AUTOMATION IN

MICROBIOLOGY
(for blood cultures)

Dr.T.V.Rao MD
 Beginning of
Microbiology
 Almost exactly 300 years
ago Anton van
Leeuwenhoek
described the first
bacteria seen through the
microscope, thus
providing the technical
basis for studying the
morphology of micro-
organisms
 Knowledge explosion in
Microbiology

The explosion of knowledge in the
last century, pioneered by Pasteur,
Koch and many others immortalised
in modern generic and specific
names was dependent on
improvements in procedures for
isolating and identifying organisms
of importance in industry and
medicine.
 Rapid Methods are
Emerging

Rapid methods and automation is a
dynamic area in applied
microbiology dealing with the study
of improved methods in the
isolation, early detection,
characterization, and enumeration of
microorganisms and their products
in clinical, food, industrial, and
environmental samples.
 Changing perceptions,

Microbiology labs are beginning to
accept the shift toward automation
for reasons as numerous and varied
as microbiology itself.
Microbiologists and lab technicians
recognize that automated solutions
are not intended to replace cognitive
decision-making but rather, simply
replace tedious, repetitive steps.
Man has Evolved So also the
Microbes, so the need for
Automation
 Beginning of Automation
 The field started around mid-1960s and with
the development of a variety of miniaturized
microbiological techniques developed
 Streamlining workflow maintains consistency
but allows microbiologists to devote more time
to operations that require their unique skills
and experience
Hospital Acquired Infection a threat
to Medical Profession- needs faster
methods to Identify.
 Microbiology labs play a crucial role by
establishing a front line of defence against the
threat of Nosocomial infections. According to the
Centres for Disease Control and Prevention, in
American hospitals alone, HAIs account for an
estimated 1.7 million infections and 99,000
associated deaths annually. Of these infections,
32% are urinary-tract, 22% are surgical-site,
15% are pneumoniae, and 14% are bloodstream.
The Clinicians need Quicker
Results
 The shift from manual test
processing to automated
solutions can aid in
reducing HAIs by providing
health systems with
standard, consistent lab
processing that yields
quicker, more accurate
test results.
 Automation enters into
several areas in
Microbiology
 Rapid Methods and Automation in
Microbiology has developed into an
important sub-discipline of applied
microbiology in the past 15 years. The field
deals with improved methods in the isolation,
early detection, characterization, and
enumeration of microorganisms and their
products in clinical, food, industrial, and
environmental samples.
Automation reduces errors
and innovative
 Automated processes have gone well beyond
changing outdated procedures. They
minimise potentially dangerous practices,
lower turnaround time, reduce errors,
enhance quality control, improve specimen
handling and boost accuracy.
Moreover, technologists in automated labs
tend to embrace innovation more readily.
 Lesser Manpower More
volume of work

Because automation largely circumvents
repetitive manual processing, lab
technicians find it easier to focus on
complex tasks that require their specific
skills.
It is therefore remarkable that, despite
shortages of skilled personnel and
increases in the volume of work, it has
taken years for automation to become
acceptable to microbiologists.
 Desired Objectives in
Automation
 Reexamination of laboratory functional steps
– Phlebotomy
– Sample labeling
– Transportation
– Pre-, peri-, and post-analytical processing
 Laboratory automation for improved efficiency and
error reduction
 Create an informatics continuum
– Process Control vs. LIS function
– Auto-verified and auto-interpreted data
 Predictive genomics and the passive home
monitoring paradigm
 Adding Value to Lab Tests Through
Automation
 Lab Test
– Faster TOT
– Accuracy, Precision,
Safety
 Add information
value
– Auto validation
– Trending Lab Test
 Effecting change Auto validation
using lab results Trending
– Lifestyle changes Life Style Adjustments
– Selection of
therapeutics Appropriate Therapeutics
 Every Body is a Learner to New
Technologies, Enthusiasm
Makes Difference
Blood culturing most
important and live
saving Investigation
Needs optimal Methods for
Diagnosis of Blood Borne
Pathogens
 Why Blood Culture
 Physician can find source of
infection
 Physician
can initiate life-saving
support measures
 Physician can start targeted
antibiotic therapy
 What is a Blood Culture?

