Journal of medical microbiology最新文献

Introduction. Pleural empyema is common but microbiological diagnosis is challenging, often leading to prolonged empiric broad-spectrum antimicrobial use.Hypothesis. 16S rRNA PCR on operative pleural tissue will increase diagnostic yield and improve antibiotic stewardship in patients with surgically managed pleural empyema.Aim. The objective was to characterize the clinical and microbiological characteristics of surgically managed pleural empyema, assess the diagnostic yield of 16S rRNA PCR and determine its impact on antimicrobial use.Methodology. This retrospective study identified patients with pleural empyema at a tertiary thoracic referral unit in North London, UK, between March 2019 and March 2023. Demographic, clinical and microbiological characteristics were collected.Results. One hundred eighty-three patients underwent surgery for pleural empyema at University College Hospital at Westmoreland Street over a 4-year period. Most empyemas were community-acquired, and the main surgical modality was minimally invasive video-assisted thoracoscopic surgery (151/183, 82.5%). Thirty-day all-cause post-operative mortality was 0.6%. Microbial aetiology was ascertained in 47%, with Streptococcus anginosus group, Streptococcus pneumoniae and anaerobes most frequently identified. Operative pleural tissue 16S rRNA PCR had a high diagnostic yield compared to conventional culture alone (68.2% vs. 26.4%). Post-operatively, antibiotics were prescribed for a median of 14 days (interquartile range 10-18), the majority broad spectrum (169/181, 93.4%). 16S PCR impacted antimicrobial prescribing in one-tenth of cases when used (4/32, 12.5%); however, turnaround times limited its impact.Conclusion. Molecular diagnostics improve bacterial detection and antibiotic stewardship in pleural empyema. Streamlining molecular diagnostics pathways or developing pleural-specific multiplex PCR panels could further enhance management.

Introduction. Carbapenem-resistant Acinetobacter baumannii (CRAB) represents a critical healthcare threat with limited treatment options, particularly challenging in Southeast Asia where resistance rates exceed 65%.Hypothesis/Gap Statement. Current synergy testing methods are labour-intensive and poorly standardized, limiting their clinical application. We hypothesize that synergistic interactions between antibiotics follow predictable mathematical patterns derivable from separate MIC determinations for each antibiotic.Aim. To evaluate the efficacy of colistin-meropenem-ampicillin/sulbactam combinations at standard dosages and develop a predictive mathematical model for synergistic interactions against CRAB.Methodology. A cross-sectional study was conducted using 61 CRAB clinical isolates from a Vietnamese tertiary hospital. MICs were determined using broth microdilution, and synergy was assessed via checkerboard assays. Mathematical models were developed to predict fractional inhibitory concentration (FIC) values from separate MIC determinations for each antibiotic.Results. All isolates demonstrated high-level meropenem resistance (MICs 32-≥128 µg ml^-1) and ampicillin/sulbactam resistance (98.4% with MICs≥64/32 µg ml^-1) but remained intermediate to colistin (MICs 0.0625-0.25 µg ml^-1). The triple combination achieved 100% synergy at standard ampicillin/sulbactam doses (8/4 µg ml^-1). Our log-transformed power model accurately predicted synergistic interactions (R²=0.928) using the equation log(FIC) = -2.52+(-1.02) × 1/√Mero+0.43×1/√Col+4.32×1/√As.Conclusion. The triple combination achieves universal synergy at standard dosages, potentially reducing toxicity risks. Our mathematical model enables rapid prediction of effective combinations from routine susceptibility tests, offering a transformative approach to optimizing therapy against multidrug-resistant pathogens.

Introduction. The abnormal proliferation of Cutibacterium acnes, a human skin commensal bacterium, aggravates acne. Prompt and aggressive treatment of acne in its initial stages is essential because of the increased psychological distress experienced by patients. Over-the-counter medications containing disinfectants are sometimes used to treat acne because they are widely available, exhibit broad-spectrum activity and have a likelihood of causing resistance.Gap statement. Limited information is available regarding the bactericidal effects of disinfectants against C. acnes.Aim. In the present study, we comprehensively evaluated the efficacy of various disinfectants.Methodology. C. acnes ATCC6919 and eight clinical isolates with different genotypes obtained from patients with acne were used. Benzethonium, chlorhexidine, resorcinol, homosulfamine, isopropyl methylphenol and olanexidine were used as disinfectants. The bactericidal activity of these disinfectants against C. acnes was assessed using a time-kill kinetic assay. Three independent experiments were conducted to ensure reproducibility of the results.Results. Benzethonium, chlorhexidine, isopropyl methylphenol and olanexidine exhibited high efficacy. However, under in vitro acne conditions, with the addition of artificial sebum, the bactericidal efficacy of the disinfectants was significantly reduced. However, olanexidine retained bactericidal activity at concentrations as low as 0.2%, comparable with that at 1.5%.Conclusion. This study showed that the disinfectants benzethonium, isopropyl methylphenol, chlorhexidine and olanexidine have high bactericidal activity against C. acnes. In particular, olanexidine demonstrated a strong bactericidal effect even under in vitro acne conditions. Further in vivo validation is required to determine whether olanexidine could be a new treatment option for managing acne.

