European Journal of Clinical Microbiology & Infectious Diseases最新文献

Purpose: People living with HIV (PWH) experience a disproportionate burden of sexually transmitted infections (STIs), leading to more severe health outcomes and increasing the risk of HIV transmission. The presence of untreated STIs can accelerate HIV disease progression, while HIV infection can complicate STI diagnosis and treatment. Despite this interconnectedness, comprehensive data on the global prevalence of specific STIs among PWH remain limited. This systematic review aims to synthesize existing data to provide a more accurate picture of the prevalence of co-infection with Treponema pallidum, Neisseria gonorrhoeae, Chlamydia trachomatis or Trichomonas vaginalis in PWH, while also identifying critical knowledge gaps and informing future research priorities.

Methods: We searched databases for eligible studies reporting the prevalence of Treponema pallidum, Neisseria gonorrhoeae, Chlamydia trachomatis, or Trichomonas vaginalis among PWH, published from January 1, 2000, to February 1, 2023. From 22,290 identified articles, 127 independent studies meeting the inclusion criteria were included in this meta-analysis.

Results: The overall global co-infection prevalence of Treponema pallidum, Neisseria gonorrhoeae, Chlamydia trachomatis, and Trichomonas vaginalis in PWH, was 4.8% (95%CI: 4.7-5.0%), 0.8% (95%CI: 0.6-0.9%), 2.5% (95%CI: 2.2-2.7%), and 3.0% (95%CI: 2.7-3.3%), respectively. The global prevalence of these four STIs in PWH is high, especially in Africa and Southeast Asia and in MSM and TGW populations. Based on the subgroup analyses, we further found that there was a high prevalence of Treponema pallidum and Chlamydia trachomatis in Southeast Asia and a high infection of Trichomonas vaginalis in the whole of Africa. Treponema pallidum infection was more common in males than females, and Chlamydia trachomatis and Trichomonas vaginalis infections were more common in females than males. Besides, high infection rates of Treponema pallidum, Neisseria gonorrhoeae, and Chlamydia trachomatis were detected in men who have sex with men (MSM) + transgender women (TGW), while high infection rates of Trichomonas vaginalis were found in sex workers and pregnant women.

Conclusion: The study confirmed high prevalence of four sexually transmitted pathogens in PWH, noting regional, gender, and subpopulation-specific differences. It offered insights for targeted interventions and healthcare strategies. The research underscored the necessity for enhanced data collection and expanded screening/treatment for vulnerable populations and regions.

Rapid identification of pathogens in acute meningitis is critical for timely treatment. However, traditional methods often face limitations in differentiating closely related species such as Streptococcus pneumoniae and Streptococcus pseudopneumoniae. We report a case of community-acquired meningitis caused by S. pseudopneumoniae secondary to a cerebrospinal fluid fistula, highlighting the microbiological diagnostic challenges.

Enteroviruses (EVs) are a large group of genotypes that cause a variety of pathologies, some of them very serious. This study analyzed the last 10 years (2014-2023) of EVs diagnosis and classification. In 166,674 samples collected, EVs were found in 9,535 (5.7%) by rt-RT-PCR, and 332 (3.5%) were classified by Sanger methods. Symptoms were analyzed in 7623 cases. EVs were found in 5718/63,829 (8.9%) before, 1384/42,373 (3.3%) during and 2433/60,472 (4%) after the Covid pandemic (p < 0.0001), and in 7249/69,700 (10.4%) children under 6 years and in 2286/96,974 (2.35%) in oldest (p < 0.0001). The positive rate of EVs was high but decreased during the Covid period. In the youngest children EVs-A (associated with exantematohous disorders as well as respiratory manifestations and febrile syndromes) was most common, while EVs-B (frequent in neurological symptoms) was most common in children aged 6-15 years and EVs-D (associated to respiratory manifestations) in adults.

Background and purpose: Clostridioides difficile infection (CDI) is a leading cause of healthcare-associated infections worldwide, with hypervirulent strains linked to severe disease and higher mortality. This study aims to analyze the epidemiology of CDI at a tertiary-care hospital in Italy and compare clinical outcomes between patients infected with hypervirulent and non-hypervirulent strains.

