Blue WF Mod3 F13

General topic:

antibiotic resistance; How do we kill/detect antibiotic resistant bacteria?

Background:

Antibiotic resistance is a critical problem facing modern medicine, with an increase in number of recent cases involving antibiotic resistant bacteria resulting from overuse of antibiotics. The causes of resistance are still mostly unknown, as are the mechanisms by which it arises and how best to counter it without exacerbating the situation by exerting selective pressure. When dealing with infections in the clinic, determining the nature of the infection is important for applying the most efficient treatment. Current methods for detecting antibiotic resistance, such as phenotypic analysis or molecular detection by PCR of affected genes, tend to be slow or limited to searching for a single known mutation.

In the event of ubiquitous resistance to antibiotics, we would have no way to combat bacterial infections. This would leave us without a good way to combat many prevalent diseases. Additionally, there are currently antibiotic resistant, disease-causing bacteria (MRSA, certain strains of tuberculosis, and certain strains of E. coli, among others) that it would be useful to have the ability to easily detect the presence of or kill.

Specific idea:

Use known resistance mutations to target antibacterial-resistant bacteria in order to detect or kill them. Create a more specific and/or faster assay to detect the presence of antibacterial-resistant bacteria in a bacterial infection Target known resistance mutations to (kill cells expressing mutations/detect specific resistance mutations in the clinic) Alternatively do something with the fact that approach from TB paper can be used to detect resistance (easier assay to detect resistance)?

General Approach:

Generate a Zn finger that specific to the mutation sequences in antibiotic-resistant bacteria Attach a marker (in the case of detection) or a cytotoxic/antibiotic agent (in the case of killing antibiotic-resistant bacteria) to the Zn finger Deliver the Zn finger to the cells Use the results of Zn finger treatment appropriately

References

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC89006/ Describes current methods for detecting antibiotic resistance - phenotypic analysis is still the method of choice for most clinical applications, but molecular methods (PCR and similar) have the advantage in detecting specific mutations.

http://www.nature.com/ng/journal/v45/n10/full/ng.2747.html After sequencing 47 strains of TB, researchers found that there were multiple resistance sequences that were conserved throughout the different strains. Resistance sequences were shown to provide specific drug resistance.

http://pubs.acs.org/doi/abs/10.1021/ac048703c Bacterial genomic DNA was attached to a chip. The microarray chip was used to detect the bacterial species whose genome was attached to the chip, and showed a low proportion of cross-hybridization.

http://openwetware.org/wiki/Preparing_chemically_competent_cells Protocol to generate chemically competent cells. In the event that we need to transform the Zn fingers into the cells, they need to be chemically competent.

http://www.nature.com/nmeth/journal/v9/n8/full/nmeth.2030.html Describes the generation and delivery of Zinc fingers to cultured cells. Zinc fingers were generated using PCR amplification from mammalian expression vectors and fusing the DNA binding sequence with a DNA cleavage domain. They were then transformed into chemically competent cells, and the of the cleavage protein were quantified.

http://www.ncbi.nlm.nih.gov/pubmed/23912527 On-chip culturing methods were combined with Surface Plasmon Resonance (SPR) to detect low levels of a bacterial pathogen. This decreased the number of processing steps and the processing time needed to detect bacterial pathogens.

http://www.sciencedirect.com/science/article/pii/S0925400507002456 Description of a chip to detect bacteria using microfluidics and monoclonal antibodies. A sample containing bacteria is passed through a well on the chip. Antibodies hold cells in place, which changes the impedance of the well. This change can then be measured to determine whether and how many bacteria were present. The chip is used for concentrations down to 10^4 CFU/mL, roughly appropriate for a urinary tract infection.

http://en.wikipedia.org/wiki/List_of_antibiotics