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Dr.T.V.Rao MD
ESTABLISHING
DIAGNOSTIC MICROBIOLOGY LABORATORY
DR.T.V.RAO MD 1
WHAT IS MEDICAL MICROBIOLOGY
• Medical Microbiology may overlap with parasitology,
generally considered the Study of Diseases caused by
multi-cellular parasites, where a parasite is defined as
an organism that derives its nutrients from another
living organisms, often but not always to the detriments
of its host. Microbes are continually probing our
defenses and commensals that get into the "wrong"
place can do untold damage. A very small Minority of
microbes are primary pathogens. These are capable of
infecting individuals and causing disease.
DR.T.V.RAO MD 2
CHALLENGES IN MEDICAL MICROBIOLOGY
• Medical Microbiology is a challenging profession
deals with all aspects of infection, through initial
diagnosis, to treatment. It includes hands on bench
work in the laboratory, which is often neglected and
close involvement with clinical staff in a variety of
acute and community settings to effectively
manage infections and ensure effective
surveillance and infection prevention and control
across the healthcare community.
DR.T.V.RAO MD 3
KNOW WHAT YOU ARE DOING
• Laboratory medicine in general and
microbiology in particular is presently subject
to rapid evolution.
• •Do we know where we are going?
• •What are the driving forces?
• •Is it good, bad or just plain necessary?
• •Who is gaining and who is losing?
DR.T.V.RAO MD 4
COMPONENTS OF DIAGNOSTIC
MICROBIOLOGY
• It is the analysis of a sample, the synthesis of results
(of several samples) and the clinical consultation.
Together these form the basis for
• -diagnosis,
• -therapy,
• -infection control
• -advice on and surveillance of antimicrobial resistance
and several other ‖Public health” issues on a national
and European level.
DR.T.V.RAO MD 5
• Clinical microbiologists are
engaged in the field of
diagnostic microbiology to
determine whether
pathogenic microorganisms
are present in clinical
specimens collected from
patients with suspected
infections. If
microorganisms are found,
these are identified and
susceptibility profiles, when
indicated, are determined.
ROLE OF CLINICAL MICROBIOLOGISTS
DR.T.V.RAO MD 6
• During the past two decades, technical
advances in the field of diagnostic
microbiology have made constant and
enormous progress in various areas,
including bacteriology, mycology,
mycobacteriology, parasitology, and
virology. The diagnostic capabilities of
modern clinical microbiology laboratories
have improved rapidly and have
expanded greatly due to a technological
revolution in molecular aspects of
microbiology and immunology. In
particular, rapid techniques for nucleic
acid amplification and characterization
combined with automation and user-
friendly software have significantly
broadened the diagnostic arsenal for the
clinical microbiologist.
COPING WITH PROGRESS IN DIAGNOSTIC
MICROBIOLOGY
DR.T.V.RAO MD 7
• The conventional diagnostic model for clinical microbiology has been labor-intensive and frequently required days to weeks before test results were available. Moreover, due to the complexity and length of such testing, this service was usually directed at the hospitalized patient population.
CONVENTIONAL DIAGNOSTIC
MICROBIOLOGY
DR.T.V.RAO MD 8
DESIGN THE LABORATORY TO SUIT THE
CIRCUMSTANCES – AND WORK LOAD
DR.T.V.RAO MD 9
Over the past two decades, Biosafety in Microbiological and Biomedical Laboratories (BMBL) has become the code of practice for biosafety—the discipline addressing the safe handling and containment of infectious microorganisms and hazardous biological materials.
ESTABLISH THE BIOSAFETY IN
MICROBIOLOGY LABORATORY
DR.T.V.RAO MD 10
• Biosafety level 1
(BSL-1) is the basic
level of protection
and is appropriate
for agents that are
not known to cause
disease in normal,
healthy humans
BIOSAFETY LEVEL 1
DR.T.V.RAO MD 11
• Biosafety level 2 (BSL-
2) is appropriate for
handling moderate-risk
agents that cause
human disease of
varying severity by
ingestion or through
percutaneous or
mucous membrane
exposure
BIOSAFETY LEVEL 2
DR.T.V.RAO MD 12
• Biosafety level 3 (BSL-3) is appropriate for agents with a known potential for aerosol transmission, for agents that may cause serious and potentially lethal infections and that are indigenous or exotic in origin.
