Sketching out changes in the microbiology checklist
Many CAP checklist questions for lab inspectors can
be traced to requirements set by the Clinical Laboratory Improvement
Amendments of 1988.
But when Thomas A. Merrick, MD, education commissioner for the
CAP Commission on Laboratory Accreditation, instructed laboratorians
earlier this year on how to inspect the microbiology laboratory,
he chose to focus on questions that might not be covered by the
CLIA ’88 regulations.
"The emphasis of late has been on clinically relevant questions
that address the very important interface between the microbiology
lab and the medical staff, pharmacy, and infection control committee,"
says Dr. Merrick, director of the microbiology department at Presbyterian/St.
Luke’s Medical Center, Denver.
Working with CAP staff, Dr. Merrick crafted 13 vignettes that
highlight recent changes to the microbiology checklist. This includes
questions that he and the CAP’s technical specialists are often
asked to clarify during inspections and others that have been raised
in discussion groups on the American Society for Microbiology’s
Now for the first vignette:
1. Review of the laboratory’s quality control
records show that the gram-stain procedure is checked and recorded
for each new batch of stains and at least weekly against known gram-positive
and gram-negative control organisms. The inspector notes that the
laboratory is also performing other bacteriology stains and is checking
these stains weekly. Is this acceptable?
The laboratory inspector can choose to:
Two microbiology checklist questions apply. MIC.21540, a Phase I question,
asks, "Is the gram-staining procedure checked and recorded for each
new batch of stains and at least weekly against known gram-positive
and gram-negative control organisms?" The lab here is checking the
gram-stain procedure at least weekly, so the answer to this checklist
question is yes.
- Not cite a deficiency because the laboratory is in compliance.
- Not cite a deficiency and informally make an oral recommendation.
- Not cite a deficiency but make a written recommendation.
- Cite a deficiency.
The other, MIC.21560, is a Phase II question. It asks, "Are all
bacteriology stains checked with a positive control and negative
control (when appropriate) for intended reactivity each day of use
or weekly, whichever is less frequent?"
Centers for Medicare and Medicaid Services staff reviewed the
checklist and found this question to be "less stringent than the
CLIA requirements," Dr. Merrick says. Future versions of the checklist
will specify that gram stains can be checked weekly but that all
other bacteriological stains, such as for Legionella, Nocardia,
and Bordetella, must be checked daily or on each day of use.
Of the lab in the vignette, Dr. Merrick says he would not cite
it as deficient because it is compliant with the question as written.
"But obviously I would make a strong recommendation to them that
the next version of the checklist will require them to show that
they check these daily," he says.
This change notwithstanding, Dr. Merrick expects there will be
relief from excessive QC testing in other areas within the next
An American Society for Microbiology membership survey found the
rates of QC failures for common laboratory reagents, such as catalase,
oxidase, indole, and coagulase, were less than one percent, and
it was presented with a subsequent survey to the Clinical Laboratory
Improvement Advisory Committee and the Centers for Disease Control
and Prevention. CLIAC and CDC agreed with ASM’s recommendation that
new lots of commercial reagents with a 99 percent or greater success
rate need to be tested only once. "However, we must wait until the
regulations are published in the Federal Register before we can
make a change in the checklist," Dr. Merrick adds. Surveys are being
done now on QC failure rates for miniaturized or automated bacterial
identification systems and on laboratory protocols for media QC
that might result in less frequent quality testing of these products
within the next year.
Two changes to the laboratory-general checklist about the review
of QC data have already taken effect. Instead of weekly review of
QC data by a supervisor, the lab must prove oversight review at
least monthly. In addition, there’s no longer a requirement to label
reagents with date received or date opened-only the date prepared
or reconstituted, expiration date, and storage requirements are
needed. "Those are changes that will help us cut back on some of
our unnecessary paperwork," Dr. Merrick says.
2. While reviewing the laboratory’s
performance on a recent CAP Survey, the inspector notices that the
laboratory submitted a result of "gram-positive cocci present" from
a sterile body site and the result was graded as acceptable. As
the inspector questions the supervisor and reviews the procedure
manual, she discovers that the gram-positive cocci isolated from
a body site are routinely identified to the genus and species level.
