I would seriously, seriously doubt this story.
In order for this to happen, the underwear would have to have wet discharge on it - once it's dry, the bacteria would die. In addition, that bacteria would have to align perfectly with his urethra in order to enter it.
And where did he get this dirty underwear?
For herpes, pretty much the same, except that the person who had worn the underwear would have to have herpes AND chlamydia, would have to have had either a herpes outbreak or had viral shedding, and somehow, all of that survived the air, and perfectly aligned with his skin and urethra to create the perfect storm of infection. There'd also have to be enough bacteria (chlamydia) and enough virus (herpes) surviving the air, the friction, etc., to be able to infect him.
If it were my partner, I'd call it a big fat lie from a big fat liar who lies. That's just me, though.
How did you test for herpes? Did you get a type specific IgG blood test? Make sure it is a type specific test, and not one that gives you one result for both types. (This is not for his benefit, but for yours.) You may have hsv1, which could have been an infection you acquired as a child or something, and not a genital infection.
This is not to alleviate his big lie, but to make sure you are aware of what you may or may not have.
I'm sorry you are dealing with this. :(