A method of extracting microbial cells from a whole blood sample and performing an assay on the extracted microbial cells, the method comprising: adding the whole blood sample to a pretreatment vessel, the pretreatment vessel comprising a pretreatment mixture, the pretreatment mixture comprising a blood cell lysis reagent configured for the selective lysis of non-microbial cells and a hydrophobic cushioning liquid having a density greater than that of the whole blood sample and the blood cell lysis reagent; agitating the contents of the pretreatment vessel; centrifuging the pretreatment vessel such that the cushioning liquid forms a first liquid interface below a first supernatant, wherein microbial cells from the whole blood sample are removed from suspension and collected adjacent to the first liquid interface; withdrawing a substantial quantity of the first supernatant without removing the collected microbial cells; performing washing steps comprising: (i) adding a volume of wash buffer to the pretreatment vessel; (ii) agitating the contents of the pretreatment vessel; (iii) centrifuging the pretreatment vessel such that the cushioning liquid forms a second liquid interface below a second supernatant, and such that microbial cells are transported to and collected at the second liquid interface; and (iv) withdrawing a substantial quantity of the second supernatant without extracting the collected microbial cells; agitating the contents of the pretreatment vessel and allowing the cushioning liquid to re-establish the liquid interface below a suspension containing the microbial cells; extracting a least a portion of the suspension without extracting a substantial portion of the cushioning liquid, thereby obtaining an extracted suspension comprising microbial cells; lysing the microbial cells within the extracted suspension to obtain a lysate; and performing at least one nucleic acid amplification assay to detect at least one analyte that may be present in the lysate. adding the whole blood sample to a pretreatment vessel, the pretreatment vessel comprising a pretreatment mixture, the pretreatment mixture comprising a blood cell lysis reagent configured for the selective lysis of non-microbial cells and a hydrophobic cushioning liquid having a density greater than that of the whole blood sample and the blood cell lysis reagent; agitating the contents of the pretreatment vessel; centrifuging the pretreatment vessel such that the cushioning liquid forms a first liquid interface below a first supernatant, wherein microbial cells from the whole blood sample are removed from suspension and collected adjacent to the first liquid interface; withdrawing a substantial quantity of the first supernatant without removing the collected microbial cells; performing washing steps comprising: (i) adding a volume of wash buffer to the pretreatment vessel; (ii) agitating the contents of the pretreatment vessel; (iii) centrifuging the pretreatment vessel such that the cushioning liquid forms a second liquid interface below a second supernatant, and such that microbial cells are transported to and collected at the second liquid interface; and (iv) withdrawing a substantial quantity of the second supernatant without extracting the collected microbial cells; (i) adding a volume of wash buffer to the pretreatment vessel; (ii) agitating the contents of the pretreatment vessel; (iii) centrifuging the pretreatment vessel such that the cushioning liquid forms a second liquid interface below a second supernatant, and such that microbial cells are transported to and collected at the second liquid interface; and (iv) withdrawing a substantial quantity of the second supernatant without extracting the collected microbial cells; agitating the contents of the pretreatment vessel and allowing the cushioning liquid to re-establish the liquid interface below a suspension containing the microbial cells; extracting a least a portion of the suspension without extracting a substantial portion of the cushioning liquid, thereby obtaining an extracted suspension comprising microbial cells; lysing the microbial cells within the extracted suspension to obtain a lysate; and performing at least one nucleic acid amplification assay to detect at least one analyte that may be present in the lysate.