Clinical Microbiology and Infection最新文献

Objectives: This study evaluated the in vitro activity of cefiderocol against clinical carbapenem-resistant Pseudomonas aeruginosa (CRPA) isolates in China before its clinical introduction, and investigated the mechanisms underlying resistance.

Methods: A total of 557 nonduplicate CRPA isolates were collected from central China between 2021 and 2024. Antimicrobial susceptibility testing, whole-genome sequencing, transcriptional and functional assays, enzyme kinetics, molecular docking, and site-directed mutagenesis were performed to identify molecular determinants of cefiderocol resistance.

Results: Among the antibiotics tested, cefiderocol exhibited the highest in vitro activity against CRPA, with 99.10% (552/557) of isolates being susceptible. Multilocus sequence typing (ST) revealed extensive diversity (203 STs), with ST235 as the predominant lineage (19.93%, 111/557). Notably, ST266 isolates displayed markedly reduced susceptibility (MIC₅₀ = 4 mg/L; MIC₉₀ = 32 mg/L) compared with ST235 (MIC₅₀ = 0.5 mg/L; MIC₉₀ = 1 mg/L; p= 0.0006) and uniquely coharboured bla_AFM-1 and bla_IMP-45. Functional assays indicated that bla_AFM-1 overexpression was a major driver of cefiderocol resistance, increasing MICs to 16 mg/L. Long-read sequencing localized bla_AFM-1 to an IncP-2 plasmid, and the elevated expression observed in cefiderocol-non-susceptible isolates was associated with increased gene copy number instead of promoter variation. Kinetic assays showed that AFM-1 exhibited higher catalytic efficiency against cefiderocol than NDM-1, and molecular docking predicted a strong binding affinity (-9.2 kcal/mol) between cefiderocol and AFM-1. Whole-genome sequencing of CRPA isolates with cefiderocol MICs ≥2 mg/L further revealed frequent alterations in iron-uptake systems, efflux pump regulators, and OprD porin. Reversion of the FptA G273R substitution restored cefiderocol susceptibility (MIC reduction from 16 to 4 mg/L) and upregulated pyochelin-related iron-uptake genes.

Conclusions: Cefiderocol remains highly active against CRPA in China; however, resistance can emerge through diverse mechanisms even without prior exposure. Early molecular surveillance will be crucial to ensure its rational use and sustained clinical efficacy.

Objectives: The emergence of extensively drug-resistant Enterobacterales, particularly carbapenemase-producing Klebsiella pneumoniae, poses a serious global health threat. Cefiderocol (FDC), a sideromycin antibiotic, employs a 'Trojan horse' strategy by using bacterial iron transport systems to enter the cell and inhibit cell wall synthesis. Although initially promising, resistance to FDC has rapidly emerged in the clinics and in the environment, necessitating a comprehensive understanding of the underlying resistance mechanisms.

Methods: In this study, we used transposon-directed insertion-site sequencing in an extensively drug-resistant FDC-susceptible K. pneumoniae ST258 strain to systematically identify genetic networks that modulate FDC resistance.

Results: Our transposon-directed insertion-site sequencing analysis revealed 299 chromosomal genes significantly impacting FDC resistance, with 143 identified as conditionally resistant modulators (CRMs) and 156 as conditionally essential genes. CRMs notably included genes associated with FDC influx, such as the siderophore uptake genes cirA and tonB, and porin channels such as ompK36 and tolB. Importantly, we identified several CRMs involved in bacterial capsule synthesis and expression (e.g. csrD and glnD), suggesting that capsule overexpression is a novel resistance mechanism. Phenotypic characterization of cirA, csrD and glnD knockout mutants confirmed increased FDC resistance. Furthermore, disruption of csrD and glnD resulted in enhanced capsule production, increased resistance to human serum and, in particular, increased virulence in a Galleria mellonella infection model.