 A blood culture is a
laboratory test in which
blood is injected into
bottles with culture
media to determine
whether
microorganisms have
invaded the patient’s
bloodstream.
 Need for Blood Culture?
No microbiological test is more essential to the
clinician than the blood culture. The finding of
pathogenic microorganisms in a patient’s
bloodstream is of great importance in terms of
diagnosis, prognosis, and therapy.”

- L. Barth Reller, Clin. Infect. Diseases, 1996

 Proof in Blood borne
Infection
A clinically suspected infection is ultimately
confirmed by isolation or detection of the
infectious agent. Subsequent identification of the
microorganism and antibiotic susceptibility tests
further guide effective antimicrobial therapy.
Bloodstream infection is the most severe form of
infection and is frequently life-threatening, and
blood culture to detect circulating
microorganisms has been the diagnostic
standard.
Blood culture is a Important a
Diagnostic tool in Infectious
diseases
 Bloodculture is a microbiological
culture of blood. It is employed to
detect infections that are spreading
through the bloodstream
(such as bacteraemia, septicaemia
amongst others). This is possible
because the bloodstream is usually
a sterile environment.
 What are We doing Now is
not optimal – Needs Rapid
Methods
 Most microbiological culture procedures
Most microbiological culture procedures
require the use of solid media, like blood agar
and MacConkey agar plates that need to be
visually monitored by trained personnel at
intervals of 24 hours. These conventional
cultures using normal media take at least a
minimum of 72 hours to isolate the pathogen
and carry out susceptibility test to know the
efficacy of antibiotics on simple aerobic
bacteria
 Optimal Methods of Blood
Collection makes difference
 The physicians consent with filled in request with details
for culturing the Blood
 Gloves will be worn in accordance with standard
precautions..
 Appropriate verification of the patient's identity, by
means of an armband or area specific procedure, will
occur before the specimen collection.
 Cultures should be drawn before administration of
antibiotics, if possible.
 If at all possible, blood cultures should not be drawn
from lines, but should be drawn only via venepuncture
PHLEBOTOMY TRAINING
PROGRAMS
WHO?

WHAT?

WHERE?
 NEW CATEGORY OF
LAB PERSONNEL Phlebotomist

Defined as a person who collects blood for clinical laboratory test or examination
purposes
 Principles for Collection

 Gloves will be worn in accordance with standard

precautions.
 •A physician’s order must be obtained for specimen
collection.
 •Appropriate verification of the patient's identity, by
means of an armband or area specific procedure, will
occur before the specimen collection.
 •Cultures should be drawn before administration of
antibiotics, if possible.
 •If at all possible, blood cultures should note drawn
from lines, but should be drawn viavenipuncture.
 Materials
 Chlorhexidine swabs (1-2 packages)
 Alcohol swabs
 Blood culture bottles (2 bottles per set)
 2 syringes (adult: 20 cc, paediatric: 5 cc)
 2 needles (adult: 22 gauge or preferably larger butterfly
or standard needle; pediatric: 25 or 23 gauge butterfly
or standard needle)
 Gloves (sterile &nonsterile)
 Tourniquet
 Sterile gauze pad
 Adhesive strip or tape
 Self-sticking patient labels
 Plastic zip lock specimen bags
Steps 1 – 3, Check, Explain,
Wash

 1.Identify the patient by

checking the arm band or
area-specific procedure.
 2.Explain the procedure to
the patient.
 3.Wash hands with soap and
water with friction for 15
seconds or use alcohol
based hand rub
Step 4 –Prep Cap

 Prep the rubber

cap of the blood
culture bottles with
an alcohol pad in a
circular motion.
Allow the alcohol to
dry.
 Step 5 -Prep the Puncture
Site
 Prep the puncture site with Chlorhexidine:
– •Using aseptic technique, remove the applicator
from its package.
– •Holding the applicator downward, gently squeeze
the wings to release the solution.
– •Scrub with a back & forth motion using friction
for 30 seconds on dry skin or 2 minutes on wet
skin.
 •Do not wipe the site after cleansing the skin
with Chlorhexidine.
 Step 6 -Gloves

 Apply gloves:
 If palpation of site prior
 to puncture is
 anticipated, wear sterile
 gloves.
 If palpation of site prior
to puncture is not
anticipated, wear
nonsterile gloves.
 Step 8 -Mix

 Gently rotate the

bottles to mix the
blood & the broth
(do not shake
vigorously).
 Step 9 and 10 (Label)

