CLINICAL BACTERIOLOGY 1

QUALITY ASSURANCE AND INFECTION CONTROL

LEC 20 BY MS NIÑA CHRISTINE O. ORILLA
November 29, 2022

LESSON OUTLINE ● Focuses on continuous quality improvements for achieving

near perfection by restricting the number of possible defects
to fewer 3.4 defects per million
1. QUALITY ASSURANCE AND INFECTION CONTROL
1.1. Lean Methodology ● DMAIC - Define, measure,analyze, improve, control
1.2. Six Sigma ● This acronym helps in making precise measurements, identify
1.3. Total Quality Management (TQM) exact problems and providing measure solutions
1.4. Quality Control vs Quality Assurance ● So when your six sigma is implemented correct;y, it can help
1.5. Continuous Quality Improvement (CQI) organizations reduce operational costs by focusing on reducing
1.6. Individualized Quality Control Program (IQPC) defects, minimizing turnaround time and trimming costs.
2. QUALITY PROGRAM ● Remember your 6 sigma revolves on restricting the number of
2.1. Specimen Collection and Transport possible defects.
2.2. Criteria for Unacceptable Specimen ● While your lean methodology, eliminating redundant motion,
2.3. Standard Operating Procedure Manual recognizing ways and identifying what creates value from the
3. PERSONNEL COMPETENCY ASSESSMENT client’s perspective.
4. REFERENCE LABORATORIES ● Your lean methodology is mostly on the client’s perspective.
4.1. Reference Laboratories in the Philippines
● Your 6 sigma rotates or revolves more on near perfection on
5. PATIENT REPORTS
the laboratory side.
6. PROFICIENCY TESTING
7. PERFORMANCE CHECKS
8. ANTIMICROBIAL SUSCEPTIBILITY TESTS Total Quality Management (TQM)
9. MAINTENANCE OF QC RECORDS & QC STOCKS ● Improve quality by ensuring conformance to internal
10. QUALITY ASSURANCE PROGRAM requirements
11. EXTERNAL QUALITY ASSESSMENT SCHEME (EQAS) ● Whereas your six sigma focuses on improving quality by
12. BENCHMARKING reducing the number of defects and impurities.
13. CONTINUOUS DAILY MONITORING ● Six sigma is also fact based,data driven and results oriented,
14. INFECTION CONTROL providing quantifiable and measurable bottom line results
15. HEALTHCARE ASSOCIATED INFECTIONS linked to strategy and related to customer requirements.
16. COMMUNITY ACQUIRED INFECTIONS
17. CENTERS FOR DISEASE CONTROL AND PREVENTION Focus on the differences between these three. Your six sigma or faction
18. ANTIBIOTIC RESISTANT MICROORGANISMS restricting defects, total quality management is conformance to internal
19. INFECTION CONTROL PROGRAM requirements. So if tao pani siya, your total quality management is a
20. BIOSAFETY person who does things by the book or by the law. While six sigma is a
20.1. Principle of Biosafety
perfectionist prison.
20.2. Classification of Biosafety Levels
20.3. Kinds of Biosafety Cabinets (BSCs)
20.4. Waste Disposal QC vs QA
20.5. Waste Segregation and Storage ➔ QC is associated with the internal activities that ensure
20.6. Color Coding Scheme diagnostic test accuracy.
20.7. Spillage Control ➔ QA is associated with external activities that ensure positive
patient outcomes.

Since the publication of the report To Err is Human by the Institute of Positive patient outcomes in the microbiology laboratory include
Medicine, the endeavor for a safer and a more efficient healthcare ● Reduced length of stay
delivery system has been in full force. The issue of quality in the ❖ Because with the service and the testing now na gi
medical laboratory has evolved over more than 4 decades after the provide so naayo siya dayon, the length of stay will
publication of the Recommendations of Quality Control in 1965 be reduced
.
QUALITY ASSURANCE AND INFECTION CONTROL ● Reduced cost of stay
❖ Directly proportional to the length of stay.
Lean Methodology
● Concentrates on eliminating redundant motion, recognizing ● Reduced turnaround time for diagnosis of infection
waste, and identifying what creates value from the client’s ● Appropriate antimicrobial therapy
perspective ● Customer (physician or patient) satisfaction
● The main objective of the clinical laboratory is to deliver quality
patient results at the lowest cost within the shortest time ➢ So this is where your quality assurance mostly
frame while maintaining client satisfaction revolves (customer satisfaction of our
● Involves five principles: Value, Value stream, Flow, Pull, and patient/physician) so mostly external.
Continuous Improvement ➢ Your quality control is internal.

Six Sigma CQI AND PI

● Relatively new concept compared to TQM ● Continuous Quality Improvement or Performance Improvement
● Originated in 1986 from Motorola Drive to reduce the fax by ● Through well thought out programs of QC and QA, are part of
minimizing variation in processes through metric measurement the requirements for laboratory accreditation under Clinical
Laboratory Improvement Amendments (CLIA, 1988)

