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31A
Verification and
Validation of
Procedures in the
Clinical Microbiology
Laboratory
RICHARD B. CLARK, MICHAEL A. LEWINSKI,
MICHAEL J. LOEFFELHOLZ, AND
ROBERT J. TIBBETTS

COORDINATING EDITOR
SUSAN E. SHARP

Cumitech
CUMULATIVE TECHNIQUES AND PROCEDURES IN CLINICAL MICROBIOLOGY
31A_Coverpg_Cumitech_557049 6/24/10 9:18 AM Page 2

Cumitech 1C Blood Cultures IV (2005) Cumitech 31A Verification and Validation of Procedures
Cumitech 2C Laboratory Diagnosis of Urinary Tract in the Clinical Microbiology Laboratory
Infections (2009) (2009)
Cumitech 3B Quality Systems in the Clinical Cumitech 32 Laboratory Diagnosis of Zoonotic
Microbiology Laboratory (2005) Infections: Viral, Rickettsial, and Parasitic
Agents Obtained from Food Animals and
Cumitech 7B Lower Respiratory Tract Infections (2004)
Wildlife (1999)
Cumitech 10A Laboratory Diagnosis of Upper Respiratory
Tract Infections (2006) Cumitech 33 Laboratory Safety, Management, and
Diagnosis of Biological Agents Associated
Cumitech 12A Laboratory Diagnosis of Bacterial Diarrhea with Bioterrorism (2000)
(1992)
Cumitech 34 Laboratory Diagnosis of Mycoplasmal
Cumitech 13A Laboratory Diagnosis of Ocular Infections
Infections (2001)
(1994)
Cumitech 16A Laboratory Diagnosis of the Cumitech 35 Postmortem Microbiology (2001)
Mycobacterioses (1994) Cumitech 36 Biosafety Considerations for Large-Scale
Cumitech 18A Laboratory Diagnosis of Hepatitis Viruses Production of Microorganisms (2002)
(1998) Cumitech 37 Laboratory Diagnosis of Bacterial and
Cumitech 21 Laboratory Diagnosis of Viral Respiratory Fungal Infections Common to Humans,
Disease (1986) Livestock, and Wildlife (2003)
Cumitech 23 Infections of the Skin and Subcutaneous Cumitech 38 Human Cytomegalovirus (2003)
Tissues (1988)
Cumitech 39 Competency Assessment in the Clinical
Cumitech 24 Rapid Detection of Viruses by Microbiology Laboratory (2003)
Immunofluorescence (1988)
Cumitech 40 Packing and Shipping of Diagnostic
Cumitech 26 Laboratory Diagnosis of Viral Infections Specimens and Infectious Substances (2004)
Producing Enteritis (1989)
Cumitech 41 Detection and Prevention of Clinical
Cumitech 27 Laboratory Diagnosis of Zoonotic
Microbiology Laboratory-Associated Errors
Infections: Bacterial Infections
(2004)
Obtained from Companion and Laboratory
Animals (1996) Cumitech 42 Infections in Hemopoietic Stem Cell
Cumitech 28 Laboratory Diagnosis of Zoonotic Transplant Recipients (2005)
Infections: Chlamydial, Fungal, Viral, and Cumitech 43 Cystic Fibrosis Microbiology (2006)
Parasitic Infections Obtained
from Companion and Laboratory Animals Cumitech 44 Nucleic Acid Amplification Tests for
(1996) Detection of Chlamydia trachomatis and
Neisseria gonorrhoeae (2006)
Cumitech 29 Laboratory Safety in Clinical Microbiology
(1996) Cumitech 45 Infections in Solid-Organ Transplant
Recipients (2008)
Cumitech 30A Selection and Use of Laboratory Procedures
for Diagnosis of Parasitic Infections of the Cumitech 46 Laboratory Procedures for Diagnosis of
Gastrointestinal Tract (2003) Blood-Borne Parasitic Diseases (2008)

Cumitechs should be cited as follows, e.g.: Clark, R. B., M. A. Lewinski, M. J. Loeffelholz, and R. J. Tibbetts, 2009. Cumitech 31A, Verification and Vali-
dation of Procedures in the Clinical Microbiology Laboratory. Coordinating ed., S. E. Sharp. ASM Press, Washington, DC.
Editorial Board for ASM Cumitechs: Alice S. Weissfeld, Chair; Maria D. Appleman, Vickie Baselski, Mitchell l. Burken, Roberta Carey, Lynne Garcia, Larry
Gray, Amy L. Leber, Andrea J. Linscott, Yvette S. McCarter, Susan E. Sharp, James W. Snyder, Allan L. Truant, Punam Verma.
Effective as of January 2000, the purpose of the Cumitech series is to provide consensus recommendations regarding the judicious use of clinical micro-
biology and immunology laboratories and their role in patient care. Each Cumitech is written by a team of clinicians, laboratorians, and other interested
stakeholders to provide a broad overview of various aspects of infectious disease testing. These aspects include a discussion of relevant clinical consid-
erations; collection, transport, processing, and interpretive guidelines; the clinical utility of culture-based and non-culture-based methods and emerging
technologies; and issues surrounding coding, medical necessity, frequency limits, and reimbursement. The recommendations in Cumitechs do not repre-
sent the official views or policies of any third-party payer.
Copyright © 2009 ASM Press Address editorial correspondence to ASM Press,
American Society for Microbiology 1752 N St. NW, Washington, DC 20036-2904, USA
1752 N St. NW E-mail: books@asmusa.org
Washington, DC 20036-2904, USA Send orders to ASM Press, P.O. Box 605, Herndon, VA 20172, USA
ISBN 978-1-55581-530-1 Phone: (800) 546-2416 or (703) 661-1593 • Fax: (703) 661-1501
Online: estore.asm.org
All Rights Reserved
10 9 8 7 6 5 4 3 2 1
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Verification and Validation


of Procedures in the
Clinical Microbiology
Laboratory

Richard B. Clark
Quest Diagnostics Nichols Institute, Chantilly, VA 20151
Michael A. Lewinski
University of California, Los Angeles, CA 90095
Michael J. Loeffelholz
University of Texas Medical Branch, Galveston, TX 77555
Robert J. Tibbetts
Henry Ford Health System, Detroit, MI 48202
COORDINATING EDITOR: Susan E. Sharp
Kaiser Permanente—NW, Portland, OR 97230

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Definitions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Federal Regulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Role of the FDA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Role of CLIA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Selection of a Laboratory Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Verification of Common Microbiology Tests . . . . . . . . . . . . . . . . . . . . . . . . . 10
Verification Study Design . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Verification Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
AST Systems (Unmodified, FDA Cleared) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
AST System Verification Studies Not Arbitrated with a Reference Method
(Test 30 or More Isolates per Panel/Card) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
AST System Verification Studies Arbitrated with a Reference Method
(Test up to 100 or More Isolates per Panel/Card) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Diagnostic Microbiology and Microbial Identification Tests . . . . . . . . . . . . . . . . . . . . . . . . 14
Verification of Unmodified, FDA-Cleared Tests . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Verification of LDTs, Modified FDA-Cleared Tests, and Commercially
Available Kits That Are Not FDA Cleared . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .17
Validation of Diagnostic Tests Used in Clinical Microbiology . . . . . . . . . . . . 18
Components of the Validation Process . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Frequency of Test Validation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Summation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Appendix A: Method Selection and Verification Example . . . . . . . . . . . . . . 21
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Appendix B: Process for Selection of a Test Method . . . . . . . . . . . . . . . . . . 23

INTRODUCTION tors, as defined below, that are readily measurable


and have become the hallmarks for analyzing tests as
well as determining laboratory and technologist pro-

T
he most important attributes of a laboratory
test are its ability to produce accurate, precise, ficiency. When a new laboratory test is introduced,
and reproducible results with rapid turnaround these factors may be weighed with other issues, such
time and clinical utility. There are a number of fac- as clinical relevance, cost, instrumentation, and ease

1
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2 Clark et al. CUMITECH 31A

of performance. Laboratories are required to estab- idation of the performance of existing test methodol-
lish policies and procedures to maintain or improve ogy. However, before these processes can be dis-
the reliability, efficiency, and clinical utility of labo- cussed in detail, relevant definitions must be estab-
ratory tests. Two of the most important analyses per- lished.
formed in the laboratory are verification and valida-
Accuracy (22, 23): Technical accuracy is the nearness
tion. While the definitions of these processes are
of an individual measurement to the true value, as
often used interchangeably they are in fact two sepa-
determined by a reference method, or the agreement
rate processes. Verification is the one-time process
between two tests. Clinical accuracy is the overall
performed to determine or to confirm a test’s ex-
ability of a test to both rule in and rule out an ana-
pected performance prior to implementation in the
lyte or a specific disease. Accuracy is synonymous
clinical laboratory; simply put, it asks “does the test
with test efficiency and can be expressed mathemati-
work?” Validation is an ongoing process of monitor-
cally as a percentage:
ing a test, procedure, or method to ensure that it con-
tinuously performs as expected; simply put, it asks No. of correct results
“does the test still work?” Validation is achieved  100
Total no. of results
through normal quality control, proficiency testing,
staff competency testing, and instrument calibration. Analyte (22): The component of a specimen or organ-
The purpose of this Cumitech is to provide guid- ism which is to be measured or demonstrated. An ana-
ance on the necessary criteria that may be required as lyte may be a particular antigen, antibody, nucleic
new tests are considered for clinical use and as old acid, organism, enzyme, species, or metabolic product.
tests are reevaluated for their clinical relevance. Once
verified, additional analyses can be performed to de- ASR: The Food and Drug Administration (FDA) de-
termine the test’s sensitivity and specificity compared fines an analyte-specific reagent (ASR) as “antibodies,
to an existing test or to the gold standard. Addition- both polyclonal and monoclonal, specific receptor
ally, positive and negative predictive values (PPV and proteins, ligands, nucleic acid sequences, and similar
NPV, respectively) can be determined based on the agents which, through specific binding or chemical
relative prevalence of a particular disease. The guide- reaction with substances in a specimen, are intended
lines within this Cumitech apply equally to simple for use in a diagnostic application for identification
single-reagent tests and the most complex of instru- and quantification of an individual chemical sub-
ments generating a variety of analytic results and in- stance or ligand in biological specimens” (http://
terpretations. However, these are simply guidelines www.fda.gov/downloads/MedicalDevices/Device
and should be used in addition to other criteria or RegulationandGuidance/GuidanceDocuments/UCM
policies which regulatory, accrediting, licensing, or 071269.pdf; accessed 6 August 2009). In simpler
standard-setting agencies use in assessing either the terms, from a clinical standpoint, ASRs are the sepa-
compliance of a laboratory or the accuracy of indi- rate building blocks of a laboratory-developed test
vidual tests or instruments. (LDT) used to identify a particular analyte. Examples
Lastly, the information in this Cumitech is not all- are the primers and probes used to detect and iden-
inclusive. Much information can be found in the lit- tify Bordetella pertussis in a nasopharyngeal swab
erature regarding the verification and validation of specimen. Guidance on the use of ASRs can be found
test methods; however, this information often applies in the “Guidance for Industry and FDA Staff Com-
to quantitative analyses more commonly found in the mercially Distributed Analyte Specific Reagents
chemistry laboratory. When these processes are ap- (ASRs): Frequently Asked Questions,” which can be
plied to microbiology, where qualitative results are found at the website above.
more common, where subjective interpretations are Gold standard: A commonly used term generally in-
required, or where the results include the identifica- dicating a test method currently accepted as reason-
tion of microorganisms with biological variation, ably, but not necessarily 100%, accurate (15, 22). It
more flexibility is required. Thus, the focus of this is used as the reference method for assessing the per-
Cumitech is on the common qualitative and semi- formance characteristics of another test method. See
quantitative test procedures performed in the clinical also “Reference method.” A caveat regarding the
microbiology laboratory. gold standard method of analysis: when the true dis-
ease status of a patient is unknown and the disease
state is being determined by using a test compared
DEFINITIONS
with an imperfect gold standard, the results will be
The primary processes addressed in this Cumitech skewed and errors of the gold standard or reference
are the verification of a new test or method prior to method will be magnified. As is often the case with
introduction into the laboratory and the ongoing val- new and improved technologies, the new test may be
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CUMITECH 31A Verification and Validation of Procedures in the Clinical Microbiology Laboratory 3

