Annals of Clinical Microbiology and Antimicrobials最新文献

The prevalence of carbapenem-resistant Klebsiella pneumoniae (CRKP) infections has surged in China over the past decade, posing a significant public health concern. However, comprehensive data on CRKP antimicrobial resistance patterns and the impact of the COVID-19 pandemic on these patterns in China remain unclear. We conducted a systematic review of CRKP infections in China, utilizing data from PubMed spanning 2006 to July 2023. We focused on resistance rates of CRKP causing infections, examining variations across time, regions, and age groups, as well as factors contributing to antimicrobial resistance. Our analysis included 68 studies from 19 provinces in China, comprising 1,284 CRKP isolates obtained from 779 patients. The overall mortality rate for CRKP infections in China was 27% (95% CI: 0.14-0.41, I² = 73%, k = 47), with ST11 being the predominant sequence type (Pooled Rate: 80%, 95% CI: 0.67-0.90, I² = 86%, k = 31). Temporal and spatial analyses indicated increased resistance to ciprofloxacin (Random effects model: Q_b = 9.88, df = 1, P < 0.010) and levofloxacin (Random effects model: Q_b = 7.69, df = 1, P < 0.010) during the COVID-19 pandemic. Resistance to chloramphenicol (Random effects model: Q_b = 4.97, df = 1, P = 0.030) and ceftazidime-avibactam (Random effects model: Q_b = 8.58, df = 1, P < 0.010) was lower in southern regions, while tetracycline resistance (Random effects model: Q_b = 9.69, df = 1, P < 0.010) was lower in the north. Higher resistance rates were observed in adults and the elderly. Age and geographic location were key factors associated with antimicrobial resistance. Fourteen out of thirty-five drugs showed a positive correlation with mortality rates, emphasizing their significant impact on CRKP infection mortality. This study underscores the need for targeted interventions to address regional and age-related variations in CRKP resistance and highlights the critical role of antimicrobial resistance in influencing mortality outcomes.

Background: Candidozyma auris is an emerging multidrug-resistant fungal pathogen responsible for nosocomial outbreaks worldwide. In addition to antifungal resistance, its ability to persist in the hospital environment and tolerate commonly used biocides presents a critical challenge for infection control. However, the relationship between biocide tolerance, antifungal resistance, and virulence traits in C. auris remains poorly understood.

Methods: In this study, 47 C. auris Clade 1 isolates were evaluated using phenotypic and genotypic methods. ITS region sequencing was performed using Oxford Nanopore technology. Susceptibility testing was conducted for seven antifungal agents and four biocides using the CLSI reference microdilution method. Virulence factors including biofilm formation, secreted aspartyl proteinase, esterase, caseinase, phospholipase, and hemolysis were assessed.

Results: All isolates were identified as Clade 1. MIC values for antifungals ranged from 0.015 to 64 µg/mL, and for biocides from 0.0078 to 128 mg/L. Fluconazole resistance was found in 31% of isolates, while amphotericin B resistance was 4%; no echinocandin resistance was observed. Biofilm and SAP activity were detected in all isolates; esterase was positive in 87%, and caseinase in 4%. Statistically significant correlations were observed between amphotericin B and isavuconazole MICs (ρ = 0.32, p = 0.028), amphotericin B and triclosan MICs (ρ = 0.35, p = 0.018), and amphotericin B MICs and caseinase activity (ρ = 0.31, p = 0.035). These findings suggest potential phenotypic links between antifungal resistance and specific virulence traits.

Conclusions: This is the first study from Türkiye to evaluate the antifungal and biocide susceptibility alongside virulence characteristics of Clade 1 C. auris. While statistically significant associations were observed, we acknowledge that resistance mechanisms and pathogenicity pathways are distinct. Therefore, these correlations should be interpreted cautiously and warrant further investigation at the molecular level.

Background: Heteroresistance can lead to treatment failure and has brought a rigorous challenge to clinical laboratories for detecting them. The aim of this study was to investigate the potential for tigecycline-susceptible Klebsiella pneumoniae (K. pneumoniae) clinical isolates to develop heteroresistance under antibiotic pressure.

