United States Department of Agriculture

Agricultural Marketing Service, Science & Technology

Microbiological Data Program

SOP No.: MDP-QA-03 Page 1 of 8

Title: Quality Assurance (QA) Controls 

Revision: 07 Replaces: 09/25/09 Effective: 10/01/10

1. Purpose

To provide minimum requirements and standard procedures for quality assurance 

(QA) controls used in the USDA/AMS Microbiological Data Program (MDP).

2. Scope

This standard operating procedure (SOP) shall be followed by all laboratories 

conducting microbiological studies for MDP, including support laboratories 

conducting non-routine activities that may impact the program. This SOP represents 

minimum MDP requirements and is presented as a general guideline. Each 

laboratory shall have written procedures that provide specific details concerning how 

the procedure has been implemented in that laboratory.

3. Principle

3.1 QA controls have known values that ensure the accuracy and reliability of a test 

system. MDP QA controls consist of an uninoculated media control, a negative 

cultural control, a positive cultural control, and a positive produce control for each 

batch/set of samples analyzed by each test method. Reagent controls are added 

when required.

3.2 QA controls are expected to exhibit known well-characterized results. If a QA 

control does not exhibit the expected result, that control does not meet the MDP 

acceptability criteria and is considered unacceptable.

3.3 If any control yields an unacceptable result, appropriate investigative/re-testing 

measures, as outlined in subsection 5.3 of this SOP, must be taken. If a control 

result is unacceptable for either the original or rerun analysis, the Monitoring 

Programs Office (MPO) shall be notified. Results associated with unacceptable 

controls shall be appropriately coded in Remote Data Entry (RDE) as described in 

subsection 5.4 of this SOP.

4. References

4.1 AOAC International Guidelines for Laboratories performing Microbiological 

and Chemical Analyses of Food and Pharmaceuticals, An Aid to Interpretation of 

ISO/IEC 17025:2005 (Rev 09/2006), Section: General requirements for the 

competence of testing and calibration laboratories 

4.2 A2LA Food Microbiology Program Requirements, subsection 5.10, Reporting 

the Results, June 2001
United States Department of Agriculture

Agricultural Marketing Service, Science & Technology

Microbiological Data Program

SOP No.: MDP-QA-03 Page 2 of 8

Title: Quality Assurance (QA) Controls 

Revision: 07 Replaces: 09/25/09 Effective: 10/01/10

4.3 Memorandum, Requirement to Notify MPO of QA Control Failure, February 3, 

2004

4.4 Memorandum, Quality Assurance Control Requirements, January 21, 2004

5. Procedures

 5.1 Controls Required per Set

5.1.1 Each analytical batch/set of samples shall include uninoculated media 

controls, a negative cultural control, a positive cultural control, and a positive 

produce control for each method used to test that batch/set of samples. 

5.1.2 The uninoculated media controls are intended to demonstrate the sterility of 

the medium and the results also may be used as a baseline within the analytical 

system.

5.1.3 The negative cultural control is intended to demonstrate suitable microbial 

conditions for growth, but differing biochemical reactions than the target 

organism in a given environment.

5.1.4 The positive cultural and positive produce controls are intended to reflect 

the expected behavior of a target organism in a given environment (e.g., substrate, 

temperature, pH) within the analytical system. An additional intent of the positive 

produce control is to demonstrate that no inhibitory effects occur from the 

produce.

5.1.5 Characteristics of control strains are detailed in Attachment 1, Current QA 

Control Strain Information.

5.2 Procedures for Handling QA Controls for All PCR-Based Methods

5.2.1 A separate area away from the general microbiological work is required for 

processing samples for polymerase chain reaction (PCR). If space is limited a 

hood or a chamber or a Biosafety cabinet can be used. To avoid crosscontamination, transfer of cultures and DNA samples should be performed with 

extreme care.

