Journal of medical microbiology最新文献

Introduction. Adherence is a major virulence trait in Candida glabrata that, in many strains, depends on the EPA (epithelial adhesin) genes, which confer the ability to adhere to epithelial and endothelial cells of the host. The EPA genes are generally found at subtelomeric regions, which makes them subject to subtelomeric silencing. In C. glabrata, subtelomeric silencing depends on different protein complexes, such as silent information regulator and yKu complexes, and other proteins, such as Repressor/activator protein 1 (Rap1) and Abf1. At the EPA1 locus, which encodes the main adhesin Epa1, we previously found at least two cis-acting elements, the protosilencer Sil2126 and the negative element, that contribute to the propagation of silencing from the telomere to the subtelomeric region.Hypothesis. Abf1 binds to the regulatory regions of EPA1 and other regions at the telomere E-R, thereby negatively regulating EPA1 transcription.Aim. To determine whether Abf1 and Rap1 silencing proteins bind to previously identified cis-acting elements on the right telomere of chromosome E (E-R subtelomeric region), resulting in negative regulation of EPA1 transcription and infer Abf1 and Rap1 recognition sites in C. glabrata.Methodology. We used chromatin immunoprecipitation (ChIP) followed by quantitative PCR to determine the binding sites for Abf1 and Rap1 in the intergenic regions between EPA1 and EPA2 and HYR1 and EPA1, and mutants were used to determine the silencing level of the EPA1 promoter region.Results. We found that Abf1 predominantly binds to the EPA1 promoter region, leading to negative regulation of EPA1 expression. Furthermore, the mutant abf1-43, which lacks the last 43 amino acids at its C-terminal end and is defective for subtelomeric silencing, exhibits hyperadherence to epithelial cells in vitro compared to the parental strain, suggesting that EPA1 is derepressed. We also determined the motif-binding sequences for Abf1 and Rap1 in C. glabrata using data from the ChIP assays.Conclusion. Together these data indicate that Abf1 negatively regulates EPA1 expression, leading to decreased adhesion of C. glabrata to epithelial cells.

Introduction. Laboratory participation in external quality assessment (EQA) programmes including proficiency testing (PT) is a requirement of clinical laboratory conformance to ISO 15189:2022 Medical laboratories - Requirements for quality and competence. PT is one EQA method whereby laboratories are sent blinded samples for characterization by routine laboratory diagnostic methods. Importantly, PT enables a laboratory's performance to be evaluated in comparison to the standard reference methods and to the performance of other peer laboratories using similar diagnostic methods.Gap statement. The desired outcome of participating in PT is to help laboratories identify possible sources of error in each step of the total testing process and particularly in their test methods during the analytical phase.Aim. This cross-sectional study investigated the impact of using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) compared to conventional phenotypic biochemical testing on laboratory performance in a clinical bacteriology PT scheme.Methodology. During a 6-year period from 2017-2022, the Canadian Microbiology Proficiency Testing implemented 112 PT challenges comprising 22 different sample types and included 61 different bacterial species. This was translated into 5883 graded test events for analysis. Multiple logistic regression techniques were employed to explore the association between the test method employed and laboratory performance. The sample type and aerobic classification of challenge organisms were included as confounding variables.Results. Laboratories using MALDI-TOF MS performed significantly better in characterizing microorganisms than laboratories using phenotypic biochemical testing alone [odds ratio OR = 5.68, confidence interval (CI): 3.92, 8.22] regardless of the sample type and aerobic classification. Notably, our analysis identified a significant association between anaerobic organisms and laboratory performance (OR: 0.24, CI: 0.17-0.35), suggesting that culturing and identifying fastidious organisms remains a significant obstacle for many clinical microbiology laboratories.Conclusions. Although no method is infallible and its performance will depend on the validation and quality assurance procedures, this finding may help the management in the decision for implementing MALDI-TOF MS in the microbiology laboratory. This study highlights the important role PT providers play in the objective assessment of laboratory performance and how it can provide evidence for quality improvement.

