Yup, they sure can carry pathogenic bacteria. Salmonella is the most commonly discussed, but all reptiles can carry it...and snakers55 is absoluetly right - everything carries bacteria of some kind. It's uncommon for it to pose a problem though, unless small children or immune comprimised people are involved. Proper hand washing (and not kissing the turtles!) combined with good water quality maintenace should prevent most problems.
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