more accurate than the accepted gold standard. Dis- .html (accessed 8 July 2009) for further information
agreement between the two tests will manifest them- regarding IUO and RUO test kit use in the clinical
selves as false positives or false negatives. As such, it microbiology lab and the role of such tests in clinical
has been suggested that the concepts of sensitivity diagnostics.
and specificity should not be used when the true dis-
ease state of the patient is unknown (15). In this sit- Medical device: An instrument, apparatus, implement,
uation, it may be more appropriate to display the machine, contrivance, implant, in vitro reagent, or
agreement and disagreement between the gold stan- other similar or related article, including a compo-
dard and new test in graphic or tabular form such as nent part, or accessory which is recognized in the of-
a 2-by-2 table. Areas of disagreement may then be ficial National Formulary, the United States Pharma-
further investigated by other tests or by monitoring copoeia, or any supplement to them intended for use
the patient’s condition to determine if disease devel- in the diagnosis of disease or other conditions or in
ops. In those instances in which it cannot be deter- the cure, mitigation, treatment, or prevention of dis-
mined whether the new test is better than the gold ease in humans or other animals intended to affect
standard, a decision to use the new test alone or in the structure or any function of the body of humans
combination with the gold standard may be made by or other animals, which does not achieve any of its
using a cost-benefit analysis (15). Problems associ- primary intended purposes through chemical action
ated with use of an imperfect gold standard are more within or on the body of humans or other animals
fully discussed in the CLSI publication I/LA 18-A2 and which is not dependent upon being metabolized
(22) and in references 1, 14, and 19. for the achievement of any of its primary intended
purposes.
Home-brew test: See “LDT.”
New test: A new test includes any test not previously
Incidence (8): The number of new cases over a period offered by a laboratory, a procedure or methodology
of time. It is most often given as the incidence rate or change, or a test performed in-house that was previ-
the number of new cases of infection in a specified ously performed at a reference laboratory. Such tests
population at risk during a defined period relative to include detection or identification of a totally new
the overall number of people in the population at risk. analyte, the use of totally new methodology, a new
In vitro diagnostic (IVD) product: Any medical de- approach to detecting an analyte, a change from a
vice which is a reagent, reagent product, calibrator, manual method to an automated one, a new applica-
control material, kit, instrument, apparatus, equip- tion of existing technology, or the test of a new ma-
ment, or system, whether used alone or in combina- trix (old analyte in a different specimen).
tion, intended by the manufacturer to be used in vitro Old test: An old test is any procedure for detection of
for the examination of specimens, including blood a disease, analyte, or characteristic (e.g., antimicro-
and tissue donations, derived from the human body, bial susceptibility) that had been in use before 24 April
solely or principally for the purpose of providing in- 2003, the effective date of the final Clinical Labora-
formation concerning a physiological or pathological tory Improvement Amendments (CLIA). Laborato-
state or a congenital abnormality, determining safety ries are not required to verify or establish perfor-
and compatibility with potential recipients, or moni- mance specifications for any test system used by the
toring therapeutic measures. laboratory before 24 April 2003.
LDT (13): Procedures developed in-house that use Precision (22): A measure of the extent to which
reagents that are either commercially available or replicate analyses (using identical procedures) of a
produced in-house. Since an LDT is not reviewed homogeneous analyte agree with each other. Preci-
and/or approved by the FDA and since the reagents sion implies freedom from inconsistency and random
used therein cannot be reviewed for their intended error but does not guarantee accuracy. Precision is
use, these tests require more extensive performance synonymous with reproducibility; however, the use
verification (4). LDTs routinely use reagents pro- of the term precision is generally applied to quantita-
vided by companies for either investigative use only tive assays, while reproducibility is used with quali-
(IUO) or research use only (RUO); however, this does tative analyses. Mathematically, precision can be ex-
not deem the LDT an IUO or RUO test. Conversely, pressed as a percentage:
IUO or RUO kits typically carry with them manu-
facturer’s limitations and, therefore, must be used in No. of repeated results in agreement
 100
accordance with these guidelines described by the Total no. of results
company and/or the FDA and must not be used for
IVD testing. Please refer to the document located Predictive value (15, 22): The predictive value of a
at http://www.devicelink.com/ivdt/archive/08/03/004 test is the probability that a positive result (PPV)
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4 Clark et al. CUMITECH 31A

accurately indicates the presence of an analyte or a experience and observation, and the subsequent use
specific disease or that a negative result (NPV) accu- of this knowledge to make and verify procedural
rately indicates the absence of an analyte or a specific changes for improved test performance.
disease. PPV is expressed as a percentage:
Reference method: A thoroughly investigated method
No. of true-positive results in which exact and clear descriptions of the necessary
 100 conditions and procedures are given for the accurate
No. of true-positive plus
determination of one or more values; the docu-
false-positive results
mented accuracy and precision of the method are
commensurate with the method’s use for assessing
NPV is expressed as a percentage:
the accuracy of other methods for measuring the same
No. of true-negative results property values or for assigning reference method val-
 100 ues to reference materials. A currently used method
No. of true-negative plus
is unacceptable as a reference method unless there is
false-negative results
on-site or peer-reviewed-journal documentation of
an acceptable level of accuracy and precision of the
Predictive values can vary significantly with the
method. See also “Gold standard.”
prevalence of the disease or analyte unless the test is
100% sensitive (for NPV) or specific (for PPV). The Reproducibility: See “Precision.”
highest predictive values are desired when inappro-
priate treatment due to false-positive or -negative re- Sensitivity (2, 15, 22, 23): Clinical sensitivity is a
sults has serious clinical, emotional, epidemiological, measure of a test’s ability to accurately detect pa-
public health, or economic consequences. Predictive tients with a specific disease. Analytic sensitivity
values are most meaningful in evaluating a test’s per- measures the smallest quantity of an analyte that can
formance in specific risk population groups. be reproducibly distinguished from background levels,
or a zero calibrator, in a given assay system; it is usu-
Prevalence (8): The frequency of a disease in the pop- ally defined at the 0.95 confidence level (2 standard
ulation of interest at a given point in time (point deviations) and is more appropriately called the limit
prevalence) or during a defined period of time (pe- of detection. In microbiology, for example, the detec-
riod prevalence). tion limit can be correlated to the number of colonies
in culture or the lowest quantity of antigen, antibody,
Quality assurance (10, 17): A system for continuously or nucleic acid a test can detect. The highest sensitiv-
improving and monitoring the reliability, efficiency, ity is desired when a disease is serious and treatable
and clinical utilization of laboratory tests. Quality and when false-positive results will not lead to seri-
control, quality improvement, and method validation ous clinical or economic problems. Mathematically,
are integral components of quality assurance. sensitivity is expressed as a percentage:
Quality control (10, 17): The process of ongoing per-
formance checks, including personnel performance, No. of true-positive results
 100
using known organisms or analytes to ensure on a No. of true-positive plus
regular and frequent basis that a method which has false-negative results
gone through the verification process (see below) and
is now part of the laboratory’s routine test battery is Specificity (2, 15, 22, 23): Clinical specificity is a
performing as expected. Quality control systemati- measure of a test’s ability to accurately identify all
cally detects deficiencies in testing by setting limits of noninfected patients. Analytic specificity is the ability
acceptable performance (accuracy and precision). It of an analytical method to detect only the analyte
thus allows detection and corrective action, where that it was designed to measure. The highest speci-
appropriate, of major problems or errors with test ficity is desired when the disease is serious but not
systems and their performance. Quality control im- treatable, when disease absence has either psycholog-
plies that there exist standard analytes that have ical or public health value, or when false-positive re-
known reactions or reactivity. Quality control is an sults might cause serious clinical or economic prob-
integral part of the test validation process. lems. Mathematically, specificity is expressed as a
percentage:
Quality improvement (10, 17): The prevention of test
deficiencies and enhancement of a test’s clinical util- No. of true-negative results
 100
ity by establishing a thorough understanding of the No. of true-negative plus
test’s capabilities and limitations, as gathered from false-positive results
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CUMITECH 31A Verification and Validation of Procedures in the Clinical Microbiology Laboratory 5

User-modified test: Any procedure that incorporates the role of the FDA to regulate medical devices under
modifications of the manufacturer’s FDA-cleared or the appropriate control levels necessary to ensure
-approved package insert instructions. safety and effectiveness. The Safe Medical Devices
Act of 1990, a major revision of the 1976 amend-
Validation: The documentation that a test which has
ments, added new provisions to better ensure that de-
already been verified is repeatedly giving the ex-
vices entering the market were safe and effective. It
pected results as the test is performed over a period
also provided means for the FDA to discover serious
of time. Validation confirms that the test continues to
problems more quickly and remove defective devices
perform satisfactorily according to the laboratory’s
from the market. More recently, the ASR Rule, en-
requirements or the manufacturer’s claims or, for
acted 23 November 1998 and updated on 15 Septem-
LDTs, according to its intended use. The require-
ber 2008 (21 CFR §809), defines the FDA’s approach
ments for test validation may include personnel com-
to regulate manufacturers of reagents that are used as
petency assessment, quality control, internal and ex-
components in LDTs. The FDA considers clinical lab-
ternal proficiency testing, and correlation with
oratories that develop in-house tests to be manufac-
clinical findings. Validation thus becomes an integral
turers of medical devices and they are subject to FDA
part of the laboratory’s quality assurance program.
jurisdiction under the FD&C Act. However, the FDA
Verification (4): The documentation of either com- has generally exercised enforcement discretion over
mercial or LDT performance. For FDA-cleared or LDTs and decided to ensure the quality of the reagents
-approved tests, it is the process of examination or used in LDTs through the ASR Rule. Before a test can
evaluation of a test system to determine whether the be marketed (commercially distributed) in the United
claims stipulated by the manufacturer in the package States, it must first be reviewed and cleared by the
insert as they relate to the product, the process, the FDA for IVD use. However, laboratories are permit-
results, or the interpretation can be achieved. Verifi- ted to verify and validate user-developed procedures
cation requires determination or confirmation of the and offer testing services (as opposed to the commer-
test performance characteristics, including sensitivity, cial distribution of their test) providing they meet the
specificity, and where appropriate, the predictive val- regulatory requirements defined by both CMS in
ues, precision, and accuracy of the test. Verification CLIA (discussed previously) and the FDA. The FD&C
is a one-time process, completed before the test or Act, the Safe Medical Devices Act, and the ASR Rule
system is used for patient testing (see Appendix A). are administered by the FDA’s Center for Devices and
Radiological Health through the Office of Device
It is important to note that the definitions for val-
Evaluation/Division of Clinical Laboratory Devices.
idation and verification as written above are accepted
Analogous to the regulatory requirements for IVD
by CLSI, the CLIA, and the International Organiza-
clearance in the United States, the In Vitro Diagnos-
tion for Standardization. However, the definitions ac-
tic Directive (98/79/EC) (IVDD) was introduced in the
cepted by The Joint Commission and the College of
European Union as one in a series of medical device
American Pathologists (CAP) are the inverse.
directives intended to ensure that only safe and effec-
tive products are sold in the European market. The
FEDERAL REGULATION IVDD includes strict regulations regarding manufac-
turing, import, and marketing. The “CE” mark on the
Role of the FDA manufacturer’s product indicates compliance with
The FDA and the Centers for Medicare and Medi- the IVDD, just as the marking of products with “For
caid Services (CMS) are two principal agencies in the In Vitro Diagnostic Use” indicates compliance with
U.S. Department of Health and Human Services re- the FDA in the United States. However, a CE-marked
sponsible for regulating laboratory tests. This section product is not automatically granted FDA clearance,
attempts to eliminate some of the confusion that of- and premarket review is still required and vice versa.
ten exists between the regulatory requirements for
FDA Clearance or Approval of an IVD
FDA clearance or approval of an IVD product while
introducing the different requirements for laborato- Medical Device Classification
ries to implement tests already approved or cleared The FDA recognizes three classes of medical de-
by the FDA relative to those that have not been vices based on the level of control necessary to ensure
cleared for IVD use. the safety and effectiveness of the device. Unless they
Laboratory tests are considered medical devices are deemed exempt, the FDA will classify IVD prod-
and, as such, are under the regulatory control of the ucts as class I, class II, or class III devices. This clas-
FDA. The Medical Device Amendments to the Food, sification determines the process the manufacturer
Drug, and Cosmetic (FD&C) Act in 1976 expanded must complete to obtain FDA clearance or approval
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6 Clark et al. CUMITECH 31A

