You are dealing with confidential patient data. You are also dealing with the necessity to secure your data and...
provide tiered access to that data. I would not under ANY circumstances place anything but publicly accessible data into MySQL. I'm sure one of your patients would not be happy if your Web site were hacked, and confidential information was stolen from your database. If someone is recommending using MySQL for something this critical to your business, I certainly hope you find someone else to work with for every aspect of IT related to your business.
Your options for the backend of a Web site with such sensitive data would be Microsoft SQL Server, Sybase, Oracle or DB2. If I were ever working with a medical firm or any other business for that matter that held my confidential data in their databases, and I found out they were using MySQL for storage, I would find another business to work with and would immediately launch an investigation into how my confidential data was handled and secured.
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