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MICRO 1: QUALITY ASSURANCE AND INFECTION CONTROL
IQPC (Individualized Quality Control Program)
● Provides a mechanism for the laboratory to review the
preanalytical, analytical and post analytical phases of testing
and environment.
● Must include a risk assessment, quality control and quality
assessment plan.
It must assess the following:
➔ Specimen
➔ Test system
➔ Reagents
➔ Environment
➔ Testing personne
● Clinical Laboratory Improvement Amendment (CLIA) does not
require any specific types of tools or assessment be utilized
as long as the lab demonstrates that the quality control plan
meets the CLIA requirements.
○ It is the laboratory director’s job to be responsible for
ensuring that the plan meets the guidelines.
QUALITY PROGRAM
● Each lab must establish and maintain written procedures and
policies that implement and monitor quality systems for all
phases of the total testing process (pre-analytical, analytical,
post-analytical as well as general lab systems).
● Lab director
○ Primarily responsible for the QC and QA programs
● Lab personnel
○ Must actively participate in both programs
● Federal guidelines are considered minimum standards are
superseded by higher standards imposed by states or private
certifying agencies.
BASIC ELEMENTS OF QC PROGRAM
SPECIMEN COLLECTION AND TRANSPORT
● The lab is responsible for providing written policies and
procedures that ensure (+) ID and optimum integrity of a
patient specimen from the time of collection or receipt of the
specimen for completion of testing and reporting of results.
● The guidelines for specimen collection and transport as well
as the instructions should be available for health care
providers for use when specimens are collected.
The written collection instructions should be in detail and must
include the ff: (examples on the right)
1) Test purpose and limitations
2) Patient Respiratory Syncytial Virus (RSV) = stool culture,
selection criteria Nasopharyngeal Swabs (NPS), or oropharyngeal
swabs
↓ reference or normal range or such (we'll
Category for patient selection: 2 y.o. and below
3) Timing of Before antimicrobials are administered, doctors
specimen would order blood culture at the height of fever or
collection before the administer antibiotics to know whether
pre- and post-antimicrobial administration if there
is growth of a certain bacteria.
4) Optimal Blood culture → collected left and right
specimen
collection sites
5) Approved Urine culture → needs to use a sterile container
specimen
or follow proper procedures in collecting
collection
methods
6) Specimen Bacterial collection: swabs (for viral), swabs with
transport calcium alginate, those that do not contain
medium criteria wooden shafts
7) Specimen Most specimens require a cold chain throughout
transport time the transport. So the appropriate temperature
and temperature must be maintained along the way, especially for
long travel distances – there must be a certain
temperature that is allowed for a certain
specimen (e.g. Room temperature is required for
the test. Therefore, it must be followed). This is
because some specimens are viable only for a
certain time at a certain temperature.
8) Specimen It will also be indicated on the guide or the
holding instructions – how long will these specimens be
instructions if it held? (e.g. hold at 4 degrees celsius for 24
cannot be hours). It must be written in detail.
transported
immediately
9) Minimum acceptable volume requirements where applicable
10) Availability of There are some tests that are available on site or
test sometimes, other tests are sent to a reference
laboratory – as there are tests that are not
available in the laboratory so you have to indicate
if the specimen is for “send out”. At the same
time we have to again, follow the transport
temperature and the proper medium required.
11) Turnaround Do you think that bacterial cultures would grow in
time 1 hour or in a matter of minutes? One must know
the specific or the corresponding turn around
time for tests. Mostly culture tests, blood
culture, urine culture will take at least 24 hours
for an initial result. Same goes with your viral
testing, mostly those testing would take 24-48
hours to generate a result.
12) Result Every institution or laboratory must have a
reporting uniform reporting procedure.
procedures
● What must be indicated on the result?
– the name of the medical technologist
who processed the result, the
signature, and the result with the
be tackling that along the way).
**additional information as something went wrong with the slides
● Verbatim: the collection instruction should include how our
requisition should be filled out electronically or by hand. The
laboratory must also include a statement indicating that the
requisition must be filled out entirely. So in addition to
standard information such as your patient name…
● Verbatim: hospital or laboratory number, ordering physician
and other critical information that includes whether the patient
was receiving antimicrobial therapy, the suspect agent or
syndrome, immunization history, and travel history when
certain microorganisms or parasites are suspected.
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MICRO 1: QUALITY ASSURANCE AND INFECTION CONTROL
● Verbatim: sometimes during specimen collection, there will be
a case investigation for included or an additional form that
contains the patient details and supporting documents for the
testing. But mostly, if not for surveillance purposes, along with
the specimen will always be the laboratory request.
CRITERIA FOR UNACCEPTABLE SPECIMEN
● Unlabeled, mislabeled, or incompletely labeled specimens
○ One of the grave mistakes in the medical technology
world is mislabelling or no label. Check the label
always. Remember that us medical technologists or
future medical technologists, must ensure that there
should always be a label. Ok ra nga inyong
relationship walay label basta make sure that the
samples you process and receive in the lab have
labels.
○ This is always the first sign that a specimen must be
rejected.
● Quantity not sufficient for testing (QNS)
○ For example you take up urine culture, it is only 0.5
ml volume or just a small amount — so you need to
also to consider the appropriate volume that would
be enough for repeat testing and for storage at the
appropriate span of time
○ ex. CSF - critical specimens (do you directly reject a
critical specimen that has a small amount of
volume?)
○ Along with that, the laboratory must have a way or
another set of instructions when it comes to critical
samples (those samples that cannot be collected
right away such as your CSF unlike blood or urine you
could immediately collect those again. But CSF and
biopsy are different tissue specimens that are most
likely difficult to collect and there have to be
considerations and exclusions in this matter)
● Use of improper transport medium, such as stool for ova and
parasites not submitted in preservatives
● Use of improper swab such as use of wooden shaft or calcium
alginate tip for viruses
○ The use of wooden shaft or calcium alginate tip for
viruses would inhibit the process. Wooden or wood
are inhibitors because they contain a certain type of
enzyme. So you have your RNA test and these are
inhibitors of your RNA? which will be the one that you
will be detecting on — ??
● Inappropriate handling of specimen with respect to
temperature, timing,or storage requirements
● Improper collection site for tests requested, such as stool for
respiratory syncytial virus
● Specimen leakage for transport container
○ One of the most common specimen under the
rejection criteria
○ Most of the time if the cap is not properly closed it
will cause specimen leakage. So this is a criteria for
rejection especially for cultures or some tests that
