In an example method, a series of time-based clustering images is generated for a plurality of library fragments from a genome sample. Each time-based clustering image in the series is sequentially generated. To generate each time-based clustering image in the series: i) a respective sample is introduced to a flow cell, the respective sample including contiguity preserved library fragments of the plurality of library fragments, wherein the contiguity preserved library fragments are attached to a solid support or are attached to each other; ii) the contiguity preserved library fragments are released from the solid support or from each other; iii) the contiguity preserved library fragments are amplified to generate a plurality of respective template strands; iv) the respective template strands are stained; and v) the respective template strands are imaged.

In an example method, a series of time-based clustering images is generated for a plurality of library fragments from a genome sample. Each time-based clustering image in the series is sequentially generated. To generate each time-based clustering image in the series: i) a respective sample is introduced to a flow cell, the respective sample including contiguity preserved library fragments of the plurality of library fragments, wherein the contiguity preserved library fragments are attached to a solid support or are attached to each other; ii) the contiguity preserved library fragments are released from the solid support or from each other; iii) the contiguity preserved library fragments are amplified to generate a plurality of respective template strands; iv) the respective template strands are stained; and v) the respective template strands are imaged.

The present invention relates to methods for the qualitative and quantitative determination of the susceptibility of microbial organisms such as bacteria to antimicrobial agents such as antibiotics. For example, the present invention provides a method of determining the susceptibility of a unicellular or multicellular microorganism to an antimicrobial agent by acoustic flow cytometry. The method comprising exposing cells of the microorganism to at least one antimicrobial agent, wherein said cells of the microorganism are in and/or derived from a sample obtained from a subject having or suspected of having an infection with said microorganism; measuring effect of said at least one antimicrobial agent on cellular morphology of said cells of the microorganism by acoustic flow cytometry; and determining susceptibility of the microorganism to the at least one antimicrobial agent from the acoustic flow cytometry data output.

In an example method, a series of time-based clustering images is generated for a plurality of library fragments from a genome sample. Each time-based clustering image in the series is sequentially generated. To generate each time-based clustering image in the series: i) a respective sample is introduced to a flow cell, the respective sample including contiguity preserved library fragments of the plurality of library fragments, wherein the contiguity preserved library fragments are attached to a solid support or are attached to each other; ii) the contiguity preserved library fragments are released from the solid support or from each other; iii) the contiguity preserved library fragments are amplified to generate a plurality of respective template strands; iv) the respective template strands are stained; and v) the respective template strands are imaged.

The present invention relates to a combination of fluorescent dyes for identifying, or differentiating between, different bacterial strains, wherein the combination comprises two or more of the following fluorescent dyes: SYBR Green I, SYTO 13 or 9, and/or DiSC3(5) and/or FM4-64. The device is particularly suited for identifying the type of bacterial infection causing a Urinary Tract Infection (UTI) and can be used to help identify which antimicrobial agents would be suitable for the treatment the infection.