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Establishing Diagnostic Microbiology Laboratory


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Title: Establishing Diagnostic Microbiology Laboratory

diagnostic microbiology laboratory
  • Dr.T.V.Rao MD

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

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.

Know what you are doing
  • Laboratory medicine in general and microbiology
    in particular is presently subject to rapid
  • 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?

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.

Role of clinical microbiologists
  • 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.

Coping with progress in diagnostic microbiology
  • 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

Conventional diagnostic microbiology
  • 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.

Design the laboratory to suit the circumstances
and work load
Establish the biosafety in microbiology laboratory
  • Over the past two decades, Biosafety in
    Microbiological and Biomedical Laboratories
    (BMBL) has become the code of practice for
    biosafetythe discipline addressing the safe
    handling and containment of infectious
    microorganisms and hazardous biological

Biosafety level 1
  • 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

Biosafety level 2
  • 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 3
  • 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 4
  • 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

optimal utilization of the available resources
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.

Optimal specimen collection increases the
capabilities of diagnostic reporting
  • 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

Errors in specimen collection increases morbidity
and economic loses
  • 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.

Update the bacteriology laboratories can save
several lives
  • 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.

Turn to fluorescent microscopy for rapid
diagnosis of several life threating infections
  • 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.

Good bench work is the strength of diagnostic
  • 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.

Unfamiliar and uncommon isolates
discard with wisdom
  • 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.

Improve the potentials of mycobacteriology and
  • 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.

Anaerobes are equally important in diagnostic
  • 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.

Reporting the Microbiology Results
(No Transcript)
Reporting the laboratory results
  • 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.

Quality control helps in progress of Laboratory
Molecular methods is diagnosis of Infectious
  • 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

Laboratories in developing countries should
support the epidemiological studies
  • 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.

  • Working with WHONET make you familiarize with
    optimal drug choice, zone sizes, easier to
    understand in interpretation in precise reporting.

Tele diagnostic services in Infectious Diseases
  • 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.

CDC helps in Telediagnosis of parasitic infections
  • 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.

Caring for self is equally important
  • 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.

Publishing your work
  • 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.

Internet and e-learning.
  • 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

Organizational change Consequences to be
  • Quality of ordering and taking samples
  • Acceptable dispersion of samples
  • Transportation time and frequency of analysis
  • Total laboratory throughput time (including
    timeliness of report)

Array of competences
  • Competence for performing analysis
  • Competence for synthesis and evaluation of
  • Competence for clinical consultation
  • Availability for consultation (staffing, working
  • Education and training
  • Public health service -including infection
    control, HCAI (health care infections) and AMR
    (antimicrobial resistance).
  • Recruitment of competent staff
  • Cost

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

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

Trends in clinical microbiology
"the good, the tedious and the ugly.
  • Concentration of resources
  • Amalgamation of services
  • Outsourcing of services
  • Accreditation of laboratories
  • Explosion of staff competences
  • Automation of analysis

  • 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
  • Outsourcing became part of the business lexicon
    during the 1980s.

The future and growing needs of the Microbiology
  • Antimicrobial resistance development and health
    care associated infectionswill demand more of
  • The compromised host of todays medicine requires
    effecive antibiotics for profylaxis and/or
  • 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.

Shorten time to diagnosis
  • Transportation of samples -distance, service,
    24h-availability of blood culture cabinets.
  • Availability -opening hours (24 h service, 7 d).
  • Analytical methods process time, random
  • Timeliness of reporting (and making sure reports
    are looked at)
  • Shorten time to susceptibility test results
  • Rapid detection of susceptibility
  • Rapid exclusion of resistance

The way forward
  • 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

Beware Laboratory results can create
controversies and legal challenges
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
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