5.2.2 Acceptability Criteria for QA Controls - QA controls are expected to exhibit 

known values as specified in Attachment 1. If a QA control does not exhibit the 

expected result and/or does not fall within the categories as described in Sections 

5.2.3 through 5.2.5, that control does not meet MDP acceptability criteria and is 

considered unacceptable.
United States Department of Agriculture

Agricultural Marketing Service, Science & Technology

Microbiological Data Program

SOP No.: MDP-QA-03 Page 3 of 8

Title: Quality Assurance (QA) Controls 

Revision: 07 Replaces: 09/25/09 Effective: 10/01/10

5.2.3 For Internal Control (IC) failures associated with SOP MDP MTH-11, the 

laboratories should check the PCR amplification results for target genes (Stx-1 

and/or Stx-2). If the target gene(s) are amplified and the non-template control has 

worked as expected, the laboratories may treat the IC control failure as 

acceptable. Samples and controls need not be restested/repeated; however, 

laboratories are encouraged to determine appropriate concentrations of genomic 

DNA preparations from the control strains for PCR assays and to document those 

procedures in internal laboratory SOPs.

5.2.4 For uidA gene amplification failure in the positive produce culture control 

associated with SOP MDP MTH-11, the laboratories shall check PCR 

amplification results from the positive culture control and positive DNA control. 

If these results are positive for uidA amplification and the non-template control 

has worked as expected the laboratories may treat this failure as acceptable. 

Samples and controls need not be retested/repeated; however, laboratories are 

encouraged to determine appropriate spike levels for setting up overnight positive 

produce control cultures for use in PCR assays (refer to section 6.4 Controls in 

SOP MDP-LABOP-02). 

5.2.5 For PCR results yielding non-specific amplification(s) in the non-template 

control or suspicious amplifications (specific or non-specific) in several test 

samples, all samples along with appropriate controls must be repeated. In 

addition, the laboratory must institute a plan for cleanup of the pipettes used in the 

PCR assay, the PCR workstation, and other surfaces that may come in contact 

with aerosols and amplicons. Other steps must include discarding suspect buffers 

and reagents used in the PCR assay and initiation of retesting with new or freshly 

reconstituted reagents and buffers. All investigative steps and results must be 

reported to MPO.

5.3 Response to Failure to Meet Acceptability Criteria (Comments, observations, 

corrective actions, etc., should be recorded as part of sample data transmitted to 

MPO)

5.3.1 If any of the controls (media, negative cultural, positive cultural or positive 

produce control) fail to yield the expected results, the situation must be 

investigated.

5.3.2 If the problem is easily identified (e.g., typographical error), it shall be 

corrected. If the problem is not readily identified or able to be corrected, and does 

not fall under situations as described in Section 5.2, that batch of samples must be
United States Department of Agriculture

Agricultural Marketing Service, Science & Technology

Microbiological Data Program

SOP No.: MDP-QA-03 Page 4 of 8

Title: Quality Assurance (QA) Controls 

Revision: 07 Replaces: 09/25/09 Effective: 10/01/10

re-analyzed. Complete Attachment 2, QC Control Failure Reporting Form and 

fax to the MPO laboratory liaison at (703) 369-0678, with a copy to the Deputy 

Director. Fax notification shall be followed by a telephone call to the MPO 

laboratory liaison(s) at (703) 330-2300. Alternatively, Portable Document Format 

(PDF) copies of Attachment 02 with the signature may be e-mailed to both the 

liaison(s) and the Deputy Director.

5.3.3 For all MDP procedures, the appropriate sample wash/broth or aliquot of the 

wash/broth for each test must be saved under refrigeration; each laboratory should 

determine the best method for accomplishing this requirement (e.g., transfer to 

sterile centrifuge tube). Discard samples only after controls have yielded 

satisfactory results. 

5.3.4 The recommended timeframe for initiating investigation/re-testing is within 

two business days of control failure. It is recognized that there could be a change 

(e.g., growth of bacteria) in the sample wash/broth; however, re-testing is required 

and re-sampling is not acceptable.

