Browse
Submit Data
Databases
API
Help

Dataset Information

27 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Broth Microdilution and Gradient Diffusion Strips vs. Reference Agar Dilution Method: First Evaluation for Clostridiales Species Antimicrobial Susceptibility Testing.

ABSTRACT: Antimicrobial susceptibility testing of anaerobes is challenging. Because MIC determination is recommended by both CLSI and EUCAST, commercial broth microdilution and diffusion strip tests have been developed. The reliability of broth microdilution methods has not been assessed yet using the agar dilution reference method. In this work, we evaluated two broth microdilution kits (MICRONAUT-S Anaerobes^® MIC and Sensititre Anaerobe MIC^®) and one gradient diffusion strip method (Liofilchem^®) for antimicrobial susceptibility testing of 47 Clostridiales isolates (Clostridium, Clostridioides and Hungatella species) using the agar dilution method as a reference. The evaluation focused on comparing six antimicrobial molecules available in both microdilution kits. Analytical performances were evaluated according to the Food and Drug Administration (FDA) recommendations. Essential agreements (EA) and categorical agreements (CA) varied greatly according to the molecule and the evaluated method. Vancomycin had values of essential and categorical agreements above 90% for the three methods. The CA fulfilled the FDA criteria for three major molecules in the treatment of Gram-positive anaerobic infections (metronidazole, piperacillin/tazobactam and vancomycin). The highest rate of error was observed for clindamycin. Multicenter studies are needed to further validate these results.

SUBMITTER: Baquer F

PROVIDER: S-EPMC8388896 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Evaluation of Calcium-Enhanced Media for Colistin Susceptibility Testing by Gradient Agar Diffusion and Broth Microdilution.

Project description:Despite the increasing reliance on polymyxin antibiotics (polymyxin B and colistin) for treatment of multidrug-resistant Gram-negative infections, many clinical laboratories are unable to perform susceptibility testing due to the lack of accurate and reliable methods. Although gradient agar diffusion is commonly performed for other antimicrobials, its use for polymyxins is discouraged due to poor performance characteristics. Performing gradient agar diffusion with calcium enhancement of susceptibility testing media has been shown to improve the identification of polymyxin-resistant isolates with plasmid-mediated resistance (mcr-1). We therefore sought to evaluate the broad clinical applicability of this approach for colistin susceptibility testing by assessing a large and diverse collection of resistant and susceptible patient isolates collected from multiple U.S. medical centers. Among 217 isolates, the overall categorical and essential agreement for calcium-enhanced gradient agar diffusion were 73.7% and 65.5%, respectively, compared to the results for reference broth microdilution. Performance varied significantly by organism group, with agreement being highest for Enterobacterales and lowest for Pseudomonas aeruginosa Nevertheless, even for Enterobacterales, there was a high rate of very major errors (9.2%). Performance was similarly poor for calcium-enhanced broth microdilution. While calcium enhancement did allow for more accurate categorization of mcr-1-resistant isolates, there were unacceptably high rates of errors for both susceptible and non-mcr-1-resistant isolates, raising serious doubts about the suitability of these calcium-enhanced methods for routine colistin susceptibility testing in clinical laboratories.

| S-EPMC6989058 | biostudies-literature

Klebsiella pneumoniae and Colistin Susceptibility Testing: Performance Evaluation for Broth Microdilution, Agar Dilution and Minimum Inhibitory Concentration Test Strips and Impact of the "Skipped Well" Phenomenon.

Project description:The emergence of multidrug resistant Gram-negative pathogens, particularly carbapenemase producers, has forced clinicians to use last line antibiotics, such as colistin. Since colistin susceptibility testing presents several challenges, this study aimed at evaluating the performance of two alternative susceptibility methods for Klebsiella pneumoniae, namely, agar dilution (AD) and MIC test strips (MTS). These approaches were compared with the reference method, broth microdilution (BMD), and provide a quantitative description for the "skipped well" (SW) phenomenon. Colistin susceptibility was evaluated by BMD and AD in parallel and triplicate, using 141 K. pneumoniae clinical isolates while MTS performance was evaluated only for a subset (n = 121). Minimum inhibitory concentration analysis revealed that a substantial part (n = 26/141; 18.4%) of the initial isolates was deemed undetermined by BMD due to the following: discordance between replicates (1.4%); presence of multiple SWs (7.8%); and the combination of both events (9.2%). Both AD and MTS revealed a high number of false-susceptible strains ("very major errors"), 37.5% and 68.8%, respectively. However, AD agreement indices were reasonably high (EA = 71.3% and CA = 94.8%). For MTS these indices were lower, in particular EA (EA = 41.7% and CA = 89.6), but the approach enabled the detection of distinct sub-populations for four isolates. In conclusion, this study provides the most comprehensive study on the performance of AD and MTS for colistin susceptibility testing in K. pneumoniae, highlighting its limitations, and stressing the importance of sample size and composition. Further, this study highlights the impact of the SW phenomenon associated with the BMD method for K. pneumoniae.