to market its product; namely, either premarket noti- class III medical devices (e.g., a preamendment de-
fication [510(k)] or premarket approval (PMA). vice). The 510(k) submission identifies characteristics
Most devices are cleared for commercial distribution of the new or modified medical device compared to a
in the United States by the premarket notification medical device with similar intended use currently
[510(k)] process. legally marketed in the United States. The currently le-
Class I devices present minimal potential harm to gally marketed device is referred to as the “predi-
the user, are typically simple in design and manufac- cate” device. If the device is a high-risk device and
ture, and have a history of safe use. Examples of class has been found to be not substantially equivalent to
I devices include tongue depressors, arm slings, and a class I or II device or class III device requiring
handheld surgical instruments. Most class I devices 510(k), then the device must have an approved PMA
are exempt from the 510(k) requirement by regulation before being marketed in the United States. Some de-
but are not exempt from other general controls, such vices that are found to be not substantially equivalent
as product registration and device listing. However, a to a cleared class I, II, or III (not requiring PMA) de-
class I device may require a premarket notification vice may be eligible for down classification to a class
[510(k)] based on its stated or purported use. Such I or class II device. If the FDA assessment of the
devices are referred to as reserved class I devices. 510(k) submission indicates that it is substantially
A class II device is any device for which reasonable equivalent to a legally marketed device, the device is
assurance of safety and effectiveness can be obtained cleared and the manufacturer is free to market it in
by applying both general controls, as for class I devices, the United States. The FDA has granted exemptions
and special controls. Special controls may include spe- from the requirement for 510(k) notification for a
cial labeling requirements, mandatory performance variety of generic-type devices, including such micro-
standards, development of patient registries, and a biology products as anaerobic chambers, incubators,
requirement for postmarket surveillance. Examples gas-generating devices, and most media.
of class II devices include physiologic monitors, X-ray
systems, gas analyzers, pumps, and surgical drapes. PMA Process
Most class II devices require premarket notification PMA is the most stringent type of device market-
by submission and FDA review of a 510(k) for clear- ing application required by the FDA. Unlike premar-
ance to market the IVD. A few class II devices are ex- ket notification [510(k)], PMA approval is based on
empt from the premarket notification. Information the FDA’s determination that the PMA submission
on class II exempt devices is located within the device contains sufficient valid scientific evidence that pro-
regulation (21 CFR 862–892). vides reasonable assurance that the device is safe and
Class III devices are in the most stringent regula- effective for its intended use(s). A PMA is required to
tory category and are usually devices that “support receive clearance to market or continue to market a
or sustain human life, are of substantial importance class III medical device in the United States. How-
in preventing impairment of human health, or which ever, as previously mentioned, there are some class III
present a potential, unreasonable risk of illness or in- devices currently being marketed without a PMA,
jury.” Due to the higher level of risk associated with primarily due to commercial distribution prior to the
class III devices, the FDA has determined that general FD&C Act, but these devices must have a cleared
and special controls alone are insufficient to ensure premarket notification 510(k) prior to marketing.
the safety and effectiveness of class III devices. There- Before approval, a PMA receives an in-depth scien-
fore, these devices require a PMA application to ob- tific review, and the manufacturer’s facilities must
tain marketing clearance in the United States. Some undergo a comprehensive inspection compliance with
class III medical devices, such as a preamendment de- current good manufacturing practices. Finally, the
vice (a device in use before 1976), require only a PMA is reviewed by an FDA advisory panel of outside
510(k) clearance by the FDA to be marketed. Exam- experts who provide recommendations to the FDA
ples of class III devices that require a PMA include re- for approval with or without conditions or for disap-
placement heart valves, silicone gel-filled breast im- proval of the application. Examples of microbiology
plants, and implanted cerebellar stimulators. For devices requiring PMA applications are those in-
more information on test complexity and to research tended for the detection or typing of human papillo-
specific products, go to http://www.accessdata.fda mavirus; all hepatitis and human immunodeficiency
.gov/scripts/cdrh/cfdocs/cfCLIA/search.cfm (accessed virus diagnostic, detection, and monitoring devices;
8 July 2009). and devices using nucleic acid amplification tech-
niques for direct detection of Mycobacterium tuber-
Premarket Notification or 510(k) Clearance Process culosis from clinical material. Refer to the FDA web-
The 510(k) clearance process is required for re- site above for regulatory requirements of class III
served class I and class II medical devices and select devices prior to commercial distribution in the
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CUMITECH 31A Verification and Validation of Procedures in the Clinical Microbiology Laboratory 7

United States and refer to section 515(c)(1) of the require more extensive performance verification. The
FD&C Act for the required contents of a PMA. laboratory’s responsibility for proficiency testing ex-
FDA Clearance and Product Labeling tends to LDTs, and this proficiency testing should be
performed at least two times a year.
After all analytical and clinical data have been
critically reviewed, the final step of the FDA review ASRs
is to clear or approve the product labeling. That is, ASRs are the active ingredients of tests that are
the FDA review process confirms that sufficient evi- used to identify one specific disease or condition. ASRs
dence was presented which supports the claims of the include “antibodies, both polyclonal and mono-
manufacturer and does not establish claims or con- clonal, specific receptor proteins, ligands, nucleic
firm test performance. The FDA pays particular at- acid sequences, and similar agents which, through
tention to the following components of the package specific binding or chemical reaction with substances
insert, all of which are required by law (21 CFR in a specimen, are intended for use in a diagnostic ap-
809.10): intended use; specimen collection, trans- plication for identification and quantification of an
port, and storage recommendations; warnings and individual chemical substance or ligand in biological
limitations; expected values; validation of cutoff; re- specimens.” ASRs are purchased by manufacturers
sults and their interpretation; quality control recom- who use them as components of tests that are cleared
mendations; and specific performance characteristics. or approved by the FDA and also by clinical labora-
All microbiology products which undergo a scientific tories that use the ASRs to develop LDTs used exclu-
evaluation of data to substantiate product perfor- sively by that laboratory. As mentioned previously, the
mance claims as stated in the product insert (i.e., FDA classifies medical devices, including diagnostic
moderate- and high-risk devices) are expected by the devices such as ASRs, into class I, II, or III according
FDA to maintain that performance throughout the to the level of regulatory control that is necessary to
life of the product. Failure to maintain that expected provide a reasonable assurance of safety and effec-
performance could result in compliance or regulatory tiveness. These classifications include consideration
action. Promotional and advertising materials also of the level of risk associated with the device. The
fall under the labeling regulation. Such material can classification of an ASR determines the appropriate
only be reflective of the information contained in the premarket process. ASR class I devices are subject to
package insert for the device. general controls but exempt from premarket notifi-
RUO and IUO Products cation. The manufacturer must label class I, exempt
ASRs with the statement “Analyte Specific Reagent.
Devices which are in the laboratory research phase
Analytical and performance characteristics are not
of development may not be represented as effective
established.” An ASR class II device is a reagent used
diagnostic products, and the statement “For Research
as a component in a blood banking test of a type that
Use Only (RUO). Not for use in diagnostic proce-
has been classified as a class II device (e.g., certain cy-
dures” must be prominently placed in product label-
tomegalovirus serological and Treponema pallidum
ing. A product being shipped or delivered for prod-
nontreponemal test reagents). An ASR class III
uct testing prior to full commercial marketing must
reagent is one intended as a component in tests in-
prominently bear the statement “For Investigational
tended either (i) to diagnose a contagious condition
Use Only (IUO). The performance characteristics of
that is highly likely to result in a fatal outcome for
this product have not been established.” Only in
which prompt, accurate diagnosis offers the oppor-
vitro devices which have been 510(k) cleared or have
tunity to mitigate the public health impact of the con-
received PMA from the FDA may legally include the
dition (e.g., human immunodeficiency virus or M. tu-
statement “For In Vitro Diagnostic Use” as part of
berculosis) or (ii) for use in donor screening for
their product labeling and package insert. In the clin-
conditions for which the FDA has recommended or
ical laboratory, results from the following must not
required testing to safeguard the blood supply or es-
be reported without verification: (i) tests or proce-
tablish the safe use of blood and blood products (e.g.,
dures that have been developed in-house and use
tests for hepatitis or for identifying blood groups).
class I reagents that do not have an indicated use for
All ASRs require manufacturing under current good
that test or (ii) reagents or tests provided by compa-
manufacturing practices, and both class II and class
nies for IUO or RUO that are not used within the
III reagents require special controls.
guidelines described by the company or by the FDA.
Reports of such results should indicate that the test is LDTs and Special Considerations
not FDA cleared or approved but has been developed LDTs are procedures developed in-house that have not
and verified in-house. Since LDTs are not reviewed been reviewed and/or approved by the FDA. This in-
by the FDA and since the reagents used therein can- cludes the use of a laboratory-modified, FDA-cleared
not be reviewed for their use in those tests, these tests test (e.g., off-label use of an FDA-cleared test) or a
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8 Clark et al. CUMITECH 31A

