Hasil untuk "Microbiology"

A. Möller

M. Bertoldi, G. Vallini, A. Pera

M. Speck

Weitong Yao, Yujun Li, Huize Sun et al.

IntroductionThe beta-coronavirus SARS-CoV-2 has been revealed to infect mammals and other species, which potentially promotes the virus adaptation to broader species and the emergence of new variants. The host range of different SARS-CoV-2 variants are mainly determined by the affinity of the receptor-binding domain (RBD) of the spike protein to the host receptor angiotensin-converting enzyme 2 (ACE2). Thus, this study aims to elucidate the detailed mechanisms of such dynamic adaptation of indicated SARS-CoV-2 variants.MethodsIn this study, flow cytometry and surface plasmon resonance (SPR) assays were used to assess the binding affinity between RBDs and avian ACE2. Then, infection assays with MLV-based SARS-CoV-2 spike pseudovirus or authentic viruses were performed to verify the avian ACE2 mediated viral entry. Finally, mutagenesis studies were conducted to identify key amino acids of avian ACE2 orthologs and RBDs.ResultsOur previous findings revealed that wild-type SARS-CoV-2 RBD does not bind chicken ACE2. Here, we found that ACE2 orthologs from chicken and mallard were capable to support binding to RBDs of the Alpha, Beta, and Gamma variants, which further enabled the viral entry. On the contrary, the RBD of BA.1 failed to bind avian ACE2. Whereas, a triple-residue reversal mutant (S446G, S496G, H505Y) restored ACE2 binding and enabled efficient viral entry. Additionally, several key residues within RBD were characterized as the determinant of its affinity to avian ACE2.DiscussionOur findings reveal that higher mutation rates in emerging variants might lead to future cross-species receptor usage or even spillover. Understanding such cross-species transmission mechanisms provides new insights to the virological features and potential host range of emerging SARS-CoV-2 variants.

Elaheh Karimzadeh‐Soureshjani, Farab Pourhasan, Pouria Ahmadi Simab et al.

ABSTRACT Helicobacter pylori infection has been extensively studied in relation to various gastrointestinal disorders, with emerging evidence suggesting a significant association with inflammatory bowel disease (IBD). Epidemiological studies consistently demonstrate an inverse relationship between H. pylori infection and IBD development, particularly Crohn's disease (CD). Meta‐analyses reveal a significantly lower prevalence of H. pylori among IBD patients compared to healthy controls, supporting the hypothesis of a potential protective effect. This negative correlation appears particularly strong for virulent strains expressing CagA, suggesting strain‐specific immunomodulatory properties. The protective mechanisms may involve H. pylori's ability to modulate host immune responses and maintain gut microbial homeostasis. Experimental models show that H. pylori colonization can induce regulatory T‐cell responses and downregulate pro‐inflammatory cytokines, potentially creating an immunological balance that protects against IBD development. Conversely, H. pylori eradication has been associated with increased IBD incidence and disease flares, possibly through disruption of established microbial ecosystems and immune regulation. Clinical observations further support this relationship, demonstrating that H. pylori‐positive CD patients often experience milder disease courses with fewer complications. However, the interaction remains complex, as H. pylori infection may also exert detrimental effects in certain contexts. The bacterium's influence appears to depend on multiple factors, including infection timing, strain characteristics, and host genetic background. Current evidence highlights the crucial interplay between H. pylori, gut microbiota composition, and mucosal immunity in shaping IBD pathogenesis. Future research should focus on elucidating precise molecular mechanisms and evaluating whether targeted modulation of H. pylori could offer therapeutic potential, while considering potential risks.

Jennifer Guiraud, Caroline Piau, Cécilia Enault et al.

