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Any pros and cons? One puts the test substance in sterile discs, while the other one puts it directly into wholes in the agar. Any thoughts?

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I came across a nice Master's thesis that investigated precisely that. The conclusion reads as follows:

Automated microbroth dilution-based testing methods are increasingly used by many clinical microbiology laboratories to determinate antimicrobial susceptibility. Thus, it is vital that these methods are able to accurately determine the correct antibiotic susceptibility patterns of microorganisms being tested. In our laboratory, we use the Trek Sensititre system (Well Plate Method). However, if this system cannot accurately detect resistance visualized as inner colonies on the Kirby Bauer Assay, then the clinical importance of the Trek Sensititre may be called into question.

Our study showed that the Trek Sensititre was unable to detect the additional resistance of inner colonies that are detected using the Kirby Bauer Assay. Nevertheless, there are a number of important limitations associated with the study: Firstly, the inner colonies used in the study were pooled from all inner colonies from the Kirby Bauer plate. Because the colonies were pooled, in some cases from different antibiotic zones, it is possible that a mixed population of resistant organisms that were selected for by the different antibiotics were tested. This possible mixture of multiple different subpopulations may make the results difficult to interpret. Secondly, some inner colonies were selected from antibiotics that do not have any CLSI- 47 approved interpretations and would be considered inappropriate to report. For example, some Pseudomonas aeruginosa isolates displayed inner colonies to ertapenem, an antibiotic that has no CLSI interpretations and a drug that would not be used clinically. The Trek Sensititre results from those inner colonies showed additional issues with multiple different antibiotics. Clinically, the patient would not have been treated with that antibiotic, so that this resistant set of subpopulations may not have been selected for. Thus the results from the study may not be clinically significant but it does open up questions to the possibility that the Trek Sensititre may not detect clinically significant resistant subpopulations.

Given that the Trek Sensititre can miss resistant subpopulations in Gram negative bacilli, it is important to establish the clinical relevance of this finding. If the inner colonies selected for by each of the antibiotic discs was sub-cultured individually instead of pooled together and then run on the Trek Sensititre, then the following results may possibly differ from the pooled inner colonies. An important future direction would be to determine whether the unreported resistance from the organisms in the study had an effect on patient care however, this was beyond the scope of this thesis study. Thus, the clinical significance of this study’s findings require future study. Nevertheless, laboratories should be aware of the potential for missing sub-populations of antimicrobial resistant organisms using broth-based microdilution methods.

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