laboratory-verified procedure that incorporates either oratories now also play a critical role in ensuring that
commercially available reagents not cleared by the devices and medical products previously cleared or
FDA for IVD use (e.g., RUO reagents or ASRs) or approved by the FDA are performing as expected.
reagents produced in-house. Since LDTs are not re- Laboratories have the responsibility of reporting de-
viewed and/or approved by the FDA and since the vice problems to the FDA and manufacturers. Con-
reagents used as components in the test cannot be re- cerns about the quality, performance, or safety of any
viewed for their intended use, these tests require more medical device should be reported. There are both
extensive performance verification (4). Moreover, voluntary and mandatory reporting systems through
federal regulations require that LDTs that incorpo- the FDA’s adverse event reporting program, Med-
rate an ASR are required to include a statement on the Watch (http://www.fda.gov/medwatch; accessed 8
report. For example, an LDT incorporating an ASR July 2009).
class I reagent would include “This test was developed
and its performance characteristics determined by Role of CLIA
[Laboratory Name]. It has not been cleared or ap- The CMS regulates all laboratory testing (except re-
proved by the U. S. Food and Drug Administration.” search) performed on humans in the United States
Although the use of an RUO reagent as a compo- through the CLIA regulations. The final CLIA qual-
nent in an LDT remains controversial and is subject ity system regulations became effective on 24 April
to the terms defined in the written agreement be- 2003 (4). The objective of the CLIA program is to en-
tween the manufacturer and the laboratory, the CAP sure quality laboratory testing. Since 13 November
established rules for its accredited labs regarding the 2003, the FDA has assumed primary responsibility
use of RUO reagents when no comparable FDA- for performing the CLIA complexity categorization
cleared product is available. According to the CAP’s functions that include the process of assigning com-
anatomic pathology checklist, RUOs “purchased mercially marketed IVD test systems to one of three
from commercial sources may be used in laboratory- CLIA regulatory categories based on their potential
developed tests only if the laboratory has made a rea- risk to public health: waived, moderate complexity,
sonable effort to search for IVD- or ASR-class or high complexity.
reagents and that these efforts should be documented Sections 493.1200 through 493.1299 of subpart K
by the laboratory director” (http://www.devicelink of the regulation set forth the quality control re-
.com/ivdt/archive/08/03/004.html; accessed 8 July quirements for tests of moderate or high complexity
2009). Although there are no federal regulations to (waived tests are not subject to quality control). Ef-
include a statement on an LDT incorporating an RUO fective 24 April 2003, quality control (including ver-
reagent, it is strongly recommended that the labora- ification) of moderate- and high-complexity tests was
tory use language analogous to that described above merged into one standard. Section 493.1253 of the
for a class I ASR. It is important to note that the use CLIA regulations describes the requirements for the
of unmodified kits provided by companies for RUO establishment and verification of method perfor-
or IUO are not considered LDTs, are not to be used mance specifications. For unmodified, FDA-cleared
for diagnostic purposes, and are subject to federal reg- or -approved tests (either moderate or high complex-
ulations and the language specified in the certifica- ity), the laboratory is required to verify the manufac-
tion program for each product. Please refer to http:// turer’s performance specifications provided in the
www.devicelink.com/ivdt/archive/08/03/004.html package insert before reporting patient test results.
(accessed 8 July 2009) for further information re- These specifications are:
garding IUO/RUO test kit use in the clinical micro-
• Accuracy
biology lab and the role of such kits in clinical
• Precision
diagnostics.
• Reportable range
Since LDTs have not been reviewed or cleared by
• Reference range
the FDA, they require more extensive verification be-
fore patient testing. Moreover, FDA clearance or ap- This requirement applies when the laboratory replaces
proval of a laboratory test does not predict perfor- a test system or instrument (with the same model or a
mance in a particular laboratory’s patient population different model), adds a new test, or changes the man-
and therefore does not substitute for verification of ufacturer of a test system.
test performance before use. Thus, laboratories are For LDTs (not FDA cleared or approved) or FDA-
required to verify the performance of tests, FDA cleared or -approved tests modified by the labora-
cleared or otherwise, prior to patient testing and tory, the laboratory must establish applicable perfor-
must maintain an active quality assurance program mance characteristics. The requirement only applies
that validates the test performance over time. In ad- to instruments, kits, or test systems introduced on or
dition, test verification and validation by clinical lab- after the effective date of the quality control regula-
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CUMITECH 31A Verification and Validation of Procedures in the Clinical Microbiology Laboratory 9

tions, 24 April 2003. Prior to reporting patient test 1. Define the purpose for which the method is to be
results for methods that fall within these categories, used. Common purposes for tests include the fol-
the laboratory must establish the following perfor- lowing (22):
mance characteristics, as applicable (see Appendix A Screening: Screening is used for testing large pop-
for more details): ulations of patients for the presence of a disease
• Accuracy state or analyte (such as an infectious agent). In
general, screening tests should have high (i.e.,
• Precision greater than 95%) clinical sensitivity and NPVs. In
• Analytical sensitivity most cases, the recommended specificity and PPV
can be lower than those of diagnostic and confir-
• Analytical specificity, to include interfering sub- matory tests. Thus, a negative screening test result
stances should indicate that the person has a high proba-
• Reportable range of patient test results bility of being free of the characteristic, whereas a
positive test result might reflect only the need for
• Reference range(s) confirmatory testing.
• Any other characteristic required for test perfor- Diagnosis: Diagnosis is used for the evaluation of
mance and interpretation of results persons suspected of having a given disease state
or characteristic (e.g., a particular type of infec-
In addition, control procedures for patient testing
tion). If the characteristic is important, either for
must be established on the basis of the verified perfor-
treatment or for prognostic considerations, sensi-
mance specifications. The laboratory is required to
tivity should be as high as possible. When diag-
have documentation of the verification of the manu-
nostic test results are not confirmed by additional
facturer’s specifications or establishment of perfor-
laboratory or clinical data, specificity may also
mance specifications for LDTs or modified FDA-
need to be very high. However, if an accurate con-
cleared or -approved tests. All laboratory accrediting
firmatory test is readily available, a high degree of
programs which have been granted deemed status by
specificity might not be necessary. The majority of
CMS (including CAP, The Joint Commission, and the
clinical tests for infectious diseases are for diag-
Commission on Laboratory Accreditation) must in-
nostic use.
clude these requirements as part of their inspection cri-
teria. For example, the CAP Laboratory General Supplemental: Supplemental (may also be referred
checklist includes verification and establishment of to as confirmatory) testing is used after obtaining
performance specifications (http://www.cap.org/apps a positive screening or diagnostic test result to en-
/docs/laboratory_accreditation/checklists/laboratory sure the accuracy of that initial result. Specificity
_general_sep07.pdf; accessed 25 March 2009). and PPV, rather than sensitivity and NPV, are usu-
ally the primary considerations for supplemental
tests; specificity should exceed 98%. Supplemen-
SELECTION OF A LABORATORY METHOD tal tests may not be necessary when the screening
Once a laboratory has reached the decision to offer a or diagnostic test has high specificity and PPVs.
new test, the next step in the process is generally the The specificity of supplemental tests is, by defini-
selection of the method by which the test will be per- tion, established when the test is used in conjunc-
formed. Few laboratories have the time or resources tion with, and subsequent to, a screening or diag-
to perform in-house evaluations of the large number nostic test. Supplemental tests should generally
of available test systems, kits, or methods which may not be used in lieu of screening or diagnostic tests,
be available to the microbiology laboratory for de- unless their performance has been thoroughly ver-
tection of an organism, antigen, or other analyte of ified for this purpose in well-defined patient pop-
interest. Thus, it becomes crucial to approach the se- ulations (e.g., treponemal tests for diagnosis of la-
lection of a new method in an organized fashion, tent or late syphilis).
making use of all available information to narrow 2. Decide what analyte (e.g., organism, antigen, or
down the selection without performing expensive in- nucleic acid, etc.) is to be detected and what the
house studies. The following steps are designed to reference method or gold standard will be for com-
serve as a guide for the initial selection of a labora- parison. Note, if the new test is likely to be more
tory method. Although all steps may not be necessary sensitive than the gold standard, then scientifically
for every test method under consideration by a labo- valid ways to arbitrate discrepant results (e.g.,
ratory, the basic process can be followed for the ma- clinical data or other assays, etc.) should be de-
jority of tests utilized by the microbiology laboratory. fined prior to beginning verification studies (1, 14,
19, 22).
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10 Clark et al. CUMITECH 31A

3. In collaboration with the end user of the test (e.g., • Quantities of reagents and controls needed for
the physician) combined with the information from test; storage requirements
steps 1 and 2, determine the medical usefulness of • Shelf life of reagents and controls before and
the test (e.g., whether the test will lead to im- after opening
proved patient care and/or shortened hospital stay)
and preliminary clinical and/or microbiological • Availability of supplies, service, and/or techni-
requirements for test sensitivity, specificity, and cal support
predictive values (as appropriate). • Possible safety hazards related to performing test
4. Survey the technical and medical literature for per- • Whether a reference range is appropriate for
formance claims of various methods that may in- the test and how it will be determined for the
dicate that one or more methods will meet the ini- institution
tial requirements for sensitivity and specificity, etc. 6. Make a preliminary selection of a test method,
When reviewing the literature, confirm that the perform the in-house verification (see Appendix
method described is actually the test (unmodified) A), and write a report to include, but not neces-
that is to be evaluated in the laboratory. sarily limited to, data and conclusions. The labo-
5. Determine the characteristics of the method(s) of ratory director or designee must sign the report. It
interest. The choice of method may also be based is recommended that a verification study protocol
on the following practical parameters (3, 16, 26). be written prior to conducting the study. The pro-
The laboratory should prioritize these parameters tocol should include the study design, methods for
based on their patient population and institution’s data analysis, and performance expectations.
mission. A brief outline of the laboratory method selection
• Cost of the method process is provided in Appendix B.
What are the comparative costs for material
and labor relative to alternatives to the test?
If applicable, what are costs of service contracts? VERIFICATION OF COMMON
For instrumentation, what are the comparative MICROBIOLOGY TESTS
costs of purchase versus reagent rental versus
CLIA regulations require that laboratories verify the
lease?
manufacturer’s performance specifications for new
What is the extent of reimbursement?
unmodified tests prior to reporting patient test re-
• Practicality in the laboratory setting sults. These performance specifications include accu-
Can the test be performed on all necessary shifts? racy (agreement), precision (or reproducibility), re-
Does the test require special equipment? portable range, and reference range (normal values)
What is the turnaround time for the test? (4) (http://www.cms.hhs.gov/clia/downloads/6064bk
What are the personnel and training require- .pdf; accessed 5 March 2009).
ments? The accuracy portion of test verification is usually
Are quality control and proficiency test mate- accomplished by performing the new or revised test
rials available? method in parallel with a reference method that has
What is the extent of quality control that will an established and satisfactory level of accuracy. How-
need to be performed? ever, in the absence of a suitable reference method,
What is the extent of preventive maintenance analytic performance characteristics can be estab-
that will need to be performed? lished using previously characterized clinical samples,
Is there adequate space in the laboratory to per- characterized clinical isolates, or simulated samples
form the test? prepared by spiking the appropriate test matrix with
Can the test be automated to reduce labor? various concentrations of characterized clinical iso-
Does the system have an indication for all of the lates or the analyte of interest. That is, the accuracy
uses and/or organisms that are of interest? of a new test can be established by either method
comparison or recovery studies and is a measure of
• Specimen requirements concordance between observed and expected results.
Volume and type of specimen needed Precision (or reproducibility) should be verified
Collection requirements within runs, between runs, and between operators, if
Transport requirements the test system is considered to be highly operator de-
Storage requirements pendent. Fully automated systems are generally not
Quality of specimen considered to be operator dependent. Precision can
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CUMITECH 31A Verification and Validation of Procedures in the Clinical Microbiology Laboratory 11

be verified by testing several negative and positive tains biochemicals that are then used to differentiate
specimens (or for quantitative tests, various levels of or presumptively identify the organism). This would
analyte) at least in duplicate in the same run and in include Campylobacter agar, media for the selective
different runs. For operator-dependent tests, this isolation of the pathogenic Neisseria spp., and any
process is performed by at least two different opera- other media not listed in Table 3 of reference 21.
tors. The comparability of repeated results (either In the following sections, suggested methods are
qualitative or quantitative, as appropriate) is assessed included for verification of many of the commonly
relative to the manufacturer’s specifications. used tests and test systems found in the microbiology
The reportable range is verified by testing charac- laboratory. These suggestions are not meant to be all-
terized samples with known values near the lower inclusive, and alternative approaches may be utilized
and upper ends of the manufacturer’s reportable range in individual laboratories. In addition, it is recog-
as well as samples in the normal range (usually neg- nized that the verification process can be timely and
ative for analyte). expensive, often complicated by a paucity of specimens
The reference range (normal values) provided by containing (or lacking in some circumstances) the de-
the test manufacturer or as published in textbooks or sired analyte. In some cases, laboratories will need to
scientific articles can be used by the laboratory, pro- make difficult choices about the extent of verification
vided the laboratory’s patient population is similar. If that is possible, taking into consideration how widely
the laboratory chooses to evaluate specimens from the test has been used and accepted by the micro-
known healthy patients, the results should be within biology community, the extent and results of pub-
the test’s reference range. lished evaluations, and the impact of an incorrect test
With careful planning, all of these test characteris- result on the patient. In some cases, repeat testing of
tics may be verified using the same set of samples. For selected control material near the test cutoff value(s)
example, the laboratory can test samples with known may give a level of satisfaction. In other cases, labo-
values at the lower and upper ends of the manufac- ratories may decide that they are unable to perform
turer’s reportable range along with samples in the a reasonable verification and may choose to refer the
normal range for the institution’s patient population, test to another laboratory. Whenever possible, the
in different runs, on different days, and by different purchase of a new system or test methodology should
personnel. be made contingent upon the results of the verifica-
The results of test verification should indicate one tion studies. Records of the actual test verification re-
of three possibilities: sults must be maintained for at least 2 years after re-
tirement of the test system.
• The test is acceptable for routine use.
• Further verification studies are required.
• Immediate corrective action is required by the Verification Study Design
manufacturer (if commercially obtained), the user,
The verification study design, the statistical analysis
or both. The test is unsuitable for routine use un-
of study results, and the criteria establishing accep-
til its performance parameters can be verified.
table performance of a new test will depend on the
Certain commonly used microbiology items are type of assay and its intended use. The verification
not considered instruments, kits, or test systems under study of an assay should demonstrate that it can de-
the CLIA of 1988 and may not require a complete tect or accurately characterize the analyte of interest,
verification process prior to use. Items such as media and the verification plan and acceptance criteria
or individual reagents used as components of the should be established prior to beginning the verifica-
identification process (e.g., oxidase or catalase) may tion studies, if possible. The studies and the accep-
instead be monitored through the quality control tance criteria should be consistent with the industry
protocols of the laboratory. However, each labora- standard for the assay at the time and/or as estab-
tory must assess the nature and purpose of each of lished by peer-reviewed publications. One approach
these components and may choose to perform more for defining acceptance criteria is the concept of total
elaborate in-house verification. For example, a deci- allowable error for a test, based on medical or clinical
sion may reasonably be made not to perform verifi- requirements (28). While generally applied to quan-
cation on common media with a history of limited titative testing, this approach can be used to assess the
failures, such as most of the media listed in Table 3 performance of a new antimicrobial susceptibility test
of CLSI document M22-A3 (21), but it should be (AST) system where one considers concordance be-
strongly considered for some of the more highly com- tween methods to mean a result within 1 doubling
plex media which are multifunctional (e.g., a dilution and there is no difference in the interpreta-
medium which is selective for an organism and con- tion of resistance. The implication for laboratory
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12 Clark et al. CUMITECH 31A