Method: In this study, inducing experiment in vitro was used to acquire tigecycline heteroresistance phenotype. Population analysis profiling was used to confirm heteroresistance. Potential tigecycline heteroresistance mechanism through whole-genome sequencing and quantitative reverse-transcription PCR (qRT-PCR) were explored. Time-kill assay was used to explore the effect of tigecycline monotherapy or combination with other antibiotics.

Result: Two clinically isolated K. pneumonia strains were found to change from tigecycline susceptible to resistance during treatment of tigecycline in vivo. Experimental-evolved tigecycline heteroresistant colonies were successfully obtained by exposing to concentration of tigecycline at usual therapy of tigecycline (serum concentration of 0.1 mg/L). Heteroresistant phenotypes were stable, and the minimal inhibitory concentration sustained at resistant after 7 days serially passed in tigecycline-free medium. Frequency of heteroresistant subpopulation ranged from 7.0 × 10^-7 to 1.41 × 10^-6. Genome sequencing and analysis showed mutations of ramR, acrR and rpsJ could be responsible for the stage from tigecycline susceptible to heteroresistance and further to resistance in K. pneumoniae. Quantitative reverse-transcription PCR analysis revealed that the increased expression of tigecycline resistance genes detected in tigecycline resistant subpopulations might be associated with tigecycline heteroresistance. Time-kill assay showed the impaired efficacy of serum concentrations of 0.1 mg/L tigecycline (50 mg/q12h intravenously [i.v.]) monotherapy on tigecycline susceptible K. pneumoniae. 1 mg/L tigecycline could be effective in preventing susceptible strain but failed on heteroresistance. Combination with other antibiotics which are susceptible to target strains such as tigecycline-polymyxin B and tigecycline-amikacin can effectively inhibit the growth of resistant subpopulations.

Conclusion: The findings reveal the phenomenon where tigecycline may induce resistance in initially susceptible strains during clinical treatment, associated with several mutations of ramR, acrR and rpsJ, resulting in treatment failure. The heteroresistant strains induced by low concentrations of tigecycline in vitro provide a perspective for exploring the molecular mechanisms of tigecycline resistance in K. pneumoniae. Combination with other antibiotics like polymyxin B and amikacin would show synergistic effects in evading regrowth of resistant subpopulations.

Background: This study evaluated the performance of the simultaneous amplification and testing (SAT) assay for detecting common Candida species in vaginal specimens compared with culture (gold standard) at the Obstetrics and Gynecology Hospital of Fudan University from December, 2024 to January, 2025.

Methods: Speimens were analyzed by both Candida culture (with MALDI-TOF MS identification) and the SAT-Candida assay. Discordant results were further confirmed by real-time polymerase chain reaction (RT-PCR) and bidirectional sequencing. A comparative analysis (kappa coefficient) was conducted as well. We assessed the limit of detection, technical specificity, repeatability and the clinical diagnostic effectiveness, including sensitivity, specificity, diagnostic accuracy, positive predictive value (PPV), and negative predictive value (NPV) of SAT-Candida assay.

Results: In our study, among the 472 initially collected specimens, 5 were excluded because the presence of the Candida species were outside the detection spectrum of the SAT-Candida assay. The ages of the rest 467 cases ranged from 13 to 77 years old, and by comparison with SAT-Candida assay and Candida culture, 444 concordant results and 23 discordant results were discovered. After the reconfirmation, the SAT-Candida assay presented a overall sensitivity of 98.7%, specificity of 97.8%, PPV of 97.9%, NPV of 98.7%, and diagnostic accuracy of 98.3% in detecting Candida species. The kappa value between Candida culture and SAT-Candida assay in detecting Candida species was 0.91.

Conclusions: This SAT-Candida assay is acute, highly sensitive, and specific, which can be applied as an optimal diagnostic tool for detecting and identifying common Candida species from vaginal samples of vulvovaginal candidiasis (VVC) suspected patients.

