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ESTABLISHING   DIAGNOSTIC MICROBIOLOGY                LABORATORY                 Dr.T.V.Rao MDDR.T.V.RAO MD               ...
WHAT IS MEDICAL MICROBIOLOGY• Medical Microbiology may overlap with parasitology,     generally considered the Study of Di...
CHALLENGES IN MEDICAL MICROBIOLOGY• Medical Microbiology is a challenging profession  deals with all aspects of infection,...
KNOW WHAT YOU ARE DOING• Laboratory medicine in general and  microbiology in particular is presently subject  to rapid evo...
COMPONENTS OF DIAGNOSTIC                     MICROBIOLOGY• It is the analysis of a sample, the synthesis of results  (of s...
ROLE OF CLINICAL MICROBIOLOGISTS• Clinical microbiologists are  engaged in the field of  diagnostic microbiology to  deter...
COPING WITH PROGRESS IN DIAGNOSTIC               MICROBIOLOGY•    During the past two decades, technical     advances in t...
CONVENTIONAL DIAGNOSTIC                     MICROBIOLOGY                             • The conventional                   ...
DESIGN THE LABORATORY TO SUIT THE       CIRCUMSTANCES – AND WORK LOADDR.T.V.RAO MD                             9
ESTABLISH THE BIOSAFETY IN                MICROBIOLOGY LABORATORYOver the past twodecades, Biosafety inMicrobiological and...
BIOSAFETY LEVEL 1                         • Biosafety level 1                           (BSL-1) is the basic              ...
BIOSAFETY LEVEL 2• Biosafety level 2 (BSL-  2) is appropriate for  handling moderate-risk  agents that cause  human diseas...
BIOSAFETY LEVEL 3                         • Biosafety level 3                           (BSL-3) is appropriate            ...
BIOSAFETY LEVEL 4• Exotic agents that pose  a high individual risk of  life-threatening disease  by infectious aerosols  a...
OPTIMAL UTILIZATION OF THE AVAILABLE                 RESOURCESDR.T.V.RAO MD                              15
BE FAMILIAR WITH STERILIZATION                          PRACTICES• Scientific sterilization practices will certainly cut s...
OPTIMAL SPECIMEN COLLECTION INCREASES THE    CAPABILITIES OF DIAGNOSTIC REPORTING• Specimen collection and aseptic  precau...
ERRORS IN SPECIMEN COLLECTION INCREASES        MORBIDITY AND ECONOMIC LOSES                        • For patients, specime...
UPDATE THE BACTERIOLOGY LABORATORIES          CAN SAVE SEVERAL LIVES                     •    Bacteriology departments    ...
TURN TO FLUORESCENT MICROSCOPY FOR RAPID   DIAGNOSIS OF SEVERAL LIFE THREATING               INFECTIONS• Advantages of flu...
GOOD BENCH WORK IS THE STRENGTH OF                DIAGNOSTIC MICROBIOLOGY• Bench work Is the most  important component of ...
UNFAMILIAR AND UNCOMMON ISOLATES                DISCARD WITH WISDOM                           • All uncommon isolates shou...
IMPROVE THE POTENTIALS OF    MYCOBACTERIOLOGY AND MYCOLOGY•    The diagnostic work on     Mycobacteriology and Mycology la...
ANAEROBES ARE EQUALLY IMPORTANT IN        DIAGNOSTIC MICROBIOLOGY                     • The anaerobic culture             ...
REPORTING THE MICROBIOLOGY              RESULTSDR.T.V.RAO MD                     25
DR.T.V.RAO MD   26
REPORTING THE LABORATORY                RESULTS• Reporting the results  should be done with  caution as the Physicians  ar...
QUALITY CONTROL HELPS IN PROGRESS OF             LABORATORYDR.T.V.RAO MD                       28
MOLECULAR METHODS IS DIAGNOSIS OF                   INFECTIOUS DISEASES• he PCR is the most sensitive of the existing rapi...
LABORATORIES IN DEVELOPING COUNTRIES        SHOULD SUPPORT THE EPIDEMIOLOGICAL                      STUDIES• The emphasis ...
COMPUTER DOCUMENTATION WITH USE OF                                   WHONET•    Continuous surveillance of local antimicro...
WHONET• Working with  WHONET make  you familiarize  with optimal drug  choice, zone  sizes, easier to  understand in  inte...
TELE DIAGNOSTIC SERVICES IN               INFECTIOUS DISEASES•    When a laboratory would like     assistance in identifyi...
CDC HELPS IN TELEDIAGNOSIS OF                PARASITIC INFECTIONS                            • If you are a               ...
CARING FOR SELF IS EQUALLY                IMPORTANT• Our health and disease is a  concern to us and family  member apart f...
PUBLISHING YOUR WORK                    • Always publish your genuine                      work in Journals and periodical...
INTERNET AND E-LEARNING.• All young and senior  professionals should refer  the good potential of  information high way, t...
ORGANIZATIONAL CHANGE –     CONSEQUENCES TO BE EVALUATED                             • Quality of ordering and            ...
ARRAY OF COMPETENCES•    –Competence for performing analysis•    –Competence for synthesis and     evaluation of results• ...
COMPUTERIZED DECISIONS A             EMERGING NEED …..• Computerized decision  support can preserve  physician autonomy an...
