The present invention relates to methods and kits for providing high throughput quantitative analysis of impact (e.g., by application of materials which affect — positively and/or negatively — microbial species) on human microbiome.

The present disclosure relates to an assay method for the antimicrobial activity of an antimicrobial agent. The assay method for the antimicrobial activity of an antimicrobial agent according to the present disclosure comprises: injecting an antimicrobial agent into a culture medium in which a strain is grown; shaking the culture medium according to time and sampling the culture medium according to the time; after the sampling, centrifuging the culture medium into which the antimicrobial agent is injected; and after the centrifuging, measuring the number of microorganisms after culturing a bacterial solution from which the antimicrobial agent is removed, wherein the antimicrobial activity can be evaluated depending on the type and content of the antimicrobial agent, and the antimicrobial activity of the antimicrobial agent can be accurately and reliably evaluated.

The present disclosure relates to an assay method for the antimicrobial activity of an antimicrobial agent. The assay method for the antimicrobial activity of an antimicrobial agent according to the present disclosure comprises: injecting an antimicrobial agent into a culture medium in which a strain is grown; shaking the culture medium according to time and sampling the culture medium according to the time; after the sampling, centrifuging the culture medium into which the antimicrobial agent is injected; and after the centrifuging, measuring the number of microorganisms after culturing a bacterial solution from which the antimicrobial agent is removed, wherein the antimicrobial activity can be evaluated depending on the type and content of the antimicrobial agent, and the antimicrobial activity of the antimicrobial agent can be accurately and reliably evaluated.

A method for antibacterial susceptibility testing includes preparing a set of two or more samples of a plurality of bacterial cells from a patient; adding a different amount of a selected drug to each sample; illuminating at least a portion of a sample using a coherent illumination source; capturing a series of speckle images over time of at least a portion of the illuminated sample; and determining an inhibition status of the sample using a machine-learning classifier applied to the series of speckle images. The steps of illuminating the sample, capturing a series of images, and determining an inhibition status are repeated for each sample of the set of two or more samples. The method may include transforming the series of speckle images to a frequency series of speckle images; and determining the inhibition status of the sample uses the machine-learning classifier applied to the frequency series of speckle images.

A method for antibacterial susceptibility testing includes preparing a set of two or more samples of a plurality of bacterial cells from a patient; adding a different amount of a selected drug to each sample; illuminating at least a portion of a sample using a coherent illumination source; capturing a series of speckle images over time of at least a portion of the illuminated sample; and determining an inhibition status of the sample using a machine-learning classifier applied to the series of speckle images. The steps of illuminating the sample, capturing a series of images, and determining an inhibition status are repeated for each sample of the set of two or more samples. The method may include transforming the series of speckle images to a frequency series of speckle images; and determining the inhibition status of the sample uses the machine-learning classifier applied to the frequency series of speckle images.

A method for determining the susceptibility of a bacteria to an antibiotic, comprising transferring one portion of a sample containing living bacterial cells into a bacterial growth medium to create a control sample; transferring another portion of the sample into a bacterial growth medium to which a predetermined amount of antibiotic or predetermined amount of a library of antibiotics has been added to create a test sample; adding an alkyne-modified non-canonical amino acid to both the control sample and test sample during bacterial growth, wherein the alkyne-modified non-canonical amino acid incorporates into surface proteins, internal proteins, or both; reacting the alkyne-containing proteins with an azide-modified detection molecule using click-chemistry to label the cells; detecting the labeled cells using a method that generates a detectable signal; and comparing the signal generated by the control sample to the signal generated by the test sample, wherein a decrease in detectable signal between the control sample and the test sample is indicative of susceptibility of the living bacteria to the predetermined antibiotic or predetermined library of antibiotics.

A method for determining the susceptibility of a bacteria to an antibiotic, comprising transferring one portion of a sample containing living bacterial cells into a bacterial growth medium to create a control sample; transferring another portion of the sample into a bacterial growth medium to which a predetermined amount of antibiotic or predetermined amount of a library of antibiotics has been added to create a test sample; adding an alkyne-modified non-canonical amino acid to both the control sample and test sample during bacterial growth, wherein the alkyne-modified non-canonical amino acid incorporates into surface proteins, internal proteins, or both; reacting the alkyne-containing proteins with an azide-modified detection molecule using click-chemistry to label the cells; detecting the labeled cells using a method that generates a detectable signal; and comparing the signal generated by the control sample to the signal generated by the test sample, wherein a decrease in detectable signal between the control sample and the test sample is indicative of susceptibility of the living bacteria to the predetermined antibiotic or predetermined library of antibiotics.

Provided herein are devices and methods that enable co-incubation of microorganisms. Also provided are methods of making such devices for co-incubation of microorganisms, and various applications of such devices.

Provided herein are devices and methods that enable co-incubation of microorganisms. Also provided are methods of making such devices for co-incubation of microorganisms, and various applications of such devices.

The present invention provides a method for determining the resistance of a microorganism to a drug by detecting at least a transcript of a drug resistance gene from a microorganism in a biological sample, the method comprising the steps of: (i) lysing the cells by means of a chemical or a mechanical method, thereby obtaining a lysate and cell debris; (ii) obtaining a ribosome-antibody complex from the lysate using an antibody or a fragment thereof which binds specifically to a microorganism-ribosomal protein; (iii) purifying the mRNA associated to the ribosome-antibody complex by means of a nucleic acid extraction method; and (iv) submitting the resulting mRNA to a specific gene detection method, thereby identifying the at least one drug resistance gene transcript of the biological sample. Provided methods and kits allow determining the resistance to antibiotics of a biological sample in a rapid and reliable manner, thereby minimizing the risk of AMR and allowing the definition of the therapeutic potential of a selected antibiotic