Clinical Microbiology and Infection最新文献

Objectives: Aimed to trace the clonal dissemination of ceftazidime-avibactam-resistant Klebsiella pneumoniae and clarify the complex ceftazidime-avibactam-resistance mechanism caused by multiple β-lactamase variants.

Methods: This study isolated six ceftazidime-avibactam-resistant K. pneumoniae clinical strains from six inpatients in the hepatobiliary surgery department. The antimicrobial resistance phenotypes, genotypes and single nucleotide polymorphisms (SNPs) of the strains were analyzed. The resistance mechanism of K. pneumoniae strains to ceftazidime-avibactam was clarified through molecular cloning and enzyme kinetic measurement. The transferability of ceftazidime-avibactam resistance in the strains was verified by conjugation test, S1-pulsed-field gel electrophoresis (PFGE) and plasmid sequence analysis. Fitness was determined using bacterial growth curves and plasmid stability tests.

Results: The number of SNPs between all six K. pneumoniae strains was less than six, indicating a nosocomial clonal dissemination incident. KPC-157 was proven to be unable to mediate resistance to ceftazidime-avibactam. We revealed that CTX-M-249 which mutated from CTX-M-65 (Ser130Gly & Pro167Ser) could mediate resistance to ceftazidime-avibactam, since avibactam could not efficiently inhibit the enzyme activity. Under the selective pressure of ceftazidime-avibactam, the plasmid carrying bla_CTX-M-249 could be transfer into the recipient cell. Based on the analysis of genomic evolution and medical history, the selective pressure exerted by ceftazidime-avibactam during transmission may contribute to the mutation, replication and truncation of the resistance gene region especially the complex evolution of bla_CTX-M-65. The coexistence of bla_CTX-M-65 and bla_CTX-M-249 alleles on different plasmids could evolve into two copies of bla_CTX-M-249, enhancing the resistance to ceftazidime-avibactam.

Conclusions: This study reported the clonal dissemination of KPC-157-producing ceftazidime-avibactam-resistant K. pneumoniae strains and revealed the resistance mechanism of the novel variant CTX-M-249 for the first time. The dissemination of these mutant strains posed an alarm for global infection prevention and control.

Objectives: Chest-X ray (CXR) and/or C-reactive protein (CRP) could help general practitioners (GPs) distinguish community-acquired pneumonia (CAP) from other lower respiratory tract infections (LRTIs). This study aims to explore whether CXR and/or CRP in clinically suspected CAP reduce antibiotic initiation by GPs.

Methods: We conducted a prospective, randomised, controlled, digital case vignette study assigning French GPs to patients' vignette with clinically suspected CAP and 1) no further examination, 2) CXR as first line test, 3) CRP as first line test, or 4) CRP in addition to CXR. The primary endpoint was antibiotic initiation rate.

Results: Among the 3,729 included GPs (median age= 40 years [IQR 34-50], 66% women), 2,472 GPs were assigned to "CXR as first line test" arm (1,238 with "CXR negative" and 1,234 with "CXR positive") of whom 71.4% (1,765) initiated antibiotics as compared to 90.2% (1,134) of the 1,257 GPs assigned to "no CXR" arm (21% reduction; RR= 0.79, 95% confidence interval [95%CI]: 0.77-0.82]). In the 1,238 GPs with "negative CXR", the reduction achieved 51% (RR= 0.49, 95%CI: 0.46-0.52]) as compared to no CXR. Among the 1,228 GPs assigned to "CRP as first line test", 76.3% (937) initiated antibiotics (15% reduction in the antibiotic initiation (RR= 0.84, 95%CI: 0.81-0.87)) as compared to no CXR. Adding CRP as a reflex test to CXR systematically increased antibiotic initiation when CRP was positive and decreased it when negative.

Conclusion: In patients with clinically suspected CAP, systematic CXR as first line test independently of its result, and to a lesser extent CRP as first line test or as reflex test, significantly reduce antibiotic use.

Objectives: Streptococcus suis is an emerging zoonotic porcine pathogen and a leading cause of adult bacterial meningitis in Southeast Asia, associated with raw pork consumption. Most zoonotic S. suis infections globally are caused by strains from lineage CC1 carrying a serotype 2 capsule. However, in Thailand, ∼40% of the reported zoonotic infections are caused by two endemic lineages, CC104 and CC233 which also have a serotype 2 capsule. In this study, we aimed to identify the drivers of the emergence and recent evolution of these two lineages.