Methods: A retrospective comparative study was conducted on patients diagnosed with CDI at ASST Spedali Civili di Brescia, Italy, from January 2015 to June 2023. Hypervirulent strains were identified using the GeneXpert assay as positive for cytotoxin gene (tcdB), binary toxin genes (tcdA and tcdB) and a single nucleotide deletion at position 117 in the tcdC gene and compared to a randomized matched control group with non-hypervirulent CDI. Clinical data were collected and analyzed, with multivariate logistic regression employed to identify risk factors for hypervirulent CDI.

Results: Of 1,059 positive C. difficile specimens, a statistically significant trend between January 2015 to June 2023 was found in the increasing incidence of CDI cases per 1,000 hospital admissions and 10,000 bed-days. Notably, a remarkable increase of hypervirulent strains was recorded in 2021 and 2022 when compared to previous years. A total of 130 patients were analyzed: 62 (47.7%) with hypervirulent CDI and 68 (52.3%) controls. Hypervirulent CDI was associated with higher 30-day mortality (18% vs. 5.8%, p = 0.03). Multivariate analysis showed that hypervirulent CDI significantly increased 30-day mortality risk (OR = 9.915, CI = 2.37-61.05, p = 0.005) and that prior antibiotic therapy was a significant risk factor (OR = 5.49, CI = 1.19-39.96, p = 0.047).

Discussion: Our epidemiological data, while suggesting a potential resurgence in CDI transmission during COVID-19 pandemic, are derived from a single-center experience with limited generalizability to the broader population. Nonetheless, they highlight the need for strengthened antimicrobial stewardship and national surveillance systems to effectively monitor and manage these strains.

Purpose: To review the risk factors, clinical characteristics, and microbiological profiles of microbial keratitis cases, as well as the antibiotic resistance patterns of bacterial isolates in the region of Galicia, Spain.

Methods: This retrospective case series includes patients with culture-positive non-viral microbial keratitis between 2010 and 2020, treated at nine hospitals within the region of Galicia, North-West Spain. The standard protocol involved Gram staining for bacterial infections and calcofluor white staining for fungal or amoebal infections, identification by MALDI-TOF mass spectrometry or microscopy, and antimicrobial susceptibility interpreted according to EUCAST or CLSI guidelines.

Results: 780 microorganisms were isolated from corneal scraping cultures from 654 patients. 36.9% resided in urban areas, and 63.1% in rural areas. Isolates were more frequently collected in spring and summer. The median time to corneal scraping was 0 days (IQR 0-2), and the median time to epithelialisation was 24.0 days (IQR 11-49). Most cases had a single corneal infiltrate (509 cases; 77.8%) and affected the stroma (432; 66.1%), with small (< 3 mm) epithelial defects (347; 53.1%). Significant risk factors included contact lens wear (24.2%) and exposure to organic matter (4.9%). The most frequent bacteria was CoNS (207; 26.4). Fungi (77; 9.9%) and amoebae (6; 0.8%) were less common. Steroid use and eyelid disease increased resistance in CoNS species. An increase in the percentage of MRSA (compared to MSSA) was detected over the study period (p = 0.045).

Conclusions: In Galicia (Spain), microbial keratitis was mostly attributed to CoNS. An increase in MRSA keratitis was observed. Analysis of risk factors may help in suspecting antibiotic resistance. Surveillance programs for detecting the development of antimicrobial resistance are necessary to provide treatment guidelines based on local data.

Purpose: Mycobacterial liquid culturing typically requires six weeks or longer, primarily because of the slow growth rate of Mycobacterium tuberculosis. This study aimed to evaluate the potential of shortening the duration of mycobacterial liquid culturing in healthcare settings with high prevalence rates of non-tuberculous mycobacteria.

Methods: We retrospectively analyzed the relationship between mycobacterial species and time to positive testing of liquid cultures from sputum samples using the Mycobacteria Growth Indicator Tube system over a 3.5-year period beginning in July 2020 at a university hospital in Japan.