Introduction. Bloodstream infections (BSIs) caused by multidrug-resistant Gram-negative bacteria (MDR-GNB) are a major cause of mortality, with limited treatment options.Gap/Hypothesis. Despite the global rise of MDR-GNB, prospective data on their clinical impact in North Africa remain scarce, restricting evidence-based guidance for empiric therapy.Aim. To assess the prevalence, resistance patterns and clinical outcomes of MDR-GNB BSIs in Libya, and to identify predictors of 30-day mortality.Methodology. A prospective cohort study was conducted in two Libyan hospitals between November 2022 and November 2024. Adult patients with positive blood cultures were enrolled. Isolates were identified using standard microbiological methods, and antimicrobial susceptibility testing was interpreted according to Clinical and Laboratory Standards Institute (CLSI) 2023 guidelines. Multivariable logistic regression was applied to identify independent predictors of 30-day mortality.Results. Among 673 BSI episodes, 37.4% were multidrug resistance (MDR). Escherichia coli (32.0%) and Klebsiella pneumoniae (25.9%) predominated, while carbapenem resistance was highest in Acinetobacter baumannii (42.4%). Overall, 30-day mortality was 23.8%, and was significantly higher in MDR infections (32.1% vs 18.8%; P<0.001). Independent predictors of mortality were MDR infection [adjusted odds ratio (aOR), 1.9], Intensive care Unit (ICU) admission (aOR, 2.6), Charlson Comorbidity Index ≥3 (aOR, 1.7) and inappropriate empiric therapy (aOR, 2.3).Conclusion. MDR-GNB BSIs are highly prevalent in Libya and substantially worsen outcomes. These findings highlight the urgent need for improved empiric therapy, antimicrobial stewardship and infection control programmes.

Introduction. Klebsiella pneumoniae, Klebsiella quasipneumoniae and Klebsiella variicola are closely related species (collectively referred to as 'PQV') but exhibit distinct clinical presentations and epidemiological profiles. These distinctions are important for proper diagnosis and treatment of infections and other Klebsiella-related diseases. The ability to differentiate between these species is becoming more important as we better understand their unique roles in disease.Hypothesis/Gap statement. Despite the importance of accurate taxonomic classifications, both traditional and modern laboratory techniques fail to accurately delineate between the PQV species, which can lead to treatment failures. Conversely, taxonomy via whole-genome sequencing is highly accurate but is both costly and resource-intensive. Thus, there is a lack of a widely adopted method that balances both cost-effectiveness and accuracy for differentiating PQV species.Aim. To assess the taxonomic accuracy of existing genome databases and classification tools for PQV species and to develop a rapid, cost-effective method for accurate species differentiation.Methodology. To address these challenges, we extracted 78 representative PQV genomes from the Integrated Microbial Genomes and Microbiomes database. We used multiple comparative genomic comparison techniques, phylogenetic tree constructions and pangenome profiling to accurately phylogenetically and subsequently taxonomically classify the genomes. After establishing accurate taxonomic classifications, we identified species-specific marker genes (SSMGs) represented by KEGG Orthologies (KOs).Results. The Genome Taxonomy Database (GTDB) classifications were consistent with our comparative genomic benchmarks, while the National Center for Biotechnology Informationdatabase originally contained six misclassified genomes. The GTDB-Tk tool also showed reliability for systematic classification of the genomes. Our KO-based screening identified 22 candidate SSMGs. Four markers (K05306, K07507, K13795 and K09955) exhibited significant specificity. ATP-binding proteins showed slightly higher maximum percentage identity values due to conserved domains but were still valuable within multi-locus SSMG panels.Conclusion. Our findings establish the GTDB as the gold standard taxonomic reference for PQV classification when complete genomes are available. Additionally, we developed a practical panel of genetic markers that enables rapid, cost-effective and accurate species differentiation. These SSMGs represent practical tools that can be implemented in diagnostic laboratories for both clinical specimens and environmental surveillance, addressing a critical gap in clinical microbiology.