Background: Many rifampicin (RIF)-resistant (RR) tuberculosis (TB) patients remain sensitive to isoniazid (INH), which challenges the strategy of using RR as an instant indicator of multiple-drug resistance tuberculosis (MDR-TB). A molecular test capable of concurrently detecting RIF and INH resistance is urgently needed.

Methods: The performance of a novel rapid molecular test, Innowave MTB/RIF/INH (InnowaveDX) was evaluated prospectively in three tertiary hospitals. Its capability of detecting resistance to RIF and INH was assessed.

Results: In 767 pulmonary tuberculosis (PTB) patients, InnowaveDX showed significantly higher sensitivity than the Xpert MTB/RIF assay (Cepheid, USA) (74.97% versus 68.18%; p = 0.003, χ² = 8.664). This difference was particularly notable in culture-negative PTB cases (52.73% versus 41.29%; p = 0.001, χ² = 10.565). Both tests demonstrated high specificity in 286 non-TB patients. The overall consistency in RIF susceptibility prediction between InnowaveDX and the Xpert assay was 97.3% (505/519). InnowaveDX identified 83.05% (98/118) of INH-resistant cases as predicted by phenotypic drug susceptibility testing (pDST) and 95.45% (105/110) by another molecular method (MeltPro, Zeesan, China) for INH resistance detection on isolates. In addition, InnowaveDX showed a 99.35% consistency (154/155) with katG, inhA, and ahpC sequencing on sputum samples. The consistency rate for MDR-TB prediction between InnowaveDX and pDST was 93.25% (332/356). The accuracy of using RR to predict MDR-TB varied between 64.1 and 80.5%, depending on the reference method.

Conclusion: InnowaveDX is an easy, rapid, and sensitive molecular test for PTB diagnosis that can detect INH and RIF resistance within 3 h, facilitating MDR-TB diagnosis on the first day of hospital admission.

Background: Legionella gormanii (L. gormanii) is an emerging pathogen causing legionellosis, yet it is much less studied than the predominant species, L. pneumophila. Clinical treatment guidelines for legionellosis are primarily based on data from L. pneumophila and recommend macrolides and fluoroquinolones. However, the intrinsic antimicrobial susceptibility of L. gormanii is not well-defined, creating uncertainty about whether these guidelines are directly applicable. Establishing a baseline understanding of its susceptibility patterns is a prerequisite for effective epidemiological surveillance and for identifying non-wild-type resistance. This study aims to address this fundamental knowledge gap by characterizing the in vitro susceptibility profiles of a large collection of environmental L. gormanii isolates.

Methods: This study systematically evaluated the in vitro activity of ten representative antimicrobials against 207 environmental L. gormanii isolates collected in China between 2019 and 2021. Minimum inhibitory concentrations (MICs) were determined by the broth microdilution (BMD) method, and species-specific epidemiological cutoff values (ECOFFs) were established using the ECOFFinder tool.

Results: Most tested agents demonstrated good in vitro activity. Rifampin was the most potent agent, while clarithromycin was the most active macrolide. Conversely, tetracyclines showed limited activity. Comparative analysis revealed that L. gormanii exhibited markedly higher MICs for rifampin (approximately 9.58-fold) than typically reported for L. pneumophila. Species-specific ECOFFs were determined for nine antimicrobials: rifampin (0.016 mg/L); ciprofloxacin, levofloxacin, and clarithromycin (0.063 mg/L); moxifloxacin (0.125 mg/L); erythromycin (0.25 mg/L); azithromycin (0.5 mg/L); trimethoprim-sulfamethoxazole (4 mg/L); and tigecycline (16 mg/L).

Conclusions: This study establishes the first large-scale susceptibility dataset and species-specific ECOFFs for L. gormanii. The findings highlight key inter-species differences in susceptibility, particularly for rifampin, underscoring that treatment paradigms cannot be safely extrapolated from L. pneumophila. These ECOFFs provide a critical tool for surveillance of non-wild-type resistance. However, these data, derived from environmental isolates, are intended for epidemiological and hypothesis-generating purposes and must be supplemented with clinical and pharmacokinetic/pharmacodynamic (PK/PD) studies before informing changes to clinical practice.