performance is that the laboratory should verify that that the microbiologist be confident that the system
analytical variation is low enough so as not to cause chosen is able to provide accurate and reliable results
a clinically significant change in results. This means in the user’s own laboratory. Within the past 15 years,
that estimates of inaccuracy (bias or lack of trueness) a number of recommendations for verification of sus-
and imprecision (repeatability and reproducibility) ceptibility test systems have been discussed in the lit-
should show that they are sufficiently small and erature (18, 20, 26). Although it may be difficult for
within the defined allowable total error. For quanti- laboratories to perform a rigorous study of a new
tative methods, a stringent criterion has been recom- system, use of selected controls (i.e., those obtained
mended where the test value (3 standard devia- from the American Type Culture Collection [ATCC]
tions) is within the established allowable total error or other reputable sources) and clinical isolates can
(28). Other examples of acceptance criteria are dis- aid in the effort to verify the claims made in the lit-
cussed in the following sections. erature and by the manufacturer regarding the accu-
racy and reproducibility of a system (18). Isolates
Verification Samples saved from proficiency surveys may also be used for
verification studies. The evaluation design (two are
Samples used for method verification should be well-
suggested below for comparing AST systems) should
characterized clinical specimens or culture isolates
allow for the detection of categorical errors (18, 25).
from either retrospective or prospective clinical spec-
Though not recommended, it is possible to verify an
imens or studies whenever possible. All samples should
AST system against disk diffusion testing, even
be collected in compliance with local, regional, and
though only categorical agreement and not essential
federal statutes. Proficiency and/or commercially pre-
agreement will be verified.
pared reference panels characterized by one or more
Evaluation of susceptibility test methods should
methods are suitable for method verification studies.
be done using a distribution of organisms similar to
However, they may not reflect the sample matrix
those commonly isolated and representing resistant
or reference range for the user institution’s patient
phenotypes observed in the institution. For example,
population.
verification of gram-positive antibiotic panels should
The FDA permits the use of remnant samples in
include methicillin-resistant Staphylococcus aureus
certain circumstances (including method verification
(MRSA), D-test-positive S. aureus, coagulase-negative
studies) provided the specimens are collected for rou-
staphylococci, and vancomycin-resistant enterococci;
tine clinical care, they would otherwise have been
verification of gram-negative panels should include
discarded, and they are not individually identifiable.
extended-spectrum beta-lactamase-, carbapenemase-,
In the case of a rare event or analyte, the use of
and AmpC-producing Enterobacteriaceae, along with
archived and/or retrospective samples in addition to
multidrug-resistant Pseudomonas aeruginosa and
prospective patient samples may be required to gen-
Acinetobacter to the extent that these are encoun-
erate data from a large enough sample set for statis-
tered in the institution. Other rare antibiotic-resistant
tical analysis. Alternatively, simulated specimens pre-
isolates (such as vancomycin-resistant S. aureus and
pared using sample matrix spiked with characterized
beta-lactamase-positive enterococci) may also be in-
clinical isolates or analyte may be used (often re-
cluded in the evaluation. In total, at least 30 isolates
ferred to as spiking, recovery, or seed-and-recovery
should be tested with each antibiotic panel/card.
studies). In these studies, simulated specimens are
While institutions should make every effort to con-
prepared using sample matrix collected from patients
duct studies using their own isolates, those with lim-
presumed to be without disease, and positive samples
ited resources may consider assistance from the ven-
are prepared by seeding (spiking) negative sample
dor in the form of reagents, characterized bacterial
matrix with various concentrations of analyte. A
strains, and technical support. However, only labora-
panel of simulated positive and negative specimens is
tory personnel, not the vendor technical experts,
randomized and tested blindly. Caution must be
should perform the verification studies.
taken when extrapolating assay performance from
Precision (reproducibility) studies may be per-
simulated specimens. Laboratories using simulated
formed by testing five isolates in triplicate for 3 to 5
samples as part of assay verification should docu-
days. Isolates with known antibiotic resistance phe-
ment the potential limitations of their findings.
notypes such as quality control strains from ATCC
can be used. It would be preferable that at least two
AST Systems (Unmodified, FDA Cleared) of the precision test isolates be antibiotic resistant
The generation of AST results is one of the most im- (for example, MRSA and carbapenemase-producing
portant functions of the microbiology laboratory, Enterobacteriaceae). Acceptable precision results
as the results may directly affect the therapy chosen should be 95%, at a minimum (including both es-
for the treatment of a patient (9). Thus, it is critical sential and categorical agreement; see below).
31A_Cumitech_557040-rpt 6/24/10 9:17 AM Page 13

CUMITECH 31A Verification and Validation of Procedures in the Clinical Microbiology Laboratory 13

Precision (reproducibility) essential agreement (PEA): No. of comparisons within 1 well


Agreement within 1 twofold dilution of the preci- EA   100
Total tested
sion test isolate antibiotic MIC.
The total tested can be calculated for all organisms
No. of comparisons within 1 and drugs combined or for each drug.
well of known reference MIC
PEA   100
Total no. of results CA: Agreement of interpretative results (SIR) between
the new AST system under evaluation and the current
AST system using FDA/CLSI interpretive criteria.
The total tested can be calculated for all organisms
and drugs combined or for each drug.
No. of categorical result matches
CA   100
Total tested
Precision (reproducibility) categorical agreement
(PCA): Agreement with the interpretative results
The total tested can be calculated for all organisms
(susceptible/intermediate/resistant [SIR]) of the preci-
and drugs combined or for each drug.
sion test isolate using FDA/CLSI interpretive criteria.
ME: One AST system under evaluation indicates a
No. of categorical result matches susceptible or resistant response and the other AST
PCA   100
Total no. of results system indicates the opposite result as a resistant or
susceptible response.
The total tested can be calculated for all organisms
and drugs combined or for each drug. No. of ME discrepancies
ME   100
Total no. of resistant organisms
tested by both methods
AST System Verification Studies Not Arbitrated
with a Reference Method (Test 30 or More MinE: One AST system indicates an intermediate re-
Isolates per Panel/Card) sponse, and the other AST system indicates either a
Many evaluations (due to limited resources) do not susceptible or resistant response.
compare the test AST system under evaluation against
a reference method but only compare it against the No. of MinE discrepancies
MinE   100
current AST system of the laboratory. For this rea- Total no. of organisms tested
son, the test AST system may not be incorrect when
results are discrepant between both AST systems. The total tested can be calculated for all organisms
One cannot automatically call the existing system and drugs combined or for each drug.
correct when the new AST system result differs. For
this type of evaluation when a reference method is
not used, the following types of discrepancies can be AST System Verification Studies Arbitrated
substituted for the traditional error rates (see below). with a Reference Method (Test up to 100 or
A minor discrepancy is defined when one AST system More Isolates per Panel/Card)
result is intermediate and the other AST system result In larger microbiology laboratories with a higher
is susceptible or resistant. A major discrepancy is throughput and potentially higher normal back-
having one result susceptible and the other resistant. ground of antibiotic-resistant isolates, it may be prefer-
For this type of evaluation, there are no very major able to perform larger studies of up to 100 or more
errors (VME). Overall, there should be less than 5% isolates per panel/card type. Ideally, at least 50% of
major errors (ME) and an overall essential agreement the comparison isolates should exhibit some form of
(EA) and category agreement (CA) of 90%. Both antibiotic resistance. Discrepancies between AST sys-
ME and minor errors (MINE) should be a combined tems need to be arbitrated with a reference method
10%. In addition, both the within-1-dilution agree- (i.e., microbroth dilution, macrobroth dilution,
ment (EA) and the CA (agreement of interpretative and/or agar dilution). It is acceptable to verify a new
results [SIR] between both AST system results) AST system against a reference MIC method alone.
should be 90%. The traditional error rates defined below may be
utilized for these larger arbitrated studies between
EA: Agreement within 1 twofold dilution of the AST systems or an AST system versus a reference
new AST system under evaluation with the current MIC method. Acceptable performance rates for EA
AST system. and CA should be 90%, whereas acceptable
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14 Clark et al. CUMITECH 31A

performance for the VME rate should be 3% (min- MinE: Either the new AST system under evaluation
imum of 35 resistant isolates); not more than 1 in 33 or the current AST system as verified by the reference
of these antibiotic-resistant isolates should repeatedly method indicates an intermediate response. The
test falsely susceptible (18). The ME rate should be other method indicates either a susceptible or resis-
3%. For ME and MinE combined (a minimum of tant response.
100 strains), the error rate should be a combined
7%. Additional detailed FDA recommendations No. of MinE discrepancies
MinE   100
for industry AST system evaluations can be found at Total no. of organisms tested
http://www.fda.gov/MedicalDevices/DeviceRegulation
andGuidance/GuidanceDocuments/ucm080564.htm The total tested can be calculated for all organisms
(accessed 8 July 2009). and drugs combined or for each drug.