ABSTRACT Accurate identification of non-tuberculous mycobacterial (NTM) species is crucial for the diagnosis and appropriate management of NTM infections. This study aimed to evaluate the performance of two assays, FluoroType Mycobacteria VER 1.0 and Maldi BioTyper (MBT) Mycobacteria. The two assays were evaluated using 119 NTM, including 85 slow-growing mycobacteria and 34 rapid-growing mycobacteria, representing a total of 33 species isolated in three French clinical laboratories. We used the GenoType assays as reference method for species identification, followed by 16S rRNA gene sequencing if the GenoType kits returned Mycobacterium sp. Compared to the reference method, the FluoroType Mycobacteria assay provided correct species identification in 89.9% of cases (107/119). Among the most frequently encountered species in clinical settings, low concordance was obtained for Mycobacterium intracellulare (82.4%, 14/17), Mycobacterium gordonae (66.7%, 6/9), and Mycobacterium xenopi (75%, 6/8). Misidentification was obtained in two cases (Mycobacterium smegmatis instead of Mycobacterium mageritense, and Mycobacterium mucogenicum instead of Mycobacterium phocaicum). Using the MBT Mycobacteria assay, 78.1% (93/119) of NTM isolates were correctly identified at the species level. One Mycobacterium europaeum isolate was misidentified as M. intracellulare/Mycobacterium chimaera. In five cases, the assay provided more accurate NTM identification compared to GenoType assays, in which closely related species are identified as a group. The FluoroType Mycobacteria VER 1.0 and the MBT Mycobacteria assays are useful tools for NTM identification from positive cultures, reducing handling time compared to GenoType assays. Their routine use in laboratories must take into consideration their performance and limitations in clinical settings.

Samuel Degregori, Melissa B. Manus, Evan B. Qu et al.

ABSTRACT The human facial skin microbiome is remarkably similar across all people sampled to date, dominated by facultative anaerobe Cutibacterium. The origin of this genus is unknown, with no close relatives currently described from samples of primate skin. This apparent human-specific bacterial taxon could reflect the unique nature of human skin, which is significantly more oily than that of our closest primate relatives. However, previous studies have not sampled the facial skin microbiome of our closest primates. Here, we profiled the skin microbiome of zoo-housed chimpanzees (Pan troglodytes) and gorillas (Gorilla gorilla gorilla), alongside their human care staff, using both 16S and shotgun sequencing. We showed that facial skin microbiomes differ significantly across host species, with humans having the lowest diversity and the most unique community among the three species. We were unable to find a close relative of Cutibacterium on either chimpanzee or gorilla facial skin, consistent with human specificity. Hominid skin microbiome functional profiles were more functionally similar compared to their taxonomic profiles. However, we still found notable functional differences, including lower proportions of fatty acid biosynthesis in humans, consistent with microbes’ reliance on host-derived lipids. Our study highlights the uniqueness of the human facial skin microbiome and supports a horizontal acquisition of its dominant resident from a yet unknown source.IMPORTANCEUnderstanding how and why human skin bacteria differ from our closest animal relatives provides crucial insights into human evolution and health. While we have known that human facial skin hosts distinct bacteria—particularly Cutibacterium acnes—we did not know if these bacteria and their associated genes were also present on the faces of our closest relatives, chimpanzees and gorillas. Our study shows that human facial skin hosts markedly different bacteria than other primates, with C. acnes being uniquely abundant on human faces. This finding suggests that this key bacterial species may have adapted specifically to human skin, which produces more oils than other primates.

Shuyan Sheng, Bangjie Chen, Ruiyao Xu et al.