require sterile specimens. Leakage could be a sign
of contamination
● Sera excessively hemolyzed, lipemic, or contaminated with
bacteria
○ This will be some indication of contamination with
bacteria capability, hemolysis or a different color of
the serum
○ The rejected specimen will be logged electronically or
manually in a rejection of specimen report will be
sent to the ordering clinician
○ One must need to have a process flow for specimen
rejection. Its either you record it electronically or
there’s a log book for this and after that you inform
the clinician on the reason of the rejection
○ The rejected specimens remember that it will not be
retained. Sometimes specimens not meeting the
requirements may be accepted by the laboratory if
the specimen is irretrievable or it has been acquired
through an invasive procedure as well as what
mentioned earlier, such as your CSF specimens.
○ If this happens again, approval with ordering
physician and laboratory director must be secured
with a disclaimer on the final report indicating that a
specimen was not collected properly and the result
should be interpreted with caution (this is how you
will report you have to consider the specimen but
with a disclaimer on the report)
○ Remember who will you inform when you receive a
critical or irretrievable specimen that fits the criteria
for rejection? Inform the clinician also your
laboratory director, proceed with the testing then put
a disclaimer on the final report regarding the status
of the specimen received
STANDARD OPERATING PROCEDURE MANUAL
● Every department/section in a lab must have one
○ Holy Grail for every department
● Part of the quality control program
● Defines test performance, tolerance limit, reagent preparation,
required quality control, result reporting, and references
● should be written again in the format of CLSI and must be
reviewed and signed
● Must be available in the work areas
● Definitive lab reference
● Used for questions related to individual tasks
● Any obsolete procedure should be dated when removed from
the SOP and retained for at least 2 years
Checkpoint Questions:
● How often must the SOP be reviewed and signed?
○ Annually or biannually by lab director who appears on
the CLIA certificate
● Who reviews, signs, and approves all changes in the SPO?
○ Lab director
PERSONNEL COMPETENCY ASSESSMENT
● It is the lab director’s responsibility to employ sufficient
qualified personnel for the volume and complexity of the work
performed.
○ For example, public staffing of Virology labs such as
one technologist per 500 to 1000 specimens per
year
○ Technical on the job training must be documented
and the employer’s competency must be assessed
twice.
■ Twice in the first year and annually
thereafter
○ Continuing education programs should be provided
and verification of attendance should be maintained
in the employee’s personnel file. Examples of this
are free seminars and training with corresponding
CPD units. These can serve as refresher courses.
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Lab competency must be include the following:
● Direct observation of task performance to include patient
preparation if applicable.
○ Ex. Phlebotomy. How do you prepare a patient for
phlebotomy?
○ Specimen handling, processing and testing
● There will also be direct observation on the performance or
instrument maintenance and function checks
● Monitoring the recording and reporting of results
● Review of intermediate test results or worksheets, QC results,
patient results, and preventive maintenance records
● Assessment of test performance through testing previously
analyzed specimens and internal blind testing of samples or
external patient samples
○ This incorporates known negatives or positives.
○ A given sample will be tested normally, just like in
treating an unknown.
○ A kind of competency assessment
● Assessment of problem-solving skills.
These competency assessments must be documented and completed
by qualified personnel.
● Some medical technologists attend competency assessments
for certification and as a requirement for licensing.
● There are different departments or areas in the lab that
require competency assessment or competency certificate
before you can continue to process in that specific area or
specialty.
REFERENCE LABORATORIES
● Not all testing can be completed in one facility. A laboratory
test that cannot be performed “in-house,” lab or in the same
institution and needs to be sent somewhere else is
considered a reference laboratory test.
● The reference laboratory is a separate entity from the facility
that collects specimens. It must be accredited or licensed. (In
the PH, it must be accredited or licensed by the DOH.)
● The referral labs need address and licensure number which
are included in a patient’s final result.
REFERENCE LABORATORIES IN THE PHILIPPINES
Antimicrobial Resistance Surveillance Reference Laboratory (ARSRL)
● Correlates with Microbiology
● Aims to form a professional network of sentinel regional and
central laboratories that will provide quality antimicrobial
resistance surveillance data
● Yearly, they will have a summary of reports of the antimicrobial
resistance in the PH. Stated in the summary reports include
bacteria “hotspots” for the year and which locations are
affected.
National Reference Laboratory for Emerging and Re-emerging Diseases
(NRL-ERBD)
● At the forefront in the diagnostic surveillance for notifiable
diseases which includes diphtheria, atypical pneumonia,
leptospirosis, and anthrax. So the NRL-ERBD is the reference
laboratory for these.
RITM-National Influenza Center (RITM-NIC)
● Was established through the support of the DOH, WHO, and
the United States Center for Disease Control to perform
routine virologic surveillance of influenza-like illnesses. So this
is your Severe Acute Respiratory Infection (SARI) which includes
influenza A, B and the likes.
Department of Medical Entomology
● Primarily involved in the conduct of basic and applied research
on vectors of infectious diseases such as dengue, filariasis,
Japanese encephalitis, and malaria.
Department of Virology of the Research Institute for Tropical Medicine
● Designated as the national reference laboratory for measles
and other exanthems (reactive rashes) in 2000 continue to
provide support in the measles elimination program
National Reference Laboratory for Mycology
● The lead laboratory for the diagnosis of medically important
fungi
● Povides technical and laboratory support for the isolation and
identification of fungi
Schistosomiasis National Reference Laboratory
● Aims to form a professional network of sentinel regional
laboratories set up to provide quality diagnostic tests for
schistosomiasis.
So we have a lot of reference laboratories that aren't on the list. For
example the reference laboratory for TB which is the National
Tuberculosis Reference Laboratory or the NTRL. Another is for
transfusion transmissible infections for blood donors and units is the
Research Institute for Tropical Medicine (RITM). For polio and other
enteroviruses, the Department of Virology still of RITM. Another is
dengue which is the same, the RITM. In the Philippines, the national
unit for reference laboratories would be the Research Institute for
Tropical Medicine. So if you could go and visit, I think they allow visits to
the RITM but you cannot see how they perform the tasks. So, RITM
caters on trainings and seminars for laboratories and medical
technologists.
PATIENT REPORTS
● There should be an established system for supervisory review
of all laboratory reports.
● This review involves checking the specimen workup to verify
the correct conclusions were drawn, and no clerical errors
were made in reporting results.
● Reports should be released only to individuals authorized by
