Annals of Clinical Microbiology and Antimicrobials最新文献

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.

The mcr-9 allele is typically located on IncHI2 type plasmids, but there are only few reports describing the co-occurrence of the bla_NDM gene on the same plasmid. Our aims were to describe the spread of an IncHI2A plasmid harboring both the mcr-9 and the bla_NDM-1 genes in a multicenter study in Israel. All New-Delhi Metallo-β-lactamase-producing Enterobacterales (NDME) isolated from three medical centres in Israel between January 2018 and July 2019 were included. The mcr-9.1 gene was identified in 37/212 (17.4%) of the isolates, mostly in Enterobacter cloacae (34/37, 92%). The mcr-9.1 gene was also identified in Klebsiella pneumoniae sequence types (ST)-76 (n = 2) and Escherichia coli ST-69 (n = 1). In one hospital, out of 32 E. cloacae isolates, 19 (51.35%) were clustered into five transmission clusters of the ST-511, ST-1261 and ST-1750. Four subtypes of a ~ 290 kb IncHI2A type plasmid were identified in all isolates that co-harbored the mcr-9.1 and the bla_NDM-1 genes. This plasmid was identified in all isolates, with four sub-communities (sc), with sc-4 identified in all three species. The resistance genes were surrounded by the IS26 (mcr-9.1) or by the ISAba125 and the IS300 (bla_NDM-1) mobile elements. The dissemination of the mcr-9.1 and the bla_NDM-1 genes was accelerated via clonal spread and the dual carriage on a single plasmid.

Background: The emergence of MDR K. pneumoniae poses a critical challenge in treating respiratory-associated pneumonia. Bacteriophages are promising antibiotic alternatives with unique features. This study aimed to isolate new bacteriophages from the hospital environment and investigate their therapeutic potential and mechanisms.

Methods: We employed plaque assays, transmission electron microscopy, and whole-genome sequencing to systematically characterize the biological properties, morphology, and genomic profiles of the phages in parallel. The bacteriostatic curve, biofilm staining quantification, and biofilm inhibition rate assay were employed to evaluate the in vitro lytic efficacy of the phage. More importantly, we established the murine pneumonia infection models through nasal instillation, assessed the therapeutic potential of the phage in vivo by observing pathological morphology via HE staining, detecting pro-inflammatory cytokine levels via qPCR and ELISA, and monitoring bacterial load changes in lung tissue through PCR analysis.

Results: Phages vB_KpnP_XY3 and vB_KpnP_XY4, taxonomically classified as Siphoviridae, demonstrated broad temperature (4-60 °C), pH (4-11) tolerance, chloroform resistance, latent periods of 40/35 min, and burst sizes of 340/126 PFU/cell. Both genomes contained circular dsDNA genomes (47,466 bp/50,036 bp) without virulence or antibiotic resistance genes. The bacterial concentration markedly decreased at 2 h post-treatment, reaching its biological nadir by 6 h. Concurrent biofilm assays demonstrated 80% biofilm inhibition and rapid bacterial clearance. In murine pneumonia models, both phage monotherapy and phage-antibiotic combinations significantly reduced bacterial loads compared with antibiotics alone (P < 0.05), concurrently attenuating inflammation (IL-1β/IL-6/TNF-a. P < 0.0001) and restoring alveolar architecture with reduced necrosis.

Conclusion: The phages vB_KpnP_XY3 and vB_KpnP_XY4 demonstrated robust environmental adaptability. Its antibacterial effect is related to its specific biofilm dissolution performance in vivo and in vitro. These findings provide strong evidence for the precise phage treatment of MDR K. pneumoniae infections.

Background: Mycobacterium abscessus (Mab) is a multidrug-resistant bacterial pathogen capable of causing widespread infections, often with a poor prognosis in susceptible populations. Mab comprises three distinct subspecies that exhibit phenotypic diversity and genetic heterogeneity.

Methods: We performed whole-genome sequencing and phenotypic antimicrobial susceptibility testing on 109 Mab isolates collected at zhongshan hospital from 2018 to 2023.

