Yes, flies apparently carry all kinds of bacteria on their mouthparts and feet, including Streptococcus, Staphylococcus, Salmonella, and E. coli. Common houseflies do not bite but they still absorb moist materials with their mouthparts when they eat, and these materials can get transferred to wherever they choose to land. Flies that hang around dairies are biting flies, and this page (pdf file) explains that they’re able to transmit disease between cows, so I would guess that they can transmit it to humans too.
Yes, flies are known as vectors and so carry and transmit diseases. For instance, tse-tse flies are notorious for transmitting trypanosomiasis, a protozoa responsible for the disease known as sleeping sickness. House flies (Musa domestica) thrive in filthy places and some disease-causing organisms come through them.
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