Should the laboratory be confronted with this discrepancy?
"If you report isolates to the species level, you must do so for
the Survey specimens as well," says Dr. Merrick. "But if the organism
is one that you normally identify to genus or presumptive genus
level on a patient sample—for example, grampositive bacilli
resembling Corynebacteria—with referral to a reference
lab for further identification if clinically indicated, it is acceptable
to report likewise for a Survey specimen."
The relevant microbiology checklist question is MIC.00350, a Phase
II question that asks, "Are organisms in proficiency testing specimens
identified to the same level as those from patient samples?"
For the lab in vignette No. 2, Dr. Merrick would look closely
at the Survey results and cite a deficiency only if this level of
reporting was found to be a trend. "If this is a one-time event
and the supervisor has a reasonable explanation for it, then I would
make a recommendation only. But it’s certainly something to be taken
A related microbiology checklist question, MIC.01100, asks, "For
areas where graded proficiency testing is not available, are other
procedures used to validate performance at least semiannually?"
Examples include fastidious, difficult-to-grow microorganisms, such
as Helicobacter pylori, or hazardous organisms, such as
In those situations a laboratory must perform an alternative form
of proficiency testing, Dr. Merrick says. That can include ungraded
PT programs, split sample analysis with other laboratories, split
sample with established in-house materials, or clinical validation
by chart review. For more ideas on how to meet this requirement,
he recommends a new NCCLS document, GP29-A, titled "Validation of
laboratory tests when proficiency testing is not available."
3. The laboratory has purchased a new bacterial
antigen kit that contains positive and negative onboard controls.
Staff members are uncertain about the level of complexity of the
test system, and this information is not in the package insert.
They are running positive and negative liquid QC with each new lot
There are two updated questions in the microbiology checklist
about rapid bacterial antigen tests. One is MIC.21760, a Phase II
question, which asks, "For direct bacterial antigen tests on patient
specimens that do include internal positive and negative controls,
and are not classified as high complexity under CLIA ’88, is a positive
and negative external control tested with each new kit lot number
or separate shipments of a given lot number?" High-complexity tests
that include an extraction phase must be checked each day of use
with a positive organism, Dr. Merrick says.
The second is MIC.21770, also a Phase II question, which asks,
"For direct bacterial antigen tests on patient specimens that do
not include internal positive and negative controls, is a positive
and negative control tested with each run of patient specimen?"
The laboratory must first determine the test’s complexity level.
If the manufacturer hasn’t provided this information, it can be
found on the Food and Drug Administration’s Web site. "In this case
I would cite a deficiency until they have done that," Dr. Merrick
says. If the test complexity is not defined, it becomes high complexity
Another question that’s fairly new to the microbiology checklist
and poses difficulties for labs, MIC.21620, a Phase II question,
asks, "Are new reagent lots checked against old reagent lots or
with suitable reference material before or concurrent with being
placed in service?" Suitable reference materials include previously
tested patient samples with known readings or control materials
that have been tested on the old reagent lot. "The purpose of this
parallel testing is to determine if a new lot has the same specificity
and sensitivity as the last lot," explains Dr. Merrick. "This way
if there’s a change in patient results over time, you know it is
due to a change in the patient and not the sensitivity level of
the new lot."
4. The inspector reviews quality control
records for the antimicrobial susceptibility tests and notes that
a few weekly control tests are circled. The supervisor says these
results were out of control, but when asked to provide evidence
of corrective action, he says the control organism was faulty and
a new one had been ordered. In the meantime, results from the susceptibility
tests were being reported.
The relevant microbiology checklist question, MIC.21910, is a
Phase II question that asks, "For antimicrobial susceptibility testing
of either disk or dilution type, are control organisms tested with
each new lot or batch of antimicrobials or media and each day the
test is performed thereafter?"
