Sad to hear this. It is safe, with proper use. I learned the hard way, using what water I had available with me while travelling. I used water purification drops. However I made 2 mistakes.
1. Using anything but filtered water.
2. Not cleaning the neti pot (sinus pump in this case)
I've had a raging sinus infection the last few months since I began travelling Thailand, after getting checked out I had 6 different infectious bacteria in my sinuses. I always have a bit of a sinus issue so seeing maybe a couple wouldn't surprise me but 6 and one of them being e.coli! Thankfully I've figured out my mistakes and making progress in eliminating it but geez. Can never be too careful it seems when putting something into your body.