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Although there is a well-established connection between the gut microbiome and obesity, the specific mechanisms by which microbes regulate cell signalling, inflammation and adipocyte growth to influence disease severity in obese patients remain largely unclear. Subsequently, while obesity itself is a well-established risk factor for various cancers, the exact mechanisms by which it drives disease progression are not yet definitively known. In this study, we explored the link between obesity-associated microbiome alterations and cancer progression by analysing microbial abundance in tissue samples from obese and cancer patients, and we identified specific microbes correlated with body mass index (BMI) that are associated with key cancer-related pathways. Notably, BMI-associated microbial species such as Pseudomonas fluorescens and Lactobacillus sakei were linked with both pro-tumour and anti-tumour progression in cancer patients. Additionally, microbes found to be abundant in cancer and obese tissue, such as Pseudomonas baetica, were significantly associated with the upregulation of certain oncogenic signalling pathways. BMI-associated microbes were also correlated with chemokine signalling and TFR2/NFkB-related genes. Both of these have well-established roles in inflammatory activity and inflammasome expression, a critical step in obesity-related cancer progression. Therefore, these microbes were found to be associated with variations in disease prognosis and patient survival. This study provides new insights into how obesity-related microbiome dysbiosis may be associated with cancer development and aims to introduce novel potential avenues for precision medicine approaches in cancer treatment.

Fresh produce-associated outbreaks of the foodborne pathogen Escherichia coli O157 are responsible for a number of disease cases, hospitalizations and deaths. In many cases, the source of contamination can be linked to the growing media of the food, although pathogen detection is problematic in these complex soil ecosystems. In this study, direct quantitative real-time PCR without pre-enrichment was used to detect 310 copies of the Tir gene, using a primer sequence specific to E. coli O157, in horticultural compost purchased from a commercial supplier. The pathogen could not be cultured on selective media but was visualized using peptide nucleic acid fluorescence in situ hybridization and cell elongation viability assay, confirming the viability. Enumeration of elongated E. coli O157 determined that there were 205 live cells per gram of compost. The nonculturability and confirmation of viability of the pathogen indicates its viable but nonculturable (VBNC) status. The detection of VBNC foodborne pathogens in environmental samples challenges current understanding of the nature of foodborne pathogen contamination.

Cryptococcus albidus, an emerging pathogen, poses diagnostic and therapeutic challenges, especially in immunocompromised patients. We report a case of C. albidus meningitis in a young T-cell acute lymphoblastic leukaemia patient, initially suspected to have Herpes Simplex Virus (HSV) encephalitis. CSF analysis confirmed C. albidus, leading to antifungal therapy with liposomal amphotericin B and flucytosine, resulting in clinical improvement. Elevated procalcitonin levels suggest a potential role in fungal infections. This case underscores the importance of early identification and appropriate treatment in C. albidus meningitis.

Ticks are arthropod vectors that transmit pathogens important to human and animal health. The objective of this work was to identify Uukuvirus lihanense in the metatranscriptome of hard ticks. Between October 2022 and June 2023, ticks were collected from rural areas of the Colombian Caribbean area of the departments of Córdoba and Cesar. High-throughput sequencing (next-generation sequencing) was performed using MGI's DNBSEQ-G50RS. Bioinformatics analyses were performed in Galaxy, diamond and IQ-TREE2. A total of 766 ticks were collected; 87.33% (669/766) were Rhipicephalus microplus, 5.4% (42/766) Dermacentor nitens, 4.2% (32/766) Rhipicephalus sanguineus and 3.0% (23/766) Amblyomma dissimile. Complete and partial L and S segments of Uukuvirus lihanense (LITV) were detected in the metatranscriptome of A. dissimile, D. nitens and R. microplus. The LITV sequences found are phylogenetically related to those detected in R. sanguineus and A. variegatum from the French Antilles, in R. microplus from Trinidad and Tobago and R. microplus from Brazil. LITV was identified in D. nitens and R. microplus; the first report was in A. dissimile. Although LITV is not considered necessary in public health, the virus belongs to the Phenuiviridae family, which includes viruses of public health importance, such as Dabie banda-virus and Bandavirus heartlandense.

Introduction. Antimicrobial resistance (AMR) is a complicated public health challenge. This study aimed to obtain a baseline assessment of undergraduate health and science students' knowledge and attitudes of antibiotic use, resistance and stewardship across European countries and to evaluate education methods. Methods. A 43-item cross-sectional multilingual survey of healthcare practitioners and undergraduates studying dentistry, medicine, nursing, pharmacy and science subjects was conducted by Public Health England (now UK Health Security Agency) in 2018 across 30 EU/EEA countries. Of the 43 questions developed for healthcare workers, a subset of 33 questions directly relevant to students was available for student completion. Results. A total of 1,222 students from 27 EU/EEA countries participated in the survey, with 50% studying medicine (379/760). The mean score across seven knowledge questions was 6.04 out of 7 (sd, 1.14). Knowledge scores differed by the degree being studied and were higher among students in the later years of their degree programme. Knowledge was significantly higher (P<0.001) in those who had received training on prudent antibiotic use and infection management. Most students had not heard about AMR awareness campaigns, including European Antibiotic Awareness Day, and felt they did not have a key role in addressing AMR. Conclusion. Although students demonstrated good overall knowledge of antibiotic use and AMR, many lacked awareness of their role in tackling AMR. Designing more effective targeted educational interventions for these students, such as curriculum development and interprofessional education and training, could be beneficial to support appropriate antibiotic use and efforts to tackle AMR.