To clarify this question and further define out-of-control results,
the checklist says: "The overall performance of the susceptibility
test system should be monitored by testing appropriate reference
strains each day the test is performed. However, the frequency of
test monitoring may be reduced to weekly, including the testing
of new lots or batches of antimicrobials or media, if the laboratory
can document satisfactory performance with daily control tests as
suggested by NCCLS guidelines." Performance is considered satisfactory
if all reference strains were tested for 30 consecutive test days
and this is documented, and, for each drug/microorganism combination,
no more than three of the 30 values (zone diameter or minimum inhibitory
concentrations) are outside the accuracy ranges. These limits can
be established by the laboratory or by NCCLS guidelines M2-A7 or
The laboratory in vignette No. 4 first must be able to give the
inspector documentation showing that it has completed the 30-day,
daily QC tests. And, if new antimicrobials have been added since
these tests were done, it needs to document that these new panels
have been tested.
When a weekly test is found to be out of control because of an
obvious error such as the wrong drug or control stain having been
used, positive contamination, or an incorrect atmosphere of incubation,
the QC test should be repeated. "If it’s OK, then the lab can continue
with weekly quality control testing," Dr. Merrick says.
However, if there’s not an obvious explanation for out-of-control
results, the lab must return to daily QC testing long enough to
define the source of the adverse result and to document its resolution.
This documentation should include testing of appropriate reference
organisms for five consecutive test days and proof that for each
drug/microorganism combination all five of the disk diameters and
minimum inhibitory concentration values are within the accuracy
"The important point is that during the retesting period, the
out-of-control antibiotic should not be reported on patient samples,"
says Dr. Merrick. Another microbiology checklist question, MIC.21480,
a Phase II question, directly addresses that. It asks, "Are the
results of controls reviewed for acceptability before reporting
Because the laboratory in the vignette has not done this, Dr.
Merrick would cite two deficiencies: one for not having evidence
of corrective action and another for reporting results on out-of-control
5. Review of routine antimicrobial susceptibility
test results shows that the laboratory is reporting second- and
third-generation cephalosporins on all gram-negative isolates, even
when the organism is susceptible to a first-generation cephalosporin.
Should the inspector cite a deficiency?
Two Phase I microbiology checklist questions apply. MIC.21900
asks, "Are guidelines established for the number and type of antibiotics
reported for organisms isolated from different sites of infection?"
To address this question, the laboratory should refer to the latest
supplement of NCCLS M100-S11 titled "Performance standards for antimicrobial
susceptibility testing," which contains current information on antibiotic
selection, interpretation, and QC testing. But each laboratory should
set its own guidelines.
"Selection of the most appropriate antimicrobial agents to test
and report is a decision best made by each local laboratory in consultation
with infectious disease practitioners, the pharmacy, and infection
control committee of the medical staff," Dr. Merrick says. Cascade
reporting, or reporting no more than four agents, improves the clinical
relevance of test reporting and minimizes the selection of multiresistant
nosocomial strains by overuse of broad-spectrum antibiotics.
Also implicit in microbiology checklist question MIC.21900 is
the requirement that laboratories only report antimicrobial agents
that are effective at the infection site where the organism was
isolated. This means reporting drugs such as penicillin, cefotaxime,
or ceftriaxone and meropenem for a Streptococcus pneumoniae
isolate found in a cerebrospinal fluid specimen from a patient with
meningitis and not antimicrobial agents that have poor penetration
of the meninges and CSF.
The second checklist question, MIC.21950, asks, "Does the procedure
manual address unusual or inconsistent antimicrobial testing results?"
A new NCCLS document, M39-P, includes a section on data verification
that addresses the intent of this question.
"It’s important for a laboratory to have a procedure for cumulative
antimicrobial susceptibility test data, and it should address in
its procedure manual how it’s going to handle unusual or inconsistent
test results," Dr. Merrick says. These supplementary protocols can
include checking for transcription errors, satisfactory growth,
or the absences of subtle contamination on plates or trays and reproducibility
of results by repeating the test or using an alternative test method.
For the laboratory reporting second- and third-generation cephalosporins
on all gram-negative isolates, Dr. Merrick says he wouldn’t cite
a deficiency if the medical staff has insisted on this information.
However, in circumstances where this is not the case, he would strongly
recommend that the laboratory decide which group A agents to report
routinely and which group B agents to report only selectively in
consultation with the medical staff. "They’re not doing anyone a
favor by reporting antibiotics that aren’t necessary," he adds.