 Place the patient label on each bottle &

label each culture bottle with the site of
specimen collection. When applying
patient identification labels, do not cover
the bar code label on the blood culture
bottles. Attach the laboratory requisition.
 Send the blood cultures to the Clinical
Microbiology receiving area as soon as
possible.
 Step 11
 11.Document the following in the medical
record Date & time specimen obtained
 –Site of specimen collection
 If 2 sets of blood cultures have been ordered,
obtain the second set in the same manner as
the first, making a new venepuncture at a
different site
 Techniques of Paediatric
Collections

Tourniquet Application
 Need to maximize chances of successful
collection
 Remember that the vein is still developing
and might need to rely on firm tightness
 Ideally, tourniquet should not be kept on
for more than one minute
 If possible, apply heat
 If using a hand, consider a bucket of warm
water
 Techniques of Paediatric
Collections

Insertion Principles
 Cantilevering of elbow
 The option factor:
-Choose your options of direction before insertion
-Minimize the odds of unnecessary “digging”
 Avoid plunging the needle right up to the hilt
 Often, a drawback does the trick
 If vacutainer is slowing down, replace with a
syringe
 Self
Protection
A few ways to make sure
your role in the collection
process is carried out with
efficiency, orderliness and
safety
 The Contaminated Blood
Culture

 If the skin is not adequately cleansed before

drawing blood for culture, bacteria on the
skin will be injected into the bottle,
producing a false positive blood culture.
 It is sometimes difficult for the physician to
determine whether the bacteria growing in
the blood culture is a real pathogen causing
bloodstream infection or whether bacteria
on the skin have contaminated the culture.
This can lead to excess use of antibiotics
and prolongation of hospital stay.
 Sample Labeling
Efficiencies
 Bar coding at the
point-of-phlebotomy B-D id
 2D vs. 1D bar codes
– Reduce the number
of computer
interfaces
– Self directing
specimens
 Technological Improvements for
All Steps in the Diagnostic
Process
Just in Time Supplies
Automated Process Control
EMR
Phlebotomy
Trays Instruments
Reporting Designed for
Automation
Storage
RFID

2D-Codes
Recording
Analysis
Biorepository
Transportation
Pre-analytical
Mobile Robot Analytical and
Automation
Accessioning
 What is a Blood Culture?

 A blood culture is a
laboratory test in which
blood is injected into
bottles with culture
media to determine
whether
microorganisms have
invaded the patient’s
bloodstream.
Blood & Body Fluid Cultures

Blood cultured by the BacT/Alert 3D leads to early
detection of pathogens (>89 per cent within 24
hours and 97 per cent within 48 hours) especially
in cases of septicaemia, enteric fevers, bacterial
endocarditis and other pyrexias of bacterial origin.

Activated charcoal neutralises antimicrobials and
toxins enhancing early recovery of pathogens.
Positives are detected faster than Bactec even at
low concentrations in blood and body fluids like
CSF, CT guided aspirates etc.

Delayed transport does not compromise results.

The instrument is capable of recovering
significantly more organisms that resin.
 BacT/AlerT 3D culture
system
 BacT/AlerT 3D culture system. This is
the first automated non-radiometric
and non-invasive culture system that
continuously monitors system for
culture of bacteria (both aerobic and
anaerobic), fungi and mycobacteria.
All these bacteria can be cultured
using different media as prescribed..
Principles in BacT/AlerT 3D
culture system
 Thisis a closed system and works on
the colorimetric principle of detection
of CO2 produced by the organisms.
The CO2 causes a lowering of the pH
of the medium, which in turn
produces a colour change in a sensor
attached to the CO2-sensitive base of
each bottle.
 You are guided by
Computerized Systems
 Theinstrument reacts before this
colour change is apparent by means
of an audible or visible alert flagged
by the computer. The bottles are
constantly agitated and are read at
10-minute intervals. The readings are
transmitted to a computer compiler,
which computes results. This
bioMérieux BacT/ALERT® 3D
 The bioMérieux BacT/ALERT® 3D
provides an optimal environment for
the recovery of a wide range of
pathological organisms, including
bacteria, yeasts and mycobacteria;
utilizing proprietary plastic culture
bottles ensuring added safety to the
user.
Principles of functioning of BacT
alert Monitors
 Microorganisms multiply in
the media, generating CO2.
As CO2 increases, the
sensor in the bottle turns a
lighter colour.
 Measuring reflected light,
the BacT/ALERT 3D monitors
and detects color changes in
the sensor.
 Algorithms analyze the data to
determine positivity, and the
laboratory is notified immediately
with visual and audible alarms.
Automation becomes more
complex
Automation becomes need of the
Hour
 Full
microbiology laboratory automation
needs have never been so apparent, with
financial constraints and increasing testing
volumes at the same time that labour is
becoming both harder to find and more
expensive. Implementation of full
microbiology lab automation is one solution,
as fewer technologists are required to
process automated tests..
 Automation improves
quality of services

