Establishing Diagnostic Microbiology Departments

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Establishing diagnostic microbiology laboratory :

Dr.T.V.Rao MD Establishing diagnostic microbiology laboratory Dr.T.V.Rao MD 1

What is Medical Microbiology:

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:

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:

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:

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

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. Role of clinical microbiologists Dr.T.V.Rao MD 6

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. Coping with progress in diagnostic microbiology Dr.T.V.Rao MD 7

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. Conventional diagnostic microbiology Dr.T.V.Rao MD 8

Design the laboratory to suit the circumstances – and work load :

Design the laboratory to suit the circumstances – and work load Dr.T.V.Rao MD 9

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 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:

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:

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:

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

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 biosafety level 4 Dr.T.V.Rao MD 14

optimal utilization of the available resources :

optimal utilization of the available resources Dr.T.V.Rao MD 15

Be familiar with sterilization Practices:

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

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. Optimal specimen collection increases the capabilities of diagnostic reporting Dr.T.V.Rao MD 17

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. Errors in specimen collection increases morbidity and economic loses Dr.T.V.Rao MD 18

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. Update the bacteriology laboratories can save several lives Dr.T.V.Rao MD 19

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. Turn to fluorescent microscopy for rapid diagnosis of several life threating infections Dr.T.V.Rao MD 20

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 . Good bench work is the strength of diagnostic microbiology Dr.T.V.Rao MD 21

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. Unfamiliar and uncommon isolates discard with wisdom Dr.T.V.Rao MD 22

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. Improve the potentials of mycobacteriology and Mycology Dr.T.V.Rao MD 23

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. Anaerobes are equally important in diagnostic microbiology Dr.T.V.Rao MD 24

Reporting the Microbiology Results:

Reporting the Microbiology Results Dr.T.V.Rao MD 25

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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. Reporting the laboratory results Dr.T.V.Rao MD 27

Quality control helps in progress of Laboratory:

Quality control helps in progress of Laboratory Dr.T.V.Rao MD 28

Molecular methods is diagnosis of Infectious diseases:

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 :

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:

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

Whonet :

Working with WHONET make you familiarize with optimal drug choice, zone sizes, easier to understand in interpretation in precise reporti ng. Whonet Dr.T.V.Rao MD 32

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. Tele diagnostic services in Infectious Diseases Dr.T.V.Rao MD 33

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 . CDC helps in Telediagnosis of parasitic infections Dr.T.V.Rao MD 34

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. Caring for self is equally important Dr.T.V.Rao MD 35

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 . Publishing your work Dr.T.V.Rao MD 36

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 . Internet and e-learning . Dr.T.V.Rao MD 37

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) Organizational change – Consequences to be evaluated Dr.T.V.Rao MD 38

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 Array of competences Dr.T.V.Rao MD 39

Computerized Decisions a Emerging Need …..:

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

Computerize your laboratory to suit the demands of the hospital:

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.

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 Trends in clinical microbiology "the good, the tedious and the ugly”. Dr.T.V.Rao MD 42

Outsourcing :

S ubcontracting 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:

The future and growing needs of the Microbiology Antimicrobial resistance development and health care associated infections will 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

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 Shorten time to diagnosis Dr.T.V.Rao MD 45

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 The way forward Dr.T.V.Rao MD 46

Beware Laboratory results can create controversies and legal challenges :

Beware Laboratory results can create controversies and legal challenges Dr.T.V.Rao MD 47

For Articles of Interest on diagnostic microbiology follow me on:

Dr.T.V.Rao MD 48 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 Dr.T.V.Rao MD 49

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