Results: We analyzed 15,147 sputum culture samples and found a 1.1% positivity rate for Mycobacterium tuberculosis complex, while the rates for Mycobacterium avium complex and Mycobacterium abscessus were 17.6% and 2.1%, respectively. The median time to positivity was 17 days for Mycobacterium tuberculosis complex, 9 days for Mycobacterium avium complex, and 4 days for Mycobacterium abscessus. Comparing a 4-week culture period with an eight-week period, the positivity rates for Mycobacterium avium complex and Mycobacterium abscessus were 97.0% and 99.4%, respectively.

Conclusion: In settings with a high incidence of non-tuberculous mycobacteria, the basic liquid culturing period can be safely shortened to 4 weeks without significantly compromising detection sensitivity, except for the samples that are highly suspected to contain tuberculosis, extremely slow-growing mycobacteria, smear-positive, or nucleic acid amplification testing positive.

Purpose: We investigated how the microscopic quality of endotracheal aspirates (ETA) impacts the performance of the Filmarray® pneumonia plus panel (FA-PP) in patients undergoing mechanical ventilation (IMV) with suspicion of lower respiratory tract bacterial infection (LRTBI).

Methods: The quality of ETA was categorized according to the number of leukocytes and buccal squamous epithelial (BSE)/field (100x magnification). G5 (< 10 BSE cells and > 25 leukocytes/field) and G4 (10-25 BSE cells and > 25 leukocytes/field) ETA were tested in parallel by the FA-PP and conventional semiquantitative culture.

Results: In total, 153 ETA were graded as G5 (from 115 patients) and 56 as G4 (from 48 patients). Focusing on "conventional" bacterial species, a trend towards more positive results (P = 0.16), and co-detections (P = 0.18) was returned by G5 ETA. Although more targets were detected on G5 ETA (P = 0.005), the spectra of bacteria detected was comparable across G5 and G4 specimens. A trend towards higher bacterial burdens as quantitated by the FA-PP, and irrespective of the target, was observed in G5 (median, 10⁶ genome copies/ml) vs. G4 ETA (median, 10⁵ genome copies/ml). The degree of full agreement between FA-PP and culture was higher for G5 ETA (Kappa value, 0.54; 95% CI, 0.43-0.66) than for G4 ETA (Kappa value, 0.31; 95% CI, 0.11-0.49). For all bacterial targets detected, genome copy/ml numbers exceeded colony forming units (CFU)/ml counts in 1-2 log₁₀, irrespective of ETA grading. The degree of correlation between genome copies/ml and CFU/ml was slightly better for G5 ETA (Rho = 0.65; P = 0.001) than for G4 ETA (Rho = 0.54; P = 0.11).

Conclusion: FA-PP testing of G5 ETA may provide more comprehensive and clinically useful information compared with G4 specimens in patients undergoing IMV with suspected LRTBI and receiving antimicrobial therapy. Yet G4 ETA may still provide useful microbiological information.

Purpose: The present study investigated the role of resistance-nodulation-cell division (RND) efflux pumps in tigecycline resistance of Acinetobacter baumannii clinical isolates recovered from three Western Balkan countries (Serbia, Bosnia and Herzegovina and Montenegro).

Methods: A total of 37 A. baumannii isolates recovered from seven tertiary care hospitals in 2016 and 2022 were tested against tigecycline using broth microdilution method. Then, efflux pump inhibitor carbonyl cyanide 3-chlorophenylhydrazone (CCCP) was used to determine the involvement of efflux pumps in tigecycline resistance. Molecular typing was performed by pulsed-field gel electrophoresis (PFGE) and multiplex PCR-based determination of clonal lineage. Regulators of efflux pumps were analyzed for amino acid substitutions, while reverse transcription-quantitative PCR (RT-qPCR) enabled quantification of RND efflux pumps expression.

Results: All tested isolates were interpreted as resistant to tigecycline and showed reduced tigecycline minimum inhibitory concentration (MIC) values in the presence of CCCP. PFGE analysis showed significant diversity among isolates grouped in cluster I including IC2 (n = 32) and IC3 (n = 1) isolates, while cluster II was comprised of four IC1 isolates. The most prevalent substitutions in AdeR were V120I and A136V and in AdeS G186V and N268H (n = 33). The Q262R substitution was detected in AdeL proteins of IC1 isolates, whereas no alterations were observed within AdeN. The expression of the adeB, adeG, and adeJ genes in selected isolates was upregulated in five (1.16- to 3-fold), sixteen (1.35- to 2.82-fold), and twelve isolates (1.62- to 4-fold) compared to ATCC19606, respectively.