law to receive them. It's either the physicians and various mid
level practitioners.
● Clinicians should be notified about panic values immediately.
Panic values are potentially life threatening results. For
example, (+) gram stain for CSF or a (+) blood culture. Inform
immediately the clinician, either you call the department and
inform for panic values immediately.
● Reference ranges must be included on the report where
appropriate.
● All patient records should be maintained for at least 2 years
before being archived. However, maintaining records for at
least 10 years may be needed to support medical necessity in
the event of a post payment building audit. So there are
exceptions to these. So just remember that most patient
records are maintained for at least 2 years. 2 years is also
stated for audit.
PROFICIENCY TESTING
● Proficiency testing is a quality assurance measure used to
monitor the laboratory's analytic performance compared to its
peers and reference standards.
● It provides an external validation tool and objective evidence of
the laboratory competence for patients and accrediting
oversight agencies.
● Laboratories are required to participate in a Proficiency Testing
(PT) program for each analyte through which a program is
available.
● The passing rate for your proficiency testing is 80 %.
○ Average core: 80 %
○ This is to maintain licensure in any subspecialty
area.
○ For example: proficiency testing for malaria,
proficiency testing for influenza
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MICRO 1: QUALITY ASSURANCE AND INFECTION CONTROL
○ In proficiency testing, you will be given unknown
samples wherein you would process the samples as
is (usually samples from RITM from reference labs)
→ the results must be the same with their results
(so it should coincide).
Doc’s experience: it's good to know that we have done proficiency
testing for influenza viruses and MERS-COV, and humbly speaking, for 3
consecutive years we have performed 100% proficiency testing for this.
So, this is also a way to determine the processes performed with the
laboratory practices and skills and expertise of the laboratory
personnel.
● In proficiency testing, we call the samples as blind unknowns.
○ These unknowns are to be treated exactly as patient
specimens from accessioning into the laboratory
computer or manual logbook, to work up and
reporting of results.
● The testing personnel and laboratory director are required to
sign a statement when the proficiency testing is completed -
attesting to the fact that the specimen was handled exactly
like a patient specimen.
● So in this way, proficiency testing specimen established the
accuracy and reproducibility of laboratories day to day
performance.
○ TAKE NOTE : accuracy and reproducibility.
● The laboratory procedure, reagents, equipment and personnel
are all checked in the proces.
● However, what happens if there are errors in your proficiency
testing?
○ Errors on proficiency testing help point out
deficiencies and the subsequent education of the
staff can lead to overall improvements in the
laboratory quality.
○ Doc said that it is not the end of the world when you
are able to encounter errors in proficiency testing.
○ Errors for any test is a room for improvement - it's
always a lesson learned.c
PERFORMANCE CHECKS
Performance checks is applicable for :
Instruments
❖ Equipment logs should contain the following information:
➢ Instrument name
➢ Serial number of instrument
➢ Date of implementation in the lab (must be visible -
may be a sticker note/ sticker paper)
➢ Procedure
➢ Periodicity of function checks
➢ there would be a table near the instrument where
you would input how often you use the computer . for
example: on this day, you use the machine and you
put the date, your initials etc on this worksheet.
➢ Acceptable performance ranges
➢ Instrument function failures
■ E.g. There are failures on the run, indicate
on the remarks that there is an invalid run
or failed run.
➢ Date and time of service request
➢ Response and Maintenance records
■ As defined with at least the minimum
frequency specified by the manufacturer.
■ Instrument maintenance records should be
retained in the laboratory for the life of the
instruments.
■ Specific guidelines regarding the periodicity
of testing for autoclaves, biological safety
cabinets, centrifuge, incubators,
microscopes, refrigerators, freezers, water
baths, heat blocks, and other microbiology
laboratory equipment can be found in a
number of the references listed in the SOP.
■ There are different periodic tracking of
different instruments, so it is good to ask
the manufacturer or look at the
manufacturers data.
Commercially prepared media exempt from QC
❖ Based on findings a list of media that did not require retesting
in the user’s laboratory is if it was purchased from a
manufacturer who follows CLSI guidelines.
❖ For example, there are different commercially prepared media
that are exempted from quality control. The job of the
laboratory is to inspect each shipment for cracked media or
Petri dishes, hemolysis, freezing, unequal filing, excessive
bubbles, clarity and visible emission.
User - prepared and non - exempt, commercially prepared media
❖ Quality control forms should contain the:
➢ Amount prepared
➢ Source of each ingredient
➢ Lot number
➢ Sterilization method
➢ Preparation date
➢ Expiration date (1 month for agar plates, 6 months
for tube media)
➢ Name of the preparer
❖ Both user-prepared and non-exempt commercially prepared
media should be checked for proper color, consistency, depth,
smoothness, hemolysis, excessive bubbles, and
contamination.
❖ Sterility is examined by incubating the medium for 48 hours
under the environmental conditions and temperature routine
used in the laboratory.
❖ Both should be tested with quality control organisms of known
physiologic and biochemical properties
ANTIMICROBIAL SUSCEPTIBILITY TESTS
Goal of quality control testing of antimicrobial susceptibility tests is to
ensure precision and accuracy of the supplies and microbiologists
performing the test . The laboratory must check each lot number and
shipment of microbial agent before or concurrent with initial use using
an approved control organism.
Stains and Reagents
● Containers should be labeled as to contents, concentration,
storage requirements, date prepared or received, date placed
in service (commonly called date opened).
● It should be stored according to the manufacturer's
recommendation and tested with positive and negative
controls before use.
○ Note: Incorporating positive and negative controls
are ways of quality control measures in the
laboratory.
● Outdated materials or reagents that fail QC even after testing
with fresh organisms = Discarded immediately.
Antisera:
● Lot number, Date received, Condition received, Expiration date
for all shipments of antisera should be recorded.
● New lots must be tested concurrently with previous lots, and
testing must include positive and negative controls.
○ Note: Everytime there is a new shipment or lot
number, we need to test it with the known or
previous lots.
○ Note: Positive and negative controls are always
incorporated because it is the measure of knowing
whether or not certain reagents, stains, or antisera
are functioning properly.
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Kits:
● They need to be tested as specified in the manufacturer’s
package insert.
● Each shipment of kits must be tested even if it is the same lot
number as a previously tested lot because temperature
changes during shipment may affect the performance.
● Components of reagent kits of different lot numbers must not
be interchanged unless otherwise specified by the
manufacturer.
MAINTENANCE OF QUALITY CONTROL RECORDS & QUALITY CONTROL
STOCKS
