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At the end of the events of The Girl Who Waited, we see Rory and (younger) Amy coming back into the TARDIS after

they have been out walking in a Chen7-ridden world.

Towards the beginning of the episode a Handbot identifies that Amy is indeed carrying the bacteria even if she is immune, and even if this was not the case it's still most likely that they'd have some on their skin or clothes.

In this case, how did the Doctor not contract the disease from Amy and Rory?

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Because she's not been exposed to Chen-7.

The two-streams facility was designed to provide an individual living space for the 40,000(ish) people on Apalapucia who had become infected with the Chen-7 disease. Each person gets their own sculpted environment, separated in time by a few miliseconds. This means that someone entering the facility would be largely protected from the other inhabitants (e.g. those who're infected).

The bots identify that Amy is carrying 'unregistered bacteria' but don't indicate that she's carrying Chen-7. Assuming her impressions are correct, it's simply detecting her normal human biologicals:

HANDBOT: You are carrying unregistered bacteria. Please let me help you.

AMY: No, I'm not from this world. Your medicine'll kill me.

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  • But if this is the case, why couldn't the Doctor walk freely around Two-Streams?
    – theage
    Commented Feb 23, 2015 at 19:55
  • @theage - An abundance of caution, probably.
    – Valorum
    Commented Feb 23, 2015 at 19:57
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    @theage it was never stated that he COULDN'T, but that he WOULDN'T. Walking around a facility probably infested with bacteria that would kill him and make him unable to regenerate sounds like a terrible idea when Rory is around to do the walking for you. And the TARDIS would be probably be capable of scanning Amy and Rory upon re-entrance to ensure safety.
    – Dave Johnson
    Commented Feb 23, 2015 at 23:13

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