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General guidelines for a microbiological


laboratory of optimal capacity
The suggested space for a microbiological testing laboratory of optimal capacity 130 sq. m.

Food testing laboratory


Reference culture room
Changing/entry room
Media preparation room
Washing/decontamination room
Office /td>
Head

40 sq. m.
10 sq. m.
10 sq. m.
10 sq. m.
10 sq. m.
10 sq. m.
14 sq. m.

Interior passages
TOTAL
Sample receipt room
GRAND TOTAL

16 sq. m.
120 sq. m. (approx)
10 sq. m.
130 sq. m.

Arrangements of the different areas to carryout functions preventing contamination are


identified in the layout plan (Fig. 5). The plan identifies locations for the main testing
laboratory, media preparation room, glassware washing and decontamination room, culture
maintenance room, head's room, staff room/ office and other facilities. The required
specifications in designing of the laboratory complex are given below in relation to Fig 58.

Set up partitions as in Fig 5, using aluminium and glass panelling. Put aluminium
or cement brick up to 1.2 meters from the floor and then glass up to the ceiling. At
ceiling level all the panels should fit tightly and be sealed with appropriate material
to prevent air leaks that may lead to contaminations.
All doors to be of aluminium /glass, opening outward. The door marked A should
have a width of 150 cm and the doors marked B a width of 130 cm to allow large
equipment to be carried in. Other doors could be of standard size.
Fix the central workbench in the main laboratory as indicated in the layout
diagram. (Fig. 5). There should be cupboards and drawers under the benches.
Construct workbenches along the wall in the glassware washing room, culture
maintenance room, media preparation rooms and in the main laboratory. These
should be 90 cm (height) x 90 cm (width) and suit the length to the walls as in Fig.
5. They may be of concrete or wood with push-in cupboards and drawers
underneath.
All bench and table tops in the testing laboratory, culture maintenance room, media
preparation room and washing room need to be laid with granite, formica or a
similar non-porous material.

The testing laboratory, the media preparation room and the culture maintenance
room need to be air-conditioned to maintain a continuous temperature of 25 oC and
RH (55 + 5)%.
In locations where an uninterrupted power supply is not available day and night, a
backup generator with automatic switch gear needs to be used.
The floor of the testing laboratory, the media preparation room and culture
maintenance room should be done with epoxy resin. In all other areas, use smooth
floor tiles, preferably white and of dimension 30cm x 30 cm.
The locations for electricity outlets for 15 amps and 3-phase supply are indicated in
Fig 6. Provide adequate lighting, using fluorescent or low energy bulbs to provide
light intensity of 750 lux. The lights should be fixed at ceiling level and not
hanging (to avoid collection and release of dust).
Locations of sinks are given in Fig 5. Stainless steel sinks are preferred. In the
washing room a sink with a draining board will be more useful. It is preferable to
fix two-way or three-way laboratory type taps for the sinks.
The water delivered to the laboratories should be at a minimum pressure of 2.0 bar
(Where the pressure of the public supply is low and not continuous, install an
overhead tank at 11metre height (equivalent of approximately the 4th floor of a
building).
The gas lines should carry two-way or four-way taps. The supply tank should be
located outside the laboratory with suitable safety valves and protection from
mishandling.
All water exhaust down pipes from the sinks should be of 50 mm diameter leading
down to 100 mm diameter horizontal pipes with no bends, and opening directly out
of the laboratory so that they can be cleaned from outside.
All surfaces in the testing laboratory, culture room and media preparation room
where dust could accumulate (window panes and sharp corners in the floor) need to
be made at an angle and curved.
No pipelines and conduits should be laid on the surface of the floor or along the
surface of walls in the laboratories as they permit dust and dirt to accumulate and
are impossible to clean. They should be embedded.
Storage cupboards for glassware and chemicals should be put up at appropriate
places above 1.6 meters on the walls in the testing laboratory, washing room,
sampling room and media preparation room (height 100 cm x depth 45 cm).

Tint the glass windows in the outer walls to prevent direct sunlight entering the
laboratory
There should be no ceiling fans in the testing laboratories and the ceilings should
be smooth.
Extraction fans may be fixed in washing and media preparation room, but kept
closed except during operation.
Enamel paints are preferable on the walls since they can be washed.
The proposed layout of equipment is given in Fig. 7.
FIG 5- LAYOUT PLAN FOR A MICROBIOLOGICAL LABORATORY OF
CAPACITY 130 sq. m.