Abstract Background Numerous studies have shown that Schistosoma japonicum infection correlates with an increased risk of liver hepatocellular carcinoma (LIHC). However, data regarding the role of this infection in LIHC oncogenesis are scarce. This study aimed to investigate the potential mechanisms of hepatocarcinogenesis associated with Schistosoma japonicum infection. Methods By examining chronic liver disease as a mediator, we identified the genes contributing to Schistosoma japonicum infection and LIHC. We selected 15 key differentially expressed genes (DEGs) using weighted gene co-expression network analysis (WGCNA) and random survival forest models. Consensus clustering revealed two subgroups with distinct prognoses. Least Absolute Shrinkage and Selection Operator (LASSO) and Cox regression identified six prognostic DEGs, forming an Schistosoma japonicum infection-associated signature for strong prognosis prediction. This signature, which is an independent LIHC risk factor, was significantly correlated with clinical variables. Four DEGs, including BMI1, were selected based on their protein expression levels in cancerous and normal tissues. We confirmed BMI1's role in LIHC using Schistosoma japonicum-infected mouse models and molecular experiments. Results We identified a series of DEGs that mediate schistosomiasis, the parasitic disease caused by Schistosoma japonicum infection, and hepatocarcinogenesis, and constructed a suitable prognostic model. We analyzed the mechanisms by which these DEGs regulate disease and present the differences in prognosis between the different genotypes. Finally, we verified our findings using molecular biology experiments. Conclusion Bioinformatics and molecular biology analyses confirmed a relationship between schistosomiasis and liver hepatocellular cancer. Furthermore, we validated the role of a potential oncoprotein factor that may be associated with infection and carcinogenesis. These findings enhance our understanding of Schistosoma japonicum infection's role in LIHC carcinogenesis.

Saskia F. Erttmann, Nelson O. Gekara

Summary: Bacterial membrane vesicles have emerged as gadgets allowing remote communication between the microbiota and distal host organs. Here we describe a protocol for enriching vesicles from serum and colon that could widely be adapted for other tissues. We detail pre-clearing of serum or colon fluids using 0.2-μm syringe filters and their concentration by centrifugal filter devices. We also describe vesicle isolation with qEV size exclusion columns and finally the concentration of isolated vesicle fractions for downstream analyses.For complete details on the use and execution of this protocol, please refer to Erttmann et al. (2022).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Li Tan, Meng-Mei Zhong, Qiong Liu et al.

ObjectivesThe purpose of this study was to evaluate available evidence on the association between the human oral microbiota and coronavirus disease 2019 (COVID-19) and summarize relevant data obtained during the pandemic.MethodsWe searched EMBASE, PubMed, and the Cochrane Library for human studies published up to October 2022. The main outcomes of the study were the differences in the diversity (α and β) and composition of the oral microbiota at the phylum and genus levels between patients with laboratory-confirmed SARS-CoV-2 infection (CPs) and healthy controls (HCs). We used the Human Protein Atlas (HPA), Gene Expression Profiling Interactive Analysis (GEPIA) database, Protein−protein interaction (PPI) network (STRING) and Gene enrichment analysis (Metascape) to evaluate the expression of dipeptidyl peptidase 4 (DPP4) (which is the cell receptor of SARS CoV-2) in oral tissues and evaluate its correlation with viral genes or changes in the oral microbiota.ResultsOut of 706 studies, a meta-analysis of 9 studies revealed a significantly lower alpha diversity (Shannon index) in CPs than in HCs (standardized mean difference (SMD): -0.53, 95% confidence intervals (95% CI): -0.97 to -0.09). Subgroup meta-analysis revealed a significantly lower alpha diversity (Shannon index) in older than younger individuals (SMD: -0.54, 95% CI: -0.86 to -0.23/SMD: -0.52, 95% CI: -1.18 to 0.14). At the genus level, the most significant changes were in Streptococcus and Neisseria, which had abundances that were significantly higher and lower in CPs than in HCs based on data obtained from six out of eleven and five out of eleven studies, respectively. DPP4 mRNA expression in the oral salivary gland was significantly lower in elderly individuals than in young individuals. Spearman correlation analysis showed that DPP4 expression was negatively correlated with the expression of viral genes. Gene enrichment analysis showed that DPP4-associated proteins were mainly enriched in biological processes, such as regulation of receptor-mediated endocytosis of viruses by host cells and bacterial invasion of epithelial cells.ConclusionThe oral microbial composition in COVID-19 patients was significantly different from that in healthy individuals, especially among elderly individuals. DPP4 may be related to viral infection and dysbiosis of the oral microbiome in elderly individuals.

