MEDICAL MICROBIOLOGYDIAGNOSTIC CHALLENGES

Dr.T.V.Rao MD

Role of Microbiology

➲ Medical Microbiology deals with all aspects of infection, through

initial diagnosis, through to treatment. It includes hands on bench work in the laboratory and close involvement with

clinical staff

Microbes can infect any one ?

Where we stand Today

Most neglected and least invested

specialty Reasons can be

many

Are we Doctors or Technologists?

Goal of Microbiologists

➲The goal of microbiologic evaluation is to provide accurate,

clinically pertinent results in a timely manner. The quality of the

specimens submitted to the microbiology laboratory is critical

for optimal specimen evaluation

Sterilization practices

Microbiologists have greater say in Sterilization Practices

• Be a educator on Sterilization practices

Universal PrecautionsTeach simple facts to your staff

Follow the CDC Manual

• Guideline for Disinfection and Sterilization in Healthcare Facilities, 2008

Diagnostic Challenges

Fishing for Diagnosis in Laboratories, Is it worth?

The physicians and Microbiologists should be aware of the clinical manifestations, before undertaking the test.

Microbiological tests are expensive and technically demanding

Causal testing of Microbiological tests are counterproductive.

Good Microbiology begins with Good specimen collection

• Emphasize that obtaining sensitive and specific microbiology results begins with the patient and not at the door of the microbiology laboratory.

• Accentuate the importance of proper collection and transport of specimens in both local and referral environments

•

Poor sample quality from Young ones

Have you though how difficult to collect

a Urine specimen from young child ?

Scientific specimen collection makes difference

Describe common pitfalls in specimen collection and transport

Discuss What rules or principles must be followed in order to collect microbiology specimens which will accurately reflect the pathogenesis of the microbiological agent.

Is the Microbiology Reports entirely in our domain?

The practice of sensitive, specific and cost effective clinical microbiology is intimately tied to the submission and proper handling of optimal specimens for analysis. Unfortunately, these aspects of clinical microbiology are not as critically controlled as our laboratory assays.

Overcoming inferior quality results

It is our responsibility to educate and notify our healthcare colleagues when specimens arrive at the laboratory that will yield inferior results.

Communication is a never ending process

• Communicate, communicate, communicate! – Real time feedback– Contact the health

care worker who collected the suboptimal specimen

Be Bold to tell the Clinicians which is right ……

➲ To fill out all requisitions completely and precisely, including requested details on patient history, antimicrobial therapy, and specimen source, so that the laboratory can best determine the appropriate method for processing the specimen.

Why Proper written Request

Any request is a legal document. Identifies all the outcome of test. No interchange of results. Short forms are dangerous Signature of the Doctor / Nurse is essential in

legible form, can help to contact in case of results which can save a patient.

When the patient is serious, write a Tele contact number which can help in prompt delivery of results

Specimens is the source of strength to Microbiology

Department➲ Valid interpretation of the results of

culture can be achieved only if the specimen obtained is appropriate for processing. As a result, care must be taken to collect only those specimens that may yield pathogens, rather than colonizing flora or contaminants.

Who is responsible for the Specimen collection

Bench Work

Patience paysReference Laboratories Helps

• 1.Isolation & Identification of Vibrocholarae0139 strains from Tirupati in 1995 & again in October,2000

Named as Tirupathi strain by NICED Kolkata in 1993

Terminally ill patients contribute to knowledge

may help to know what we missed

Impress with your organization for more funding to the

Laboratory

Gram Staining

Gram Staining – Most rapid method of Diagnosis

➲ The Gram stain is almost always the first step in the identification of a bacterial organism.

➲ How much attention paid ?

➲ Several rare isolates can be observed, possible to publish as articles under Case studies

Gram staining gives major clues in Bacterial and Fungal diagnosis

1Streptococcus pneumonia 2.Psudomonas pseudomallei 3 Cases of bacterial and fungal meningitis 4.Listeria Monocytogenes 5.Cryptococcus neoformans. 6.Common microbes at uncommon sites. 7.Uncommon microbes at common sites

Blood Cultures

• A blood culture may be helpful in determining the specific bacteria causing an infection and selecting the appropriate antibiotic to treat it.

A biphasic medium is the best option in resource poor settings

Blood Culture collect two specimens

➲ Two sets of blood cultures should be drawn. Number of sets positive correlates with true sepsis (except for coagulase negative Staph?) (Clin Microbial. Rev 19:788-802, 2006)

Automation in Bacterial Infections

Automation for Bacterial and Mycobacterial Cultures is a Urgent

Need

Are we ignoring Anaerobes ?

Antibiotic Policy

Conserve Antibiotics for future use

Increasing antimicrobial resistance and the cost pressures of managed care have led to increased needs to assess and ensure appropriate antimicrobial use

Having an antibiotic policy helps in limiting the use of powerful antibiotics as initial treatment, saves the powerful antibiotic for later treatment for resistant organisms and saves money for the patients.

Detection of MRSA

Methicillin-resistant Staphylococcus aureus (MRSA) is a bacterium responsible for several difficult-to-treat infections in humans. MRSA is by definition any strain of Staphylococcus aureus bacteria that is resistant to a large group of antibiotics called the beta-lactams , which include the penicillin's and the cephalosporin

Detection of ESBL

The ESBL enzymes are plasmid - mediated enzymes capable of hydrolyzing and inactivating a wide variety of beta lactams, including third generation cephalosporins, penicillin's and aztreonam. These enzymes are the result of mutations of TEM-1 and TEM-2 and SHV-I. All of these ß-lactamase enzymes are commonly found in the Enterobacteriaceae family.