BIOSAFETY LEVEL 3
DR.T.V.RAO MD 13
• Exotic agents that pose
a high individual risk of
life-threatening disease
by infectious aerosols
and for which no
treatment is available
are restricted to high
containment
laboratories that meet
biosafety level 4
(BSL-4) standards
BIOSAFETY LEVEL 4
DR.T.V.RAO MD 14
OPTIMAL UTILIZATION OF THE AVAILABLE
RESOURCES
DR.T.V.RAO MD 15
BE FAMILIAR WITH STERILIZATION
PRACTICES
• Scientific sterilization practices will certainly cut short the rate of infection reduce the costs to the hospital and reduces morbidity and mortality. The recent document on Sterilization released by
CDC Atlanta with title Guideline for Disinfection and Sterilization in Healthcare Facilities, 2008 will clarify all the doubts of practice, including the decreasing role of bio hazardous chemical and use of environmentally safe agents. Fumigation which we practice without knowing its biohazards needs a rethinking. Microbiologists should learn more; educate the Paramedical and Nursing staffs who are our greater partners in infection control.
DR.T.V.RAO MD 16
• Specimen collection and aseptic
precautions in collection is a
major concern to valid
microbiology reporting, several
life threatening septic
complications including blood
cultures in bacterial infections
are contaminated due to lapses
in specimen collection. A
frequently contaminated blood
culture reports losses the
confidence of Physicians on
Microbiology Departments.
OPTIMAL SPECIMEN COLLECTION INCREASES THE
CAPABILITIES OF DIAGNOSTIC REPORTING
DR.T.V.RAO MD 17
• For patients, specimen
collection errors during
the pre-analytical phase
can lead to medication
errors, inappropriate or
delayed therapy,
missed therapy,
possibly prolonged
hospital stays,
increased disability or
worse.
ERRORS IN SPECIMEN COLLECTION INCREASES
MORBIDITY AND ECONOMIC LOSES
DR.T.V.RAO MD 18
• Bacteriology departments should be updated, as most of the life threatening infections are bacterial in developing world, effective early diagnosis reduce the cost of antibacterial agents, on many occasions are most costlier than hospital occupancy rates. However it is certainly need of the hour.
UPDATE THE BACTERIOLOGY LABORATORIES
CAN SAVE SEVERAL LIVES
DR.T.V.RAO MD 19
• Advantages of fluorescence
microscopy are due to its
sensitivity, specificity, rapid
testing, and easy use. It is
easy to set up and do,
provides rapid diagnostic
tests, and can be very
specific. Modern
technology allows
conversion of most
compound microscopes
easily and economically
into effective fluorescence
microscopes.
TURN TO FLUORESCENT MICROSCOPY FOR RAPID
DIAGNOSIS OF SEVERAL LIFE THREATING
INFECTIONS
DR.T.V.RAO MD 20
• Bench work Is the most
important component of the
Diagnostic Microbiology
Typical tasks: include logs
in sample or specimen
noting date, time, and tests
to be performed; based on
quantitative growth patterns
and effective reporting. A
good control on the bench
work by Senior
Microbiologists keeps
everybody under check.
GOOD BENCH WORK IS THE STRENGTH OF
DIAGNOSTIC MICROBIOLOGY
DR.T.V.RAO MD 21
• All uncommon isolates should be
studied to species level with
extended biochemical testing,
and will be a boon to publish
case reports in good academic
journals.
• All uncommon isolates should
not be reported without the
wisdom of the senior
Microbiologists.
• All upcoming Microbiologists
should seek the help of reference
centres for assistance and
guidance as all we think may not
be correct.
UNFAMILIAR AND UNCOMMON ISOLATES
DISCARD WITH WISDOM
DR.T.V.RAO MD 22
• The diagnostic work on Mycobacteriology and Mycology lags the advances to the growing needs of the physicians. Tuberculosis being a major health problem in the country, yet no dedicated laboratories to diagnose the disease beyond smear examination, and increasing drug resistant tuberculosis is a concern to the treating physician. The attention and dedicated work of the young Microbiologists will certainly supported by every one. However we certainly need new generation of Microbiologists to take up the Tuberculosis related work.
IMPROVE THE POTENTIALS OF
MYCOBACTERIOLOGY AND MYCOLOGY
DR.T.V.RAO MD 23
• The anaerobic culture
work remains least
attempted and younger
generation of
Microbiologists should
explore this division of
bacteriology as many
anaerobes are
developing drug
resitance.
ANAEROBES ARE EQUALLY IMPORTANT IN
DIAGNOSTIC MICROBIOLOGY
DR.T.V.RAO MD 24
REPORTING THE MICROBIOLOGY
RESULTS
DR.T.V.RAO MD 25
DR.T.V.RAO MD 26
• Reporting the results
should be done with
caution as the Physicians
are not familiar with what
really we mean and matters
to be made clear and
understandable. The
greatest communication
gap between clinicians and
microbiologists remain with
terminology.