Wiwik Swastiwi Anastasia, Febriyandi Febby YS, Angela Siringo Ringo Evy

The Siak District Government has long tried to advance the tourism sector by utilizing the rich heritage of the Malay cultural history of the Kingdom of Siak Sri Indrapura. These efforts have strengthened since the establishment of the vision of becoming the centre of Malay culture and the mission of Siak Regency to become a major tourism destination in Riau Province. This research aims to offer a development strategy for Malay historical and cultural heritage museums in Siak Regency to support the achievement of Siak's vision as a Malay cultural centre. This research uses a qualitative method to analyze the potential of Malay historical and cultural heritage in Siak for the development of the Balairung Sri Museum of Siak Regency. Data were obtained through observation, FGD, survey, literature study and documentation. The results of this study indicate that Siak Regency needs a museum that presents Malay historical and cultural heritage comprehensively, including history and 11 objects of cultural promotion, thus distinguishing it from the previous museum. The development of the museum needs to pay attention to various important aspects related to the presentation of collections, distinctiveness and the role of Balairung Sri in its time.

Haoyu Zhou, Haoyu Zhou, Ruohan Ren et al.

Comprehensive identification of possible target cells for viruses is crucial for understanding the pathological mechanism of virosis. The susceptibility of cells to viruses depends on many factors. Besides the existence of receptors at the cell surface, effective expression of viral genes is also pivotal for viral infection. The regulation of viral gene expression is a multilevel process including transcription, translational initiation and translational elongation. At the translational elongation level, the translational efficiency of viral mRNAs mainly depends on the match between their codon composition and cellular translational machinery (usually referred to as codon adaptation). Thus, codon adaptation for viral ORFs in different cell types may be related to their susceptibility to viruses. In this study, we selected the codon adaptation index (CAI) which is a common codon adaptation-based indicator for assessing the translational efficiency at the translational elongation level to evaluate the susceptibility to two-pandemic viruses (HIV-1 and SARS-CoV-2) of different human cell types. Compared with previous studies that evaluated the infectivity of viruses based on codon adaptation, the main advantage of our study is that our analysis is refined to the cell-type level. At first, we verified the positive correlation between CAI and translational efficiency and strengthened the rationality of our research method. Then we calculated CAI for ORFs of two viruses in various human cell types. We found that compared to high-expression endogenous genes, the CAIs of viral ORFs are relatively low. This phenomenon implied that two kinds of viruses have not been well adapted to translational regulatory machinery in human cells. Also, we indicated that presumptive susceptibility to viruses according to CAI is usually consistent with the results of experimental research. However, there are still some exceptions. Finally, we found that two viruses have different effects on cellular translational mechanisms. HIV-1 decouples CAI and translational efficiency of endogenous genes in host cells and SARS-CoV-2 exhibits increased CAI for its ORFs in infected cells. Our results implied that at least in cases of HIV-1 and SARS-CoV-2, CAI can be regarded as an auxiliary index to assess cells’ susceptibility to viruses but cannot be used as the only evidence to identify viral target cells.

Iva Ganeva, Koini Lim, Jerome Boulanger et al.

Summary: Lipid droplets (LDs) are intracellular organelles responsible for storing surplus energy as neutral lipids. Their size and number vary enormously. In white adipocytes, LDs can reach 100 μm in diameter, occupying >90% of the cell. Cidec, which is strictly required for the formation of large LDs, is concentrated at interfaces between adjacent LDs and facilitates directional flux of neutral lipids from the smaller to the larger LD. The mechanism of lipid transfer is unclear, in part because the architecture of interfaces between LDs remains elusive. Here we visualize interfaces between LDs by electron cryo-tomography and analyze the kinetics of lipid transfer by quantitative live fluorescence microscopy. We show that transfer occurs through closely apposed monolayers, is slowed down by increasing the distance between the monolayers, and follows exponential kinetics. Our data corroborate the notion that Cidec facilitates pressure-driven transfer of neutral lipids through two “leaky” monolayers between LDs.

Verónica Saludes, Antoni E. Bordoy, Elena Yela et al.