| S-EPMC8700027 | biostudies-literature

Variability of Daptomycin MIC Values for Enterococcus faecium When Measured by Reference Broth Microdilution and Gradient Diffusion Tests.

Project description:Daptomycin has become a mainstay therapy for the treatment of serious vancomycin-resistant Enterococcus faecium infections. However, concern exists that current testing methods do not accurately predict the clinical success of daptomycin therapy. We evaluated a collection of 40 isolates of E. faecium across three centers by reference broth microdilution (BMD), and two gradient strips, to determine the precision of daptomycin MICs by these methods and the correlation of daptomycin MIC testing with mutations in the liaFSR system, one of the primary daptomycin resistance mechanisms among the enterococci. Daptomycin MICs spanned 3-log2 dilutions by BMD for 60.0% of isolates, 17.5% spanned 4 dilutions, 2.5% spanned 5 dilutions, and 20.0% spanned 6 or more dilutions. Fifteen isolates had MICs interpreted as susceptible by some tests and nonsusceptible by others. Neither BMD nor gradient diffusion tests could reliably differentiate isolates with or without mutations in liaFSR, resulting in a 59.8% very major error rate compared to determination of genotype by BMD, 63.5% by Etest, and 68.5% by MIC test strip. Imprecision in daptomycin MIC determination for E. faecium make establishment of a revised breakpoint challenging. Clinicians should be aware of this testing variability when making treatment decisions for patients with serious infections caused by this organism.

| S-EPMC6125562 | biostudies-literature

Comparison of Agar Dilution to Broth Microdilution for Testing In Vitro Activity of Cefiderocol against Gram-Negative Bacilli.

Project description:Cefiderocol (CFDC) is a siderophore cephalosporin with activity against Gram-negative bacterial species that are resistant to carbapenems and other drugs. The MICs of CFDC were determined for 610 Gram-negative bacilli, including 302 multinational Enterobacterales isolates with characterized mechanisms of beta-lactam resistance, 180 clinical isolates from the Mayo Clinic and Mayo Clinic Laboratories not characterized for specific resistance mechanisms, and 128 isolates with CFDC MICs of ≥8 μg/ml obtained from International Health Management Associates, Inc. (IHMA, Schaumburg, IL). Broth microdilution using standard cation-adjusted Mueller-Hinton broth (BMD) and iron-depleted cation-adjusted Mueller-Hinton broth (ID-BMD), and agar dilution (AD) using standard Mueller-Hinton agar were performed according to Clinical and Laboratory Standards Institute (CLSI) guidelines. MICs were interpreted according to the investigational CLSI, FDA, and EUCAST breakpoints, and results were compared. MICs inhibiting 50 and 90% of organisms (MIC50 and MIC90, respectively), essential agreement (EA), categorical agreement (CA), and error of different types were determined. Results showed considerable discordance between AD and ID-BMD. CFDC showed low EA and CA rates and high error rates for AD in comparison to ID-BMD. Overall, this study does not support use of standard AD for determining CFDC MICs.

| S-EPMC7771473 | biostudies-literature

Gradient diffusion susceptibility testing for <i>Neisseria gonorrhoeae</i>: an accurate alternative to agar dilution in high-MIC strains?

