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

Effecting change using lab results– Lifestyle

changes– Selection of

therapeutics

Lab TestAuto validation

TrendingLife Style Adjustments

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 CulturePhysician 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 Blood culture 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 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

PhlebotomistDefined 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

2D vs. 1D bar codes–Reduce the

number of computer interfaces

–Self directing specimens

B-D id

Technological Improvements for All Steps in the Diagnostic

ProcessJust in Time Supplies

Reporting

Analysis

Transportation

Accessioning

BiorepositoryRecording

Process Control

Pre-analyticalAnalytical and Automation

AutomatedPhlebotomyTrays

RFID

Mobile Robot

Storage

2D-Codes

Instruments Designed for Automation

EMR

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

This is 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

The instrument 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 For example, 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

DATA Accessioning Specimen tracking Data logging and reporting Quality control

documentation

PROCESS MANAGEMENT Sample quality

assessment Optimal routing and

scheduling Intelligent reporting

Automation

Data

Information

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

Emaildoctortvrao@gmail.com