Prospects for standardisation of methods and guidelines for disc susceptibility testing

The influence of the phylum Planctomycetota in the environmental resistome

Antimicrobial resistance is one of the leading causes of death worldwide and research on this topic has been on the spotlight for a long time. More recently and in agreement with the One Health Approach, the focus has moved towards the environmental resistome. Members of the phylum Planctomycetota are ubiquitously present in the environment including in hotspots for antimicrobial resistance selection and dissemination. Furthermore, phenotypic broad-range resistance has been observed in diverse members of this phylum. Here we review the evidence available on antimicrobial resistance in the underexploited Planctomycetota and highlight key aspects for future studies.

How To: ECOFFs - the why, the how and the don´ts of EUCAST epidemiological cutoff values

BACKGROUND

Identifying the MIC wild type distribution and its delineation of species targeted for receiving antimicrobial agent breakpoints is an important first step for determining clinical breakpoints. Having the main responsibility in EUCAST for characterizing the wild-type distributions and the setting of epidemiological cutoff values (ECOFFs), we explain the why, the how and frequent misconceptions of wild-type MIC distributions and ECOFFs.

OBJECTIVES

To clarify how wild type MIC distributions and ECOFFs for agents and important target organisms are defined and determined and why these are important tools in microbiology, as well as to point to common misunderstandings and inappropriate use.

SOURCES

The EUCAST database of >40 000 MIC distributions, publications addressing the definition of wild-type MIC distributions and ECOFFs in bacteria and fungi. The EUCAST Standard Operating Procedure 10. Documents published by the European Centre for Disease Control and the European Food Safety Agency.

CONTENT

The rationale for defining wild-type distributions and ECOFFs is explained. Setting breakpoints that bisect wild-type MIC distributions lead to poor methodological reproducibility and poor correlation between clinical outcome and susceptibility testing results. The methods applied by the European Committee on Antimicrobial Susceptibility Testing (EUCAST) to selecting distributions for aggregation and website display are described, highlighting the importance of incorporation of data from multiple sources and methods. The methods used by EUCAST to estimate ECOFFs are outlined. Finally, the common misunderstandings of these processes are addressed.

IMPLICATIONS

The international community needs to agree on the phenotypic definitions of wild-type distributions. Systematic methods for developing and applying ECOFFs are essential to the conduct of phenotypic antimicrobial susceptibility testing and interpretation, which will remain the dominant laboratory method for the foreseeable future.

Toward Decentralizing Antibiotic Susceptibility Testing via Ready-to-Use Microwell Array and Resazurin-Aided Colorimetric Readout

In the face of the global threat from drug-resistant superbugs, there remains an unmet need for simple and accessible diagnostic tools that can perform important antibiotic susceptibility testing against pathogenic bacteria and guide antibiotic treatments outside of centralized clinical laboratories. As a potential solution to this important problem, we report herein the development of a microwell array-based resazurin-aided colorimetric antibiotic susceptibility test (marcAST). At the core of marcAST is a ready-to-use microwell array device that is preassembled with custom titers of various antibiotics and splits bacterial samples upon a simple syringe injection step to initiate AST against all antibiotics. We also employ resazurin, which changes from blue to pink in the presence of growing bacteria, to accelerate and enable colorimetric readout in our AST. Even with its simplicity, marcAST can accurately measure the minimum inhibitory concentrations of reference bacterial strains against common antibiotics and categorize the antibiotic susceptibilities of clinically isolated bacteria. With more characterization and refinement, we envision that marcAST can become a potentially useful tool for performing AST without trained personnel, laborious procedures, or bulky instruments, thereby decentralizing this important test for combating drug-resistant superbugs.

Normalized resistance interpretation, the NRI method: Review of NRI disc test applications and guide to calculations

The normalized resistance interpretation (NRI) method was developed in response to a call for a method to calibrate disc diffusion test results making inter-laboratory comparisons possible. The main use of NRI so far has been in individual laboratories, in medical and veterinary medicine and in the field of marine microbiology. The applications of NRI for disc diffusion tests are reviewed and, in addition, a detailed description of the calculation procedure is presented. NRI provides a fully objective method for ECOFF calculations of disc diffusion antimicrobial susceptibility test results.