EA: Agreement within 1 twofold dilution of the Furthermore, users should investigate all categori-
new AST system under evaluation with the current cal errors for all of the above types of AST system ver-
test AST system as verified by the reference method. ifications. If the specified limits are exceeded for any
antibiotic, the test must be considered unverified and
No. of comparisons within  1 well withdrawn from consideration or corrective action
EA   100
Total no. of organisms tested must be taken in conjunction with the manufacturer
to attempt to resolve the discrepancies. Following cor-
The total tested can be calculated for all organisms rective action, the new or revised test should be run
and drugs combined or for each drug. again in parallel with the reference method on a min-
imum of 20 appropriate isolates (isolates which will
CA: Agreement of interpretative results (SIR) be- demonstrate that the problem[s] has been corrected).
tween the new AST system under evaluation and the Error rates may not be significant with certain anti-
current AST system as verified by the reference microbial agent-organism combinations (i.e., these
method using FDA/CLSI interpretive criteria. types of errors may be considered for elimination
from the study). In addition, if a significant number of
No. of categorical result matches organisms have MICs near the breakpoint, the cate-
CA   100
Total no. of organisms tested gorical agreement may be 90% due to the inherent
plus-minus dilution variabilities of AST systems.
The total tested can be calculated for all organisms
and drugs combined or for each drug. Diagnostic Microbiology and Microbial
Identification Tests
VME: The new AST system under evaluation indi- Processes for verifying diagnostic microbiology tests
cates a susceptible response while the current AST and microbial identification tests are similar.
system, as verified by the reference method, indicates Examples of analytes detected by diagnostic micro-
a resistant response. Clinically, VME are the most se- biology tests include the following:
rious type of error and can only be detected by test-
ing organisms resistant to each antimicrobial agent. • Microorganisms
• Microbial antigens
No. of VME discrepancies • Nucleic acids
VME   100
Total no. of resistant organisms • Antibodies
by current AST system as verified Examples of microbial identification test formats
by the reference method include the following:

ME: The new AST system under evaluation indicates • Antisera


a resistant response, while the current AST system • Antigens
verified by the reference method indicates a suscepti- • Chemicals
ble response. ME can only be detected by testing or- • Stains
ganisms susceptible to each antimicrobial agent. • Instruments
• Reagents
No. of ME discrepancies • Kits
ME   100
Total no. of susceptible organisms The process for verifying a microbiology test may
by current AST system as verified be relatively straightforward for analytes which are
by the reference method common in the population or for organisms fre-
31A_Cumitech_557040-rpt 6/24/10 9:17 AM Page 15

CUMITECH 31A Verification and Validation of Procedures in the Clinical Microbiology Laboratory 15

quently encountered. When the new test will be de- sess sensitivity, specificity, and predictive values, it is
tecting a relatively uncommon analyte or organism only required to assess overall accuracy (agreement)
(for example, a direct test for the detection of Cryp- of unmodified FDA-cleared tests. If the accuracy study
tosporidium), assessment of the sensitivity or accu- includes samples with known values at the lower and
racy of the test in the user’s own patient population upper ends of the manufacturer’s reportable range
becomes difficult. In these circumstances, the manu- (weakly and strongly positive), the laboratory is also
facturer, other laboratories, or commercial sources able to verify the reportable range. Together with a
may be able to provide specimens of known content precision (reproducibility) study and package insert
or isolates to be used in the evaluation. data on the reference range, the verification require-
It is important to remember that a test may be ments are met.
suitable for one population of patients and not for The laboratory should also establish a procedure
another. Laboratories must evaluate this individually and acceptance criteria for the precision/repro-
and be prepared to provide physicians with the spec- ducibility study. Precision should be verified within
ifications of the test for individual populations with runs, between runs, and between operators, if the test
different disease prevalences if pertinent. system is considered to be highly operator depen-
dent. To assess within-run precision, several mem-
Verification of Unmodified, FDA-Cleared Tests bers of the 20-specimen panel (such as two negative
Diagnostic Tests specimens and two positive specimens) should be run
The new test should be performed in parallel with the at least in duplicate. This process is then repeated on
existing test or a reference method on at least 20 a different run and, if necessary, by a different opera-
specimens (http://www.cms.hhs.gov/clia/downloads/ tor. For qualitative diagnostic assays, the same or
6064bk.pdf; accessed 5 March 2009), generally di- comparable results should be obtained. Any devia-
vided equally among those positive for the analyte tions should be investigated. For quantitative diag-
and those negative for the analyte. Flexibility in the nostic assays (a value is reported), the laboratory
distribution of positives and negatives is important should calculate the percent coefficient of variation
to account for such factors as rare analytes and the (within runs, between runs, and total) and compare
institution’s patient population. Both weakly and the results to the manufacturer’s package insert data.
strongly positive specimens should be included to The test may be considered verified if it meets the
verify the reportable range of the assay. If weakly requirements initially established for performance by
positive specimens are unavailable, dilution of the manufacturer of the test (22) or as defined by the
strongly positive specimens with the appropriate user in the verification protocol.
specimen matrix can achieve the same effect. In some
circumstances, it may be necessary to test more spec- Microbial Identification Tests
imens to document that the test meets the required Verification of automated, multi-analyte test systems
level of sensitivity, specificity, or PPV and NPV. An for identification of microorganisms to the species
example of this decision-making process can be level should be conducted with a minimum of 20 iso-
found in Appendix A. lates representing a wide-range of clinically relevant
After the results of the new test are compared with organisms for the institution (http://www.cms.hhs
those of the reference method (gold standard), the .gov/clia/downloads/6064bk.pdf; accessed 5 March
number of true-positive, true-negative, false-positive, 2009). This may include gram-positive organisms such
and false-negative results obtained with the test to as S. aureus, coagulase-negative staphylococci, ente-
be verified should be documented. Total accuracy rococci, and Streptococcus pneumoniae and gram-
should be at least 90% relative to the reference negative organisms such as members of the Entero-
method (3). When the reference method is known to bacteriaceae and non-lactose fermenters. Note that
be an imperfect standard, an attempt to resolve dis- large institutions with complex patient populations
crepancies should be made. The calculated predictive and a wide variety of clinically relevant organisms
values may not be indicative of the performance of would likely need to evaluate more than 20 isolates.
the test in an actual patient population if the preva- In addition, the appropriate quality control organ-
lence of the target analyte is different from that used isms should also be tested and included during the
in the verification study. A test with a specificity of verification process. For identification methods that
95% when the prevalence of a target disease is only detect only one analyte (e.g., immunofluorescent
1% will have a predictive value of a positive result of reagents), the new test should be run in parallel with
only 16.7%. Individual predictive values may be cal- the existing test or a reference method on a minimum
culated from the sensitivity and specificity data for of 20 microbial isolates (http://www.cms.hhs.gov/
known different prevalences, as seen in the example clia/downloads/6064bk.pdf; accessed 5 March 2009)
in Appendix A. Note that while it is common to as- generally divided equally among those positive for
31A_Cumitech_557040-rpt 6/24/10 9:17 AM Page 16

16 Clark et al. CUMITECH 31A

the analyte and those negative for the analyte. Flexi- • Will the media used by the system support the
bility in the distribution of isolates containing and growth of organisms (including yeasts, anaerobes,
lacking the analyte is important to account for such and fastidious organisms, where appropriate)
factors as rare analytes and the institution’s patient commonly seen in the user’s patient population?
population. • Will the instrument (for automated systems) de-
For microbial identification tests, there should be tect, in a timely fashion, the majority of patho-
at least 90% agreement with the existing system or genic organisms from blood cultures which con-
reference method before the new method is consid- tain these microorganisms?
ered verified (3). Due to a variety of factors, the level
Two approaches for verification of blood culture
of misidentification deemed acceptable should be de-
systems are discussed below. Laboratories may also
termined by each laboratory, and should take into ac-
choose to combine these approaches to take advan-
count the manufacturer’s performance specifications
tage of the strong points of each (e.g., perform paral-
provided in the package insert. Certain groups of or-
lel studies to assess the ability of the system to detect
ganisms may be more challenging for new systems to
commonly isolated organisms and perform seeded
identify (e.g., nonfermenters, corynebacteria, coagu-
blood cultures to assess less common pathogens).
lase-negative staphylococci), and greater flexibility
There may be circumstances in which the labora-
may be necessary in assessing the accuracy of the new
tory is implementing a newer version of a test system.
method (i.e., identification to the genus level only
Blood culture systems may be a good example of this.
may be acceptable performance). In addition, the types
Depending on the changes to the new system version, a
of disagreements encountered with the new system
verification study may not be necessary. If the differ-
should be scrutinized. The new system may misiden-
ences between the current and new systems are lim-
tify an organism, may require further tests before
ited to the blood culture instrument (e.g., hardware
identifying an organism, or may give no identifica-
and software) and the blood culture bottles are not
tion at all. Misidentification is the most serious error
changed, then an instrument function check by a ven-
for an identification system; however, a laboratory
dor technical representative is sufficient to verify ad-
may choose to accept a certain number of isolates
equate performance of the complete blood culture
with no or appropriate partial identification if other
system in the user’s laboratory. The functional check
factors (e.g., cost or speed) outweigh the inconven-
would verify that the incubation and optical systems
ience of further testing and would have minimal im-
and the software are operating per the manufac-
pact on patient care.
turer’s specifications.
If the accuracy (agreement) of the new or revised
test does not satisfy the verification requirements, the
test must be considered unverified and withdrawn Seeded Blood Culture Studies
from consideration or corrective action must be Select a minimum of 20 isolates representative of
taken by the manufacturer, the user, or both. Follow- blood culture isolates normally seen in the institu-
ing corrective action, the new or revised test should tion. Include both gram-positive and gram-negative
be run again in parallel with the reference method bacteria and yeasts, as appropriate. To the greatest
and interpreted as described above. extent possible, use actual patient isolates rather than
stock strains. Prepare seeded blood cultures with iso-
Blood Culture Systems lates of each of the above species. To challenge the
Meaningful verification of a new blood culture sys- system, the minimum amount of sterile, antibiotic-
tem is one of the most difficult tasks facing the clini- free human blood recommended by the manufacturer
cal microbiologist. Parallel testing requires collection should be placed in each bottle. In addition, the
of additional blood from each patient and may not numbers of organisms placed in each bottle should
be possible in some patients or institutions. The low approximate those found in cases of septicemia
level of positivity for clinical pathogens (usually in (which can be less than 0.1 CFU per ml of blood) (3).
the range of 8 to 14%) (3) means that most of the This is accomplished by making serial dilutions of
specimens collected will be of little value in the com- the organisms prior to inoculation to achieve ap-
parison. In addition, the incidence of contamination proximately 5 to 30 CFU per bottle.
(usually 1 to 3%) and predominance of a limited The method is considered verified if all isolates are
number of pathogens may result in an evaluation detected within time frames specified by the user.
skewed toward only a few of the potentially clinically Times to positivity must be consistent with the liter-
significant organisms. Thus, verification studies ature for given organisms. As few as 3 days may be
should be designed to answer the following funda- sufficient to recover at least 95% of clinically rele-
mental questions: vant bacteria and yeasts (7). Any problems with de-
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CUMITECH 31A Verification and Validation of Procedures in the Clinical Microbiology Laboratory 17