Project description:IntroductionThe correlation of antimicrobial susceptibility testing (AST) between agar dilution and gradient diffusion for Neisseria gonorrhoeae is not well established, especially in strains with high MICs.AimThe objective of this study was to evaluate the accuracy of gradient diffusion for N. gonorrhoeae .MethodsFifty strains of N. gonorrhoeae , all tested by the agar dilution method according to CLSI methods and confirmed to be genetically distinct using molecular typing (NG-MAST), were selected. Isolates with high MICs were targeted. Gradient diffusion was performed for ceftriaxone (CRO), cefixime (CFX), azithromycin (AZT), tetracycline (TET) and fosfomycin (FOS) using two different commercial antimicrobial strips on different culture media (a non-commercial GC agar base with 1 % defined growth supplement and two commercial media). The performance of agar gradient diffusion was assessed based on accuracy, using essential and category agreements (EA and CA).ResultsEssential and categorical agreement were over 90 % for CRO, CFX and AZT on the two commercial agar media tested. Category disagreements were seen for CFX and AZT, mostly just very major errors. For TET, EA ranged from 80 to 96 % and CA ranged from 38 to 76 %, most of the misclassifications being minor errors. Finally, EA for FOS ranged between 80 and 98 %.ConclusionGradient diffusion is an accurate and acceptable alternative for CRO, CFX and AZT. Caution is advised when MICs are reported by gradient diffusion approach breakpoints because of the possibility of very major errors. The use of gradient diffusion is limited for TET because of the high rate of minor errors.

| S-EPMC7494190 | biostudies-literature

Impact of Variations in Test Method Parameters on In Vitro Activity of Surotomycin against Clostridium difficile and Surotomycin Quality Control Limits for Broth Microdilution and Agar Dilution Susceptibility Testing.

Project description:Test parameter variations were evaluated for their effects on surotomycin MICs. Calcium concentration was the only variable that influenced MICs; therefore, 50 μg/ml (standard for lipopeptide testing) is recommended. Quality control ranges for Clostridium difficile (0.12 to 1 μg/ml) and Eggerthella lenta (broth, 1 to 4 μg/ml; agar, 1 to 8 μg/ml) were approved by the Clinical and Laboratory Standards Institute based on these data.

| S-EPMC4767964 | biostudies-literature

Testing of In Vitro Susceptibility of Neisseria gonorrhoeae to Azithromycin: Comparison of Disk Diffusion and Reference Agar Dilution Methods.

Project description:Azithromycin in combination with ceftriaxone is recommended as the first-line treatment for uncomplicated gonorrhea in many countries. Therefore, monitoring of azithromycin susceptibility of Neisseria gonorrhoeae isolates is essential. In 2019, the Clinical and Laboratory Standards Institute (CLSI) listed the MIC breakpoint for a susceptible-only category to azithromycin, but breakpoints for disk diffusion are not yet available. In this study, we evaluated the usefulness of disk diffusion for testing the susceptibility of N. gonorrhoeae isolates to azithromycin. A total of 189 clinical isolates susceptible and nonsusceptible to azithromycin were used. Agar dilution MICs were correlated with inhibition zone diameters of azithromycin disks (15-μg) manufactured by BBL and Oxoid. In addition, an interlaboratory study involving two clinical microbiology laboratories was conducted. There was a strong correlation between disk diffusion and agar dilution for BBL disks (r = -0.74; P < 0.001) and Oxoid disks (r = -0.75; P < 0.001). Using a zone diameter breakpoint of ≥27 mm (susceptible) and ≤26 mm (nonsusceptible) yielded good separation between susceptible and nonsusceptible isolates and the least number of discrepancies. Compared to agar dilution, disk diffusion showed high agreement and kappa values of 95.2% and 0.899 (P < 0.001) for BBL disks and 96.8% and 0.933 (P < 0.001) for Oxoid disks, respectively. Major and very major discrepancies were observed in isolates with azithromycin MICs (1 and 2 μg/ml, respectively) near to the breakpoint. These data illustrate that disk diffusion could be a reliable method in clinical laboratories to test susceptibility to azithromycin in N. gonorrhoeae isolates.

| S-EPMC7587106 | biostudies-literature

Standardized methods and quality control limits for agar and broth microdilution susceptibility testing of Mycoplasma pneumoniae, Mycoplasma hominis, and Ureaplasma urealyticum.

