Electronic – arduino – Reading USB Data From Arduino

The native interface to most glucose meters (Abbott, Bayer, J&J and Roche) is a UART output. There is circuitry at one end of the cable that translates this to USB protocol. It is possible to read the data with a UART by using a 2.5 mm or 3.5 mm plug to connect directly with the meter.

The J&J uses a 3.5 mm plug with Tip being Tx and Ring being Rx (Tx and Rx wrt your UART, not the meter), and communicates at 9600 baud. Except for the various J&J One-Touch models, the signal levels for the other brands are typically neither regular UART (0 / 3.3) or RS232 (+-5) levels but some weird combination. Some models also swap Tx/Rx compared to the J&J. Note: the One Touch Ultra and Ultra 2 use a different (more text based) protocol than the binary protocol used by the Ultra Mini (see CoderTao's answer for a link to the latter).

Does your arduino use the +5V provided by the USB as power and as reference for the A/D? IME it is very unstable, varying for instance between 4.5V and 5.5V. You could try to use a wall-wart + 7805 instead.