How to use wild shape

The creature takes a standard action that doesn't provoke attacks of opportunity to use the supernatural ability wild shape. Then you make a new character sheet.

From wild shape, the druid...

• loses the ability to speak if an animal form is assumed, but while in the assumed animal form the druid can make noises and gesticulate like a typical creature of the assumed form.
• gains the ability to communicate with other animals of the same general grouping. Note: Ask the DM what a general grouping is for the assumed form. (That is, do tigers speak the same language as house cats?)

From the effect of a supernatural ability duplicating the effect of the spell beast shape I, the druid...

• gains the base land speed of the assumed form.
• gains a climb speed equal to the assumed form's climb speed but not more than 30 ft.
• gains a fly speed equal to the assumed form's fly speed but not more than 30 ft. This fly speed always has average maneuverability.
• gains a swim speed equal to the assumed form's swim speed but not more than 30 ft. The druid also gains the ability to breathe underwater while swimming.
• gains darkvision with a range equal to the range of the assumed form's darkvision but not more than 60 ft.
• gains low-light vision if the assumed form also has low-light vision.
• gains scent if the assumed form also has scent.
• gains bonuses based on the assumed form's size. Assuming the form of a Small animal grants the druid a +2 size bonus to Dexterity and a +1 natural armor bonus. Assuming the form of a Medium animal grants the druid a +2 size bonus to Strength and a +2 natural armor bonus.

From the effect of a supernatural ability duplicating the effect of a spell of the transmutation subschool polymorph, the druid...

• gains the natural attacks of the assumed form and proficiency sufficient to use those attacks. Note: The druid uses his own base attack bonus but his modified ability scores to determine attack bonus and final damage with these natural attacks.
• gains a +10 bonus on Disguise skill checks made to masquerade as an animal of the assumed form, although specific creatures' forms can't be assumed.
• gains the appropriate size modifiers to armor class and on his attack bonus, Combat Maneuver Bonus, and Stealth skill checks if the druid has changed size. Note: This should also likely include modifiers to Fly skill checks, but this goes unmentioned by the text.
• sees all his carried gear meld into his new form because the assumed form is that of an animal (or plant or elemental). The only magic items that continue functioning are those that both provide constant bonuses and do not need to be activated to function (see here). Note: Enhancement bonuses from magic armor and shields don't usually work either.
• loses the ability to cast spells because the assumed form is that of an animal (or, probably, a plant). Note: The feats Eschew Material and Natural Spell help a druid cast spells while in an assumed form that normally prohibits casting.
• loses extraordinary and supernatural abilities dependent upon on his original form, including keen senses, scent, darkvision, natural attacks, and movement modes.
• loses class features dependent upon his original form, but those class features that allow adding features to the original form can still be used to add such features to the new form. Note: Special restrictions apply to effects of the polymorph subschool (see below).
• gains immunity to other effects of the polymorph subschool. The druid can allow himself to be affected a new polymorph subschool effect, but such an allowance ends this current polymorph subschool effect. Note: This is actually a bigger deal than you might expect.
• gains immunity to effects that change his size.
• gains and loses whatever the GM says he gains and loses if there are any questions. Note: That's actually in the rules.

When the druid gains the ability to also use, for example, beast shape II, the second section is, I think, the only part that needs changing.

Nothing else changes, but the druid's Dexterity-based or Strength-based stuff will need to be adjusted for his modified ability scores. Specifically, a creature that uses the special ability wild shape does not gain the assumed form's skills, does not gain the assumed form's size-based modifiers as if it were advancing as a monster (instead using the special polymorph subschool size change rules), and does not gain the assumed form's base attack bonus nor the assumed form's saving throw bonuses (although the druid's attack bonus and saving throw bonuses may change due to the modified ability scores).

The absence of evidence is not the evidence of absence.

In this case, at least, the above is true. Since the wording for wild shape does not explicitly say conditions are removed/dispelled, and disease is a condition, that condition is not dispelled upon shifting back. It can then be surmised that status affects such as poisoned, blinded, etc, are also not removed upon shifting to and from wildshape, it can be easily concluded that those effects still persist in the original druid's form.

This is not to say a disease is a standard condition like poisoned, blinded, etc. But it is still a condition that persists on the player until the effect wears off, or is cured.

Diseases specify what creatures are affected by them. For example, Cackle Fever:

This disease targets humanoids, although gnomes are strangely immune.

Or Sight Rot:

This painful infection causes bleeding from the eyes and eventually blinds the victim. A beast or humanoid that drinks water tainted by sight rot must... etc.

After this point, the real question becomes does a mundane disease that affects a specific animal affect the druid in their humanoid form?

That goes into some science that is more theory than actual rules. So there's no easy way to say that a disease will or will not affect the druid in a different form. However, it could be said that the disease remains dormant in an unaffected or immune host, but when the host becomes a viable creature the disease persists. This is up to your DM at this point.

• If the druid is considered their race in terms of biological susceptibility in wildshape or not, then the disease would always persist.
• If the druid is not considered their race in terms of biological susceptibility in wildshape, then the disease would not persist, or would be quickly cleansed from an unsupported host.

One last observation from this can be taken from the text of Wild Shape:

You retain the benefit of any features from your class, race, or other source and can use them if the new form is physically capable of doing so.

Of course, biological susceptibility to a disease wouldn't exactly be considered a "benefit" but you could rule this to mean that if you are a Gnome you will, for the purposes of disease viability, be able to be infected as if you were a Gnome, no matter what beast you were taking the shape of.