Project description:An international multilaboratory collaborative study was conducted to develop standard media and consensus methods for the performance and quality control of antimicrobial susceptibility testing of Mycoplasma pneumoniae, Mycoplasma hominis, and Ureaplasma urealyticum using broth microdilution and agar dilution techniques. A reference strain from the American Type Culture Collection was designated for each species, which was to be used for quality control purposes. Repeat testing of replicate samples of each reference strain by participating laboratories utilizing both methods and different lots of media enabled a 3- to 4-dilution MIC range to be established for drugs in several different classes, including tetracyclines, macrolides, ketolides, lincosamides, and fluoroquinolones. This represents the first multilaboratory collaboration to standardize susceptibility testing methods and to designate quality control parameters to ensure accurate and reliable assay results for mycoplasmas and ureaplasmas that infect humans.

| S-EPMC3486213 | biostudies-literature

Cefiderocol Antimicrobial Susceptibility Testing against Multidrug-Resistant Gram-Negative Bacilli: a Comparison of Disk Diffusion to Broth Microdilution.

Project description:Antimicrobial susceptibility testing (AST) of cefiderocol poses challenges because of its unique mechanism of action (i.e., requiring an iron-depleted state) and due to differences in interpretative criteria established by the Clinical and Laboratory Standards Institute (CLSI), U.S. Food and Drug Administration (FDA), and European Committee on Antimicrobial Susceptibility Testing (EUCAST). Our objective was to compare cefiderocol disk diffusion methods (DD) to broth microdilution (BMD) for AST of Gram-negative bacilli (GNB). Cefiderocol AST was performed on consecutive carbapenem-resistant Enterobacterales (CRE; 58 isolates) and non-glucose-fermenting GNB (50 isolates) by BMD (lyophilized panels; Sensititre; Thermo Fisher) and DD (30 μg; research-use-only [RUO] MASTDISCS and FDA-cleared HardyDisks). Results were interpreted using FDA (prior to 28 September 2020 update), EUCAST, and investigational CLSI breakpoints (BPs). Categorical agreement (CA), minor errors (mE), major errors (ME), and very major errors (VME) were calculated for DD methods. The susceptibilities of all isolates by BMD were 72% (FDA), 75% (EUCAST) and 90% (CLSI). For DD methods, EUCAST BPs demonstrated lower susceptibility at 65% and 66%, compared to 74% and 72% (FDA) and 87% and 89% (CLSI) by HardyDisks and MASTDISCS, respectively. CA ranged from 75% to 90%, with 8 to 25% mE, 0 to 19% ME, and 0 to 20% VME and varied based on disk, GNB, and BPs evaluated. Both DD methods performed poorly for Acinetobacter baumannii complex. There is considerable variability when cefiderocol ASTs are interpreted using CLSI, FDA, and EUCAST breakpoints. DD offers a convenient alternative approach to BMD methods for cefiderocol AST, with the exception of A. baumannii complex isolates.

| S-EPMC7771458 | biostudies-literature

Concordance of disk diffusion, broth microdilution, and whole-genome sequencing for determination of in vitro antimicrobial susceptibility of Mannheimia haemolytica.

Project description:BackgroundExtensive drug resistance (XDR) is an emerging concern with Mannheimia haemolytica, and a variety of testing methods are available for characterizing in vitro antimicrobial susceptibility.ObjectivesTo compare the concordance among disk diffusion, broth microdilution, and whole genome sequencing (WGS) for susceptibility testing of M. haemolytica before and after mass treatment using tulathromycin.AnimalsForty-eight M. haemolytica isolates collected from high-risk beef stocker calves before and after mass treatment (metaphylaxis) using tulathromycin (Draxxin, Zoetis, Parsippany, NJ) given at the label dosage of 2.5 mg/kg body weight SC in the neck.MethodsIn vitro antimicrobial susceptibility was determined for all 48 isolates using disk diffusion, broth microdilution, and WGS. Concordance was calculated between pairs of susceptibility testing methods as follows: number of isolates classified identically by the 2 testing methods for each timepoint, divided by the number of isolates tested at that timepoint. Discordance was calculated as follows: number of isolates classified differently by the 2 testing methods for each timepoint, divided by the number of isolates tested at that timepoint.ResultsConcordance between testing methods ranged from 42.3% to 100%, depending on antimicrobial evaluated, timing of sample collection, and testing method used. Very major errors were identified in up to 7.7% of classifications whereas minor errors were seen in up to 50% of classifications depending on antimicrobial evaluated, timing of sample collection, and testing method used.Conclusions and clinical importanceOur results show that discrepancies in the results of different susceptibility testing methods occur and suggest a need for greater harmonization of susceptibility testing methods.

| S-EPMC7517867 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data