European Journal of Clinical Microbiology & Infectious Diseases最新文献

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.

Objective: To investigate the incidence, pathogen distribution, and antibiotic susceptibility of early- and late-onset neonatal bacteremia, and to analyze pathogen trends before and during the COVID-19 pandemic.

Methods: Between January 2016 to December 2022, we collected 879 blood and cerebrospinal fluid specimens from newborns with bacteremia. Bacterial identification used biochemical methods and MALDI-TOF, and antibiotic susceptibility was tested with the VITEK 2 system. Incidence per 1,000 admissions was calculated with Wilson's 95% confidence intervals, and categorical variables were compared using χ²-test or Fisher's exact test.

Results: Early-onset bacteremia incidence was 2.6 per 1,000 admissions, and late-onset bacteremia was 26.3, with a significant decline from 70.7 to 10.5 per 1,000 admissions over the study period. Late-onset bacteremia was more common before COVID-19, while early-onset bacteremia increased during the pandemic. The top five pathogens were CoNS(39.9%), E. faecalis(17.7%), E. faecium(13.7%), E. coli(8.4%), and GBS(5.8%). During the COVID-19 pandemic, the incidence of CoNS and S. aureus infections significantly decreased. Throughout the entire study period, CoNS and S. aureus showed high resistance to penicillin G and erythromycin but were sensitive to vancomycin and linezolid. E. faecalis and E. faecium were susceptible to vancomycin, linezolid, and teicoplanin but resistant to erythromycin, tetracycline, and rifampin. MRCoNS and MRSA were detected in 72.7% and 31.0% of isolates, respectively. Resistance rates of E. faecium and E. faecalis to ampicillin decreased significantly, clindamycin resistance in GBS decreased during the pandemic.

Conclusion: This study highlights notable shifts in neonatal bacteraemia patterns during the COVID-19 Pandemic that were likely influenced by increased infection control and disruptions in maternal care, leading to changes in pathogen distribution and antimicrobial resistance.

Purposes: Rapid and accurate identification of non-tuberculous mycobacteria (NTM) is crucial yet challenging, promoting the development of novel molecular techniques such as amplification-based targeted high-throughput sequencing and metagenomic unbiased high-throughput sequencing. We aimed to evaluate the diagnostic value of these molecular techniques for NTM infection.

Methods: A total of 115 clinical specimens from patients with confirmed NTM infection were subjected to multiplex polymerase chain reaction detection techniques (multi-PCR), metagenomic Next-Generation Sequencing (mNGS), targeted Next-Generation Sequencing (tNGS), and targeted Nanopore sequencing (tNanopore). Positivity rates and species identification were compared among these techniques.

Results: The sensitivity of mNGS, tNGS, and multi-PCR in NTM-infection diagnosis was 44.3%, 42.6%, and 36.5%, respectively, while the sensitivity of the three methods in combination increased to 54.8%. The pathogen identification results of mNGS, tNGS and multi-PCR were matched in 80.6% (25/31) samples at the species level, among which 14 samples (45.2%) was completely matched at the subspecies level. The results of tNanopore, tNGS and mNGS at the species level were completely matched in 73.3% (22/30) samples.

Conclusions: These molecular assays demonstrated comparable performance in precisely identifying NTM species in clinical specimens, showing their promising potential as efficient and alternative tools for the rapid diagnosis of NTM disease.

Recently, an increase in cases of multidrug-resistant Gram-negative bacteria post-neurosurgical ventriculitis and meningitis is reported. Treating these infections has become challenging due to the limited availability of antibiotics and the need to select those with optimal pharmacodynamic and pharmacokinetic profiles. There is limited evidence regarding the use of meropenem-vaborbactam in treating carbapenem-resistant Enterobacterales infections of the central nervous system. We report two new cases of shunt-related ventriculitis due to carbapenem-resistant K.pneumoniae with a favorable microbiological evolution after IV only combination therapy with meropenem-vaborbactam.

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: The role of therapeutic drug monitoring (TDM) in allogeneic hematopoietic stem cell transplantation (allo-HSCT) recipients receiving letermovir has not yet been clarified. This study is to explore letermovir trough concentration (C_min) correlation with its clinical efficacy and adverse events, and factors affecting its plasma concentrations.

Methods: A prospective, non-interventional study was performed in allo-HSCT recipients receiving letermovir prophylaxis. Plasma concentrations were determined using high-performance liquid chromatography-tandem mass spectrometry. Data analysis was performed using logistic regression, linear regression, and classification and regression tree (CART) models.

Results: 701 trough concentrations from 71 recipients were included, uncovering pronounced intra- and inter-individual variability in letermovir C_min. During 24-week follow-up, CMV infection incidence was 16.4%. A significant correlation was identified between letermovir C_min and its clinical efficacy, and the CART model showed an increased risk of CMV infection when C_min ≤ 2731 ng/mL. However, no clear correlation was found between C_min and adverse events. Gastrointestinal graft-versus-host disease, cyclosporine C_min, gender, and concomitant medications, including mycophenolate mofetil, ondansetron, caspofungin, and methylprednisolone, may impact letermovir C_min. Additionally, coadministration with cyclosporine injection significantly decreased median letermovir C_min compared with cyclosporine capsules (2311 vs. 3386 ng/mL). Moreover, with the extension of time post-transplant, trough concentrations of both cyclosporine and letermovir significantly decreased.

Conclusion: TDM for letermovir may be beneficial in allo-HSCT recipients considering the variability in letermovir C_min and its correlation with clinical efficacy. Moreover, drug interactions and the effects of changes in cyclosporine dosage forms or concentrations require careful monitoring for their effect on letermovir C_min.

There is a constant need to reduce turn-around times and keep costs as low as possible for the carriage screening of GBS in pregnant patients. Laboratory automation might provide an edge in this field. The objectives of the present study were: i) to compare the performance of the direct chromID™ Strepto B agar (CA) plating against LIM-broth enriched plating on CA for the detection of GBS from vagino-rectal screening-swabs; and ii) to assess the usage of PhenoMATRIX™ for the automated screening of GBS. Between January 2021 and December 2023, 9'107 vagino-rectal specimens were collected from pregnant women at Geneva University Hospitals and were used to address the first objective. There was a small difference in the GBS detection rates between direct CA plating (13.2%; 1'202/9'107) and LIM-broth enriched plating on CA (13.2%; 1'198/9'107). Based on the LIM-broth enrichment results, the sensitivity and specificity of the direct CA plating were 98.3% (95% CI, 97.3%-98.9%) and 99.7% (95% CI, 99.5%-99.8%), respectively. Importantly, for 25 specimens, GBS growth was only detected by direct CA plating. We used a random set of 8'768 CA plate pictures for the machine learning of PhenoMATRIX™. The validation was carried out on an additional set of 830 CA plate pictures. The sensitivity and specificity of PhenoMATRIX™ were 100% (95% CI, 96.6%-100.0%) and 90.2% (95% CI, 87.8%-92.1%), respectively. We established that for GBS screening, the performance of direct CA plating is not inferior to the LIM-broth enriched approach. By relying on PhenoMATRIX™, the negative predictive value for GBS screening reaches 100% (95% CI, 99.4%-100.0%), enabling the automatic release of GBS-negative cases within 24 h.

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.

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.

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.