(7c) Nano-Biosensors for Fast, High-Throughput Detection of Antimicrobial Resistance

Antibiotics have been an important weapon in the fight against infections for over half a century. However, the extensive use and misuse of antibiotics has resulted in selection and worldwide spread of antibiotic resistant bacteria. Bacteria and other microorganisms that are known to cause infection are remarkably resilient and can develop antibiotic resistance as an outcome of evolution via natural selection. Bacteria acquire antibiotic resistance via spontaneous or induced mutations, or horizontally transferring resistance-conferring genes from one bacterium to the other. Detection and identification of DNA sequences encoding antimicrobial resistance is the key to medical intervention. However, often resistance-causing sequences exist at trace concentrations in vivo within a microbial population, and hence their detection is a challenging pursuit. While second generation deep and ultra-deep sequencing methods, and single copy PCR amplification methods are capable of detecting single nucleotide polymorphisms, however, these methods are not applicable to the clinical laboratory setting because of cost and technical complexity.  Previously, Scanning tunneling microscopy and spectroscopy (STM and STS respectively) has long been used in physical sciences to study electron tunneling, over angstrom scale distances, to measure electronic density of states and use them as fingerprints in surface science to identify adsorbed species. Recently, several groups have started exploring the use of STM for fast, high-throughput sequencing of nucleotides in the field of biophysics. While this technique can be very useful for fast, single molecule detection and simultaneous sequencing of fast mutating pathogens, notorious for developing drug resistance, only Guanine (G) nucleotides have been identified using this technique so far. Here, we present first demonstration of nano-electronic detection of single DNA strands and sequencing of all bases (A or G,T,C), with nanometer scale precision. As a proof of concept on the DNA sequencing potential using STM and STS, we partially sequenced one copy of single stranded DNA molecule of ampicillin resistance gene with over 95% success rate.