Abstract Hepatitis C virus (HCV) reinfection may hamper HCV elimination in prisons. We aimed to (i) determine the reinfection rate in people treated for HCV in Catalan prisons, (ii) measure reinfection in people entering prisons, and (iii) characterize the molecular epidemiology of HCV in prisons and people who inject drugs (PWID) in the community. Re-HCV was a prospective study in eight prisons (2019–2020) including two groups: (1) people cured with treatment in prison and followed-up every 6 months, and (2) people testing HCV-RNA positive at incarceration. Bio-behavioral data were collected. HCV isolates were sequenced and phylogenetically analyzed with those of PWID in the community. Reinfection follow-up after treatment was achieved in 97 individuals (103.05 person-years). Two reinfections were detected, resulting in an incidence ≤ 10/100 person-years. Among people entering prison, 2% (359/17,732) were viremic, of which 334 (93.0%) were included, and 44 (13.5%) presented with reinfection (84.7% being PWID). Frequently, HCV isolates in prisons and PWID in the community were phylogenetically related. Although HCV reinfection is low after treatment, it is common in people entering Catalan prisons. To maintain a low HCV prevalence in prisons, harm-reduction services and test-and-treat programs for PWID should be strengthened both inside and outside prisons.

Valiyaveetil Anjana, Kakkoprath Thekkeveetil Madavan

Introduction: The Emergency Departments (ED) are equipped with Point-of-Care (POC) Blood Gas Analysers (BGA) which deliver fast results on multiple parameters of arterial/venous blood. There is no consensus among ED physicians on the reliability of electrolyte results by POC Arterial Blood Gas (ABG) analysis compared to venous serum electrolyte from Central Laboratory Analyser/Auto-Analyser (CLA/AA). Aim: To compare the electrolyte (sodium and potassium) by POC arterial BGA (ABL800 Flex Radiometer) with venous electrolyte by CLA (Beckman Coulter AU 5800). Materials and Methods: This cross-sectional study was performed in the ED and Central Laboratory of the tertiary teaching hospital from 1st July 2018 to 31st July 2019. A total of 254 critically ill adult patients with various aetiologies, were enrolled in the study. The arterial and venous blood samples were collected for electrolyte measurement within a span of 15 minutes. The ABG samples, anticoagulated with liquid heparin, were processed in POC BGA. The venous samples collected in plain tubes were analysed in CLA. The results of sodium and potassium were compared by the mean, correlation coefficient, p-value, and Bland Altman Plots {95% Limit of Agreement (LOA)}. Results: Out of 254 paired samples (mean age: 63±15 years), 157 (61.8%) were males and 97 (38.2%) females. The mean sodium values were 131.9±7.7 mmol/L in ABG and 132.3±7.1 mmol/L in CLA (p-value <0.0001). The mean difference was 0.4 mmol/L. The mean potassium values were 3.9±1.0 mmol/L (ABG) and 4.2±0.9 mmol/L (CLA), {p-value <0.0001}. The mean difference was 0.3 mmol/L. These differences were within the accepted range specified by the United States Clinical Laboratory Improvement Amendments. There were statistically significant strong positive correlations between the measurements of the two instruments r=0.78 for sodium and r=0.76 for potassium. The 95% LOA for sodium and potassium on both the instruments were -10.03 to 9.09 mmol/L and -1.49 to 0.97 mmol/L respectively, both wide and unacceptable. Conclusion: The arterial sodium and potassium measurements by BGA were not reliable in decision making in ED when compared to the venous serum by CLA as the 95% LOA was wide and unacceptable. Hence, sodium and potassium values by BGA alone might not be used as criteria for management without confirmation from venous serum values by CLA

M. Vargas, K. Kashefi, E. L. Blunt-Harris et al.

N. Ashbolt, W. Grabow, M. Snozzi

G. Francis, C. Thomas, D. O'beirne

N. Fabregas, S. Ewig, António Torres et al.

C. Cháfer-Pericás, Á. Maquieira, R. Puchades