REPORTING THE LABORATORY
RESULTS
DR.T.V.RAO MD 27
QUALITY CONTROL HELPS IN PROGRESS OF
LABORATORY
DR.T.V.RAO MD 28
MOLECULAR METHODS IS DIAGNOSIS OF
INFECTIOUS DISEASES
• he PCR is the most sensitive of the existing rapid methods to detect
microbial pathogens in clinical specimens. In particular, when specific
pathogens that are difficult to culture in vitro or require a long cultivation
period are expected to be present in specimens, the diagnostic value of PCR
is known to be significant. However, the application of PCR to clinical
specimens has many potential pitfalls due to the susceptibility of PCR to
inhibitors, contamination and experimental conditions. It is known that the
sensitivity and specificity of a PCR assay is dependent on target genes,
primer sequences, which are expensive. However molecular methods are
most talked, highly expensive and creating dedicated laboratories continues
to be difficult in our economy If modern methods of molecular diagnostics are
not implemented we will we out of scene in Modern Medicine.
DR.T.V.RAO MD 29
LABORATORIES IN DEVELOPING COUNTRIES
SHOULD SUPPORT THE EPIDEMIOLOGICAL
STUDIES
DR.T.V.RAO MD 30
• The emphasis is on performing quality-controlled laboratory testing for a
finite period rather than long-term, routine diagnostic testing. These surveys
can be conducted in selected hospitals or laboratories that provide a natural
gathering point to sample patients meeting these entry criteria. A cohort-
based study acting as a surveillance "probe" for a finite period may be more
effective than individual patient-directed laboratory testing in providing useful
clinical and public health information, in determining the true incidence and
prevalence rates of emerging pathogens and antimicrobial-drug resistance,
and in yielding clinical predictors for various infections in defined patient
cohorts. In addition, cohort-based studies provide the opportunity to establish
diagnostic capability in basic clinical microbiology in sentinel hospitals or
laboratories and promote surveillance activities in regions where critical
public health infrastructure has been neglected . ( CDC – guidelines )
COMPUTER DOCUMENTATION WITH USE OF
WHONET
• Continuous surveillance of local antimicrobial susceptibility patterns is a must for
combating emerging antimicrobial resistance.WHONET is an effective computerized
microbiology laboratory data management and analysis program that can provide
guidance for empiric therapy of infections, alert clinicians of trends of antimicrobial
resistance, guide –the antibiotic policy decisions and preventive measures. The
program facilitates sharing of data amongst different hospitals by putting each
laboratory data into a common code and file format, which can be merged for
national or global collaboration of antimicrobial resistance surveillance. All the
documentation can be stored retrieved and analysed with the freely avialble soft
ware from WHO, just needing computer The program supports routine entry of
susceptibility test results performed by disk diffusion, MIC, and/or Etest or by Hi
comb method The majority of laboratories in the Armed forces use comparative disc
diffusion techniques based on Stokes or Kirby Bauer method to determine antibiotic
sensitivity. Interpretation guidelines for most standardized testing methodologies are
built into the system.
DR.T.V.RAO MD 31
• Working with
WHONET make
you familiarize
with optimal drug
choice, zone
sizes, easier to
understand in
interpretation in
precise reporting.
WHONET
DR.T.V.RAO MD 32
• When a laboratory would like
assistance in identifying a
parasitic organism, or
confirmation of a presumed
diagnosis, and they have access
to a digital camera, they can use
telediagnosis. Telediagnosis
involves email transmission of
data, such as digital images
captured from samples and
clinical and travel history, to
CDC. Response to these
inquiries can be provided in a
matter of minutes to hours.
TELE DIAGNOSTIC SERVICES IN
INFECTIOUS DISEASES
DR.T.V.RAO MD 33
• If you are a Microbiologist or a Pathologist and want to use telediagnosis assistance*, please visit the Diagnostic Assistance section on the DPDx Web site.
CDC HELPS IN TELEDIAGNOSIS OF
PARASITIC INFECTIONS
DR.T.V.RAO MD 34
• Our health and disease is a
concern to us and family
member apart from the
society. All Bio
hazardous micro-
organisms and materials to
be handled with caution. Be
a champion to promote the
“Universal Precautions‖
make the best contributions
in prevention of infection in
your own working arena.
CARING FOR SELF IS EQUALLY
IMPORTANT
DR.T.V.RAO MD 35
• Always publish your genuine
work in Journals and periodicals;
do not get disappointed if you
cannot publish in a reputed
journal. Now there are good
quality on line Microbiology
Journals (e-Journals) and
periodicals which are indexed
and available for your rescue.