● All quality control results should be recorded and must include
a review of the effectiveness of corrective actions taken to
resolve problems, revision of policies, and procedures
necessary to prevent recurrence of problems.
● For reference quality control stocks, stock organisms may be
obtained from the ATCC, commercial vendors, or proficiency
programs, while defined quality isolates will also be used.
● The laboratory should have enough organisms on hand to
cover the full range of testing of all necessary materials such
as media kits and reagents.
○ Ex. Stock cultures in Microbiology
BACTERIOLOGY
● In order to maintain the control stocks of the organisms, a
long term plan of storage and requirements for each organism
is needed.
○ Ex. Non-fastidious aerobic material organisms =
saved up to 1 year on TSA slants.
● Long-term shortage less than 1 year of aerobes/anaerobes
can be accomplished by:
○ Lyophilization or freeze-drying; or
○ Freezing at -70 °C
● Frozen, non-fastidious organisms should be thawed, reisolated,
and refrozen every 5 years.
● Fastidious organisms should be thawed, reisolated, and
refrozen every 3 years.
● Non-fastidious: five years
● Fastidious: three years
● Stock isolates may be maintained by freezing in 10% skim
milk; Trypticase soy broth (TSB) with 15% glycerol; 10% horse
blood in sterile, screw-cap vials or Micro Banks.
○ There are commercially available systems like the
Micro Banks.
QUALITY ASSURANCE PROGRAM
What’s the difference between the Quality Control Program and Quality
Assurance Program? The QC is for internal, and QA is for external.
Quality Assurance
is the method by which overall process of infectious disease diagnosis
is reviewed.
● Any of the steps involved in the diagnosis of an infectious
disease may be studied.
● The steps included are: Preanalytic, Analytic, and Postanalytic
Preanalytic
● Starts from the ordering of test until the initial processing of
specimen
● From the ordering of test by the clinician, processing of test by
the clerical staff, collection of specimen by healthcare
providers or patients, transport of specimen to the laboratory,
and the initial processing of specimen in the laboratory,
including specimen accessioning
Analytic
● Starts from examination until interpretation of results
● Examination and workup of culture by the microbiologist, and
interpretation of specimen results by microbiologist
● Know who are the people involved for every phase
Postanalytic
● Formulation and interpretation of report
● Formulation of written or printed report by the microbiologist,
communication of the microbiologist’s conclusions to the
clinician in a written or printed format), interpretation of report
by the clinician, and institution of appropriate therapy by the
clinician
○ DO NOT RELAY over the phone, only in printed or
written format.
○ Nowadays, most clinicians like to relay over the
phone
○ Confidentiality and data privacy
○ As a professional, there should be a standardized
form of report - which is Printed or Written
○ Do not relay over the phone because it’s a part of
the standard operating procedures and the quality
assurance programs of an institution
EXTERNAL QUALITY ASSESSMENT SCHEME (EQAS)
● Evaluates the performance of participating laboratories by
assessing the integrity of the entire testing from sample
receipt to releasing of test results
● In the Philippines, we have different external quality
assessment programs under the Research Institute for
Tropical Medicine
○ Offers programs for Bacteriology, Parasitology,
Mycobacteriology, Transfusion Transmissible
Infections (TTIs), and SARS-CoV-2 Molecular
● Sometimes, participation in the EQAS program is required
under local regulatory policies for a laboratory to operate or
continue operating
● Allow comparison of a laboratory’s testing to the performance
of a peer, group, and/or the National Reference Laboratory
- In the Philippine setting that is your Research Institute for
Tropical Medicine.
BENCHMARKING
● Individual facilities can compare its results with those of its
peers.
● Quality assurance:
○ Summary is compiled and returned to the institution
with a comparison with other facilities of similar size
and scope of service.
CONTINUOUS DAILY MONITORING
● Daily activities of microbiologist and supervisory personnel
insure that patients get the best quality care
● Activities include:
○ Comparing results of morphotypes seen on direct
examinations with what grows on the culture to
ensure that all organisms have been recovered
○ Checking of antimicrobial susceptibility report do
verify the profiles match those expected from a
particular species.
○ Studying culture and susceptibility reports for
clusters of patients with unusual infections or
multiple drug resistant organisms.
● These and other many processes result in continual
improvement all test systems ultimately resulting in the end
product of all these programs are/is quality patient care.
● Your quality control programs, quality assurance programs, all
boils down to quality patient care.
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MICRO 1: QUALITY ASSURANCE AND INFECTION CONTROL
● In the field of healthcare, whatever department you are, your
end product will always be quality patient care because you
are handling someone’s life.
● These quality control programs and quality assurance is not
for you, as a laboratory personnel, or for the sale of
requirements.
● Remember that these programs work as one to provide quality
patient care
INFECTION CONTROL
● Part of an institution that there are a lot of infections that we
can not avoid being infected by something.
● Especially working in a healthcare institution, there is always
infection/s around us.
● It is estimated that between 1.7 and 3 million of the 35
million patients admitted annually, especially in the United
States, acquired infection that was neither present nor in the
prodromal or incubation stage where they enter the hospital.
HEALTHCARE ASSOCIATED INFECTIONS
● Has replaced all confusing terms.
● Before, your healthcare associated infections were termed as
nosocomial hospital acquired or hospital onset infection.
● Treatment is estimated to be costly
● Represents an enormous economic problem in today’s
environment of cost containment.
● Some of the earliest efforts to control infection follow the
recognition in the 19th century that women were dying of
childbirth from bloodstream infections caused by group A
Streptococcus pyogenes.
● Physicians were spreading the organism by failing to wash
their hands between examination of different patients
● Hand washing is a key component of modern multimodal
infection control program
NINETEENTH CENTURY
● Women were dying of childbirth caused by group a
streptococcus
● Isolation precautions were published in the late 1800’s when
guidelines appeared advocating placement of patients with
infections in separate hospital facilities.
○ In the past four decades, we have learned that the
addition to hospitalized patients acquire infections.
Healthcare workers are also at risk of acquiring
infections from patients.
○ Thus, present day infection control and prevention
programs have evolved to prevent the position of
infection by patients and caregivers.
● To have a successful multi modal approach it must be
supported by the hospital administration and involve all
departments on an enterprise wide basis. So infection control
is not a one man job so it needs a group of people. IT needs
teamwork for it to be successful.
COMMUNITY ACQUIRED INFECTIONS
● In contrast with your healthcare associated infection,
community acquired infection is an infection contracted
outside a healthcare setting or an infection present on
admission.
● Community acquired infections are often distinguished from
healthcare associated with the types of organisms that affect
