In all likelihood, it means that a GET or POST payload contained the signature. Whether or not the request containing the signature was successful in injecting it into your site is a question that only you will be able to answer.
You can use sigtool to find the signature and again to decode the signature to see what it's detecting to help you identify the particular request(s) to investigate further.
$ sigtool --find-sigs Php.Trojan.MSShellcode-81 | awk '{ print $2 }' | sigtool --decode-sigs
VIRUS NAME: Php.Trojan.MSShellcode-81
TARGET TYPE: ANY FILE
OFFSET: *
...