6. The laboratory’s quality improvement
plan includes a monitor of blood culture contamination rates, and
the results from last quarter showed that six percent of blood cultures
were contaminated. The supervisor said she was not involved with
the study but felt that nursing staff drew most of the contaminated
cultures. Is this problem a laboratory concern?
Yes, says Dr. Merrick, and he would cite the laboratory for a
deficiency. "The laboratory needs to work with nursing staff and
phlebotomists on ways to reduce contamination," he says. Each laboratory
should also maintain blood culture statistics that are reviewed
regularly by the laboratory director.
The relevant checklist question, MIC.22630, is a Phase II question:
"Are sterile techniques for drawing and handling of blood cultures
defined, made available to individuals responsible for specimen
collection, and practiced?"
This question’s importance is highlighted by studies that show
a false-positive blood culture increases hospitalization by an average
of five days and can increase pharmacy and laboratory costs by $1,000
if it’s a coagulase-negative staphylococci that requires vancomycin
A good quality improvement study for the lab in No. 7 would be
to find ways to lower its blood culture contamination rate. Dr.
Merrick suggests setting a threshold of 2.9 percent, the overall
contamination rate found in a CAP Q-Tracks study of 158 institutions
(2001 Annual Summary Report, Blood Culture Contamination Q-Tracks,
7. The laboratory recently received nasal
swabs and a few pulmonary specimens designated as "rule out anthrax."
You ask to see the laboratory procedures for handling organisms
that may require special engineering or work practice controls,
and the supervisor says nothing is in writing but they always use
"There are two issues here, one dealing with safety to laboratory
workers and the second dealing with security procedures that a laboratory
and hospital should have in place to deal with a suspected or real
bioterrorist attack," says Dr. Merrick.
Two checklist questions address this. MIC.19060, a Phase II question,
asks, "Have policies and procedures been developed to minimize the
occupational risk of exposure to infectious agents handled in the
microbiology laboratory, in accordance with current recommendations
regarding the biosafety levels for working with different organisms?"
MIC.19160, a Phase I question, asks, "Are engineering and work practice
controls appropriate to the biosafety level of the laboratory defined
These two checklist questions relate to the safety of laboratory
workers. Though routine handling of Bacillus anthracis
specimens carries a low risk, "all of us need to be aware of laboratory-acquired
infections," Dr. Merrick says. The CDC recently provided a list
of steps laboratories should follow if B. anthracis is
suspected. And an article from the CDC, titled "Laboratory-acquired
meningococcal disease—United States, 2000," published in the
March 13 issue of the Journal of the American Medical Association,
discusses laboratory-acquired meningococcal disease and the precautions
each laboratory should take with spinal fluid and blood culture
isolates of Neisseria meningitidis.
No checklist question addresses security issues, but most hospitals
have developed bioterrorist plans that include security throughout
the hospital, including the laboratory. Dr. Merrick refers laboratories
for guidance to the joint CDC and National Institutes of Health
document, "Biosafety in microbiological and biomedical laboratories."
The most recent edition can be found on the CDC Web site at www.cdc.gov/od/ohs/biosfty/bmbl4/bmbl4toc.htm.
Dr. Merrick says he would cite the laboratory in No. 8 for two
deficiencies and advise it to develop safety and security policies.
8. The laboratory’s procedure manuals are
well written and include all of the pertinent information about
the laboratory’s scope of testing. A face sheet at the front of
the manual is signed by all of the people working in the department.
It says all persons are knowledgeable about the manual’s contents.
Is this adequate?
Checklist question MIC.12140, a Phase II question, asks, "Does
the laboratory have a system documenting that all personnel are
knowledgeable about the contents of procedure manuals relevant to
the scope of their testing activities?"
In this case, Dr. Merrick would not cite a deficiency, "but I’d
make a strong recommendation to the laboratory to do more than just
sign the front of the manual." A good comprehensive competency assessment
program includes directly observing patient test performance and
performance of instrument maintenance and function checks; monitoring
the recording and reporting of test results; reviewing worksheets,
quality control, proficiency testing, and preventive maintenance
records; evaluating test performance by testing previously analyzed
specimens, internal blind unknowns, or external proficiency test
samples; and evaluating problem-solving skills.
