I'm not a vet but there are parasites that burrow under snake's skin, sounds like that may be what you are dealing with.

There are several anti-parasite drugs that work for snakes, panacure is probably the safest.

I can't make a diagnosis, you really should get your snakes checked out by a quailified reptile vet. You could be dealing with any number of parasites, or a fungal or bacterial infection. Your vet may need to take samples and have lab work done in order to find the proper drug.

In the mean time, I would keep them quarantined from the rest of your collection. Work there cages with disposable gloves and LAST, never touch your other snakes after you've touched them. Wash and even change clothes before you touch your other animals.

It's very easy to transfer such disease through water dishes, feeding tongs, etc. So be very vey cautious.

That's a gorgeous indigo, I'd hate to see it get this!

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