patients or recovering from a disease or infection. So usually
community acquired infection involves strains of your
Haemophilus influenzae or your Streptococcus pneumoniae
which are more usually sensitive to antibiotic treatment.
CENTERS FOR DISEASE CONTROL AND PREVENTION
● The Centers for Disease Control and Prevention has
established a program to monitor the incidence of healthcare
associated infections. The data they are able to collect are
used to improve patient safety at the local and national levels.
Your CDC analyzes and publishes surveillance data to
estimate and characterize the national burden of healthcare
associated infections.
● Regardless of a hospital’s size or medical school affiliation,
the rates of infection in each body site are consistent across
institutions.
MOST HEALTHCARE ACQUIRED INFECTIONS ARE
● Urinary Tract Infections (33%)
● Pneumonia (15%)
● Surgical Site Infections (15%)
● Bloodstream Infections (13%)
The remaining 24% or other miscellaneous infections. On average each
healthcare associated infection adds to 5-10 days to the affected
patient’s hospital stay.
PRINCIPAL FACTORS DETERMINING THE LIKELIHOOD THAT A GIVEN
PATIENTS WILL ACQUIRE INFECTION:
1. Susceptibility to infection and/or immune status of the patient
2. Virulence of infecting organism
3. Nature of the patient’s exposure to the infecting organism
● In general, hospitalized individuals have increased the
susceptibility to infections.
● Corticosteroids, cancer chemotherapeutic agents and
antimicrobial agents all contribute to the likelihood of
healthcare associated infections by suppressing the immune
system or altering the host’s normal microbiota
● Healthcare associated infection may never be completely
eliminated only controlled
ANTIBIOTIC RESISTANT MICROORGANISMS
● So organisms that cause healthcare associated infections
have changed over the years because of selective pressures
from the use and overuse
● Sometimes we take antibiotics without doctors prescription
● Risk factors for acquisition of highly resistant organisms
include prolonged hospitalization and prior treatment with
antibiotics
● If you want to know the latest updates on the organisms being
more resistant to various spectrum of antibiotics you could
search through the DOH antibiotic resistant surveillance
program so they have there the annual reports for 2021,
latest one after this year they will have a summary report for
2022.
○ It also has info on what regions house the highest
antibiotic resistant microorganism being reported
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MICRO 1: QUALITY ASSURANCE AND INFECTION CONTROL
INFECTION CONTROL PROGRAM (Multidisciplinary)
● Hospital or healthcare facility infection control programs are
designed to detect and monitor healthcare associated
infections and to prevent or control their spread and are
multimodal in nature
○ Multimodal & multidisciplinary
■ Meaning it does not work with one person
alone, it needs everyone effort
● The infection control committee is a multidisciplinary and
should include a microbiologist, an infection control
practitioner or an officer
○ Oftentimes an infection control practitioner is a
nurse or a laboratory practitioner with special
training, an epidemiologist usually an infectious
disease physician , the dietary manager, a
pharmacist, chief nursing officer, operating room
manager when applicable, and the director of
environmental services.
INFECTION CONTROL OFFICER
● Collects and analyzes surveillance data, monitor patient care
practices and participates in epidemiologic investigations
● Daily review of charts of patients with fever or positive
microbiological culture allows the infection control officer to
recognize problems with healthcare associated infections and
detect outbreaks as early as possible
● He/she is also responsible for the education of healthcare
providers in techniques such as handwashing, processing
environmental surfaces and isolation precautions.
○ All of which collectively minimize acquisition spread
of infection
● It is also his/her job to identify all cases of outbreaks
● In case of outbreak, microorganisms are spread in healthcare
facilities through different or several modes such as:
DIRECT CONTACT
● Contaminated food (not cleanly prepared; so remember
handwashing) , intravenous solution
INDIRECT CONTACT
● Patient to patient on the hands of healthcare workers
● Common for this is MRSA (Methicillin-resistant Staphylococcus
aureus) and Rotavirus
DROPLET CONTACT
● Inhalation of droplets, if your droplets are defined as greater
than 5 μm in diameter that cannot travel more than 3 feet
○ Pertussis
AIRBORNE CONTACT
● Inhalation of droplets that can travel large distances on air
currents
○ Tuberculosis
VECTOR-BORNE CONTACT
● Spread through vectors like mosquitoes, malaria or rats, rat
bite fever
● However this mode of transmission is rare in hospitals within
developed countries
● Is PH a developed country? Contemplate on that..
ROLE OF MICROBIOLOGY LABORATORY
● Once the reservoir is known, infection control practitioner or
officer can implement control measures such as education
regarding hand washing or hyperchlorination of air conditioning
cooling towers in cases of legionellosis.
● The laboratory supplies the data on organism identification
and antimicrobial susceptibility profiles that the infection
control officer reviews daily for evidence of healthcare
associated infections.
● Thus, laboratory personnel must be able to detect potential
microbial pathogens, then accurately identify them to species
level and perform appropriate susceptibility testing.
● The microbiology staff should also monitor multi traverse
systems by tabulating data on antimicrobial susceptibilities of
common isolates and studying trends indicating emerging
resistance.
INFECTION PREVENTION
● There are different published guidelines specifying precautions
in hospitals.
● If you’re handling patients, there are techniques for isolation
precautions which includes healthcare workers washing their
hands between caring for different patients or for the
laboratory setting, within handling of specimens
HANDWASHING
● Basic way to break the chain of infection
● Healthcare workers should wash hands frequently using plain
soap, except in special circumstances.
○ i.e, in handling dressings from patients on contact
isolations.
SEGREGATION OF INFECTIOUS WASTE OR WASTE SEGREGATION
● Need to throw infectious dry, infectious wet, dry non-infectious,
wet non-infectious, and sharps properly
PERSONAL PROTECTIVE EQUIPMENT
● Wearing a mask, gowns, and gloves when carrying or handling
infectious substances or patients is important.
● Healthcare workers should wear gloves when touching blood,
body fluids, secretions, excretions, and contaminated linens
● Healthcare workers should wash hands frequently with plain
soap except in special circumstances.
○ Handling on patients on contact isolations
SURVEILLANCE METHODS
● Most routine environmental cultures in a healthcare facility are
now considered to be a little off use and should not be
performed unless there are special epidemiologic implications.
● The decision to perform these cultures should be determined
by the microbiologist, infection control officer, and
epidemiologist. However, certain surveillance cultures are still
performed as a method of limiting outbreaks.
● Environmental swabs are not usually performed nowadays, but
it’s a preventive measure when it comes or if there are
instances that there will be a possible outbreak.
HAND HYGIENE
● Handwashing is the basic method to break the chain of
infection.
● It’s a way of cleaning one’s hands that substantially reduces
potential pathogens (harmful microorganisms) on the hands.
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MICRO 1: QUALITY ASSURANCE AND INFECTION CONTROL