Antimicrobial resistance (AMR) is a global threat to health, food security and economies across the world. To strengthen UK surveillance efforts, the Microbiology Society and the Pathogen Surveillance in Agriculture, Food and Environment Programme (PATH-SAFE) convened a One Health AMR Surveillance Roundtable in December 2024, bringing together 16 government agencies from the human, animal, plant, environmental and food sectors across the UK central government and devolved nations. The workshop identified key questions for a UK-focused national One Health AMR surveillance system and explored opportunities and challenges for implementation. Key challenges include fragmented data with limited sharing and underutilized microbiological samples. Participants called for greater cross-sector collaboration, a shared AMR vocabulary, sustained investment and the development of a national AMR data catalogue. Coordinated One Health surveillance, backed by political commitment, is essential to tackle AMR effectively.

Introduction. Gastrointestinal infections remain a leading cause of morbidity and mortality within the UK.Hypothesis. The Luminex^® NxTAG^® Gastrointestinal Pathogen Panel (NxTAG GPP) multiplex reverse transcriptase PCR assay performs equivalently to standard-of-care diagnostic approaches.Aim. To compare the analytical performance of the NxTAG GPP assay versus routine diagnostic testing methods in a district general hospital setting.Methodology. Gastrointestinal pathogens in 159 faecal specimens from hospital inpatients and outpatient clinics were comparatively analysed using the NxTAG GPP assay versus traditional culture, enzyme immunoassay and molecular methods.Results. Positive results were detected in 45 out of 159 specimens (28.3%) by NxTAG GPP, which was a higher positivity rate when compared with traditional diagnostic methods which detected 31 out of 159 (19.5%) positive infections (P=0.087 by Fisher's exact test). Infections were caused by a single organism in 40 out of 45 (88.9%) cases, but 5 out of 45 (11.1%) infections detected were due to coinfections. No coinfections were detected by traditional methods. Campylobacter Group was the most common enteropathogen detected with 15 out of 52 (28.9%) infections. Viruses caused 26.9% of infections, including 15.4% being norovirus. Overall sensitivity, specificity and accuracy for the NxTAG GPP assay were 97.6%, 99.7% and 99.5%, respectively, for enteropathogenic bacteria and viruses detected during this study. No parasites were detected during this study and were not included in comparisons.Conclusions. The NxTAG GPP assay demonstrated high sensitivity and specificity for identifying gastrointestinal pathogens, with comparable accuracy as more resource-intensive and time-consuming standard diagnostic approaches. The NxTAG GPP has the potential to enhance patient diagnosis, reduce turnaround time and improve clinical outcomes compared to routine diagnostic methods.

Introduction. Peri-implantitis is a prevalent and challenging complication in implant dentistry, primarily induced by biofilm-associated pathogens. Among these, Porphyromonas gingivalis and Filifactor alocis have emerged as key contributors, with evidence suggesting their potential synergistic role in exacerbating peri-implant inflammation and tissue destruction.Hypothesis/Gap Statement. While P. gingivalis is a well-characterized periopathogen, the specific role of F. alocis, alone or in combination with P. gingivalis, in peri-implantitis remains underexplored. This study addresses the gap in quantifying their presence in diseased versus healthy peri-implant sites.Aim. To assess the prevalence and microbial load of P. gingivalis and F. alocis in peri-implantitis and healthy peri-implant sites using quantitative real-time PCR (qPCR) and to investigate their correlation with clinical parameters.Methodology. This cross-sectional study included 110 participants: 52 diagnosed with peri-implantitis and 58 with healthy peri-implant tissues. Clinical examination recorded probing depth (PD), clinical attachment level (CAL) and bleeding on probing (BOP). Submucosal biofilm samples were collected and analysed using species-specific qPCR. Statistical analysis employed the Mann-Whitney U test for intergroup comparisons and Spearman's rank correlation for associations between microbial levels and clinical indices.Results. Both P. gingivalis and F. alocis were significantly elevated in peri-implantitis sites compared to healthy controls. Mean P. gingivalis levels were 4.80×10⁶ ± 4.78×10⁶ copies µl^-1 in peri-implantitis and 2.09×10³ ± 1.26×10³ copies µl^-1 in healthy sites (P<0.001). F. alocis levels averaged 4.58×10⁵ ± 3.40×10⁵ copies µl^-1 in peri-implantitis and 2.45×10³ ± 1.64×10³ copies µl^-1 in healthy sites (P<0.001). P. gingivalis showed strong positive correlations with PD, CAL and BOP, while F. alocis correlated moderately with PD and CAL but not significantly with BOP.Conclusion. The significant elevation of P. gingivalis and F. alocis in peri-implantitis supports their potential synergistic involvement in disease pathogenesis. These findings underscore the need for antimicrobial strategies that target both organisms and disrupt their cooperative biofilm behaviour. Further research should clarify their pathogenic interplay and inform the development of precise therapeutic interventions.