Conclusion: This study revealed that overexpression of RND efflux pumps underlies tigecycline resistance in A. baumannii clinical isolates from the Western Balkans.

Introduction: Although CRPA may test susceptible to other β-lactams such as ceftazidime (CAZ), cefepime (FEP), and piperacillin/tazobactam (TZP), reduced potency has been observed. We assessed the adequacy of EUCAST Susceptible (S) or Susceptible Increased Exposure (SIE)/(I) doses for CAZ, FEP, and TZP against CRPA clinical isolates.

Methods: CRPA isolates were collected from patients at three Turkish hospitals. CAZ, FEP, and TZP MICs were determined using broth microdilution. Monte Carlo simulations were performed to determine the probability of target attainment (PTA) for a free time above the MIC (fT > MIC) targets for various doses of each agent against isolates defined as susceptible. fT > MIC targets were 70% for CAZ or FEP and 50% for TZP. Cumulative fraction of response (CFR) was calculated. Optimal PTA and CFR was 90% target achievement.

Results: The percentages of isolates SIE/I to CAZ, FEP, and TZP were 49,8%, 47%, and 31,8% respectively. Reduced potency was noted with 54,1% of CAZ-S isolates having MICs of 4 or 8 mg/L. Of the FEP and TZP-S isolates, MICs at the breakpoint (8 and 16 mg/L, respectively) were the mode with 45,2 and 53,9% of isolates for each, respectively. At an MIC of 8 mg/L for CAZ, the EUCAST standard dose was insufficient (CFR of 85%). 3 h infusions of EUCAST SIE doses were required for 90% PTA at MIC of 8 mg/L and an optimized CFR of 100%. For FEP, the SIE dose of 2 g q8h 0.5 h infusion of was effective (CFR 96%), utilization of an extended 3 h infusion further optimized the PTA at 8 mg/L (CFR 99%). For TZP, the standard dose of 4.5 q6h administered as a 0.5 h infusion was inadequate (CFR 86%). A standard TZP dose with an extended infusion (4.5 g q8h over 4 h) and the SIE dose 4.5 g q6h 3 h infusion resulted in CFRs > 95%.

Conclusion: These data support the EUCAST SIE breakpoints for FEP and TZP. To optimize PTA at the SIE breakpoint for CAZ, prolonged infusion is required.

Purpose: Acute lower respiratory tract infections (ALRIs) is a leading cause of child mortality worldwide. Metagenomic next-generation sequencing (mNGS) identifies ALRIs pathogens and explores the lung microbiota's role in disease severity and clinical outcomes. This study examines the association between lung microbiota and ALRIs outcomes in children, exploring its potential as a prognostic biomarker.

Methods: We retrospectively analyzed mNGS data from the bronchoalveolar lavage fluid (BALF) of 83 pediatric ALRIs patients from 2019 to 2023. Microbial diversity and relative abundances of specific taxa were compared between survivor and non-survivor groups, as well as between varying severity levels. LEfSe was employed to identify key biomarkers related to survival and disease severity.

Results: Among the 83 patients, 68 survived and 15 died. Patients were also divided into a low severity group (n = 38) and a moderate-to-very-high severity group (n = 45) according to mPIRO score at admission. Significant differences in beta diversity were observed between the survival groups and across different severity levels. Prevotella, Haemophilus and Veillonella exhibited higher abundances in both the survivor and low severity groups, suggesting their potential as predictors of better outcomes. Conversely, Enterococcus and Acinetobacter baumannii were more prevalent in the non-survivor and moderate-to-very-high severity groups. Additionally, Streptococcus pneumoniae and Streptococcus mitis showed increased abundances in survivors. LEfSe further revealed that these microorganisms may predict outcomes and severity in ALRIs.

Conclusion: Our findings underscore the complex relationship between lung microbiota and ALRIs, with specific microbial profiles associated with disease severity and clinical outcomes. This underscores the need for further research to explore and validate its prognostic predictive capacity.

Clinical trial number: Not applicable.