Simner, Patricia J

ABSTRACT Commercial antimicrobial susceptibility testing (AST) systems for gram-negative bacteria provide operational advantages over reference broth microdilution (BMD) testing, but the results produced by commercial AST systems might not be as accurate as the reference method. Assessing and comparing the performance of AST systems can be informative for clinical microbiology practice. In total, 280 clinical isolates and 100 isolates from the U.S. Centers for Disease Control and Prevention Antimicrobial Resistance Isolate Bank, including Enterobacterales and Pseudomonas aeruginosa, were intended to be tested using disk diffusion (DD) and automated commercial AST systems, such as Selux AST System (Selux Diagnostics), MicroScan (Beckman Coulter), Phoenix (Becton, Dickinson and Company), and Vitek 2 (bioMérieux). These results were compared to BMD as the reference standard. In total, 372 isolates were assessed. For Enterobacterales, the greatest frequency of very major errors was identified with cefepime by Vitek 2 (29.0%) and ertapenem by DD (9.1%); essential agreement less than 90% was identified with the following combinations: aztreonam by MicroScan (86.4%), aztreonam by Vitek 2 (88.9%), cefepime by Selux (86.3%), cefepime by Vitek 2 (76.8%), ceftazidime by Vitek 2 (89.9%), and levofloxacin by MicroScan (83.4%). For P. aeruginosa , essential agreement less than 90% was identified with the following combinations: gentamicin by Selux (87.2%), tobramycin by Selux (86.6%), and ciprofloxacin by Phoenix (88.4%). Overall, antimicrobials that had low demonstrable bias across all automated commercial AST systems included ampicillin, amoxicillin-clavulanate, ceftazidime-avibactam, ertapenem, and trimethoprim-sulfamethoxazole. Comparing commercial testing systems head-to-head against a reference standard provides insight into the strengths and weaknesses of the performance of these test systems, and these insights can subsequently inform local decisions regarding further investigations and potential operational mitigation strategies. IMPORTANCE This study assessed and compared the performance of multiple commercial antimicrobial susceptibility testing (AST) systems and disk diffusion methods. The accuracy of determining minimum inhibitory concentrations or zone diameters of antimicrobials and the associated interpretive categories were studied for 372 isolates of Enterobacterales and Pseudomonas aeruginosa . Performance of the evaluated systems revealed that multiple antimicrobial-organism combinations were below the standards typically required by regulatory agencies and clinical laboratories. These deficiencies varied across the commercial platforms and disk diffusion methods, highlighting the importance of benchmarking studies that compare the performance using identical isolates. These identified performance weaknesses may warrant further study and/or the implementation of mitigation strategies in clinical laboratory operations to prevent the reporting of errant results.

ABSTRACT Metallo-beta-lactamase (MBL)-producing Enterobacterales are a global public health concern. Infections caused by these pathogens are often hard to treat, with few effective agents currently available. While aztreonam-avibactam only recently gained U.S. and European regulatory approval, laboratories have implemented laboratory-developed tests (LDTs) using existing aztreonam and ceftazidime-avibactam reagents. We sought to compare the performance of four phenotypic methods, up to three reagent manufacturers, and two media manufacturers. One hundred two MBL-producing Enterobacterales isolates were evaluated at two sites (Centers for Disease Control and Prevention [CDC] and Johns Hopkins University [JHU] School of Medicine). The performance of four methods was evaluated: broth disk elution (BDE), disk stacking (DS), gradient diffusion strip stacking (SS), and a strip-to-disk proximity (strip-disk) method, which were compared to reference broth microdilution (rBMD) tested in parallel. Respective category agreement for CDC and JHU was 92.2% and 96.1% for BDE, 51%–76.5% and 31%–49% for DS, 71.6%–86.3% and 83.3%–86.3% for SS, and 82.4%–87.3% and 80%–89.2% for the strip-disk method. The SS essential agreement ranged from 46.1% to 62.7% for JHU and 54.9% to 92.2% for CDC. Interlaboratory reproducibility was 93.1% for rBMD, 92.2% for BDE, 47.1%–53.1% for DS, 76.5%–80% for SS, and 87.3%–88.9% for strip-disk. BDE was the only method that exceeded acceptable performance of >90% accuracy and reproducibility. DS had the lowest and most variable performance between sites and among the different disk manufacturers used. LDTs for combination testing can be highly variable, and further work is needed to improve standardization and harmonization to achieve accurate and reliable results for clinical purposes. IMPORTANCE Carbapenem-resistant Enterobacterales are classified as an urgent public health threat in the Centers for Disease Control and Prevention’s 2019 Antibiotic Resistance Threats Report. Among the most concerning resistance mechanisms are carbapenemase enzymes encoded on mobile genetic elements, which can spread rapidly between bacteria. Of the various carbapenemases, metallo-beta-lactamases are particularly challenging, as they confer resistance to nearly all beta-lactams, and current treatment options remain limited. While aztreonam-avibactam has been U.S. Food and Drug Administration (FDA)-approved for treating certain infections with limited or no alternative treatment options, no FDA-cleared susceptibility test is yet available. In this context, laboratory-developed methods, such as combination testing of aztreonam and ceftazidime-avibactam, play a critical role in guiding therapy. Our study evaluates several of the more common laboratory-developed tests compared to reference broth microdilution and found that broth disk elution was the most accurate; in contrast, other methods had variable performance, some demonstrating limited reliability and being prone to overcalling resistance.

