I've had loads of these if you're talking about tiny little boils which develop.
Most likely it is not to do with hygiene - its Staphylococcus Aureus which is normally present on the skin not E coli from your botty.
They are caused by excessive sweating (apparently, so my GP said).
What I have found to be effective is Hibi Scrub. Get a bottle of this :
it's anti microbial skin cleanser. I coat the undercarriage of my pants with the stuff before riding - I've also found that wearing padded shorts makes things worse as I sweat more in them, therefore only wear padded shorts in winter time when it's really cold.
Also go see your GP and ask about Fucidin ointment, it's what I've been using and it kind of works ok. Fucidin ointment.
Fusidic acid is only effective on gram-positive bacteria such as Staphylococcus species and Corynebacterium species.
I find that using both seems to keep them at bay, only use the fucidin when you have to, like when a vistor turns up that proves stubborn to shift. use it on morning, noon and night 'till it goes away.
Be very careful if you decide to lance it... make sure everything which goes near it is very clean, ie use the hibiscrub. I lanced one before and it grew into a cyst which then had to surgically removed. Not a pleasant experience and nor was not being able to cycle for six weeks in the middle of summer.
hope that helps a bit,