tection should be investigated by repeating the tests well-characterized specimens and to do a complete
with the same patient strains. If detection is still not verification only if these specimens do not give satis-
obtained, corrective action must be taken by the user factory results.
and/or the manufacturer prior to instituting use of
the system in the laboratory. Microbial Identification Tests
Microbial identification tests that identify isolates to
Parallel Blood Culture Studies the species level should be tested in parallel with the
Performance of parallel blood cultures allows the existing test or another reference method on a mini-
laboratory to evaluate all aspects of the new system mum of 200 isolates (11). Whenever possible, these
under actual patient and laboratory conditions. isolates should include all species identifiable by the
When a laboratory chooses to perform parallel stud- new or revised test. The same criteria for method
ies of commercially available systems, duplicate sets agreement described for unmodified, FDA-cleared
of blood cultures inoculated with equivalent blood methods (at least 90% overall agreement) should be
volumes should be obtained until a minimum of 20 met by these tests to consider them verified (11). If
positive blood cultures (not to include contaminants the new or modified test identifies a particular ana-
[7]) representative of the blood culture isolates nor- lyte, it should be tested in parallel with the existing
mally seen in the institution are evaluated. test or a reference method on a minimum of 50 mi-
The new method is considered verified if the sen- crobial isolates that contain the target analyte and a
sitivity is at least 95%, relative to the reference minimum of 100 isolates that lack the target analyte
method, and times to detection are not significantly (11). Both positive accuracy (sensitivity) and negative
different. If the new method does not meet perfor- accuracy (specificity) should be at least 95% com-
mance requirements, it should be withdrawn from pared to the reference method (11), or as defined by
consideration or corrective action should be taken by the user in the verification protocol.
the user (and the manufacturer where appropriate) If the new or modified test does not satisfy the ver-
and the verification study should be repeated. ification requirements, the test must be considered
unverified and withdrawn from consideration or cor-
Verification of LDTs, Modified FDA-Cleared rective action must be taken. Following corrective ac-
Tests, and Commercially Available Kits tion, the new or revised test should be compared
That Are Not FDA Cleared again with the reference method as described above.
Diagnostic Tests Some state or local agencies may regulate LDTs
The accuracy of these tests should be verified as de- and provide specific requirements for verification
scribed above, except that a minimum of 50 speci- studies. For example, the New York State Department
mens that contain the target analyte and a minimum of Health/Wadsworth Center has established submis-
of 100 specimens that lack the target analyte should sion guidelines for laboratory-developed, nucleic acid
be studied (11). Both positive accuracy (sensitivity) amplification tests for infectious agents (http://
and negative accuracy (specificity) should be at least www.wadsworth.org/labcert/TestApproval/forms/
95% compared to the reference method (11), or as NAATSubmissionGuidelines.pdf; accessed 25 March
defined by the user in the verification protocol. 2009). These guidelines specify that a minimum of
Note that this section only covers accuracy. CLIA 40 specimens be evaluated, including at least 30 pos-
regulations also require that the user establish per- itive for an analyte and at least 10 that are negative.
formance specifications for precision/reproducibility, This Cumitech recommends a minimum of 50 posi-
reportable range, reference range, analytical sensitiv- tive and 100 negative specimens for verification of
ity, analytical specificity (including interfering sub- laboratory-developed diagnostic microbiology tests
stances), as well as additional characteristics for (as stated in reference 11).
quantitative tests (4). This process is described briefly
in Appendix A.
VALIDATION OF DIAGNOSTIC TESTS USED
In some instances, test verification will be required
IN CLINICAL MICROBIOLOGY
because of very small modifications (e.g., a minimal
change in incubation time) of an existing protocol While verification of a new or revised test serves to
which has been previously verified. In this situation, establish that test performance parameters are satis-
verification must be performed to the extent neces- factory, it does not provide ongoing assurance that
sary to demonstrate that the change has not affected the expected test performance is satisfactory under
the performance of the test, but it may not require routine use over extended periods of time. Test vali-
the extensive testing performed initially. It may be dation is the ongoing process used by the laboratory
useful to maintain a panel of a limited number of providing tests to provide this assurance.
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18 Clark et al. CUMITECH 31A

The components of the validation process are ad- • Review of intermediate test results or worksheets,
dressed by the CLIA regulations (http://wwwn.cdc quality control records, proficiency testing results,
.gov/clia/regs/toc.aspx; accessed 25 March 2009). and preventive maintenance records
Assays covered by CLIA comprise the following: • Direct observation of performance of instrument
FDA-cleared tests, FDA-cleared modified tests, LDTs, maintenance and function checks
IUO tests, RUO tests, and tests incorporating ASRs. • Assessment of test performance through testing
The components of this key process for laboratories previously analyzed specimens, internal blind test-
providing nonwaived testing include a total testing ing samples, or external proficiency testing sam-
process (i.e., preanalytic, analytic, and postanalytic) ples
along with general laboratory systems. Each labora- • Assessment of problem-solving skills
tory must maintain written policies and procedures
that implement and monitor these quality preana- Not every type of assessment needs to be per-
lytic, analytic, and postanalytic phases. These vari- formed for each area being reviewed, and the type of
ous components (see below) must meet the testing assessment tool used (from the above list) should be
specialty and subspecialty assay needs. selected based on whether it will provide an accurate
The end result of validation will indicate one of reflection of the performance and competence of the
three possibilities: (i) the test continues to be accept- worker. Direct observation may be more important
able for routine use, (ii) immediate corrective action when first assessing a worker’s ability to perform a
must be undertaken by the manufacturer (if commer- test to which they have been recently trained, whereas
cially obtained), the user, or both, or (iii) the test assessment of ongoing competence for a fully trained
must be considered unsuitable for continued routine and experienced worker may be performed using
use until it can be validated. some direct observation of work performed com-
bined with worksheet review, maintenance record re-
view, written examination, and/or review of profi-
Components of the Validation Process ciency testing samples in the specified area.
The standard components of a validation process Training may be divided into three parts:
have expanded since the CLIA of 1988 and now in- • Initial training occurs when a new or current em-
clude the parameters listed below (4). In addition, the ployee is trained to perform a new test or when a
laboratory must monitor and evaluate the overall new assay is introduced.
quality of the general laboratory systems on an on- • Retraining may occur when periodic competency
going basis and must identify and correct issues. The assessments are unacceptable.
quality review must include the general effectiveness • Training updates are required whenever changes
of the corrective action used to fix issues. are implemented to a procedure or when additions
are made to the training document, such as new
Personnel Competency Assessment and Training learning objectives.
The laboratory must have a written documented sys-
It is helpful to prepare a checklist for each of the
tem to establish the competency of each laboratory
above procedures to ensure competency for each crit-
employee. This is an extremely important component
ical component. Direct observation includes all as-
of laboratory quality control, since it ensures person-
pects of testing, including specimen handling, speci-
nel are trained appropriately to perform prompt and
men processing, testing, and instrument maintenance
accurate testing. All employees must be assessed for
and function checks, if applicable. Record review in-
competency semiannually during their first year in a
cludes assessing the trainee’s ability to record inter-
new laboratory department and then annually there-
mediate test results, such as on worksheets; the
after (12, 24, 27). All newly implemented assays must
recording of quality control, proficiency testing, and
have proper, documented personnel training before
preventive maintenance records; and the final record-
patient test results are reported to clients (training
ing and reporting of test results. Test performance in-
verification).
cludes the use of previously analyzed specimens, in-
The CLIA regulatory requirement lists six areas
ternal blind samples, or even proficiency samples to
that must be part of a competency assessment pro-
assess competency. Problem-solving skill assessments
gram:
may be tested through written quizzes or by the doc-
• Direct observations of performance of routine pa- umentation of a problem resolution in which the
tient tests worker participated. Any unacceptable perfor-
• Monitoring of the recording and reporting of test mance(s) noted among employees with the above six
results procedures must be addressed immediately with re-
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CUMITECH 31A Verification and Validation of Procedures in the Clinical Microbiology Laboratory 19

medial training. The appropriate supervisor (with di- samples with the specific analyte (i.e., microorganism,
rector oversight) must sign off on the appropriate antigen, or amplification target sequence), or photo-
paperwork indicating that the trainee has been graphic images obtained from a reference laboratory.
trained properly for the specific assay(s). The reader
Quality Control Organisms
is referred to three comprehensive reviews of this
For FDA-cleared or -approved tests, laboratories
topic for further details (12, 24, 27).
must minimally perform the number of tests and type
of quality control testing as described in the package
Proficiency Testing
insert. Additional controls may be considered. Each
CLIA-certified laboratories must enroll in a CMS-
laboratory should establish its own collection of
approved proficiency program for each specialty and
quality control isolates. These isolates should be ob-
subspecialty for which they seek certification. For a
tained from a reputable source (i.e., ATCC or an-
current list of proficiency testing providers, see http://
other recognized vendor). Isolates should be main-
www.cms.hhs.gov/CLIA/14_Proficiency_Testing_
tained frozen or lyophilized. For some assays (such as
Providers.asp (accessed 2 June 2009). Proficiency
antibiotic susceptibility testing), bacterial isolates
testing must be performed at least twice per year.
should be subcultured from the frozen or lyophilized
Also, the laboratory must test the proficiency sample
state on a monthly basis and then stored on a slant
in the same manner as any other sample in the labo-
for weekly testing. Other isolates used for quality
ratory. For example, if a standard patient sample
control of commercial microbial identification sys-
would not normally require a repeat analysis by an
tems may require less-frequent recovery from the
assay, then the proficiency sample should not be re-
freezer (yearly may suffice). If there is some question
peated by that same assay. If the standard operating
regarding the validity of an isolate during quality
procedure requires or accepts duplicate testing of pa-
control testing, then a new subculture should be im-
tient samples for an assay, then it is acceptable to run
mediately obtained from the freezer stock or other
the proficiency sample in duplicate by this same assay.
reputable source. If nonreference strains are used, the
In addition, laboratories must not participate in
laboratory should have a complete record of the his-
any interlaboratory communication related to the
tory of the organism including characterization, stor-
proficiency sample(s) test results until after the date
age, and recovery from storage.
on which the laboratory reports proficiency test re-
Each user needs to determine which quality con-
sults to the proficiency testing program. Failure to
trol strain(s) is to be used with each assay and how
score at least an 80% on a certain testing event in a
often the quality control testing should be per-
specialty (i.e., microbiology, parasitology, mycobac-
formed. In many instances (see package inserts), the
teriology, mycology, or virology) indicates an unsat-
vendor will recommend the specific isolates to test
isfactory performance. The laboratory must then
and how often to test. When there is no specific ven-
undertake retraining with appropriate documenta-
dor recommendation, the laboratory can research the
tion. Failure to achieve an overall satisfactory per-
appropriate CLSI document and/or obtain informa-
formance for two consecutive testing events or two
tion from authoritative sources such as the Manual
out of three consecutive testing events is unsuccessful
of Clinical Microbiology to determine the best course
performance. Depending upon the circumstances,
of action. The frequency of testing and actions to be
CMS may then impose sanctions which may include
taken after quality control failure should follow the
the suspension of testing in that specialty area.
vendor’s recommendations and those of regulatory
For tests that have no external proficiency testing
agencies (5, 6, 21).
program available, the laboratory must establish an
internal proficiency program to monitor the accuracy Quality Control Analytes
and reliability of these tests. These tests must be as- Quality control analytes are a metabolic product, nu-
sessed at least semiannually. Microbiology tests for cleic acid, enzyme, or antigen usually provided by the
which proficiency testing is not normally available manufacturer of a test or system for the routine qual-
include the serum bactericidal test, minimal bacteri- ity control of a specific procedure or instrument. The
cidal concentration test, and culture for Mycoplasma analyte should be identified with a lot number or
hominis and/or Ureaplasma. Testing material may be should have other traceable identification; further
difficult to collect for some of these assays. Alterna- description should indicate concentration, titer
tive performance assessment procedures may include (where appropriate), use, date of preparation, and
split-sample analysis with reference or other labora- storage conditions. For an analyte introduced by the
tories, split-samples with an established in-house user laboratory, a defined record of its development
method, blind testing of quality control products and assay should be available. For FDA-cleared or
obtained from another laboratory, seeded clinical -approved tests, laboratories must minimally
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20 Clark et al. CUMITECH 31A