Introduction. Tissue conditioners modified with antifungals are a potential alternative to denture stomatitis (DS) treatment.Gap Statement. Information on tissue response to this treatment before its clinical application is lacking.Aim. This study aimed to evaluate the tissue response of a tissue conditioner modified with antifungals in a rat model of DS.Methodology. After DS induction for 4 days under antibiotic therapy, Wistar rats had their intraoral devices (IODs) relined with the tissue conditioner Softone without (Soft) or with the MICs against Candida albicans of nystatin (Nys) or chlorhexidine (Chx) complexed or not with β-cyclodextrin (Nys:βCD and Chx:βCD). Three controls were included: healthy rats [negative control (Nc)], rats using a sterile IOD [sterile device (Sd)] and rats with DS that did not receive treatment (DS). After 4 days of treatment, the palatal mucosa under the IODs underwent histological processing for morphohistopathological and histometric analyses, morphology of collagen fibres (birefringence), immunohistochemistry for the expression of cell proliferation (proliferating cell nuclear antigen) and cytokine (IL-1β).Results. The Nc and Sd groups were similar (P>0.05), displaying epithelial and connective tissues without any discernible changes in the parameters assessed. The DS and Soft groups exhibited pronounced epithelial alterations, cell proliferation and expression of the cytokine IL-1β. In groups treated with drug incorporation (Nys, Chx, Nys:βCD and Chx:βCD), all samples demonstrated a reduction in tissue inflammation or complete tissue recovery, with an epithelium compatible with health. For the immunohistochemical parameters, the Chx, Nys:βCD and Chx:βCD groups were comparable with Nc (P>0.05).Conclusion. The proposed treatment could be promising for DS, as it led to the tissue recovery of the palatal mucosa. Nevertheless, much lower concentrations of complexed antifungals were required to achieve a similar or higher degree of tissue response compared with uncomplexed drugs in a modified tissue conditioner formulation.

Introduction. The human lower gastrointestinal tract microbiome is complex, dynamic and prone to disruption occurring during critical illness.Hypothesis or gap statement. The characteristics of lower gastrointestinal tract microbiome disruption and its association with clinical outcomes in patients with prolonged intensive care stay remain uncertain.Aim. To systematically review studies describing lower gastrointestinal tract molecular sequencing in patients with prolonged intensive care stay and explore associations with clinical outcomes.Methodology. This systematic review was prospectively registered and follows the Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines. OVID MEDLINE, EMBASE and The Cochrane Central Register of Controlled Trials databases were searched for eligible studies describing adults and/or children who underwent molecular sequencing of stool or rectal samples taken on or after 10 days of intensive care.Results. There were 13 studies with 177 patients included. The overall certainty of evidence was low, and no studies reported mortality. Reduced alpha diversity was observed in nine out of nine studies but was not associated with clinical outcomes in four out of four studies. Longitudinal alpha diversity decreased in five out of six studies, and inter-individual beta diversity increased in five out of five studies. After approximately one week of intensive care unit admission, rapid fluctuations in dominant taxa stabilized with trajectories of either recovery or deterioration in five studies. Pathogenic enrichment and commensal depletion were reported in all 13 studies and associated with clinical outcomes in two studies.Conclusion. Lower gastrointestinal tract microbiome disruption is highly prevalent and has consistent characteristics in patients with prolonged intensive care stay. Amongst reported metrics, only relative taxon abundance was associated with clinical outcomes.

Background. The interplay among human gut microbiota (GM) composition, osteoarthritis (OA) and OA-related medication use has been extensively discussed. However, to date, there has been no exploration of the genetic correlation among these three factors.Hypothesis/Gap. The potential causal link between GM and OA), and whether medications influence this relationship, remains unclear.Methods. We utilized bidirectional Mendelian randomization (MR) to explore the genetic associations between GM and OA. We leveraged genome-wide association study (GWAS) summary statistics from the MiBioGen and GO consortia, which provided data on GM taxa and OA cases, respectively. We identified outlier single-nucleotide polymorphisms using radial-MR and assessed causal associations using inverse variance weighting (IVW), weighted median and MR-Egger methods. Robust outcomes, consistent across these methods, were reported. We addressed potential biases through tests for horizontal pleiotropy and heterogeneity, supplemented by the Mendelian randomization pleiotropy residual sum and outlier method. Multivariable MR techniques were applied to adjust for OA medication use using UK Biobank data.Results. IVW estimates revealed a significant increase in hip OA risk for Gordonibacter and Eubacterium (brachy group) [odds ratio (OR): 1.09, 95% confidence interval (CI): 1.04-1.15, P=7.82E-04; OR: 1.09, 95% CI: 1.03-1.16, P=4.67E-03, respectively]. Conversely, Senegalimassilia, Slackia and Streptococcus exhibited protective effects (OR: 0.88, P=2.14E-02; OR: 0.88, P=3.33E-02; 0.91, P=4.29E-02). Sutterella increased the risk of knee OA (OR=1.15, 95% CI: 1.07-1.25, P=4.06E-04), while Haemophilus decreased it (OR=0.94, 95% CI: 0.88-1.00, P=4.26E-02). No significant heterogeneity or horizontal pleiotropy was observed in the results. Even after accounting for the potential confounding effect of medication, the results remained consistent. No reverse causation was detected.Conclusions. Our MR study reveals gut microbiome links to OA risk. Associations hold after adjusting for medication, indicating a potential causal connection between GM and OA.