Methods: We sequenced the whole genomes of 141 Thai S. suis zoonotic and porcine strains isolated over a 15-year period and combined them with a curated global dataset of 2761 published S. suis genomes. Using comparative genomics, Bayesian evolutionary models and multivariate analysis we investigated the emergence of zoonotic potential and multi-drug resistance in CC104 and CC233.

Results: We estimated recent emergence dates for both CC104 (1990; 95% posterior: 1987-1992) and CC233 (2002; 95% posterior: 2000-2004). Both lineages acquired a serotype capsule 2 from CC1 through a capsule locus switching event, prior to their emergence. Both lineages have also experienced multiple antimicrobial resistance (AMR) acquisition events, with some strains carrying 12 determinants encoding resistance against eight classes of antibiotics. Most importantly, CC104 and CC233 lineages are the first zoonotic lineages to have acquired increased resistance to penicillin and ceftriaxone, which form the standard therapy to treat S. suis infections in humans.

Conclusions: Horizontal transfer of multiple genomic regions can cause rapid emergence of novel multi-drug-resistant zoonotic S. suis lineages. As S. suis is mainly controlled and treated through the use of antibiotics in both pigs and humans, these findings highlight the urgent need for improved and enhanced surveillance, infection control, and treatments.

Scope: Infectious diseases consultation (IDC) services contribute to optimized infection management and are associated with improved outcomes, particularly in difficult-to-treat infections. However, there is uncertainty on how IDC should best be performed, reported, and communicated to achieve optimal impact and adherence. This consensus paper aims to provide structured expert consensus guidance on possible quality indicators (QIs) for IDC activities and reports.

Methods: A systematic literature review was performed but yielded no pertinent findings. Based on experience in clinical practice, the authors proposed 30 potential QIs in four major IDC domains. A Delphi-based anonymous online survey among ID specialists and clinical microbiologists was conducted with two evaluation rounds. QIs were evaluated on 5-point Likert scales (-2, -1, 0, +1, +2). Five possible QIs were additionally evaluated using scaling bars (from 0: only focused assessment/basic evaluation to 10: complete assessment/detailed evaluation). Consensus for a QI was reached when ≥ 80% of the responses showed a strong agreement (+2) in the first round and when ≥ 80% of responses showed a strong agreement (+2) or ≥ 85% agreement for +1 or +2 on the Likert in the second round. Three clinical case scenarios were included to estimate the time required for IDC. Additionally, options for (automated) preparation and artificial intelligence (AI) support for IDC reports were assessed.

Questions addressed by consensus and recommendations: The survey was completed by 51 IDC experts of 17 different countries in the first round and by 26 experts of 10 countries in the second round. Consensus was reached for 25 possible QIs categorized in four major domains (history and risk factors, bedside assessment, recommendations, and reporting), emphasizing a thorough conduct and documentation of IDC activities. Required time for IDC ranged from 35 minutes for simple or follow-up consultations to 55 minutes for complex cases. Almost half of 20 IDC procedures were judged as amenable to benefit from automation and AI support. This consensus paper proposes a comprehensive set of possible QIs for IDC services. The integration of these indicators may standardize evaluation, enhance the effectiveness of IDC, and facilitate international benchmarking. Further research is required to validate these QIs in diverse clinical settings and explore the integration of AI tools in clinical workflows.

Background: Antifungal susceptibility testing (AFST) is central to antifungal stewardship; however, MIC results can be variable and may require careful interpretation because endpoints can be ambiguous, clinical breakpoints are lacking for many species-drug combinations, and results may differ between methods and platforms.

Objective: To explain why fungal MICs can vary within and between methods, summarize major sources of inter-method discordance, highlight clinically relevant MIC "blind spots" (tolerance, heteroresistance, rapid adaptive states), and provide practical guidance for routine interpretation and confirmation.

Sources: Narrative mini-review based on representative PubMed literature covering reference standards (CLSI/EUCAST broth microdilution), non-reference formats (gradient diffusion), commercial platforms, reproducibility and endpoint studies, and mechanistic work on tolerance, heteroresistance, and genome plasticity.