Conclusions: These results emphasize the multifactorial nature of FDC resistance, involving both impaired drug entry and capsule-mediated protection, with potentially pleiotropic effects on bacterial virulence. Our study elucidates key genetic determinants of FDC resistance and highlights the complex interplay between antibiotic resistance and bacterial pathogenicity.

Objectives: In sub-Saharan African children aged under 5 years, nontyphoidal Salmonella (NTS) frequently cause fatal bloodstream infections. Antimicrobial resistance and absence of antibiotic treatment efficacy data challenge effective treatment. In this prospective observational study, we provide treatment efficacy data of susceptibility-matched antibiotic regimens from the treatment of NTS bloodstream infections in children in Kisantu district hospital (Democratic Republic of Congo).

Methods: Children (>28 days to <5 years) admitted with severe febrile illness were enrolled after blood culture sampling. Clinical and microbiological data of children with NTS bloodstream infection were collected in-hospital and at 1-month after discharge.

Results: NTS bloodstream infection was diagnosed in 12.7% (239/1867) of enrolled children. Extensive drug-resistance (concurrent ampicillin, cotrimoxazole, chloramphenicol, third-generation cephalosporin and fluoroquinolone nonsusceptibility) occurred in 60% (144/236), i.e. 69% (71/103) in O5-antigen positive Typhimurium, 85% (72/85) in O5-antigen negative Typhimurium but only 2% (1/48) in Enteritidis serovars. Only 64% (146/228) of children received susceptibility-matched antibiotics and overall in-hospital case fatality was 25.1% (60/239). Compared with susceptibility-mismatched antibiotic treatment, susceptibility-matched third-generation cephalosporin treatment on hospital day 0-1 had better 14-day in-hospital survival (hazard ratio at death [HR_death]: 0.37 [0.16-0.88]). Similarly, susceptibility-matched third-generation cephalosporin, ciprofloxacin or azithromycin treatment on hospital day 2-6 had better 28-day in-hospital survival (HR_death: 0.21 [0.06-0.68], 0.15 [0.02-1.10] and 0.26 [0.08-0.84], respectively). After ≥5 days of susceptibility-matched antibiotics, NTS persisted in control blood cultures in 15% (13/88).

Conclusions: NTS bloodstream infections were often extensively drug resistant, leading to susceptibility-mismatched antibiotic treatment. When NTS were susceptible, third-generation cephalosporin, ciprofloxacin and azithromycin treatment appeared to be effective.

Objectives: Cefiderocol is a novel last-resort cephalosporin antimicrobial increasingly used for difficult-to-treat infections by multidrug-resistant microorganisms, and is effective against carbapenem-resistant Enterobacterales and Pseudomonas species. Multiple chromosomally encoded genetic determinants have been implicated in cefiderocol resistance, including mutations, deletions and/or frameshifts. However, identification of these determinants remains labour-intensive and time-consuming. Therefore, we share CefiderocolFinder, a bioinformatics pipeline to detect 25 genetic adaptations implicated in cefiderocol resistance from short-read whole-genome sequencing (WGS) data.

Methods: CefiderocolFinder was built using Python, supports WGS data of Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii, and contains alignment, variant calling, annotation and filtering steps. A short-read WGS dataset (n = 98) and a validation WGS dataset (n = 21) with cefiderocol antimicrobial susceptibility testing (AST) results were used to interpret and validate CefiderocolFinder.

Results: Using CefiderocolFinder, with WGS data from 98 multidrug-resistant microorganisms collected from Ukrainian patients in 2022, six unique genetic adaptations were detected. These adaptations were associated with higher MICs in AST with cefiderocol. Loss-of-function mutations were found in the siderophore receptor cirA, the general porins oprD, ompC, ompF, negative regulator of the acrAB-tolC efflux operon acrR and a conservative in-frame insertion YRIN in ftsI encoding for penicillin-binding protein 3. The adaptations were identified in 12 of 16 E. coli (75%), 1 of 60 K. pneumoniae (1%), 6 of 17 P. aeruginosa (35%) and 0 of 5 A. baumannii (0%) isolates. CefiderocolFinder was validated using publicly available datasets.