Background: While several recent studies have documented the importance of efflux pumps as mediators of rifampin (RIF) resistance, it remains uncertain which efflux pumps play major roles in rifampin-resistant Mycobacterium tuberculosis strains harboring rpoB gene mutations.

Methods: In this study, minimum inhibitory concentration (MIC) values for RIF were calculated and the expression of 13 efflux pump genes was evaluated across 35 clinical rifampicin-resistant M. tuberculosis isolates carrying the rpoB mutation before and after efflux pump inhibitor treatment.

Results: Rv0677c and Rv0191 were identified as the efflux pump genes that were most frequently overexpressed, and treatment with the inhibitor verapamil was sufficient to synergistically enhance the antibacterial effects of RIF and downregulate efflux pump gene expression. Greater numbers of overexpressed efflux pump genes were associated with a more significant decrease in the MIC value for RIF following verapamil treatment. Levels of RIF resistance for clinical isolates with the rpoB codon 445 mutation were also found to be significantly less susceptible to the effects of verapamil as compared to the resistance of strains with the codon 450 and 170 mutations.

Conclusions: These results suggest that levels of RIF resistance in clinical RIF-resistant M. tuberculosis isolates are ultimately determined by a combination of efflux pump activity and rpoB gene mutations.

Background: Lower respiratory tract infection (LRTI) remains the leading infectious cause of morbidity and mortality globally. Key bacterial pathogens include Acinetobacter baumannii, Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli, Staphylococcus aureus and Streptococcus pneumoniae. This study examined the prevalence and antimicrobial resistance patterns of major bacterial pathogens from community- and hospital-acquired LRTIs across six major hospitals in Vietnam.

Methods: Between January 2022 and May 2023, 1000 bacterial isolates were collected through an isolate-based surveillance. Species identification and antimicrobial susceptibility testing were performed by VITEK-2/Phoenix M50, with MICs determined by E-test or broth microdilution. Multiplex PCRs were used to detect common AMR genes.

Results: A. baumannii (49.6%), P. aeruginosa (21%), K. pneumoniae (18.6%) were predominant, followed by S. aureus (6.7%), E. coli (3.9%) and S. pneumoniae (0.2%). Most isolates (94.4%) were identified from hospital-acquired cases. High prevalence of MDR and carbapenem resistance were identified in A. baumannii (96% and 95%), P. aeruginosa (56.7% and 57.1%), and K. pneumoniae (78% and 69.2%), respectively. Notably, resistance to ceftazidime-avibactam was detected in K. pneumoniae (34.3%), P. aeruginosa (29%), and E. coli (7.7%), while colistin resistance was found in K. pneumoniae (18.2%) and A. baumannii (2.8%). MRSA prevalence was 79.1%, though S. aureus remained susceptible to vancomycin, linezolid and ceftaroline. Most bla_NDM-positive K. pneumoniae (62/71, 87.3%), E. coli (2/2, 100%), and P. aeruginosa (23/25, 85.2%) showed resistance to ceftazidime-avibactam. Whole genome sequencing revealed that the bla_NDM-positive but ceftazidime-avibactam susceptible isolates (9 K. pneumoniae and 2 P. aeruginosa) carried truncated bla_NDM. Overall, ceftazidime-avibactam was effective against K. pneumoniae, E. coli, and P. aeruginosa isolates carrying ESBL, ESBL and bla_OXA-48, or ESBL and bla_KPC. Alternatively, no detectable AMR genes were found in 35 ceftazidime-avibactam resistant P. aeruginosa isolates.

Conclusions: Carbapenem-resistant Gram-negative pathogens were predominant among hospital-acquired LRTIs in Vietnam, with notable resistance to ceftazidime-avibactam and colistin. The lack of effective treatment for A. baumannii remains a major concern. We found a strong correlation between AMR phenotype and genotype among K. pneumoniae and E. coli, supporting gene-based therapy to guide ceftazidime-avibactam use. However, the presence of disrupted bla_NDM underscores the need to re-evaluate commercial PCR assays for carbapenemase detection.

