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Automation in Microbiology

Blood culturing and identifying the causative agent is a top priority in optimal treatment of several patients with severe bacterial infections

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Automation in Microbiology

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  1. AUTOMATION IN MICROBIOLOGY(for blood cultures) Dr.T.V.Rao MD

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. Man has Evolved So also the Microbes, so the need for Automation

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. Lab Test Faster TOT Accuracy, Precision, Safety Add information value Auto validation Trending Effecting change using lab results Lifestyle changes Selection of therapeutics Adding Value to Lab Tests Through Automation Appropriate Therapeutics Life Style Adjustments Trending Auto validation Lab Test

  15. Every Body is a Learner to New Technologies, EnthusiasmMakes Difference

  16. Blood culturing most important and live saving Investigation Needs optimal Methods for Diagnosis of Blood Borne Pathogens

  17. Why Blood Culture • Physician can find source of infection • Physician can initiate life-saving support measures • Physician can start targeted antibiotic therapy

  18. 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.

  19. 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

  20. 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.

  21. 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.

  22. 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

  23. 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


  25. NEW CATEGORY OF LAB PERSONNEL • Phlebotomist Defined as a person who collects blood for clinical laboratory test or examination purposes

  26. 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.

  27. 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

  28. 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 withfriction for 15 seconds or use alcohol based hand rub

  29. 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.

  30. 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.

  31. 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.

  32. Step 8 -Mix • Gently rotate the bottles to mix the blood & the broth (do not shake vigorously).

  33. 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.

  34. 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

  35. Techniques of Paediatric CollectionsTourniquet 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

  36. Techniques of Paediatric CollectionsInsertion 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

  37. Self Protection A few ways to make sure your role in the collection process is carried out with efficiency, orderliness and safety

  38. 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.

  39. 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

  40. Technological Improvements for All Steps in the Diagnostic Process Just in Time Supplies Process Control Automated Phlebotomy Trays EMR Instruments Designed for Automation Reporting Storage RFID 2D-Codes Recording Analysis Biorepository Transportation Pre-analytical Analytical and Automation Mobile Robot Accessioning

  41. 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.

  42. 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.

  43. 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..

  44. Principles in BacT/AlerT 3D culturesystem • 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.

  45. 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

  46. 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.

  47. 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.

  48. Automation becomes more complex

  49. 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..

  50. 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.

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