Introduction. Efforts to understand the burden of antibiotic use in low- and middle-income countries such as Brazil are essential for developing strategies that are effective and appropriate in the context of endemic multidrug-resistant organisms.Aim. This study aims to determine antimicrobial-prescribing practices among patients hospitalized in intensive care units (ICUs) for adults in Brazil.Methodology. A 1-day point prevalence multicentre survey was conducted in 58 adult ICUs across the five regions of Brazil. The institutions were categorized according to their type and size. Detailed antimicrobial prescription data were prospectively provided to all patients hospitalized on the day of data collection.Results. A total of 620 patients were included in the study, of whom 63.9% were receiving at least one antimicrobial. Of these, 34.6% were treated for an infection, but only 39.9% of the cases were based on microbiological criteria. Empirical treatment was applied to 72.3% of the patients. Significant differences in antibiotic usage were observed across the different hospitals included in the study. Overall, treatment was most commonly directed towards pneumonia (51.8%) and bloodstream infections (29.6%). Glycopeptides (19.4%) and carbapenems (18.5%) were the most prescribed in teaching hospitals, while in non-teaching hospitals, carbapenems (17.8%) and broad-spectrum cephalosporins (16.8%) were most frequently used.Conclusion. Our study reveals alarming data on antibiotic use in adult ICUs in Brazil, with high frequencies of severe healthcare-associated infections acquired in these units, where patients are frequently subjected to empirical treatment.

Introduction. Peri-implantitis is a plaque-associated disease that leads to implant loss and arises from bacterial biofilms on the surface of the implant. Smoking is a risk factor for peri-implantitis and impedes treatment effectiveness. Additionally, aryl hydrocarbon receptor (AHR), IL-6, and IL-22 levels are related to peri-implantitis.Aim. We aimed to investigate the effects of nicotine on inflammatory response, bacterial growth and biofilm formation.Hypothesis/Gap Statement. We hypothesized that nicotine promoted pathogenic bacterial growth and biofilm formation, thereby aggravating inflammation.Methodology. The expression of AHR, IL-6 and IL-22 was measured in peri-implant sulci fluid using quantitative PCR and Western blot analyses. The cementum was incubated with bacterial suspension including Porphyromonas gingivalis, Streptococcus sanguinis and Fusobacterium nucleatum and treated with 100, 200, 250 and 300 µg ml^-1 nicotine, and then, the absorbance and number of colony-forming units were detected. Biofilm formation was evaluated using the tissue culture plate method and safranin O staining. Carbohydrates and proteins were measured by the phenol-sulfuric acid method and the bicinchoninic acid method, respectively.Results. The results indicated that smoking increased the levels of AHR, IL-6 and IL-22. Functionally, nicotine promoted the growth of P. gingivalis, S. sanguinis and F. nucleatum. Additionally, it promoted the biofilm formation of these bacteria and increased the contents of carbohydrates and proteins.Conclusion. Nicotine promoted bacterial growth and biofilm build-up, suggesting that smoking may aggravate the progression of peri-implantitis.