perform the number of tests and type of quality con- the calibration be carried out at the specified time
trol testing as described in the package insert. Addi- intervals.
tional controls may be considered. The frequency of
testing should follow the vendors’ recommendations Use of Historical Laboratory Data
or those stipulated by one or more of the various reg- Laboratories are encouraged to utilize historical data
ulatory or advisory agencies (5, 6, 21). For LDTs, concerning recovery and detection of pathogens in
positive, negative, and other relevant controls should their own populations as an aid in confirming that
be selected from recommendations for the test found the system is operating as expected. If significant
in appropriate CLSI guidelines or the Clinical Micro- changes are seen in the distribution and/or frequency
biology Procedures Handbook (17). of recovery of isolates obtained from patients over a
period of time (for example, a substantial reduction
Comparison of Test Results or Multiple in the number of isolates of S. pneumoniae from that
Instruments and Testing Sites obtained with the old system during an equal time
If the laboratory performs the same test method us- period), a more intensive investigation into the abil-
ing multiple units of the same instrument or performs ity of the new system to support and detect these
the same test method at multiple testing sites, there species is warranted. Monthly assessments of ampli-
should be a program in place to demonstrate equiva- fication positivity rates (i.e., MRSA and Chlamydia
lency of test results. It is not necessary to duplicate trachomatis, etc.) are currently a CAP requirement in
the entire assay verification process on each instru- the microbiology laboratory.
ment or at each testing site if the sites operate on the
same CLIA certificate. However, as part of the ongo- Confidentiality of Patient Information
ing validation process, laboratories should demon- There must be a system available to maintain patient
strate that multiple instruments produce equivalent confidentiality throughout all phases of laboratory
test results, both prior to performing a new test and testing.
periodically thereafter (e.g., at least twice a year). This Specimen Identification and Integrity
can be accomplished by testing well-characterized There must be a written policy in place that protects
patient specimens (or isolates), archived proficiency the identification and integrity of each sample during
samples (or isolates), or controls. When regulations the testing process that is under the laboratory’s con-
require testing of quality control material at a certain trol. This policy must include the maintenance of test
frequency, alternating the quality control material records.
among multiple instruments can also serve to verify
equivalent performance. For example, if a laboratory Complaint Investigations
has two identical instruments for bacterial identifica- There must be a system in place to handle laboratory
tion and antibiotic susceptibility testing, one-half of complaint investigations. This system must include a
the quality control organisms could be tested on in- policy for taking corrective action whenever test re-
strument A and the other half on instrument B one sults, equipment or methodologies, or patient test
week and then reversed each week. results fall outside the reportable range of test results
Implementation of New Assays for the assay system in question. Corrective action
Manufacturers routinely introduce a number of new would also be required whenever normal values or
assays each year. Some of these assays are indeed an reference intervals for a test procedure are inappro-
improvement over current laboratory technology. priate for the laboratory’s patient population or
However, some newer tests are significantly more ex- whenever control material fails.
pensive (e.g., MRSA PCR) than standard methods
Communications
(routine MRSA culture screen). The hospital labora-
There must be a system in place to handle issues of
tory needs to work with its administration to decide
communication breakdown with an authorized indi-
whether or not to implement these new expensive as-
vidual who orders tests. Excellent communication
says. If the expense of the new testing can be justified
must exist between the laboratory and the individu-
by cost reductions in other parts of the hospital (i.e.,
als who order tests to eliminate potential errors.
lowered MRSA infection rates), then it may be justi-
When the above 12 components of the validation
fiable to implement the new test for routine testing in
process are in place, the user has assurance that the
the laboratory (see Appendix B).
test or test system meets the validation requirements.
Instrument Calibration
Certain instruments require that specific components Frequency of Test Validation
or internal systems be checked on a regular basis. It Test validation is essentially a continuous process. In-
is imperative that the manufacturer’s directions for dividual laboratories are responsible for ensuring
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CUMITECH 31A Verification and Validation of Procedures in the Clinical Microbiology Laboratory 21

that the specific components of test validation, listed and reference range (negative for C. difficile toxins A and
above, occur frequently enough to ensure the contin- B) were also obtained from the vendor (Table A2). The ref-
ued performance of a laboratory test. In most cases, erence range was verified by the negative results (n  99)
following the manufacturer’s guidelines and/or the obtained from stool specimens from patients without C.
difficile disease (n  100). The reportable range was veri-
requirements of the regulatory or accrediting agen-
fied by testing positive reference specimens with high and
cies will provide this assurance.
low values (provided by the vendor). All specimens yielded
positive results by the brand X test kit.
SUMMATION A new C. difficile assay (brand Y) became FDA cleared,
and the department management decided to test the new
This updated document provides guidance in per- assay against their Acme assay (gold standard). A precision
forming test verification and validation in the micro- (reproducibility) study was performed as described for the
biology laboratory. As stated at the outset, these are brand X kit and showed 100% reproducibility (see Table
guidelines and should not be considered regulatory 4). As the brand Y kit is FDA cleared, the department man-
standards. For those responsible for establishing and agement decided to test a total of 20 stool samples (10 pos-
maintaining standards in clinical laboratories, there itive and 10 negative for C. difficile toxins A and B by the
Acme assay) in both systems. The following was obtained
are numerous excellent documents available, many
(Table A3): accuracy (agreement)  (18/20)  100  90%.
of which are cited throughout this text. Our goal
Precision (reproducibility) was evaluated by testing five
here is to make this information more microbiology replicates of positive and negative kit controls as well as a
friendly. Ensuring good laboratory practice, which positive external control (stool sample positive for C. diffi-
includes complying with regulations from various cile toxin) on three different days. The reproducibility was
agencies, can be a challenge. The availability of clear 100% (complete concordance, qualitatively, both inter-run
and useful guidelines for performing verification and and intra-run). The laboratory management then contacted
validation which specifically address clinical micro- the vendor who provided the reference range (negative for
biology should make the accomplishment of this as- C. difficile toxins A and B) (Table A4). As the brand Y kit
pect of good laboratory practice easier to achieve. is FDA cleared, it was not necessary to document analyti-
cal sensitivity and specificity (interferences). The reportable
range was verified by testing positive reference specimens
APPENDIX A with high and low values (provided by the vendor). All
METHOD SELECTION AND
VERIFICATION EXAMPLE

Laboratory A has decided to switch enzyme immunoassay TABLE A2. Summary of verification studies for C. difficile
(EIA) kits for the detection of Clostridium difficile toxins A toxin A/toxin B EIA
and B from stool samples. Brand X (new non-FDA-cleared
Result for non-FDA-cleared
kit) is compared to the current laboratory A method (Acme
Parameter brand X assay (C. difficile
assay). Laboratory A utilizes the Acme assay as the refer-
toxin A/toxin B EIA)
ence method (gold standard) against the brand X test kit.
The department management decided to test a total of 150 Specimen type. . . . . . . . . . . . . Stool
stool samples (50 positive and 100 negative for C. difficile Accuracy (method
toxins A and B by the Acme assay) in both systems. The comparison) . . . . . . . . . . . . . 99%
following was obtained (Table A1): accuracy (agreement)  Intra-run precision . . . . . . . . . . 100%, qualitative
Inter-run precision . . . . . . . . . . 100%, qualitative
(148/150)  100  99%. Precision (reproducibility) was
Analytical sensitivity (lower
evaluated by testing five replicates of positive and negative
detection limit)a . . . . . . . . . .Toxin A, 0.4 ng/ml; toxin B,
kit controls as well as a positive external control (a stool 0.5 ng/ml (obtain from
sample positive for C. difficile toxin) on three different vendor)
days. The reproducibility was 100% (complete concor- Analytical specificity
dance, qualitatively, both inter-run and intra-run). The lab- (interference)a . . . . . . . . . . . . Not affected by blood, barium,
oratory management then contacted the vendor who pro- or treatment with antibiotics
vided them with the analytical sensitivity (lower detection (obtained from vendor)
limit) for toxin detection. Specific analytical interferences Reference range . . . . . . . . . . . Negative for C. difficile toxins A
and B, as determined by
testing specimens from unin-
TABLE A1. Non-FDA-cleared assay (brand X) fected patients (accuracy
study) representative of insti-
No. of specimens tested by
tution’s patient population
Test result (brand X) gold standard (Acme assay) with result
Reportable range . . . . . . . . . . . 100% detection of reference
Positive Negative specimens (provided by ven-
dor) with high and low values
Positive 49 1 a
Additional performance specifications that must be determined for non-
Negative 1 99
FDA-cleared assays.
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22 Clark et al. CUMITECH 31A

TABLE A3. FDA-cleared assay (brand Y) 2. Carpenter, A. B. 2007. Immunoassays for the diagno-
sis of infectious diseases, p. 257–270. In P. R. Murray,
No. of specimens tested by gold
standard (Acme assay) with result E. J. Baron, J. H. Jorgensen, M. L. Landry, and M. A.
Test result (brand Y) Pfaller (ed.), Manual of Clinical Microbiology, 9th ed.
Positive Negative American Society for Microbiology, Washington, DC.
Positive 9 1 3. Carroll, K. C., and M. P. Weinstein. 2007. Manual
Negative 1 9 and automated systems for detection and identifica-
tion of microorganisms, p. 192–217. In P. R. Murray,
E. J. Baron, J. H. Jorgensen, M. L. Landry, and M. A.
TABLE A4. Summary of verification studies for C. difficile Pfaller (ed.), Manual of Clinical Microbiology, 9th ed.
toxin A/toxin B EIA American Society for Microbiology, Washington, DC.

Result for FDA-cleared 4. Centers for Medicare and Medicaid Services. 2003.
Parameter brand Y assay (C. difficile Medicare, Medicaid and CLIA programs; laboratory
toxin A/toxin B EIA) requirements relating to quality systems and certain
personnel qualifications; final rule. Fed. Regist. 68:
Specimen type . . . . . . . . . . . . .
Stool. 3640–3714.
Accuracy (method comparison) .
90% .
Intra-run precision . . . . . . . . . . . .
100%, qualitative 5. Clinical and Laboratory Standards Institute. 2006.
Inter-run precision . . . . . . . . . . . .
100%, qualitative Methods for Dilution Antimicrobial Susceptibility
Reference range . . . . . . . . . . . . .
Negative for C. difficile toxins Tests for Bacteria That Grow Aerobically; Approved
A and B (obtained from Standard, 7th ed. CLSI document M7-A7. Clinical
vendor) and Laboratory Standards Institute, Wayne, PA.
Reportable range . . . . . . . . . . . . 100% detection of reference
specimens (provided by 6. Clinical and Laboratory Standards Institute. 2006.
vendor) with high and Performance Standards for Antimicrobial Disk Sus-
low values ceptibility Tests; Approved Standard, 9th ed. CLSI
document M2-A9. Clinical and Laboratory Standards
Institute, Wayne, PA.
7. Clinical and Laboratory Standards Institute. 2007.
specimens yielded positive results by the brand Y test kit Principles and Procedures for Blood Cultures; Ap-
(Table A4). proved Guideline. CLSI document M47-A. Clinical
After completion of both verification studies, the depart- and Laboratory Standards Institute, Wayne, PA.
ment management decided to implement the FDA-cleared 8. Diekema, D. J., and M. A. Pfaller. 2007. Infection con-
test (brand Y) due to billing reasons (non-FDA-cleared tests trol epidemiology and clinical microbiology, p. 118–
are not billable to the federal government). All of the above 128. In P. R. Murray, E. J. Baron, J. H. Jorgensen,
required parameters need to be included in a formal report. M. L. Landry, and M. A. Pfaller (ed.), Manual of Clin-
The laboratory director or designee is required to approve ical Microbiology, 9th ed. American Society for Micro-
all verification studies. Laboratory inspectors may require biology, Washington, DC.
review of verification studies during on-site audits. The
9. Doern, G. V., R. Vautour, M. Gauder, and B. Levy.
verification report should be maintained for the life of
1994. Clinical impact of rapid in vitro susceptibility
the assay but may be discarded 2 years after the assay is
testing and bacterial identification. J. Clin. Microbiol.
discontinued. In addition, for laboratories that are licensed
32:1757–1762.
to accept samples from New York State patients, the New
York State Health Department may require review of veri- 10. Dunne, W. M., and M. T. LaRocco. 2007. Laboratory
fication data for modified, FDA-cleared tests and LDTs be- management, p. 4–19. In P. R. Murray, E. J. Baron, J. H.
fore New York patient testing is initiated. Jorgensen, M. L. Landry, and M. A. Pfaller (ed.), Man-
ual of Clinical Microbiology, 9th ed. American Society
for Microbiology, Washington, DC.
ACKNOWLEDGMENTS
11. Elder, B. L., S. A. Hansen, J. A. Kellogg, F. J. Marsik,
We recognize the valuable contributions of the authors and R. J. Zabransky. 1997. Cumitech 31, Verification
of the first edition of this Cumitech: B. Laurel Elder, and Validation of Procedures in the Clinical Micro-
Sharon A. Hansen, James A. Kellogg, Frederic J. Marsik, biology Laboratory. Coordinating ed., B. W. McCurdy.
Ronald J. Zabransky, and Brenda W. McCurdy (coordinat- American Society for Microbiology, Washington, DC.
ing editor).
12. Elder, B. L., and S. E. Sharp. 2003. Cumitech 39,
Competency Assessment in the Clinical Microbiology
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CUMITECH 31A Verification and Validation of Procedures in the Clinical Microbiology Laboratory 23

APPENDIX B
PROCESS FOR SELECTION OF A TEST METHOD

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