Devices, systems, and methods for single cell bacteria analysis
Provided are devices and methods for detecting the presence, absence, and/or characteristics of bacteria. A microfluidic device for characterizing bacteria is provided. The device contains one or more bacteria trapping channels, and one or more pneumatic channels in contact with the bacteria trapping channels, wherein the one or more pneumatic channels are configured to reduce the height of the one or more bacteria trapping channels to thereby trap bacteria in the one or more bacteria trapping channels if said bacteria are present in a liquid biological sample that is introduced into the microfluidic device. Also provided is a method for identifying bacteria that may be used with the microfluidic device.
1. A method for identifying bacteria comprising:
contacting a sample comprising bacteria with a carbon nanotube and microwave energy such that a probe is introduced into the bacteria, wherein the probe comprises a double strand polynucleotide probe, wherein a first strand of the double stranded probe comprises a detectable label, and a second strand of the double stranded probe comprises a quencher moiety that quenches a signal from the detectable label when the probe is double stranded,
allowing hybridization between only the labeled strand with a polynucleotide in the bacteria if bacteria are present,
and if bacteria are present, detecting a signal from the labeled strand that is hybridized to a polynucleotide in the bacteria to thereby identify the presence of, and/or the type of bacteria in the sample, and if the bacteria are not present, determining a lack of a signal from the labeled strand, and wherein a signal from the labeled strand if present is detected in a microfluidic device, and wherein the microfluidic device comprises: i) one or more bacteria trapping channels, and ii) one or more pneumatic channels in contact with the bacteria trapping channels, wherein the one or more pneumatic channels are configured to reduce the height of the one or more bacteria trapping channels to thereby trap only a single bacterium in the one or more bacteria trapping channels if said bacteria are present in a liquid biological sample that is introduced into the microfluidic device, thereby providing at least one trapped bacterium in at least one of the bacteria trapping channels.
2. The method of claim 1 , wherein the polynucleotide in the bacteria comprises RNA.
3. The method of claim 2 , wherein the RNA is ribosomal RNA (rRNA).
4. The method of claim 3 , wherein the labeled strand comprises a sequence that is complementary to rRNA from a plurality of distinct bacteria species.
5. The method claim 3 , wherein at least two double stranded probes are introduced into the bacteria, and wherein the two double stranded probes each comprise distinctly labeled first strands that have distinct sequences relative to each other, and wherein the two double stranded probes each comprise a second strand comprising a quencher moiety that quenches a signal from the detectable label when the probe is double stranded.
6. The method of claim 1 , comprising determining the presence of the at least one trapped bacterium, and determining antimicrobial susceptibility (AST) for the at least one trapped bacterium by introducing an antimicrobial agent into the one or more bacteria trapping channels wherein the at least one bacterium is trapped, and subsequently determining viability of the at least one trapped bacterium, wherein a lack of lethality of the antimicrobial agent indicates resistance to the antimicrobial agent, and wherein lethality indicates susceptibility to the antimicrobial agent.