Introduction. Acinetobacter baumannii is a common cause of multidrug-resistant (MDR) nosocomial infections worldwide, including Vietnam.Hypothesis. Analysis of crucial genetic factors may link to epidemiological characteristics and antibiotic resistance of A. baumannii clinical strains in Vietnamese hospitals.Methodology. Fifty-one A. baumannii clinical strains from six different tertiary hospitals in Vietnam were analysed using whole genome sequencing (WGS), between 2017 and 2019.Results. Eleven sequence types (STs) were identified, including four STs reported for the first time in Vietnam based on the PubMLST database and three new STs not previously documented. ST1336, ST1260 and ST575 were found exclusively in Vietnam. These STs were widely distributed in all hospitals in Vietnam, with ST2 and ST571 being the most dominant. Resistant rates to eight antibiotics, belonging to four antibiotic groups, were very high (72.5-94.1 %) with high MIC values, while resistance to colistin was 29.4%. Fifty-one isolates were identified as MDR, with 100% (51/51) isolates carrying antimicrobial-resistant (AMR) genes, and 52 antibiotic-resistant genes were detected among these strains, including β-lactam (22 genes), chloramphenicol (5 genes), lincosamide (2 genes), aminoglycoside (11 genes), rifampicin (1 gene), quinolone (2 genes), sulfonamide and trimethoprim (4 genes) and tetracycline (5 genes) resistance. The most commonly found mobile structures carried partial or complete transposons: ISaba24/ISEc29/ISEc35 contains a series of antibiotic-resistant genes.Conclusion. The WGS results of the 51 strains of A. baumannii provided important information regarding the distribution of STs and associated antibiotic-resistant genes among A. baumannii strains.

We evaluated the Xpert MTB/Rif Ultra assay performance for Mycobacterium tuberculosis (MTB) detection in formalin-fixed paraffin-embedded tissue (FFPET) compared to mycobacterial culture or laboratory-developed MTB PCR test (LDT). FFPET samples with histological features suggestive of tuberculosis from 2018 to 2023 were selected. Five hundred microlitres of tissue lysis buffer was added to FFPET scrolls and incubated at 75 °C for 5 min. After adding 50 µl of proteinase K and overnight incubation at 56 °C, sample aliquots were processed as per the manufacturer's instructions. MTB culture or LDT assay results were used as a reference for sensitivity and specificity calculations. Of 51 eligible FFPET, 32 were positive for MTB either by culture or LDT PCR on FFPET. Xpert MTB/Rif Ultra detected MTB in 23/32 positive specimens [71.9%, 95% confidence interval (CI) 54.6-84.4%]. Of nine discordant specimens, seven were MTB positive by culture and two were identified by LDT MTB PCR only, as no specimen was submitted for MTB culture. Of 19 negative samples, 100% specificity (95% CI 83.2-100.0%) was attained via Xpert MTB/Rif Ultra. Implementation of Xpert MTB/Rif Ultra on FFPET within clinical laboratories is promising, given its improved turnaround time compared to MTB culture and ability to detect MTB in cases where no tissue is available for culture.

Introduction. Reports of β-lactamase-producing Haemophilus influenzae are increasing worldwide.Aim. This study aimed to elucidate the molecular characteristics and evolution of β-lactamase-producing H. influenzae.Methodology. A total of 159 clinical isolates were characterized using multi-locus sequence typing. Antimicrobial resistance genes and integrative and conjugative element (ICE) types were identified through PCR and DNA sequencing. The genetic structure of ICE was further investigated using whole-genome sequencing.Results. Out of 159 clinical isolates, 20.8% (n=33) were β-lactamase producers. Thirteen sequence types (STs) were identified. ST 103, 155, 165 and 388 have been identified in previous studies, suggesting that strains with these STs tend to acquire the β-lactamase gene bla _TEM-1. Among β-lactamase producers, 66.7% (n=22) of bla _TEM-1 were located on ICE. The ICEs could be classified into two groups based on their sequence (types I and II). Among these strains, 2017-Y3 harboured a macrolide resistance gene, mef (A/E), in ICE. A comparative analysis of the ICE region of this strain and those from other countries suggested that each isolate was derived from ICE type I or II. These regions, including mef (A/E), were similar to those of Tn6822, which is commonly found in Streptococcus.Conclusions. This study revealed several STs associated with the acquisition of β-lactamase genes on ICEs. Additionally, ICE evolution involved the acquisition of exogenous genes. The accumulation of resistance genes in ICE raises concerns regarding the emergence of multidrug-resistant H. influenzae.