Background: Neonatal sepsis is a major cause of morbidity and mortality worldwide. The COVID-19 pandemic has influenced its epidemiology, altering pathogen distribution and antimicrobial resistance patterns, necessitating a reassessment of neonatal infection management. This study aims to evaluate the impact of the COVID-19 pandemic on neonatal sepsis incidence, pathogen distribution, and antimicrobial resistance patterns, providing evidence to inform improved clinical management strategies in neonatal intensive care units.

Methods: This retrospective cross-sectional study analyzed neonatal sepsis cases in a tertiary hospital in Tehran, Iran, comparing pre-pandemic (2017-2019) and pandemic period (2020-2023). Clinical characteristics, pathogen prevalence, and antibiotic resistance patterns were evaluated using logistic regression models.

Results: A total of 341 neonates were included (167 pre-pandemic, 174 pandemic period). Early-onset sepsis (0-3 days after birth) significantly declined during the pandemic period (40.4% vs. 12.1%, p < 0.001), while late-onset sepsis increased, particularly between 4 and 10 days (31.0% vs. 21.7%) and beyond 30 days (21.8% vs. 9.0%). Candida and Klebsiella pneumoniae infections surged during the pandemic, contributing to heightened antimicrobial resistance. Ampicillin (OR: 5.30, p = 0.002), Piperacillin (OR: 4.14, p = 0.009), Ciprofloxacin (OR: 2.39, p = 0.027), and Co-trimoxazole (OR: 2.60, p = 0.002) resistance rates increased significantly, while Colistin resistance emerged exclusively during the pandemic period, raising concerns about limited treatment options for multidrug-resistant infections.

Conclusion: The COVID-19 pandemic significantly altered neonatal sepsis patterns, increasing late-onset infections, shifting pathogen prevalence, and exacerbating antimicrobial resistance trends. Rising resistance to key antibiotics, including Colistin, underscores the urgent need for strengthened antimicrobial stewardship in NICUs. Despite these disruptions, NICU protocols remained effective, ensuring stable neonatal mortality rates.

Background: Hypervirulent K. pneumoniae (hvKp) strains are characterized by their enhanced ability to evade immune responses and disseminate systemically. Rapid identification of hvKp strains is critical for guiding clinical management and implementing effective infection control measures. Loop-Mediated Isothermal Amplification (LAMP) assays provide a rapid and cost-effective method for detecting bacterial pathogens. This study evaluates the performance of the Eazyplex^® hvKp assay for the direct detection of hvKp strains from spiked blood cultures.

Methods: We collected 20 K. pneumoniae (Kp) isolates between December 2021 and August 2024 from two hospitals in Northern Spain. Capsular serotyping and virulence gene detection were performed using PCR and whole-genome sequencing (WGS). The Eazyplex^® hvKp LAMP assay was tested on spiked blood cultures inoculated with hvKp isolates. Virulence profiles were assessed using the Kleborate scoring system.

Results: Seventeen Kp isolates had a Kleborate score of ≥ 2, suggesting high virulence. The LAMP assay detected 87 out of 95 virulence targets, demonstrating an overall accuracy of 91.5%. Although eight target genes were not directly detected, fluorescence signals indicated amplification in all cases. The assay identified 16 strains with high virulence profiles (score ≥ 3), with 14 strains scoring 4 or 5. The LAMP-based test effectively detected hvKp directly from blood cultures, with time-to-results ranging from 6:43 to 17:11 min.

Conclussion: The Eazyplex^R hvKp LAMP assay is a rapid and effective method for identifying hvKp strains directly from blood cultures. This study supports its potential utility in clinical microbiology for early detection and epidemiological surveillance of hvKp infections. However, limitations in the Kleborate scoring system indicate that additional virulence biomarkers may be needed to improve the accuracy of hvKp classification.