Implications: MICs should be interpreted as standardized measurements with known uncertainty. Expect small, dilution-step variation; standardize inoculum preparation and reading rules; report the testing method and interpretive framework; handle near-cutoff (ECOFF/CBP/ATU) results cautiously; and confirm clinically critical or discordant findings using a reference method or an independent confirmatory method. Where available and clinically relevant, targeted resistance-mechanism testing can support confirmation (e.g., FKS hotspot sequencing for echinocandin resistance in Candida; CYP51A sequencing for azole resistance in Aspergillus fumigatus).

Objectives: We aimed to investigate a nosocomial outbreak of Mycobacterium abscessus subspecies massiliense (MAM) and to track its transmission route via genomic analyses and environmental surveys at a hospital in Osaka, Japan. The outbreak was initially detected in two patients (M1 and M2) with severe disability in 2020 and expanded to five other patients (M3‒M7).

Methods: The 34-month observation period was divided into three phases separated by two interventions. Mycobacterial culture screening was performed for 294 clinical and environmental samples. We confirmed that five patients (M1‒M5) had infections in Phase 1 (March 2020-July 2021) and implemented an initial intervention. In Phase 2 (November 2021-May 2022), new patients (M6 and M7) were identified, wherein an environmental survey identified MAM strains, prompting a second intervention. No patients were identified in Phase 3 (September-December 2022). However, MAM was isolated from the environment during follow-up surveys. A total of 52 MAM isolates were analyzed, including 11 clinical isolates (one from M1-M2 in each phase and one each from M3-M7) and 41 environmental isolates obtained from care gloves, medical devices, and room equipment surrounding patients. We sequenced the isolate genomes and identified 15 subclone clusters with a threshold of 24.5 single-nucleotide variants (SNVs).

Results: The overall SNV distribution of the clinical and environmental strains was within 61 SNVs, showing near-identical genomes. Clinical strains from patient M2 with persistent positivity were classified as the same subclone, with 0-6 SNVs. The isolate from a wagon brought into patient rooms showed the lowest number of SNVs (3-8) compared with isolates from M2. This subclone cluster, involving M2 and wagon isolates, formed the hub of the inter-cluster connection of 11 clusters comprising other clinical and environmental strains.

Conclusions: M. abscessus could persist in dry environments and might be indirectly transmitted via fomites.

Background: Current tuberculosis (TB) diagnostics have limited sensitivity in children, resulting in undiagnosed and untreated cases; host blood biomarkers have the potential to narrow this diagnostic gap.

Objectives: To conduct a systematic review to identify host blood biomarkers which diagnose childhood TB and to summarize biomarker accuracy.

Methods: Data sources: MEDLINE, Embase, Cochrane Central Register of Controlled Trials, SCOPUS, ClinicalTrials.gov, and World Health Organization (WHO) Global Index Medicus.

Study eligibility criteria: Original studies that reported biomarker concentration and/or diagnostic accuracy for childhood TB.

Participants: Children <15 years undergoing evaluation for TB disease.

Tests: Any host blood biomarker measured prior to anti-TB therapy.Reference standards: Mycobacterial culture, nucleic acid amplification tests, and/or clinical diagnosis.Assessment of risk of bias: Quality Assessment of Diagnostic Accuracy Studies-2.Methods of data synthesis: A hierarchical bivariate model was used for meta-analysis.

Results: Fifty-five studies were included, of which 42 (76.4%) studies were at high risk of bias and/or had applicability concerns. The following biomarker classes were reported: cytokine/protein (n=39 studies), mRNA (n=10 studies), miRNA (n=4 studies), and other (n=11 studies). Twelve biosignatures (seven cytokine, four metalloproteinase, one miRNA) and two individual biomarkers (one cytokine, one metalloproteinase) met the WHO target product profile (TPP) for TB disease diagnosis (sensitivity ≥95%, specificity >98%). Meta-analysis was conducted for the cytokine interferon-γ-inducible protein 10 (IP-10) from seven studies; summary estimates of sensitivity (85.2%, 95% CI, 71.1-93.1%) and specificity (59.3%, 95% CI, 44.7-72.5%) did not meet WHO TPP.

Discussion: Host blood biomarkers were identified that met WHO targets for childhood TB disease diagnosis, however, most were reported from a single centre. Meta-analysis did not support IP-10 as an accurate stand-alone biomarker. High-quality studies are needed to validate host blood biomarkers in larger cohorts, and future work should focus on the development of point-of-care tests suitable for low resource settings.