● It is considered a primary measure for reducing the risk of BIOSAFETY

transmitting infection among patients and health care PRINCIPLES OF BIOSAFETY
personnel.
● Procedures include the use of alcohol-based hand rubs ● Safety Equipment
(containing 60%-95% alcohol) and hand washing with soap and ○ Primary barriers
water ● Personal Protective Equipment
● Facility Design and Construction
TYPES OF HAND HYGIENE ○ Secondary barriers
HAND WASHING ● Facility Practices and Procedures
● Biosafety Levels
● Most common
● wash hands when it’s physically soiled with dirt or when you CLASSIFICATION OF BIOSAFETY LEVELS
feel like we've handled a pretty infectious material.

ANTISEPTIC HANDWASH

● Use of alcohol or sanitizer for non-visibly soiled hands.

ANTISEPTIC HAND SCRUB

SURGICAL HAND ANTISEPSIS

PERSONAL PROTECTIVE EQUIPMENT (PPE)

● Equipment worn to minimize exposure to hazards that cause

serious workplace injuries and illnesses Figure 1. Biosafety levels (Image from the internet.)
● Should fit the wearer comfortably
○ i.e. K95 mask which requires respective fit testing As the risk for microbes increases, the level of containment or the
● Acts as a barrier between infectious materials such as viral biosafety level also increases.
and bacterial contaminants and your skin, mouth, nose, or
eyes BSL-1
● May also protect patients who are at high risk for contracting
infections ● Microbes:
● Minimizes the spread of infection from one person to another ○ Not known to consistently cause disease in
healthy adults minimal to laboratorians and the
List of PPEs: environment.
● Organisms:
● Gloves ○ Non-pathogenic strain of Escherichia coli
● Goggles or face shields
● Particulate respirator or medical mask/ n95 ● Laboratory Practices:
● Gown or coverall ○ Standard microbiological practices are followed
○ must be long sleeves ○ Work can be performed on an open lab bench or table
○ Must have cuffs (i.e. most of the activities we perform)
○ waterproof
● Shoe covers or lab shoes STANDARD PRECAUTIONS:
● Surgical bonnet
● Hand hygiene
● Use of PPE
LABORATORY BIOSAFETY AND CHEMICAL SAFETY ● Respiratory hygiene / cough etiquette
● Sharps safety (engineering and work practice controls)
● Safe injection practices (i.e. antiseptic technique for
BIOSAFETY BIOSECURITY
parenteral medications)
● Sterile instruments and devices
Application of safety precautions One of the three components of
that reduce a laboratorian risk of biorisk management, which ● Clean and disinfected environmental surfaces
exposure to a potentially ensures the safe use and
infectious microbe and limit security of biological materials in Controlled access starts with BSL-1
contamination of the work laboratories. Biosecurity focuses
environment and, ultimately, on protecting biological agents
community. from theft, loss, or misuse.

Protects you and the specimen Protects every materials and

handled information within the laboratory

Figure 2. BSL-1 Set-up

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MICRO 1: QUALITY ASSURANCE AND INFECTION CONTROL

These are the number of biosafety level 4 facilities for the year 2022:
BSL-2
Entity Code Year BSL4 facility
● Microbes: Microbes handled pose moderate hazards to
Argentina ARG 2022 1
laboratorians and the environment
● Organisms: Staphylococcus aureus Australia AUS 2022 3
Belarus BLR 2022 1
Brazil CRA 2022 1
Canada CAN 2022 1
China CHN 2022 2
Czechia CZE 2022 1
France FRA 2022 3
Figure 3. BSL-2 Set-up Gabon GAB 2022 1
Germany DEU 2022 4
BSL-3 Hungary HUN 2022 2
● Microbes: Microbes handled can be either indigenous or exotic India IND 2022 3
and can cause serious or potentially lethal disease through Italy ITA 2022 2
respiratory transmission. Respiratory transmission is the
inhalation route of exposure. Japan JPN 2022 2
● Organisms: Mycobacterium tuberculosis Philippines PHL 2022 1
● Laboratory Practices: Russia RUS 2022 2
○ Laboratories are under medical surveillance and might
receive immunizations for microbes they work with. Singapore SGP 2022 1
○ Access to the laboratory is restricted and controlled at South Africa ZAF 2022 1
all times South Korea KOR 2022 1
Sweden SWE 2022 1
Switzerland CHE 2022 3
Taiwan TWN 2022 2
United Kingdom GBR 2022 9
United States USA 2022 14

Figure 4. BSL-3 Set-up with Risk-based Enhancements

BSL-4
● Microbes: microbes handled are dangerous and exotic, posing a
high risk of aerosol-transmitted infections
● Organisms: Ebola and Marburg viruses
● Laboratory Practices:
○ Change clothing before entering
○ Shower upon exiting
○ Decontaminate all materials before exiting.

