Procedure for penis sample ?

Hi everybody. Today I went to see a doctor for some red spots on the head of my penis.
I was diagnosed with mixt balanite, and I'm waiting for lab results regarding some streptococcus.

Now, I have a question for you guys regarding the sample taking procedure.
The doctor put a thin long stick covered with cottonwool, into my penis. It was inserted quite deep inside.
He started moving it arround inside my penis.
I started screming in pain and I did that for about 5 very long seconds, until he pulled it out.
Then he took another sample using the same procedure.

I peed 2 times since then and I scream every time because it hurts really bad just like it hurt when he took the sample.
Now I'm very confused, because looking at things it doesn't make sense to me:
It's been 2 days since I have the red spots. No other sympthoms. No pain, no itching, no soreness.
Today, before I went to the physician the red spots were almost gone. Still no pain or anything.
But now, after the aforementioned procedure I have a wound inside my penis and I suffer really badly everytime I pee.
I mention that I am 30 and I never had a STD or any other pain or sympthoms related to my penis.

My question is:
Is that the correct procedure to use for taking a penis sample ?

I am concerned about stuff like:
- what if this wound won't heal ?
- what if viruses go into my blood thorugh that wound ?
- a urine sample wouldn't have been enough ?
- what is my expectation with this wound and pain and everything ?

Thank you guys, and I wish you never experience what I did today ...