A statistical approach for determination of disk diffusion-based cutoff values for systematic characterization of wild-type and non-wild-type bacterial populations in antimicrobial susceptibility testing

In this study, we introduce a new approach for determination of epidemiologic cutoffs (ECOFFs) and resistant-population cutoffs (RCOFFs) based on receiver operating characteristic (ROC) curves. As an example, the method was applied for determination of ECOFFs for seven different beta-lactam antibiotics and wild-type populations of Escherichia coli, Klebsiella pneumoniae, and Enterobacter cloacae. In addition, RCOFFs were determined for bacterial populations with defined resistance mechanisms ("resistotypes"), i.e., extended-spectrum beta-lactamase (ESBL)-positive E. coli, ESBL-positive K. pneumoniae, and ESBL-positive E. cloacae; AmpC cephalosporinase-positive E. coli and AmpC-positive K. pneumoniae; and broad-spectrum beta-lactamase (BSBL)-positive E. coli. RCOFFs and ECOFFs are instrumental for a systematic characterization of associations between resistotypes and wild-type populations.

A self-loading microfluidic device for determining the minimum inhibitory concentration of antibiotics

This article describes a portable microfluidic technology for determining the minimum inhibitory concentration (MIC) of antibiotics against bacteria. The microfluidic platform consists of a set of chambers molded in poly(dimethylsiloxane) (PDMS) that are preloaded with antibiotic, dried, and reversibly sealed to a second layer of PDMS containing channels that connect the chambers. The assembled device is degassed via vacuum prior to its use, and the absorption of gas by PDMS provides the mechanism for actuating and metering the flow of fluid in the microfluidic channels and chambers. During the operation of the device, degas driven flow introduces a suspension of bacterial cells, dissolves the antibiotic, and isolates cells in individual chambers without cross contamination. The growth of bacteria in the chambers in the presence of a pH indicator produces a colorimetric change that can be detected visually using ambient light. Using this device we measured the MIC of vancomycin, tetracycline, and kanamycin against Enterococcus faecalis 1131, Proteus mirabilis HI4320, Klebsiella pneumoniae, and Escherichia coli MG1655 and report values that are comparable to standard liquid broth dilution measurements. The device provides a simple method for MIC determination of individual antibiotics against human pathogens that will have applications for clinical and point-of-care medicine. Importantly, this device is designed around simplicity: it requires a single pipetting step to introduce the sample, no additional components or external equipment for its operation, and provides a straightforward visual measurement of cell growth. As the device introduces a novel approach for filling and isolating dead-end microfluidic chambers that does not require valves and actuators, this technology should find applications in other portable assays and devices.

Setting interpretive breakpoints for antimicrobial susceptibility testing using disk diffusion

Antimicrobial susceptibility testing plays a key role in clinical microbiology. The disk diffusion test dates back to the 1940s and became standardised from the 1950s, with the International Collaborative Study (ICS) and National Committee for Clinical Laboratory Standards (NCCLS) as the two major standards. Interlaboratory variation of disk test results was recognised early but has never been dealt with in a satisfactory manner. The error-rate bounded method was described in 1974 and its role is discussed. Species-specific susceptibility interpretation was coined in 1980 for Proteus mirabilis and chloramphenicol. In the late 1970s, more extensive use of species-specific breakpoints was introduced in Lund (Sweden). At the same time, P. Mouton constructed species-specific regression lines and pointed out the difficulties with narrow ranges of minimal inhibitory concentration (MIC) values. A more general use of species-specific regression lines was made possible with single-strain regression analysis, using one well-defined strain tested in disk diffusion with a range of disk contents. This method made it possible to calibrate the disk test in an individual laboratory. Other methods to achieve such calibration are also described. A recent method, 'MIC-coloured zone diameter histogram-technique', has proven useful for the validation of species-specific interpretive breakpoints. The microbiological breakpoint proposed by Williams in 1990 has experienced a renaissance with the European Committee on Antimicrobial Susceptibility Testing (EUCAST) epidemiological cut-off value (ECOFF). MIC and zone diameter distributions with accompanying ECOFFs for species-antimicrobial combinations are published on the EUCAST website. A method for the reconstruction of wild-type zone diameter populations, namely normalised resistance interpretation, is described. This method can produce resistance figures that are truly comparable between laboratories.