5.3.5 Contact MPO for further guidance immediately if control results for the reanalysis are again unacceptable. For methods using automated PCR 

instrumentation, MPO may require further investigation (e.g., instrument 

parameters, melting curves, etc.).

5.3.6 All corrective actions taken as described in the preceding subsections (5.3.1 

to 5.3.5) must be properly documented in internal records and the MDP RDE 

system.

5.4 Reporting Data Associated with Failed Controls (Comments, observations, 

corrective actions, etc., should be recorded as part of sample data transmitted to 

MPO)

5.4.1 Results for each of the media, negative, positive, and positive produce

controls shall be reported as acceptable or unacceptable on the QA Results screen 

in RDE or should be entered into the comments field.

5.4.2 For controls yielding acceptable results for the initial testing, the results 

shall be reported as “acceptable.”

5.4.3 For controls yielding acceptable results for a rerun test triggered by initially 

unacceptable results, the result shall be reported as “acceptable.” In the 

comments field enter “re-tested, corrective action on file, etc.” and any additional 

details. 
United States Department of Agriculture

Agricultural Marketing Service, Science & Technology

Microbiological Data Program

SOP No.: MDP-QA-03 Page 5 of 8

Title: Quality Assurance (QA) Controls 

Revision: 07 Replaces: 09/25/09 Effective: 10/01/10

5.4.4 For controls yielding unacceptable results for a rerun test, the result shall be 

reported as “unacceptable.” In the comments field enter “re-tested, corrective 

action on file, etc.” and provide any additional details.

5.4.5 Data for samples associated with unacceptable controls will be excluded 

from the MDP central database.

Disclaimer: Reference to brand names (kits, equipment, media, reagents, etc.) does not 

constitute endorsement by this agency.
United States Department of Agriculture

Agricultural Marketing Service, Science & Technology

Microbiological Data Program

SOP No.: MDP-QA-03 Page 6 of 8

Title: Quality Assurance (QA) Controls 

Revision: 07 Replaces: 09/25/09 Effective: 10/01/10

Mary Tijerina 1 September 2010

__________________________________________________________

Revised by: Mary Tijerina Date

Microbiologist, Monitoring Programs Office

8609 Sudley Road, Suite 206

Manassas, VA 20110

(703) 330-2300 x111

Shanker Reddy 2 September 2010

___________________________________________________________

Reviewed by: Shanker Reddy Date

Molecular Biologist, Monitoring Programs Office

8609 Sudley Road, Suite 206

Manassas, VA 20110

(703) 330-2300x135

 Diana Haynes 2 September 2010

Approved By: Diana Haynes Date

Deputy Director, Monitoring Programs Office

8609 Sudley Road, Suite 206

Manassas, VA 20110

(703) 330-2300

ORIGINAL SIGNATURE PAGE MAINTAINED BY USDA, AMS, SCIENCE & TECHNOLOGY, MONITORING PROGRAMS OFFICE

ELECTRONICALLY REPRODUCED SIGNATURES
United States Department of Agriculture

Agricultural Marketing Service, Science & Technology

Microbiological Data Program

SOP No.: MDP-QA-03 Page 7 of 8

Title: Quality Assurance (QA) Controls 

Revision: 07 Replaces: 09/25/09 Effective: 10/01/10

Revision 07 August 2010 Monitoring Programs Office

 Merged Sections 5.2.2 and 5.2.3 and added bold portion, “Acceptability Criteria 

for QA Controls - QA controls are expected to exhibit known values as specified 

in Attachment 1. If a QA control does not exhibit the expected result and/or 

does not fall within the categories as described in Sections 5.2.3 through 

5.2.5, that control does not meet MDP acceptability criteria and is considered 

unacceptable.”