Every attempt to publish an
article makes you realize where
we have to improve and by going
through good references we can
certainly improve ourselves.
PUBLISHING YOUR WORK
DR.T.V.RAO MD 36
• All young and senior professionals should refer the good potential of information high way, the Internet and get the best out it. E-learning should be our next option to know what the world is thinking about. I consider it is the best emerging option for improving our knowledge in Microbiology.
INTERNET AND E-LEARNING.
DR.T.V.RAO MD 37
• Quality of ordering and taking samples
• •Acceptable dispersion of samples
• •Transportation time and frequency of analysis
• •Total laboratory throughput time (including timeliness of report)
ORGANIZATIONAL CHANGE –
CONSEQUENCES TO BE EVALUATED
DR.T.V.RAO MD 38
• –Competence for performing analysis
• –Competence for synthesis and evaluation of results
• –Competence for clinical consultation
• •Availability for consultation (staffing, working hours)
• •Education and training
• •Public health service -including infection control, HCAI (health care infections) and AMR (antimicrobial resistance).
• •Recruitment of competent staff
• •Cost
ARRAY OF COMPETENCES
DR.T.V.RAO MD 39
DR.T.V.RAO MD 40
COMPUTERIZED DECISIONS A
EMERGING NEED …..
• Computerized decision
support can preserve
physician autonomy and
has been shown to improve
antibiotic use by a number
of different measures:
fewer susceptibility
mismatches, allergic
reactions and other
adverse events, excess
dosages, and overall
amount and cost of
antibiotic therapy
DR.T.V.RAO MD 41
COMPUTERIZE YOUR LABORATORY TO
SUIT THE DEMANDS OF THE HOSPITAL
• Legacy computer systems,
quality improvement teams,
and strategies for
optimizing antibiotic use
have the potential to
stabilize resistance and
reduce costs by
encouraging
heterogeneous prescribing
patterns and use of local
susceptibility patterns to
inform empiric treatment.
• Concentration –of
resources
• •Amalgamation –of
services
• •Outsourcing –of services
• •Accreditation –of
laboratories
• •Explosion of staff
competences
• •Automation –of analysis
TRENDS IN CLINICAL MICROBIOLOGY
"THE GOOD, THE TEDIOUS AND THE UGLY”.
DR.T.V.RAO MD 42
• Subcontracting a process to a
third-party company.-the decision
to outsource is often made in the
interest of lowering cost or
making better use of time and
energy costs, redirecting or
conserving energy directed at the
competencies of a particular
business, or to make more
efficient use of land, labor,
capital, technology and
resources.
• Outsourcing became part of the
business lexicon during the
1980s.
OUTSOURCING
DR.T.V.RAO MD 43
THE FUTURE AND GROWING NEEDS OF THE
MICROBIOLOGY
• Antimicrobial resistance development and health care
associated infectionswill demand more of microbiology!
• The compromised host of today´s medicine requires effecive
antibiotics for profylaxis and/or treatment.
• Empiric therapy will fail increasingly often and its use needs to
be minimised!
• -―pre-emptive culturing‖
• -rapid diagnostics (detection + AST)
• -advice on antimicrobial mono-and combination therapy will
require outstanding competence.
DR.T.V.RAO MD 44
• Transportation of samples -distance,
service, 24h-availability of blood
culture cabinets.
• –Availability -opening hours (24 h
service, 7 d).
• –Analytical methods –process time,
‖random access‖
• –Timeliness of reporting (and
making sure reports are looked at)
• •Shorten time to susceptibility
test results
• –Rapid detection of susceptibility
• –Rapid exclusion of resistance
SHORTEN TIME TO DIAGNOSIS
DR.T.V.RAO MD 45
• The true symbiosis
between large, well
equipped and richly staffed
microbiological laboratories
and smaller hospital
based laboratories
providing ‖close-
proximity microbiology‖
and consultancy
services and the basis
for infection control
THE WAY FORWARD
DR.T.V.RAO MD 46
BEWARE LABORATORY RESULTS CAN CREATE
CONTROVERSIES AND LEGAL CHALLENGES
DR.T.V.RAO MD 47
DR.T.V.RAO MD 48
FOR ARTICLES OF INTEREST ON DIAGNOSTIC
MICROBIOLOGY FOLLOW ME ON
• The Programme created by
Dr.T.V.Rao MD for ‘e’ Learning
resources for Microbiologists in
Developing World. • Email
DR.T.V.RAO MD 49