9. While observing the specimen set-up
bench, the inspector notes that a urine specimen container is unlabeled
but is accompanied by a request form. The form includes patient
information but nothing about type of infection or organisms expected.
Is this considered a deficiency?
Yes, says Dr. Merrick. "The urine container was not labeled and
I don’t think it should be accepted."
There are three relevant microbiology checklist questions. The
one Phase II question, MIC.13050, asks, "Are there documented procedures
for the proper collection, transporting and handling of culture
specimens?" The two Phase I questions, MIC.13100 and MIC.13200,
ask, "Are there criteria for establishing specimen acceptability?"
and "Do requests for isolation include source of specimen and, when
appropriate, type of infection and/or organism expected?"
The first two questions are straightforward: Every laboratory
should have a specimen collection manual that spells out the criteria
for specimen acceptability. The final question, which relates to
getting information about the type of infection and/or organism
expected, is trickier. "If your laboratory is like my laboratory
and most of the ones I’ve inspected, we’re lucky if we get any of
that information," Dr. Merrick admits. "But the point of this is
to develop a request form that includes space for that information
and to make an effort to get more information. We all do a better
job of working up the specimen if we have that available to us."
10. A positive blood culture result was
called to a nursing floor on an evening shift, but the attending
physician did not hear about it until the next day and appropriate
treatment was not started until then. Is this a deficiency?
"This may be one of the more important questions in all the scenarios
I’ve presented," says Dr. Merrick. "It addresses the postanalytical
portion of our testing."
Microbiology checklist question MIC.22620, a Phase II question,
asks, "Are initial positive cultures reported in accordance with
laboratory policy for alert values?"
The CAP does not set standards for which results should be called.
Each lab, in consultation with its medical staff, needs to develop
a list of analytes that require immediate notification of a physician
or other clinical personnel responsible for patient care when test
results fall within established alert or critical ranges. "These
values represent those results that prompt rapid clinical attention
to avert significant patient morbidity or mortality," Dr. Merrick
Other issues that need to be considered: how to contact appropriate
health care providers and document these calls, when to release
sensitive laboratory results over the phone, and what results should
be called to infection control personnel.
Dr. Merrick would cite a deficiency if the laboratory did not
have a policy in place to handle results within alert or critical
11. Stools submitted for ova and parasitic
exam are examined by a direct wet mount and concentration procedure,
but permanent stains are not performed because, in the supervisor’s
opinion, they never yield positives that are not seen by the other
two techniques. How should the inspector respond?
This is "definitely a deficiency," Dr. Merrick says. "Permanent
stains are the most sensitive method for identifying intestinal
Checklist question MIC.52100, previously a Phase I and now a Phase
II question, asks, "Does the microscopic examination of all stools
submitted for an ova and parasitic examination include a concentration
procedure and a permanent stain?"
If the specimen is received fresh, the laboratory should perform
a direct wet mount to look for motile forms of intestinal protozoa.
If there’s going to be delay, then it’s appropriate to use a stool
preservative—but both concentration and permanent stains must
12. The hematology laboratory processes
all malaria smears. The procedure describes the preparation of both
thick and thin smears. The supervisor says they prepare both but
never look at the thick smear because nobody knows how to read them.
Is this a deficiency?
Two microbiology checklist questions, MIC.52200 and MIC.52260,
both Phase I, apply: "Are both thick and thin films made to provide
thorough examination for blood parasites?" and "Are an adequate
number of fields examined under oil immersion (e.g. 300 fields)?"
"Our parasitology consultants feel that it’s important to screen
both thick and thin blood smears, and they should be examined immediately
to detect parasites," Dr. Merrick says. "One can detect smaller
numbers of parasites on the thick smear." Therefore, he would cite
a deficiency because laboratories that don’t feel comfortable reading
a thick smear must send it out to others who can analyze it and
report back the results.
Vida Foubister is a writer in Mamaroneck, NY. Address questions
about the CAP Laboratory Accreditation Program to firstname.lastname@example.org.