Tuberculosis most neglected by Microbiology Departments

New website launched to improve diagnosis of TB among people living with HIV

A web site, Evidence-Based Tuberculosis Diagnosis, has been launched that aims to provide the most comprehensive single source of evidence synthesis, policies, guidelines and research agendas on TB diagnosis. It is also a source for complete up-to-date information on the current TB diagnostics pipeline. Standard operating procedures and package inserts for several tests also are available.

Tele Diagnosis

CDC helps in Telediagnosis

➲ The CDC now offers telediagnosis to help laboratories diagnose malaria and other parasitic diseases. When laboratories are not certain about identifying parasites on a slide, they can e-mail to the CDC images of the suspected parasites. Experts then review the images and discuss findings with the submitting lab within only a few hours, allowing near real-time diagnosis as well as an opportunity for training in microscopic diagnosis.

Many unresolved questions can be solved

Documentation in Microbiology

““If you cannot If you cannot measure it, measure it, you cannotyou cannot improve it”improve it”

Lord Kelvin, 1824-1907Lord Kelvin, 1824-1907

Documentation and Retrieval is a Challenge during Medical

Inspections

Documentation in Microbiology

• WHONET is a Windows-based database software developed for the management of microbiology laboratory data and the analysis of antimicrobial susceptibility test results.

Data can be exchanged globally

To enhance local use of laboratory data for guiding therapy, assisting infection control, characterizing resistance epidemiology and identifying laboratory testing errors; to promote collaboration in surveillance activities through the exchange of data.

WHONET is used to support surveillance activities in the countries indicated  in red.

WHONET connects to the World through WWW

These tools enable any microbiology laboratory to put its test results into a database and conduct analyses to support local infection control and antibiotic use. Laboratories can also upload files created by WHONET, to feed into national or other multi-centre surveillance networks and to inform drug policy. Such surveillance programs are now in place in many countries.

WHONET Software is free and open access

The utility, BacLink, facilitates the transfer of microbiology data from existing computer systems to avoid the need to re-enter laboratory results. Baclink can transfer data into WHONET from: common commercial database and spreadsheet software; commercial susceptibility test instruments (broth microdilution and disk diffusion readers) hospital and laboratory information systems (with ASCII text files)

All antibiotic profiles at a click

Reducing the Antimicrobial resitance is a great contribution to Medical

Profession

The WHONET experience suggests that solid drug resistance data can be collected and analyzed in resource-constrained settings, using core microbiology, if local laboratories are given appropriate support. Strengthening these laboratories is therefore a potentially cost-effective contribution to both treating drug resistant disease and preventing its further spread.

Reporting the Microbiology Results

Reporting the results should be done with caution as the Physicians are not familiar with what really we mean and. The greatest communication gap between clinicians and microbiologists remain with terminology

Molecular Methods in Microbiology

Routine Methods being replaced with Technology

➲ . The microbial community continues to evolve and adapt to changing environmental influences, and the distribution of human pathogens has become more global. Our recognition of the spectrum of microorganisms that cause invasive human disease has exploded with the use of culture-independent methods to detect and characterize pathogens.

Polymerase chain reaction changes the Medicine

Scarcely any invention has alteredbiological science so radically in

such a short period as the polymerasechain reaction, or PCR. With this

technique, minute amounts of DNAcan be replicated very rapidly and

thereby amplified to such an extentthat the DNA becomes easy to

detect, study and use for any givenpurpose.

Every Body talking about PCRIs it all true ?

➲ The 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..

Limitations of PCR

However, the application of PCR to clinical specimens has many potential pitfalls due to the susceptibility of PCR to inhibitors, contamination and experimental conditions

Success of PCR lies with

➲ For instance, it is known that the sensitivity and specificity of a PCR assay is dependent on target genes, primer sequences

Molecular Biology techniques/ training should be part of Post

graduate studies➲ The PCR assay in diagnosis involves

several critical steps, such as DNA extraction from specimens, PCR amplification, and detection of amplicons

Change to Molecular / Rapid Tests is Imminent

Need of the Hour

• Diagnostic tests need to be quick, simple to use and easy to interpret with little training. They must also be completely self-contained, with no maintenance or calibration required.

Rapid diagnostic tests

• Rapid diagnostic tests (RDTs), which can diagnose infectious diseases in as little as five minutes, are being hailed as the solution

On line HelpA boon

Newer challenges with Emerging Infectious Diseases

Emerging infectious diseases

Emerging infectious disease can be one that has recently been recognised. Or it can be a disease where cases have increased (or look as though they might be on the increase) over the last 20 years, in a specific place or among a specific population.

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Emerging and Remerging infections

• Over the past 25 years, more than 30 new, or newly-recognised, infections have been identified around the world. The pattern of known infections also changes constantly, as the areas where disease is constantly present expand beyond traditional limits.

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e-learning in Microbiology

Role of teachers, is it diminishing ?

• People love to learn but hate to be taught“

• Plato

e-learning in Microbiology

e-learning important for Student and Teacher

The development of sophisticated, web-based

learning platforms that are easy to use from a student and a teacher prospective, medical

education is beginning to embrace a new modality of

knowledge transfer.

Quality Control

Quality assurance (QA) is the total process whereby the quality of

laboratory reports can beguaranteed. The term quality control covers that part of QA, which primarily

concerns the control oferrors in the performance of tests and

verification of test results.

Standard Operating Procedures a Must for accreditation

Each laboratory must have standard operating procedures (SOPs). QA of

pre-analytical, analyticaland post-analytical stages of

microbiological procedures should be incorporated in SOPs.

Publishing your workor ?

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.

Publish or Perish

Resolve the issues with Clinicians with Ethics

Learn to survive ?

Made for Dr.T.V.Rao MD’s ‘e’ learning Programme on Infectious

Diseases

Emaildoctortvrao@gmail.com