Results: The results indicate that recombination, especially distributed conjugation transfer, promotes the formation and sustained diversity of Mab subspecies. Through pangenome analysis, the synergistic gain/loss of accessory genes was found to contribute to different metabolic profiles and the ability to adapt to oxidative stress, facilitating strain adaptation to host environments. We conducted phenotypic antimicrobial susceptibility testing, revealing resistance to macrolide antibiotics differed among subspecies. We identified 24 genes whose gain or loss may increase the likelihood of macrolide resistance, including those involved in biofilm formation, the stress response, virulence, biotin synthesis, and fatty acid metabolism. Genomic variations within Mab species may have significant implications for disease epidemiology, infection pathogenesis, and host interactions.

Conclusions: Our findings provide a valuable genetic basis for the success of Mab as a highly adaptive and drug-resistant pathogen, informing current efforts to control and treat Mab infections, including strategies targeting specific sequence types or lineages.

Background: Sepsis remains a major public health challenge, leading to high mortality and morbidity rates, particularly among low-income populations such as those in sub-Saharan Africa. Its management is complicated by the emergence of multidrug-resistant bacterial strains, necessitating microbiological surveillance and adaptation of antibiotic therapy. This study examines the microbiological profile of sepsis and the antibiotic susceptibility of pathogens among critically ill patients in Lubumbashi, Democratic Republic of Congo.

Methods: A prospective study was conducted from January 2021 to December 2023 across three ICU units in Lubumbashi. Patients suspected of having sepsis were included, and microbiological samples were collected from various sources (blood, urine, pus, biological fluids). Bacterial identification and antibiotic susceptibility testing were performed according to Clinical and Laboratory Standards Institute (CLSI) guidelines. Data were analyzed using SPSS version 23^® and Excel 365^®.

Results: Among the 76 patients included, 40% had confirmed bacterial sepsis. The predominant isolates were Gram-negative bacilli (62.7%), with Escherichia coli (28.35%) and Klebsiella pneumoniae (22.73%) being the most common species. Gram-positive bacteria accounted for 33.89%, primarily coagulase-negative streptococci (15.11%) and Enterococcus faecium (5.61%). Antimicrobial resistance profiles revealed a high level of resistance to commonly used antibiotics, particularly cephalosporins, fluoroquinolones, and cotrimoxazole. However, greater sensitivity was observed with amikacin (41.3%), fosfomycin (37%), and meropenem (33.8%).

Conclusion: This study highlights the high prevalence of Gram-negative bacteria and concerning resistance to first-line antibiotics, jeopardizing the effectiveness of empirical treatments. These findings underscore the urgency of strengthening microbiological surveillance, rationalizing antibiotic use, and implementing antimicrobial resistance control policies in the DRC. Developing treatment protocols tailored to local data and enforcing stricter antibiotic regulations are essential to improving sepsis management and reducing associated mortality.

Background: Neisseria meningitidis (Nm), traditionally recognized as a nasopharyngeal commensal causing invasive meningococcal disease (IMD), has recently emerged as an etiological agent of urethritis worldwide, with sporadic urogenital cases in China raising epidemiological concerns.

Methods: Three urogenital Nm isolates were characterized to investigate their evolutionary features and transmission patterns. Through comprehensive laboratory characterization encompassing culture identification (Gram staining, oxidase testing, MALDI-TOF MS), antimicrobial susceptibility profiling, whole-genome sequencing, and functional colonization assays on urethral epithelial cells under nitrite-supplemented microaerobic conditions, three multidrug-resistant Nm isolates were identified.

Results: All isolates demonstrated resistance to penicillin and sulfamethoxazole/trimethoprim, with isolate 24-SHSP-NM2 exhibiting additional ciprofloxacin resistance. The resistance was attributed to penA variants, mtrR promoter mutations, and gyrA substitutions. Phylogenetically, one isolate clustered with Japanese ST-11,026 strains and 2 clustered with Australian ST-1466 strains. Genomic characterization identified complete denitrification operons (aniA-norB) in all three isolates, which enable nitrite-enhanced epithelial colonization. ST-1466 isolates showed meningococcal B (MenB) vaccine component FHbp antigenic homology through FHbp variant 1.1.

Conclusions: These findings collectively demonstrate the convergent evolution of urogenital tropism, antimicrobial resistance (AMR) emergence, and metabolic adaptation to genitourinary microenvironments, underscoring the threat of genitourinary Nm infections. The study highlights the critical need to enhance molecular surveillance, implement rapid AMR screening, and prioritize MenB vaccination strategies in high-risk populations.