Normalized resistance interpretation as a tool for establishing epidemiological MIC susceptibility breakpoints

Normalized resistance interpretation (NRI) utilizes the fact that the wild-type population on the sensitive side is not affected by resistance development, and therefore a normalized reconstruction of the peak can be performed. The method was modified for MIC distributions by the introduction of helper variables, in-between values assigned the mean of the neighboring numbers of isolates. This method was used on Staphylo- coccus aureus and Escherichia coli MIC distributions for 27 antimicrobials each and obtained from the EUCAST (European Committee on Antimicrobial Susceptibility Testing) website (http://www.eucast.org/mic_distributions/). The number of isolates in each of the 54 distributions ranged from 40 to 124,472. NRI produced normalized distributions in all cases. Cutoff values were calculated for +2.0 and +2.5 standard deviations (SD) above the means and then rounded up to nearest regular MIC dilution step. EUCAST also show cutoff values, ECOFF values, which were used as the reference. The NRI generated +2.0 SD values showed the best agreement with 26 of 27 within ±1 dilution step and 17 exactly on the ECOFF values for Staphylococcus aureus, and 25 of 27 within ±1 dilution step and 14 right on the ECOFF values for Escherichia coli. NRI offers an objective method for the reconstruction of the wild-type population in an MIC distribution for a given bacterial species and an antimicrobial agent. This method offers a new tool in comparative susceptibility studies such as global surveillance of resistance, as well as in quality control in individual laboratories.

Epidemiological MIC cut-off values for tigecycline calculated from Etest MIC values using normalized resistance interpretation

OBJECTIVES

To apply the normalized resistance interpretation (NRI) method to Etest MIC results which have higher precision than conventional log2 dilution MIC tests due to the inclusion of intermediate values. If successful, NRI might provide an objective tool for the definition of epidemiological MIC cut-off values.

METHODS

MICs of tigecycline and other antimicrobial agents were determined for 4771 clinical isolates comprising five Gram-positive and 13 Gram-negative species or species groups using the Etest. Histograms of MIC values were constructed for each species and NRI calculations were applied to them. An upper MIC limit of 2.5 SD above the theoretical mean of the normalized distribution was used for setting the epidemiological cut-off values.

RESULTS

Calculated cut-off values for wild-type strains were between 0.11 and 0.96 mg/L for Gram-positive species, and between 0.44 and 8.3 mg/L for Gram-negative species, except for Pseudomonas aeruginosa, which had a cut-off value of 450 mg/L, consistent with earlier reports on the lack of activity of tigecycline against this species.

CONCLUSIONS

NRI offers an objective method for the analysis of MICs produced using Etests and the determination of epidemiological MIC cut-off values.

Determination of the real standard distribution of susceptible strains in zone histograms

The procedure for NRI, a method for normalised resistance interpretation, is presented. By means of its promising autocalibration system the method generates zone breakpoints for resistance in zone diameter histograms for bacterial species-antibiotic combinations. These breakpoints give a normalised interpretation of resistance which is independent of disc test standard chosen, disc potency, medium used, inoculum size, etc. of the individual laboratory as long as the performance shows good reproducibility and precision. The method should be further tested as a tool for setting "bacteriological breakpoints" or "epidemiological breakpoints", for calculating resistance rates for comparative purposes, e.g. in antibiotic resistance surveillance, and for quality control of the disc diffusion test.

Analysis of parameters and validation of method for normalized interpretation of antimicrobial resistance

The method of normalized resistance interpretation (NRI), uses the high-zone side of the susceptible peak in a zone diameter histogram as an internal calibrator to construct the real standard distribution of susceptible isolates even in the presence of resistant isolates. NRI parameters were optimized using control strain histograms from microbiology laboratories in Stockholm, Argentina, and the Philippines. A moving average based on four-zone values was slightly better than based on two-zone average values. The optimal peak adjustment from the switch position of the moving average was 1.0 for two-zone averages and 2.5 for four-zone averages. A comparison between true means and NRI-calculated means showed a highly significant correlation (R(2)=0.963). Coefficients of variation (CV), comparing the CV of the true distribution of control strain test results with the NRI calculated distribution, identified two types of aberrant histograms. NRI calculations on clinical isolates of Escherichia coli and Staphylococcus aureus from selected laboratories showed a good agreement between the local resistance interpretations with the NRI calculated levels. One type of deviation was most marked with cephalothin histograms for E. coli isolates where the regular zone breakpoints used cut through the population of susceptible strains. With proper markers for required quality of disc test results, the NRI method might be a valuable tool for both resistance surveillance and for quality control of the disc diffusion method.