Conclusions: CefiderocolFinder provides context to corroborate phenotypical AST from WGS data, especially when the result is in an area of technical uncertainty. For E. coli, CefiderocolFinder can be a valuable tool for informing the clinician of specific genetic adaptations associated with resistance to cefiderocol, where for K. pneumoniae and P. aeruginosa the prediction of phenotypical resistance can be improved. CefiderocolFinder is available open access at http://github.com/Bryan-vd-Brand/CefiderocolFinder.

Background: Carbapenemase-producing Enterobacterales (CPE) have emerged as critical threats to global health. These bacteria are increasingly responsible for challenging outbreaks within hospital settings, leading to increased morbidity and mortality rates. They can be found in hospital water environments, where their presence may pose significant risks for patient acquisition, potentially facilitating transmission through direct and indirect contact.

Objectives: This narrative review aimed to summarize current knowledge regarding CPE in the hospital water environment, elucidate their role in patient acquisition, and evaluate effective decontamination strategies.

Sources: A comprehensive literature search was conducted using the PubMed database, identifying studies published from inception to July 2025. Additionally, manual reference checks were performed to ensure thorough coverage of relevant literature.

Content: CPE are commonly detected in the hospital water environment, particularly in sinks, toilets, and shower drains. Evidence suggests a reciprocal relationship between environmental contamination by CPE and patient acquisition. Various decontamination methods, including chemical and thermal treatments as well as reservoir replacement, have been explored. Although some methods demonstrate efficacy, they often present challenges related to implementation and sustainability.

Implications: Addressing CPE in the hospital water environment is crucial for preventing outbreaks and protecting patient safety. Implementing comprehensive infection control measures and environmental cleaning protocols could significantly reduce the risk of CPE transmission, ultimately improving patient outcomes and public health. The findings underscore the need for ongoing research to better understand contamination dynamics and the effectiveness of decontamination strategies.

Objectives: We aimed to assess the diagnostic value of a battery of confirmatory tests included in the WHO guidelines for bubonic plague, combined and individually, including culture, PCR and serology, and the on-site and laboratory performance of the F1 antigen-based lateral flow rapid diagnostic test (F1RDT).

Methods: Bubo aspirates from patients (all ages) with suspected bubonic plague enrolled into the IMASOY trial (NCT04110340) underwent routine laboratory diagnosis complemented with serology to measure IgG F1 antibodies from blood samples taken on days 1, 11, and 21. The performance of the F1RDT done on site (on-site F1RDT) and at the Central Laboratory for Plague (reference laboratory F1RDT) was compared against two reference standards: RS1 (culture or PCR-positive), which is used in routine practice, and RS2 (RS1 and serology-positive), including all available confirmatory tests for plague.

Results: Of 438 suspected cases, 184 (42%) were confirmed by culture or PCR (RS1) and 211 (48%) by culture, PCR, or serology (RS2). PCR identified 179 cases (85%), culture 137 (65%), and serology 197 (93%). The combination of PCR and culture identified 87% of confirmed cases while the remaining 13% were identified by serology only. The sensitivity and specificity of on-site F1RDT were 94% (95% CI, 89.6-97.0) and 74% (95% CI, 68.2-79.3) against RS1 and 89.1% (95% CI, 84.1-93) and 77.5% (95% CI, 71.5-82.8) against RS2. The sensitivity and specificity of reference laboratory F1RDT were 91.8% (95% CI, 86.9-95.4), 97.6% (95% CI, 94.9-99.1) against RS1, and 82.0% (95% CI, 76.1-86.9) and 99.1% (95% CI, 96.9-99.9) against RS2.

Conclusions: PCR outperforms culture, the previous reference standard. While serology adds diagnostic value, it is impractical for routine use. The F1RDT done on site cannot be relied upon for clinical case management decisions. F1RDT performs better under laboratory conditions and could be implemented in peripheral laboratories for surveillance purposes in resource-constraint settings.