MEDICAL MICROBIOLOGY

DIAGNOSTIC 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 Precautions
Teach simple facts to your staff
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 pays
Reference 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
infections is urgent need

Results are the most important aspect of

any microbial detection system. Built on
bioMérieux's patented colorimetric
technology, the Bac T/ALERT 3D
demonstrates unsurpassed recovery of
a wide range of organisms with >95%
recovery within 24 hours and >98%
within 72 hours
 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
measure it,
you cannot
improve it”
Lord 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 altered

biological science so radically in
such a short period as the polymerase
chain reaction, or PCR. With this
technique, minute amounts of DNA
can be replicated very rapidly and
thereby amplified to such an extent
that the DNA becomes easy to
detect, study and use for any given
purpose.
 Every Body talking about PCR
Is 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 Help
A 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.
.
 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.
Subscribe to Emerging Infectious
Diseases
Free on Request
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 be
guaranteed. The term quality control
covers that part of QA, which primarily
concerns the control of
errors 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, analytical
and post-analytical stages of
microbiological procedures should be
incorporated in SOPs.
 Publishing your work
or
?

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
Email
doctortvrao@gmail.com