Comparison and evaluation of antimicrobial susceptibility testing of enterococci performed in accordance with six national committee standardized disk diffusion procedures

Studies were conducted to compare and evaluate antimicrobial susceptibility test results for enterococci obtained by six national committee disk diffusion procedures. Variations in the incidence of isolates in resistance categories and errors were associated with the use of ciprofloxacin, gentamicin, nitrofurantoin, rifampin, and teicoplanin in a number of committee procedures. Results indicate that laboratories performing disk diffusion antimicrobial susceptibility testing may have problems correctly identifying resistance in enterococci with agents used to combat infections and that it may be difficult to compare resistance data for surveillance purposes.

beta-Lactamases in laboratory and clinical resistance

beta-Lactamases are the commonest single cause of bacterial resistance to beta-lactam antibiotics. Numerous chromosomal and plasmid-mediated types are known and may be classified by their sequences or phenotypic properties. The ability of a beta-lactamase to cause resistance varies with its activity, quantity, and cellular location and, for gram-negative organisms, the permeability of the producer strain. beta-Lactamases sometimes cause obvious resistance to substrate drugs in routine tests; often, however, these enzymes reduce susceptibility without causing resistance at current, pharmacologically chosen breakpoints. This review considers the ability of the prevalent beta-lactamases to cause resistance to widely used beta-lactams, whether resistance is accurately reflected in routine tests, and the extent to which the antibiogram for an organism can be used to predict the type of beta-lactamase that it produces.

Disk diffusion susceptibility tests: need for laboratory-specific breakpoints

Significant changes were observed in the measured resistance levels of Escherichia coli and Staphylococcus aureus when the Biodisk disk susceptibility test method used in 1992 was replaced with another commercial method, Oxoid. For example, when non-species-specific breakpoints were used, the frequency of cephalotin-resistant E. coli was 12% of all isolates in 1992 but only 4% in 1993; the corresponding figures for the intermediately resistant isolates were 84% and 8%. The population distribution histograms were however, practically unchanged. Thus, the resistance percentages apparently did not reflect the real development of resistance. Similar findings were also made for several other antimicrobials. Susceptibility test breakpoints should therefore be examined separately for all bacterial species in each laboratory, and the application of adjusted laboratory-specific breakpoints should be considered. For this purpose, the WHONET computer program provides excellent assistance.

Interlaboratory variations of fluoroquinolone susceptibility testing. An international study to validate the quality of microbiology results reported during the fleroxacin clinical trials

Fleroxacin, a newer fluoroquinolone, has been investigated extensively in worldwide clinical trials by laboratories using a variety of in vitro susceptibility testing methods. These methods differ in their technical details, leading to applied interpretive criteria that can also differ from nation to nation and from method to method. This retrospective three-phase investigation was designed to assess the disk diffusion and minimum inhibitory concentration (MIC) result variations produced by European laboratories participating in fleroxacin clinical trials as compared with the results of a reference laboratory performing National Committee for Clinical Laboratory Standards (NCCLS) tests. In "phase I," 105 clinical trial strains (1988-1989) from six European investigators were processed by the reference laboratory. In comparison of participant and reference laboratory zone diameters, absolute qualitative agreement was 88.7% for the approved NCCLS interpretive criteria and 94.8% for the criteria used in the fleroxacin urinary tract infection clinical trials. Only three false-susceptible results (3.1%) were reported by the investigators. In the remaining phases of this study (unknown challenge strains and contemporary clinical isolates), the investigator laboratory zone diameters and MICs were within limits of acceptable test variation, that is, +/- 4 mm by disk diffusion and +/- 1 log2 dilution step by the MIC method. For laboratories using the German (DIN) and French (SFM) methods, however, a trend toward larger zones was observed. The greatest variation between participant and NCCLS results was produced when fastidious isolates such as Haemophilus influenzae (significantly smaller zone diameters) were tested. In general, the European fleroxacin clinical trial laboratory results (organism identification and susceptibility tests) could be considered comparable to data produced with NCCLS reference methods, indicating that clinical trial results from wider sources could be used for drug registry by the US Food and Drug Administration (FDA) or by other national agencies.(ABSTRACT TRUNCATED AT 250 WORDS)