A process for simultaneously isolating and determining the presence, non-presence and/or amount of at least a first and a second target nucleic acid selected from bacteria, DNA viruses and RNA viruses from a plurality of different types of fluid samples, said process comprising the automated steps of a. adding an identical lysis buffer having a pH between 5.5 and 6.5 and comprising a chaotropic agent, a buffer substance, an alcohol, and a reducing agent to the members of said plurality of different types of fluid samples and thereby releasing nucleic acids from their cellular and/or viral environment by lysing viral capsids potentially present in the plurality of different types of fluid samples, and combining together magnetic particles and said plurality of different types of fluid samples in a number of vessels corresponding to the number of fluid samples for a period of time and under conditions sufficient to permit nucleic acids comprising the target nucleic acids to be immobilized on the magnetic particles, b. isolating the magnetic particles from the other material present in the fluid samples in a separation station comprising one or more magnets, c. purifying the nucleic acids in a separation station by separating the fluid sample from the magnetic particles and washing the magnetic particles one or more times with a wash buffer by aspirating and dispensing the suspension comprising wash buffer and magnetic particles one or more times using a pipet, d. eluting the nucleic acids from the magnetic particles with an elution buffer, e. transferring the purified nucleic acids and optionally said magnetic particles to a plurality of reaction vessels, f. amplifying the target nucleic acids, wherein the physical conditions and said period of time are identical for the members of said plurality of different types of fluid samples and wherein the first and/or the second nucleic acid is a bacterial nucleic acid. a. adding an identical lysis buffer having a pH between 5.5 and 6.5 and comprising a chaotropic agent, a buffer substance, an alcohol, and a reducing agent to the members of said plurality of different types of fluid samples and thereby releasing nucleic acids from their cellular and/or viral environment by lysing viral capsids potentially present in the plurality of different types of fluid samples, and combining together magnetic particles and said plurality of different types of fluid samples in a number of vessels corresponding to the number of fluid samples for a period of time and under conditions sufficient to permit nucleic acids comprising the target nucleic acids to be immobilized on the magnetic particles, b. isolating the magnetic particles from the other material present in the fluid samples in a separation station comprising one or more magnets, c. purifying the nucleic acids in a separation station by separating the fluid sample from the magnetic particles and washing the magnetic particles one or more times with a wash buffer by aspirating and dispensing the suspension comprising wash buffer and magnetic particles one or more times using a pipet, d. eluting the nucleic acids from the magnetic particles with an elution buffer, e. transferring the purified nucleic acids and optionally said magnetic particles to a plurality of reaction vessels, f. amplifying the target nucleic acids,