Establishing Diagnostic Microbiology Laboratory

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Establishing
diagnostic microbiology laboratory

• Dr.T.V.Rao MD

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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.

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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.

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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?

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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.

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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.

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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
  microbiologist.

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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.

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Design the laboratory to suit the circumstances
and work load
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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
  materials.

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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
  humans

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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

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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.

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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

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optimal utilization of the available resources
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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.

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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
  Departments.

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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.

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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.

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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.

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Good bench work is the strength of diagnostic
microbiology

• 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.

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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.

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Improve the potentials of mycobacteriology and
Mycology

• 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.

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Anaerobes are equally important in diagnostic
microbiology

• 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.

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Reporting the Microbiology Results
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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.

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Quality control helps in progress of Laboratory
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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.

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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 )

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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.

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Whonet

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

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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.

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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.

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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.

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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.

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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
  Microbiology.

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Organizational change Consequences to be
evaluated

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

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Array of competences

• 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

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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

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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.

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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

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Outsourcing

• 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.

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The future and growing needs of the Microbiology

• Antimicrobial resistance development and health
  care associated infectionswill demand more of
  microbiology!
• The compromised host of todays 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.

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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
  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

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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

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Beware Laboratory results can create
controversies and legal challenges
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For Articles of Interest on diagnostic
microbiology follow me on
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• The Programme created by Dr.T.V.Rao MD for e
  Learning resources for Microbiologists in
  Developing World.
• Email
• doctortvrao_at_gmail.com