A method of detecting a biological contaminant in a test sample comprising the steps of: a) combining ingredients to make a reaction mixture, wherein the ingredients comprise (i) a nucleic acid sample derived from a test sample, (ii) oligonucleotides, and (iii) a DNA polymerase, wherein the oligonucleotides comprise: - a forward oligonucleotide primer specific for amplifying a target amplification polynucleotide sequence of the biological contaminant; - a reverse oligonucleotide primer specific for amplifying the TAP sequence of the biological contaminant; - an oligonucleotide detection probe specific for the TAP sequence of the biological contaminant; - a unique detection probe for a plasmid amplification control polynucleotide (PACP) sequence of a positive amplification control plasmid, the plasmid containing the TAP sequence and a PACP sequence; and - a set of primers and a probe to detect nucleic acid extraction control polynucleotides (NACP); b) subjecting the reaction mixture to polymerase chain reaction; c) during the PCR monitoring the production of (i) TAP, (ii) nucleic acid extraction control polynucleotides (NACP), and PACP; and d) comparing the production of TAP to the production of NACP and PACP wherein the presence of TAP, the presence of NACP, and the absence of PACP produced during the PCR signifies that the test sample contains a biological contaminant and does not contain a positive amplification control plasmid, wherein a separate, parallel positive control PCR reaction is run under identical parameters and with identical components, except that the PAC plasmid is present in place of a nucleic acid sample derived from a test sample, wherein the presence of TAP, NACP and PACP produced during the positive control PCR reaction signifies that the PCR is functioning properly, and the absence of any one or more of TAP, NACP or PACP signifies that the positive control has failed. a) combining ingredients to make a reaction mixture, wherein the ingredients comprise (i) a nucleic acid sample derived from a test sample, (ii) oligonucleotides, and (iii) a DNA polymerase, wherein the oligonucleotides comprise: - a forward oligonucleotide primer specific for amplifying a target amplification polynucleotide sequence of the biological contaminant; - a reverse oligonucleotide primer specific for amplifying the TAP sequence of the biological contaminant; - an oligonucleotide detection probe specific for the TAP sequence of the biological contaminant; - a unique detection probe for a plasmid amplification control polynucleotide (PACP) sequence of a positive amplification control plasmid, the plasmid containing the TAP sequence and a PACP sequence; and - a set of primers and a probe to detect nucleic acid extraction control polynucleotides (NACP); - a forward oligonucleotide primer specific for amplifying a target amplification polynucleotide sequence of the biological contaminant; - a reverse oligonucleotide primer specific for amplifying the TAP sequence of the biological contaminant; - an oligonucleotide detection probe specific for the TAP sequence of the biological contaminant; - a unique detection probe for a plasmid amplification control polynucleotide (PACP) sequence of a positive amplification control plasmid, the plasmid containing the TAP sequence and a PACP sequence; and - a set of primers and a probe to detect nucleic acid extraction control polynucleotides (NACP); b) subjecting the reaction mixture to polymerase chain reaction; c) during the PCR monitoring the production of (i) TAP, (ii) nucleic acid extraction control polynucleotides (NACP), and PACP; and d) comparing the production of TAP to the production of NACP and PACP wherein the presence of TAP, the presence of NACP, and the absence of PACP produced during the PCR signifies that the test sample contains a biological contaminant and does not contain a positive amplification control plasmid,