Whole Slide Imaging for High-Throughput Monitoring of Microbial Growth and Its Application to Rapid Antimicrobial Susceptibility Testing

Since conventional culture-based antimicrobial susceptibility testing (AST) methods are too time-consuming (> 24-72 h), rapid AST is urgently needed for preventing the increasing emergence and spread of antimicrobial resistant infections. Although several phenotypic antibiotic resistance sensing modalities are able to reduce the AST time to a few hours or less, concerning the biological heterogeneity, their accuracy or limit of detection are limited by low throughput. Here, we present a rapid AST method based on whole slide imaging (WSI)-enabled high-throughput monitoring microbial growth at single-cell level. The time for determining the minimum inhibitory concentration (MIC) can be sufficiently short to ensure that the growth of each individual cell present in a large population is inhibited. As a demonstration, our technique was able to monitor the growth of several thousand microbes at single-cell level. Reliable MIC for bacteria and fungi was obtained in 1 h and 3 h, respectively. In addition, the application of our method prevails over other imaging-based AST approaches in allowing accurate determination of antibiotic susceptibility for phenotypically heterogeneous samples, in which the number of antimicrobial resistant cells was negligible compared to that of the susceptible cells. Hence, our method shows great Since conventional culture-based antimicrobial susceptibility testing (AST) methods are too time-consuming (> 24-72 h), rapid AST is urgently needed for preventing the increasing emergence and spread of antimicrobial resistant infections. Although several phenotypic antibiotic resistance sensing modalities are able to reduce the AST time to a few hours or less, concerning the biological heterogeneity, their accuracy or limit of detection are limited by low throughput. Here, we present a rapid AST method based on whole slide imaging (WSI)-enabled high-throughput monitoring microbial growth at single-cell level. The time for determining the minimum inhibitory concentration (MIC) can be sufficiently short to ensure that the growth of each individual cell present in a large population is inhibited. As a demonstration, our technique was able to monitor the growth of several thousand microbes at single-cell level. Reliable MIC for bacteria and fungi was obtained in 1 h and 3 h, respectively. In addition, the application of our method prevails over other imaging-based AST approaches in allowing accurate determination of antibiotic susceptibility for phenotypically heterogeneous samples, in which the number of antimicrobial resistant cells was negligible compared to that of the susceptible cells. Hence, our method shows great promise for both rapid AST determination and point-of-care testing of complex clinical microorganism isolates.