision surgery.
PubMed: 38784887
DOI: 10.13107/jocr.2024.v14.i05.4422 -
Fish & Shellfish Immunology Jul 2024Enteritis poses a significant threat to fish farming, characterized by symptoms of intestinal and hepatic inflammation, physiological dysfunction, and dysbiosis. Focused...
Enteritis poses a significant threat to fish farming, characterized by symptoms of intestinal and hepatic inflammation, physiological dysfunction, and dysbiosis. Focused on the leopard coral grouper (Plectropomus leopardus) with an enteritis outbreak on a South China Sea farm, our prior scrutiny did not find any abnormalities in feeding or conventional water quality factors, nor were any specific pathogen infections related to enteritis identified. This study further elucidates their intestinal flora alterations, host responses, and their interactions to uncover the underlying pathogenetic mechanisms and facilitate effective prevention and management strategies. Enteritis-affected fish exhibited substantial differences in intestinal flora compared to control fish (P = 0.001). Notably, norank_f_Alcaligenaceae, which has a negative impact on fish health, predominated in enteritis-affected fish (91.76 %), while the probiotic genus Lactococcus dominated in controls (93.90 %). Additionally, certain genera with pathogenesis potentials like Achromobacter, Sphingomonas, and Streptococcus were more abundant in diseased fish, whereas Enterococcus and Clostridium_sensu_stricto with probiotic potentials were enriched in control fish. At the transcriptomic level, strong inflammatory responses, accompanied by impaired metabolic functions, tissue damage, and iron death signaling activation were observed in the intestines and liver during enteritis. Furthermore, correlation analysis highlighted that potential pathogen groups were positively associated with inflammation and tissue damage genes while presenting negatively correlated with metabolic function-related genes. In conclusion, dysbiosis in the intestinal microbiome, particularly an aberrantly high abundance of Alcaligenaceae with pathogenic potential may be the main trigger for this enteritis outbreak. Alcaligenaceae alongside Achromobacter, Sphingomonas, and Streptococcus emerged as biomarkers for enteritis, whereas some species of Lactococcus, Clostridium_sensu_stricto, and Enterococcus showed promise as probiotics to alleviate enteritis symptoms. These findings enhance our understanding of enteritis pathogenesis, highlight intestinal microbiota shifts in leopard coral grouper, and propose biomarkers for monitoring, probiotic selection, and enteritis management.
Topics: Animals; Enteritis; Fish Diseases; Gastrointestinal Microbiome; Perciformes; China; Gene Expression
PubMed: 38777252
DOI: 10.1016/j.fsi.2024.109644 -
International Immunopharmacology Jun 2024Achromobacter xylosoxidans is an aerobic, catalase-positive, non-pigment-forming, Gram-negative, and motile bacterium. It potentially causes a wide range of human...
Achromobacter xylosoxidans is an aerobic, catalase-positive, non-pigment-forming, Gram-negative, and motile bacterium. It potentially causes a wide range of human infections in cystic fibrosis and non-cystic fibrosis patients. However, developing a safe preventive or therapeutic solution against A. xylosoxidans remains challenging. This study aimed to construct an epitope-based vaccine candidate using immunoinformatic techniques. A. xylosoxidans was isolated from an auto workshop in Lahore, and its identification was confirmed through 16S rRNA amplification and bioinformatic analysis. Two protein targets with GenBank accession numbers AKP90890.1 and AKP90355.1 were selected for the vaccine construct. Both proteins exhibited antigenicity, with scores of 0.757 and 0.580, respectively and the epitopes were selected based on the IC50 value using the ANN 4.0 and NN-align 2.3 epitope prediction method for MHC I and MHC II epitopes respectively and predicted epitopes were analyzed for antigenicity, allergenicity and pathogenicity. The vaccine construct demonstrated structural stability, thermostability, solubility, and hydrophilicity. The vaccine produced 250 B-memory cells per mm and approximately 16,000 IgM + IgG counts, indicating an effective immune response against A. xylosoxidans. Moreover, the vaccine candidate interacted stably with toll-like receptor 5, a pattern recognition receptor, with a confidence score of 0.98. These results highlight the potency of the designed vaccine candidate, suggesting its potential to withstand rigorous in vitro and in vivo clinical trials. This epitope-based vaccine could serve as the first preventive immunotherapy against A. xylosoxidans infections, addressing this bacterium's health and financial burdens. The findings demonstrate the value of employing immunoinformatic tools in vaccine development, paving the way for more precise and tailored approaches to combating microbial threats.
Topics: Achromobacter denitrificans; Bacterial Vaccines; Humans; RNA, Ribosomal, 16S; Gram-Negative Bacterial Infections; Animals; Epitopes; Computer Simulation; Female; Antibodies, Bacterial; Mice; Computational Biology; Antigens, Bacterial
PubMed: 38776850
DOI: 10.1016/j.intimp.2024.112287 -
Systematic and Applied Microbiology Jul 2024The tolerance of ash trees against the pathogen Hymenoscyphus fraxineus seems to be associated with the occurrence of specific microbial taxa on leaves. A group of...
The tolerance of ash trees against the pathogen Hymenoscyphus fraxineus seems to be associated with the occurrence of specific microbial taxa on leaves. A group of bacterial isolates, primarily identified on tolerant trees, was investigated with regard to their taxonomic classification and their potential to suppress the ash dieback pathogen. Examination of OGRI values revealed a separate species position. A phylogenomic analysis, based on orthologous and marker genes, indicated a separate genus position along with the species Achromobacter aestuarii. Furthermore, analysis of the ratio of average nucleotide identities and genome alignment fractions demonstrated genomic dissimilarities typically observed for inter-genera comparisons within this family. As a result of these investigations, the strains are considered to represent a separate species within a new genus, for which the name Schauerella fraxinea gen. nov., sp. nov. is proposed, with the type strain B3P038 (=LMG 33092 = DSM 115926 ). Additionally, a reclassification of the species Achromobacter aestuarii as Schauerella aestuarii comb. nov. is proposed. In a co-cultivation assay, the strains were able to inhibit the growth of a H. fraxineus strain. Accordingly, a functional analysis of the genome of S. fraxinea B3P038 revealed genes mediating the production of antifungal substances. This potential, combined with the prevalent presence in the phyllosphere of tolerant ash trees, makes this group interesting for an inoculation experiment with the aim of controlling the pathogen in an integrative approach. For future field trials, a strain-specific qPCR system was developed to establish an efficient method for monitoring the inoculation success.
Topics: Phylogeny; DNA, Bacterial; RNA, Ribosomal, 16S; Plant Diseases; Sequence Analysis, DNA; Bacterial Typing Techniques; Genome, Bacterial; Achromobacter; Plant Leaves; Apiaceae
PubMed: 38772267
DOI: 10.1016/j.syapm.2024.126516