FIG 6 - SERVICE REQUIREMENTS FOR A MICROBIOLOGICAL


LABORATORY OF CAPACITY 130 sq. m.

FIG 7- LAYOUT OF EQUIPMENT IN A MICROBIOLOGICAL LABORATORY


OF CAPACITY 130 sq. m.

Additional Information
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General guidelines for a microbiological laboratory of optimal capacity

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Setting Up a Microbiology Lab


The first challenge that any budding microbiologist may face is that of assembling and
maintaining a useful lab. Early biologists made their names immortal just by tackling this
problem; the Petri Dish, for example, is named for its inventor, Julius Petri.
The key function of a microbiology lab is to provide a safe and efficient environment for the
culture, study, storage and disposal of micro-organisms. Addressing these requirements means
youve got yourself a lab.

Subsections:

Safety Some special safety considerations you mightnt already know!

Glassware Petri Dishes, Test Tubes, Flasks What to get and how to keep

General Equipment Sterilising, Incubating, Centrifuging and Observing

Special Equipment for DNA PCR Equipment, Electrophoresis

Chemicals, Buffers and Reagents Commonly desirable chemicals and their uses

Organic Essentials Lab strains/species, plasmids, essential enzymes

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Indie Biotech

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Setting Up a Microbiology Lab


The first challenge that any budding microbiologist may face is that of assembling and
maintaining a useful lab. Early biologists made their names immortal just by tackling this
problem; the Petri Dish, for example, is named for its inventor, Julius Petri.

The key function of a microbiology lab is to provide a safe and efficient environment for the
culture, study, storage and disposal of micro-organisms. Addressing these requirements means
youve got yourself a lab.
Subsections:

Safety Some special safety considerations you mightnt already know!

Glassware Petri Dishes, Test Tubes, Flasks What to get and how to keep

General Equipment Sterilising, Incubating, Centrifuging and Observing

Special Equipment for DNA PCR Equipment, Electrophoresis

Chemicals, Buffers and Reagents Commonly desirable chemicals and their uses

Organic Essentials Lab strains/species, plasmids, essential enzymes

Leave a Reply
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Comment

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Establishing the Diagnostic Medical


Microbiology De
Follow

by tumalapalli venkateswara rao , Professor at Travancore


Medical College, Kollam Kerala
on Jun 26, 2011
inShare

4,331 views

David K. Dansu 7 months ago

kabengo 8 months ago

Abdullah Ahmed at Sylhet MAG Osmani Medical College Hospital 1 year ago

Gehad Saad , Demonstrator at Medical Microbiology and Immunology 1 year


ago

Establishing the Diagnostic Medical Microbiology


De Presentation Transcript

ESTABLISHING DIAGNOSTIC MICROBIOLOGY LABORATORY Dr.T.V.Rao


MDDR.T.V.RAO MD 1

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 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 View slide

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 View slide

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.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.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.DR.T.V.RAO MD 8

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 andBiomedical Laboratories(BMBL) has
become thecode of practice forbiosafetythe disciplineaddressing the safehandling and
containmentof infectiousmicroorganisms andhazardous biologicalmaterials.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
humansDR.T.V.RAO MD 11

BIOSAFETY LEVEL 2 Biosafety level 2 (BSL- 2) is appropriate for handling moderaterisk agents that cause human disease of varying severity by ingestion or through
percutaneous or mucous membrane exposureDR.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.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) standardsDR.T.V.RAO
MD 14

OPTIMAL UTILIZATION OF THE AVAILABLE RESOURCESDR.T.V.RAO MD 15

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.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.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.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.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 .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.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.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.DR.T.V.RAO MD 24

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 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

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 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 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

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 reporting.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.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.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.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.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.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)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 CostDR.T.V.RAO MD 39

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

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

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

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

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.DR.T.V.RAO MD 44

SHORTEN TIME TO DIAGNOSIS Transportation of samples -distance, service, 24havailability 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

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

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 Developing World. Email doctortvrao@gmail.comDR.T.V.RAO
MD 49

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