 Added new Section 5.2.3, “For Internal Control (IC) failures associated with SOP 

MDP MTH-11, the laboratories should check the PCR amplification results for 

target genes (Stx-1 and/or Stx-2). If the target gene(s) are amplified and the nontemplate control has worked as expected, the laboratories may treat the IC control 

failure as acceptable. Samples and controls need not be restested/repeated; 

however, laboratories are encouraged to determine appropriate concentrations of 

genomic DNA preparations from the control strains for PCR assays and to 

document those procedures in internal laboratory SOPs.”

 Added new Section 5.2.4, “For uidA gene amplification failure in the positive 

produce culture control associated with SOP MDP MTH-11, the laboratories shall 

check PCR amplification results from the positive culture control and positive 

DNA control. If these results are positive for uidA amplification and the nontemplate control has worked as expected the laboratories may treat this failure as 

acceptable. Samples and controls need not be retested/repeated; however, 

laboratories are encouraged to determine appropriate spike levels for setting up 

overnight positive produce control cultures for use in PCR assays (refer to section 

6.4 Controls in SOP MDP-LABOP-02).”

 Added new Section 5.2.5, “For PCR results yielding non-specific amplification(s) 

in the non-template control or suspicious amplifications (specific or non-specific) 

in several test samples, all samples along with appropriate controls must be 

repeated. In addition, the laboratory must institute a plan for cleanup of the 

pipettes used in the PCR assay, the PCR workstation, and other surfaces that may 

come in contact with aerosols and amplicons. Other steps must include 

discarding suspect buffers and reagents used in the PCR assay and initiation of 

retesting with new or freshly reconstituted reagents and buffers. All investigative 

steps and results must be reported to MPO.”

 Revised Section 5.3.2 as shown in bold, “If the problem is easily identified (e.g., 

typographical error), it shall be corrected. If the problem is not readily identified 

or able to be corrected, and does not fall under situations as described in 

Section 5.2, that batch of samples must be re-analyzed. Complete Attachment 2, 

QC Control Failure Reporting Form and fax to the MPO laboratory liaison at 
United States Department of Agriculture

Agricultural Marketing Service, Science & Technology

Microbiological Data Program

SOP No.: MDP-QA-03 Page 8 of 8

Title: Quality Assurance (QA) Controls 

Revision: 07 Replaces: 09/25/09 Effective: 10/01/10

(703) 369-0678, with a copy to the Deputy Director. Fax notification shall be 

followed by a telephone call to the MPO laboratory liaison(s) at (703) 330-2300.

Alternatively, Portable Document Format (PDF) copies of Attachment 02 with the 

signature may be e-mailed to both the liaison(s) and the Deputy Director.”

 Revised Attachment 1, Current QA Control Strain Information

 Revised Attachment 2, QC Control Failure Reporting Form

Revision 06 September 2009 Monitoring Programs Office

 Revised Section 3, Principle

 Revised Sections 5.1 through 5.4

 Updated Attachment 02

Revision 05 March 30, 2009 Monitoring Programs Office

 Updated MDP-QA-03 Attachment 1 Current QA Control Strain Information by 

deleting the negative control strain used for SOPs MDP MTH-01A, MTH-01B. 

Deleted procedures and strains related to SOPs MDP MTH-01A, MTH-01B, 

MTH-01C and MTH-08

Revision 04 March 03, 2008 Monitoring Programs Office

 Updated MDP-QA-03 Attachment 1 Current QA Control Strain Information to 

include positive and negative controls for SOPs MDP MTH-01A, MTH-01B, 

MTH-01C and MTH-08

Revision 03 September 2005 Monitoring Programs Office

 Added control strains for MDP-MTH-07, revised attachments

Revision 02 January 2005 Monitoring Programs Office

 Replaced control strains, revised attachments

Revision 01 September 2004 Monitoring Programs Office

 Revised/condensed Excel attachments into one document

 Removed NSL as only reference laboratory

 Replaced specific references to BAX with generic terminology to apply to other 

DNA-based techniques

 Added option to save broth instead of wash

 Added response to failures to meet acceptability criteria 

 Added reporting data associated with Failed Controls 

 Revised RDE comments required to reflect current RDE reporting system