ABSTRACT Candida auris is an emerging pathogen known for causing invasive, multidrug-resistant infections and healthcare-associated outbreaks. Measuring the relatedness of C. auris strains is critical for detecting and preventing healthcare-associated transmission. Whole genome sequencing (WGS) and analysis of single-nucleotide polymorphisms (SNPs) offer high-resolution assessments of genetic relatedness and antifungal susceptibility; however, interpretation requires an understanding of inter- and intra-patient C. auris diversity and genotypic markers of resistance, respectively. This study aimed to define SNP thresholds for assessing C. auris relatedness in healthcare-associated outbreak investigations, predict antifungal resistance via genotypic markers, and evaluate patient risk factors to inform future surveillance strategies. WGS was performed on 68 C. auris isolates (clades I and III) obtained from 31 hospitalized patients across a healthcare system between 2021 and 2024. Using MycoSNP analysis, we observed a maximum intra-patient variation of 14 SNPs. Five probable transmission clusters were identified based on epidemiologic links, with patient isolates differing by a median of 5 SNPs (range: 0−12). Analysis with a commercial pipeline (refMLST, BugSeq) showed similar clustering patterns. All new detections occurring more than 1 month after admission were linked to a cluster, representing a highly specific indicator of healthcare-associated infection. WGS detected known genotypic markers for fluconazole (ERG11 Y132F, F126L, and MRR1 N647T) and micafungin (FKS1 F635C) resistance, with the latter emerging during antimicrobial therapy. In addition, putative FUR1 mutations (G207R and Q16::STOP) associated with flucytosine resistance were identified. These findings emphasize the utility of WGS for identifying healthcare-associated clusters of C. auris and predicting antifungal resistance. IMPORTANCE Candida auris is a difficult-to-treat yeast that causes invasive infections in vulnerable patient populations. Healthcare exposure is a key risk factor for becoming colonized or infected with C. auris , and infection prevention groups focus on curbing the spread of this organism within the healthcare environment. Whole genome sequencing approaches are key for supporting these efforts, as they can help define clusters of C. auris transmission and can also provide insight into antifungal resistance. Our work provides practical guidance for interpreting genomic data in this setting, helping infection prevention teams respond more effectively to outbreaks and expanding the use of genotypic predictions for antifungal resistance.