Overall, laboratories
transitioning from
conventional to
automated processes
find that technologists
and microbiologists are
more open to
innovation and
improved quality.
 Industry flourishes too..

An entire industry of
microbial diagnostic kits
flourished to the present
day. Next in the 70s the
development was in
immunological test kits
and instruments to
monitor the presence of
food borne pathogens and
biomass and to predict
microbial growth
automatically.
 Advantages of
automation

Automated solutions have recently
emerged in the marketplace that address
key areas of the microbiology lab.
Automating these processes-simple,
standard, or complex-can revolutionize
the microbiology lab with more efficient,
standardized practices that will improve
quality, safety, and cost-efficiency.
 Automation increases efficacy
and eliminates individual
variations
 Forexample, automating small, yet vitally
important tasks, can make a huge impact
on the efficiency and accuracy of
laboratories. Lab technicians streak an
estimated ??? agar plates a day, a process
that is laborious, tedious, and inconsistent.
Each lab technician has his own streaking
technique
 Automation is
Advantageous
 Include the elimination of subjective
variability,
 Savings in media and reagents, and
the earlier production of useful
information in many instances, all of
winch can make a substantial
contribution to productivity and the
control of runaway cost escalation.
 Automation combined with
Laboratory Information
management
 The combined use of laboratory
automation and laboratory
information management
software (LIMS) has been shown
to increase productivity, reduce
human error and improve
tracking and traceability in a
microbiology lab
 Workflow Management

Automation Information

Data

DATA
 Accessioning PROCESS MANAGEMENT
 Specimen tracking  Sample quality
 Data logging and reporting assessment
 Optimal routing and
 Quality control
documentation scheduling
 Intelligent reporting
 Bar coding, robotics and
computers
 Bar coding, robotics and computers that replace
manual transcription significantly reduce data
loss and errors. Automation also makes it less
likely that plate information and patient
identification will be duplicated or transposed.
Three trends will drive laboratory automation’s
future: smaller, more-flexible analysers and
automation based on next-generation
technology, including micro fluidics, easy-to-use,
powerful software for centralised lab
management, and internet-based real-time
service for better up-time.
 Bar coding replacing the
Manual reading – Reduces
errors
The key to this real-time automation was
real time barcode labelling of all sample
carriers (such as bags, tubes, dishes,
bottles) provided by Kiestra's Barcode
system. This was used in conjunction
with Auto scribe's Matrix LIMS. Real time
barcode reading is known to reduce
transcription error rates to only 1 in 36
trillion characters - compared to 1 in 300
characters with manual reading.
 Kiestra's BarcodA

Kiestra's BarcodA
automatically
places an optical
barcode on all
tubes, bottles and
petri-dishes that
contains important
information such
as composition,
sell-by date etc.
Bar-coding helps in tracing
the errors
 The barcode makes
every sample carrier
unique and recorded
meaning full
traceability for the
laboratory. Samples
are also provided
with a barcode
which is generated
by Matrix LIMS.
Quality replacing Quantitity
 Quality issues are becoming increasingly
important in diagnostic laboratories. The fact
of quality is no longer sufficient and we must
now develop mechanisms to assure
consumers, the public and, most importantly,
ourselves of the continuing quality of our
service. Moving towards a quality-assured
system is not easy, requiring a meticulous
attention to detail in all areas of a
laboratory's working and organization.
 Automation gained the
Universal acceptance
A further plus for lab automation is
that it promotes consistency and
quality. Without automation, lab
tasks that are necessarily repetitive
can lead to inconsistent or
inappropriate ways of work and, from
there, to improper treatment, longer
patient stays, medication errors and
unwanted drug side-effects.
Created by Dr.T.V.Rao
MD for “e” learning
Programme
Email
doctortvrao@gmail.com