Figure 6. Map of the Worldwide Distribution of BSL-4 Facilities

THREE KINDS OF BIOSAFETY CABINET (BSCs)

CLASS I BIOLOGICAL SAFETY CABINET

Figure 5. BSL-4 Set-up, air-tight

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MICRO 1: QUALITY ASSURANCE AND INFECTION CONTROL

● Protects the operator and the normally.

environment from exposure ● Require large laboratory spaces
● Does not prevent samples being due to their installation system
handled from being exposed to and will require elaborate ducting
contaminants that may be present works.
in room air.
○ No sample protection CLASS III BIOLOGICAL SAFETY CABINET
● There is a possibility of ● Suitable for work with
cross-contamination that may microbiological agents assigned
affect experimental consistency. to biosafety levels 1,2, 3 and 4.
Figure 7. BSC Class 1 ● Scope and application is limited ● Frequently specified for work
Airflow Diagram and largely considered obsolete. involving the most lethal biological
CLASS II BIOLOGICAL SAFETY CABINET hazards.
SUBTYPE: Type A2 ● Work is performed through glove
ports in the front of the cabinet.
● Most common Class II cabinet
● During routine operation, negative
● It has a plenum from which 30%
pressure relative to the ambient
of air is exhausted and 70%
environment is maintained within
re-circulated to the work area as
the biosafety cabinet.
the down flow.
● This provides an additional
● Stated from NSF/ ANSI 49:2010,
fail-safe mechanism in case
both the Class I Type A1 and Type
physical containment is
A2 must have the
compromised.
positively-pressurized
contaminated plenum to be ● On all Class III BSCs, a supply of
Figure 11. BSC Class III HEPA filtered air provides product
surrounded by negative pressure.
Airflow Diagram protection and prevents cross
● In case there is a leakage on the
contamination of samples.
positive plenum, the leaking
aerosol will be pulled by the ● Exhaust air is usually HEPA
negative pressure back to the filtered and incinerated.
● Alternatively, double HEPA
Figure 8. BSC Class II Type positive plenum, and it will not
leak out. filtration with two filters in series
A2 Airflow Diagram
● In the A2 cabinet, about 70% of may be utilized.
air from the positive plenum is
recirculated as downflow, and the PREPARING FOR WORK WITHIN A CLASS II BSC
remaining 30% is discharged to ● Written checklist of materials
the lab through the exhaust filter. ● Laboratory coats, preferably with knit or elastic cuffs, should
be worn buttoned over street clothing
CLASS II BIOLOGICAL SAFETY CABINET
● Latex, vinyl, nitrile, or other suitable gloves are worn to provide
SUBTYPE: Type B1
hand protection
● Has a common plenum from ● Adjust the stool height
which 70% of air is exhausted, ● Only the materials and equipment required for the immediate
and 30% re-circulated to the work work should be placed in the BSC
area as the downflow. ● Blowers should be operated at least 5 minutes before
● Also has a dedicated exhaust beginning work to allow the cabinet to purge
feature that eliminates ● Surface of ol materials and containers placed into the cabinet
re-circulation when work is should be wiped with 70%EtOH or other disinfectant
performed towards the back within determined to meet the laboratory’s need to reduce the
the interior of the cabinet. introduction of contaminants to the cabinet environment.
● Toxic chemicals employed as an
adjunct to microbiological
HORIZONTAL LAMINAR FLOW CLEAN BENCH
processes should only be allowed
Figure 9. BSC Class II Type if they do not interfere with work
B1 Airflow Diagram when recirculated in the downflow.
CLASS II BIOLOGICAL SAFETY CABINET
SUBTYPE: Type B2
● Suitable for work with toxic
chemicals employed as an adjunct
to microbiological processes
under all circumstances since no
re-circulation occurs.
● In theory, Type B2 biological
safety cabinets may be
considered as the safest of all
Class I BSCs since the total
exhaust feature acts as a fail-safe
in the event that the downflow and
Figure 10. BSC Class II
/ or exhaust HEPA filtration
Type B2 Airflow Diagram Figure 12. Horizontal Laminar Flow Clean Bench Airflow Pattern
systems cease to function

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MICRO 1: QUALITY ASSURANCE AND INFECTION CONTROL

● Not BSCS
● Pieces of equipment discharge HEPA-filtered air from the back
of the cabinet across the work surface and toward the user.
● only provide product protection
● Example for this application is template addition in your
SARS-CoV analysis. Template addition RNA or DNA template
addition on a buffer

VERTICAL FLOW CLEAN BENCH

Figure 13. Vertical Flow Clean Bench Figure 15. To-do when working with a BSC

● Also not BSC

● For preparation of intravenous solutions or for the preparation
of nucleic acid for PCR
● Air is usually discharged into the room under the sash.

CHEMICAL FUME HOOD BIOSAFETY CABINET

Used for dangerous chemicals
Protects the user
No HEPA filter
Exhausts air outside the building
Used for infectious biological
agents
- considered a primary
containment for
infectious material
Protects the user, the environment,
and the material
Must have HEPA filter
Does not exhaust air outside the
building (without decontamination)

Figure 16. Not to-do when working with a BSC

WASTE DISPOSAL
Figure 14. Fume Hood Airflow Diagram ● Universal precaution
○ Every specimen should be treated as though it's
infectious.

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MICRO 1: QUALITY ASSURANCE AND INFECTION CONTROL

BIOLOGICAL WASTE

● Biological wastes may contain a variety of pathogenic

organisms.
● Pathogens in infectious waste may enter the human body by
number of routed
○ Through a puncture, abrasion, or cut in the skin
○ Through the mucous membrane
○ By inhalation
○ By ingestion

WASTE SEGREGATION AND STORAGE

● Hazardous waste should be placed in clearly marked

containers that are appropriately labeled for the type and
weight of waste
● Except for sharps and fluids, hazardous waste are generally
put in plastic bags, plastic lined cardboard boxes or leaked
proofed containers that meet specific performance standards

COLOR CODING SCHEME

BLACK CONTAINER (NON-INFECTIOUS AND PATHOLOGICAL WASTE

- Paper, tissue, empty pen, etc

YELLOW CONTAINER (INFECTIOUS AND PATHOLOGICAL WASTE

- Any material contaminated with biological fluids such as

snap-capped tubes, PCR tubes, contaminated gauze, etc.

SHARPS CONTAINER

- Used and non-reusable sharp and pointed wastes

- Used pointes tips, etc

SPILLAGE CONTROL
BIOLOGICAL SPILL PROCEDURES

General guide for ALL biological spills:

1. Use freshly prepared 10% household bleach solution and allow
at least 20-30 minutes contact time
2. Dispose off clean-up materials as biohazard waste and place
them on a biohazard bag.
3. STAY CALM, especially when working on an experiment and a
tube with bacteria is broken
4. Alert the people/MTODS

Don’t forget about handwashing and the use of BSC as a primary

containment for infectious materials, spillage control since this may
occur any time, and know also where to throw your materials since it
can cause infection.

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