Introduction. The cagA and vacA genes encode the CagA and VacA proteins, which are the two main toxins of Helicobacter pylori. Regardless of whether the illness is benign or malignant, the majority of Asian H. pylori strains are cagA (+) and vacA s1 (vacA signal region 1 allele); hence, these genotypes cannot account for the severity of gastroduodenal disease.Gap statement. The babA2 gene encodes the important adhesin BabA of H. pylori, which is crucial for persistent colonization and facilitates the translocation of CagA into host gastric epithelial cells. The synergic interaction of toxins, including CagA, VacA and BabA, could significantly contribute to the pathogenesis of H. pylori. The investigation of cagA, vacA and babA2 genes in clinical H. pylori isolates in Asian nations, particularly Vietnam, is insufficient.Aim. To investigate the cagA, vacA and babA2 genotypes to further understand their synergistic interaction in the development of gastroduodenal disease in Vietnamese populations.Methodology. A cross-sectional study was conducted on 169 H. pylori strains isolated from patients with gastroduodenal disease. The PCR assays were performed to determine the cagA, vacA and babA2 genotypes on DNA extracted from cultured H. pylori isolates.Results. The research showed that the percentage of the cagA(+), babA2(+), vacA s1m1 and vacA s1m2 was 87.6%, 73.4%, 52.1% and 44.4%, respectively. The frequencies of cagA(+)/babA2(+)/vacAs1m1 and cagA(+)/babA2(+)/vacAs1m2 combinations were 44.4% and 28.4 %, respectively. The cagA(+)/babA2(+)/vacAs1m2 combination was associated with peptic ulcer disease [adjusted odds ratio (aOR)=5.53, 95 % confidence interval (CI) 1.09-28.16, P=0.039] in male patients and chronic gastritis with precancerous lesions (aOR=5.31, 95 % CI 1.23-22.89, P=0.025) in female patients.Conclusion. The cagA(+)/babA2(+)/vacAs1m1 and cagA(+)/babA2(+)/vacAs1m2 combinations were found to be quite prevalent among Vietnamese H. pylori strains. The synergistic effect of cagA(+), babA2(+) and vacA s1m2 in increasing the odds of both peptic ulcer disease and gastric precancerous lesions has been observed.

Introduction. In antibiotic chemotherapy, an antimicrobial agent is selected based on MIC, which is determined by a test method using the principle of the broth microdilution. However, it does not provide a viable count in the mutant selection window. In this study, we used turbidimetry and visual judgement to examine the validity of the selection of various antibiotics to treat Pseudomonas aeruginosa based on MIC determination after 24 h of incubation.Methods. The antibiotics used in this study were piperacillin (PIPC), imipenem (IPM), meropenem, ciprofloxacin and amikacin (AMK). The strains used were 30 P. aeruginosa strains clinically isolated that were susceptible to all the antibiotics used, and the standard PAO1 strain. The viable count was measured after exposure for 3 and 24 h to therapeutic concentrations of various antibiotics, at which time turbidity was examined visually or by transmittance. In addition, the MPCs of IPM and PIPC were measured.Results. In this study, 10²-10⁸ c.f.u. ml^-1 of P. aeruginosa survived exposure to PIPC, IPM and AMK at concentrations 2.5-80 times the MIC despite high drug concentrations. No turbidity was observed in the culture medium. Furthermore, both IPM and PIPC showed high mutant prevention concentration (MPC), with 64.5% of strains in IPM and 10% of strains in PIPC showing intermediate or resistance after 24 h.Conclusions. Choosing an appropriate antibiotic based on exceeding the MIC may be insufficient. While the PK/PD theory focuses on MIC, measuring MPC alongside MIC is urgent in clinical practice for optimal antibiotic selection.