COMPUTERIZE YOUR LABORATORY TO  SUIT THE DEMANDS OF THE HOSPITAL                   • Legacy computer systems,             ...
TRENDS IN CLINICAL MICROBIOLOGY     "THE GOOD, THE TEDIOUS AND THE UGLY”.• Concentration –of  resources• •Amalgamation –of...
OUTSOURCING• Subcontracting a process to a  third-party company.-the decision  to outsource is often made in the  interest...
THE FUTURE AND GROWING NEEDS OF THE             MICROBIOLOGY• Antimicrobial resistance development and health care  associ...
SHORTEN TIME TO DIAGNOSIS•    Transportation of samples -distance,     service, 24h-availability of blood     culture cabi...
THE WAY FORWARD• The true symbiosis  between large, well  equipped and richly staffed  microbiological laboratories  and s...
BEWARE LABORATORY RESULTS CAN CREATE      CONTROVERSIES AND LEGAL CHALLENGESDR.T.V.RAO MD                               47
FOR ARTICLES OF INTEREST ON DIAGNOSTIC           MICROBIOLOGY FOLLOW ME ONDR.T.V.RAO MD                                  48
• The Programme created by             Dr.T.V.Rao MD for ‘e’ Learning           resources for Microbiologists in          ...
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  1. 1. ESTABLISHING DIAGNOSTIC MICROBIOLOGY LABORATORY Dr.T.V.Rao MDDR.T.V.RAO MD 1
  2. 2. 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
  3. 3. 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
  4. 4. 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
  5. 5. 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
  6. 6. 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 determine d.DR.T.V.RAO MD 6
  7. 7. 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.DR.T.V.RAO MD 7
  8. 8. 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.DR.T.V.RAO MD 8
  9. 9. DESIGN THE LABORATORY TO SUIT THE CIRCUMSTANCES – AND WORK LOADDR.T.V.RAO MD 9
  10. 10. ESTABLISH THE BIOSAFETY IN MICROBIOLOGY LABORATORYOver the past twodecades, Biosafety inMicrobiological andBiomedical Laboratories(BMBL) has become thecode of practice forbiosafety—the disciplineaddressing the safehandling and containmentof infectiousmicroorganisms andhazardous biologicalmaterials.DR.T.V.RAO MD 10
  11. 11. 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 humansDR.T.V.RAO MD 11
  12. 12. 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 exposureDR.T.V.RAO MD 12
  13. 13. 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.DR.T.V.RAO MD 13
  14. 14. 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) standardsDR.T.V.RAO MD 14
  15. 15. OPTIMAL UTILIZATION OF THE AVAILABLE RESOURCESDR.T.V.RAO MD 15
  16. 16. 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
  17. 17. 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.DR.T.V.RAO MD 17
  18. 18. 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.DR.T.V.RAO MD 18
  19. 19. 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.DR.T.V.RAO MD 19
  20. 20. 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.DR.T.V.RAO MD 20
  21. 21. 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 .DR.T.V.RAO MD 21
  22. 22. 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.DR.T.V.RAO MD 22
  23. 23. 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.DR.T.V.RAO MD 23
  24. 24. 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.DR.T.V.RAO MD 24
  25. 25. REPORTING THE MICROBIOLOGY RESULTSDR.T.V.RAO MD 25
  26. 26. DR.T.V.RAO MD 26
  27. 27. 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.DR.T.V.RAO MD 27
  28. 28. QUALITY CONTROL HELPS IN PROGRESS OF LABORATORYDR.T.V.RAO MD 28
  29. 29. 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
  30. 30. 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 )DR.T.V.RAO MD 30
  31. 31. 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
  32. 32. WHONET• Working with WHONET make you familiarize with optimal drug choice, zone sizes, easier to understand in interpretation in precise reporting.DR.T.V.RAO MD 32
  33. 33. 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.DR.T.V.RAO MD 33
  34. 34. 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.DR.T.V.RAO MD 34
  35. 35. 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.DR.T.V.RAO MD 35
  36. 36. 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.DR.T.V.RAO MD 36
  37. 37. 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.DR.T.V.RAO MD 37
  38. 38. 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)DR.T.V.RAO MD 38
  39. 39. 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• •CostDR.T.V.RAO MD 39
  40. 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 therapyDR.T.V.RAO MD 40
  41. 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.DR.T.V.RAO MD 41
  42. 42. 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 analysisDR.T.V.RAO MD 42
  43. 43. 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.DR.T.V.RAO MD 43
  44. 44. 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
  45. 45. 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 resistanceDR.T.V.RAO MD 45
  46. 46. 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 controlDR.T.V.RAO MD 46
  47. 47. BEWARE LABORATORY RESULTS CAN CREATE CONTROVERSIES AND LEGAL CHALLENGESDR.T.V.RAO MD 47
  48. 48. FOR ARTICLES OF INTEREST ON DIAGNOSTIC MICROBIOLOGY FOLLOW ME ONDR.T.V.RAO MD 48
  49. 49. • The Programme created by Dr.T.V.Rao MD for ‘e’ Learning resources for Microbiologists in Developing World. • Email • doctortvrao@gmail.comDR.T.V.RAO MD 49
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