Understanding the basis of fungal pathogenesis requires knowledge of pathogen biology that is built through studies of gene function and regulation. The critical first step in nearly all these studies is genetic transformation: the generation of targeted DNA sequence modifications through the introduction of exogenous DNA into the cell. For research focused on gene regulation, or where small precise mutations are desired, the maintenance of genomic context (i.e. surrounding DNA sequences) is important, as the disruption of flanking DNA elements can alter gene expression and confound results. This often makes the inclusion of selectable markers that are physically linked to the sequence of interest unsuitable and complicates the transformation process. Here, we present a co-transformation strategy in the human pathogen Aspergillus fumigatus that can be used to make precise, marker-free gene edits at a locus of interest without disturbing flanking DNA sequences. By simultaneously introducing a marker-free, modified copy of the gene of interest and a plasmid that directs the integration of a selectable marker to a different locus, this approach takes advantage of the benefits of selection, with results similar to that of a truly markerless strategy.

The resurgence of syphilis has necessitated novel prophylactic strategies, such as the use of doxycycline post-exposure prophylaxis. However, the potential for increased doxycycline use to select for tetracycline resistance represents significant challenges in managing this sexually transmitted infection. This study aims to identify chromosomal mutations associated with tetracycline resistance in Spirochaetales to inform molecular surveillance tools. Whole-genome sequences (WGSs) from the Spirochaetales order, including 4,355 genomes, were analysed for the presence of mutations in 16S rRNA and non-synonymous mutations in the rpsC and rpsJ genes. The study utilized WGS from GenBank® and sequence data from the PubMLST Treponema pallidum isolate collection. Genetic resistance to tetracycline was detected using a combination of blastn searches and gene-gene analysis. A transition mutation TGA to TGG at positions 965-967 in the 16S rRNA gene was detected in 5.6% of Treponema spp. and 4.0% of Spirochaeta spp. genomes. The rpsJ gene exhibited a V57G aa substitution across a significant subset of Treponema spp. (n=14) and Spirochaeta spp. (n=1). Notably, the V57K substitution was present in Spirochaeta spp. (n=17) and Treponema spp. (n=15). The rpsC gene had the H178Q mutation and was found to be present in the Spirochaetales bacterium (n=4). The identification of putative mutations associated with tetracycline resistance in Spirochaetales provides a foundation for the development of rapid molecular tests. This study underscores the complexity of antibiotic resistance mechanisms and the critical importance of surveillance of genetic resistance determinants in the era of antibiotic prophylaxis for sexually transmitted infection management.

Background. Gingivitis is a reversible gingival inflammation that may progress to periodontitis if untreated. Diabetes mellitus alters the oral microbiota and weakens host defenses, increasing susceptibility to infection. Objectives. To investigate the prevalence and characterization of β-lactamase-producing bacteria isolated from gingival swabs of diabetic and non-diabetic patients with clinically confirmed gingivitis. Methods. Thirty-seven patients were enrolled (17 diabetics and 20 non-diabetics). Gingival swabs were cultured and identified by conventional microbiological and analytical profile index (API). Antimicrobial susceptibility was tested according to the Clinical and Laboratory Standards Institute 2023 guidelines. β-Lactamase activity was assessed using an iodometric colourimetric assay. Results. A total of 65 bacterial isolates were obtained from 37 gingivitis patients. Polymicrobial infections predominated in diabetics (82.4%) vs. non-diabetics (45.0%). Non-diabetics were mainly colonized by Streptococcus mutans (45.9%) and Staphylococcus aureus (40.5%), while diabetics harboured more Gram-negative species, particularly Pseudomonas aeruginosa (21.4%) and Enterobacteriaceae (46.4 % vs. 2.7 %). Overall, 67.7 % of isolates were β-lactamase producers. Resistance was highest to ampicillin (92.3%) and amoxicillin-clavulanate (84.6%), whereas ciprofloxacin (89.2%) and piperacillin-tazobactam (78.5%) retained the greatest activity. Conclusions. Diabetes is associated with increased microbial diversity, Gram-negative colonization, and a frequency of β-lactamase-producing bacteria in gingivitis. These findings highlight diabetes as a risk factor for resistant oral infections and underscore the need for antimicrobial stewardship, resistance surveillance and future molecular studies to clarify resistance mechanisms in high-risk groups.

Tuberculosis remains a major public health concern, particularly in countries where it is still endemic. Tuberculous bursitis and tenosynovitis are rare extrapulmonary manifestations, and their association with systemic autoimmune diseases such as scleroderma is seldom reported in the literature. We report the case of a 61-year-old patient with systemic scleroderma, complicated by diffuse interstitial lung disease and treated with mycophenolate mofetil, who developed tuberculous shoulder bursitis and wrist extensor tenosynovitis. The microbiological diagnosis was confirmed by ultrasound-guided aspiration of the subacromial-subdeltoid bursa, revealing the presence of Mycobacterium tuberculosis, detected by Ziehl-Neelsen staining, GeneXpert PCR and culture. Histological analysis of synovial tissue fragments demonstrated epithelioid granulomas with caseous necrosis, confirming the tuberculous origin.

Whole-genome sequencing (WGS) of microbial pathogens provides a high-resolution approach to antibiotic resistance profiling, lineage classification and outbreak surveillance. Identification of SNPs across the genome by alignment against a reference genome is the highest precision method of delineating strains. SNiPgenie is a bioinformatics pipeline designed to perform the entire variant calling process across many samples simultaneously. It was developed in the context of developing WGS tools to support the tracking of infection transmission of Mycobacterium bovis in livestock and wildlife, the principal causative agent of bovine tuberculosis in these populations. SNiPgenie may, however, be applied to other bacteria where evolutionary change can be tracked accurately using SNPs. The tool comes with both a command line and a user-friendly graphical interface. It can run on standard desktop or laptop computers. SNiPgenie and its documentation are available at https://github.com/dmnfarrell/snipgenie.