ABSTRACT Carbapenem-resistant organisms (CROs) pose a major threat to global health due to limited therapeutic options and their capacity for rapid dissemination. Among these, carbapenemase-producing (CP) strains are of greatest concern, as they hydrolyze most β-lactams, and carbapenemase genes are readily spread via mobile genetic elements. Historically, clinical laboratories relied solely on minimal inhibitory concentration (MIC) results and interpretive criteria to guide therapy, with carbapenemase testing performed mainly for epidemiologic purposes. However, changing carbapenemase epidemiology, the introduction of enzyme-specific novel β-lactam combination agents for treatment, and updated Clinical and Laboratory Standards Institute (CLSI) guidance have renewed the importance of carbapenemase testing among carbapenem-resistant Enterobacterales. The 2025 CLSI M100 update now recommends carbapenemase testing for most Enterobacterales resistant to at least one carbapenem, emphasizing differentiation of key enzymes, such as KPC, NDM, and OXA-48-like, to inform therapeutic decisions and support antimicrobial stewardship. This minireview summarizes the evolution of CLSI guidance from early breakpoint establishment through the “MIC-only” era to the current antimicrobial resistance mechanism-driven framework. Key issues addressed include the clinical limitations of prior clinical breakpoints, challenges in balancing sensitivity and specificity of screening criteria to guide carbapenemase testing in different settings, and the expanding role of rapid phenotypic and molecular detection methods. Revisions to the EDTA-modified carbapenem inactivation method (eCIM) are discussed in light of increasing co-production of metallo-beta-lactamase and serine-carbapenemases. Reintegration of carbapenemase testing into clinical workflows highlights the role of the clinical microbiology laboratory as a critical component of antimicrobial stewardship.

Abstract Background Legionella pneumonia is an important cause of severe pneumonia, yet contemporary data describing its clinical phenotype, diagnostic patterns, and outcomes in the modern era are limited. Methods We conducted a retrospective multicenter cohort study of adults with laboratory-confirmed Legionella pneumonia across an integrated health system between January 2019 and September 2025. The primary outcome was 30-day mortality. Severe disease was defined as having a requirement for high-flow nasal cannula, noninvasive ventilation, mechanical ventilation, or extracorporeal membrane oxygenation (ECMO). Univariate and multivariable logistic regression were used to identify predictors of mortality and severe disease. Results There were 344 patients with laboratory-confirmed Legionella pneumonia during the study period. The median age was 66.6 years, and 45.1% were immunocompromised. Most patients required hospital admission (94.2%), with 36.1% admitted to the intensive care unit; 22.7% required mechanical ventilation and 1.5% ECMO. Thirty- and 90-day mortality were 11.9% and 16.6%, respectively. In multivariable analysis, cirrhosis (OR 10.2, 95% CI 2.15–48.3, P = .003), immunocompromised status (odds ratio [OR] 2.24, 95% CI 1.05–4.77, P = .036), age (OR 1.03, 95% CI 1.00–1.06, P = .031), and lymphopenia at presentation (OR 2.09, 95% CI 1.02–4.24, P = .043) were independently associated with increased 30-day mortality. Among patients who were polymerase chain reaction (PCR) or culture positive, urinary antigen testing was positive in only 25.6%. Conclusions Legionella pneumonia was associated with substantial short-term mortality. Cirrhosis, age, immunocompromised status, and lymphopenia at presentation emerged as independent predictors of 30-day mortality, underscoring the importance of host vulnerability in determining outcomes.

Abstract Background Identification of the microorganisms causing infection in children with central nervous system infection is important. Conventional cerebrospinal fluid (CSF) tests may provide limited pathogen detection. CSF metagenomic next-generation sequencing (mNGS) may provide broader pathogen detection in a single assay. Methods Results of CSF mNGS testing performed at Mayo Clinic on patients and nonpatients between January 2024 and June 2025 were retrospectively analyzed. The subcohort of children treated at Mayo Clinic was analyzed to assess test performance as compared with conventional CSF diagnostics and potential clinical impact. Results In total 134 patients (138 CSF mNGS tests) from 22 US states and 2 international sites were included. Overall positivity was 16% with viruses representing most (59%) detections. In the Mayo Clinic subcohort (n = 15), test positivity was 27%: organisms included single detections of Streptococcus mitis group and HIV type 1, as well as 2 detections of Epstein-Barr virus, all confirmed by conventional tests. Positive results were associated with CSF pleocytosis (P = .026). Higher yield was observed in participants whose care was overseen by pediatric infectious diseases (PID) specialists (P = .026) and when a specimen hold strategy was applied (P = .033). Most results (87%) did not alter antimicrobial therapy, with 2 negative results contributing to antimicrobial de-escalation. Conclusions CSF mNGS demonstrated higher diagnostic yield in patients whose specimens showed CSF pleocytosis and in those who had PID consultation. Diagnostic stewardship strategies were applied, including specimen hold approaches and PID consultation.

The U.S. Food & Drug Administration (FDA) regulates the marketing of manufacturers’ in vitro diagnostic tests (IVDs), including assays for the detection of SARS-CoV-2.