Automation in microbiology


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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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  • The learning objectives for this presentation include a reexamination of the functional steps that are required to provide a laboratory result to a physician. These steps include phlebotomy sample labeling, transportation, centrifugation, pre-analytical processing. We will look at laboratory automation as a means to improve efficiency and error reduction not only throughout the pre-analytical and analytical steps in the diagnostic process, but in the post analytical area as well. What I hope to convey is that there is an opportunity to create an informatics continuum by monitoring and directing all steps in the process, the need to evaluate the current capabilities of your laboratory information system (LIS) and to learn how medical decision making can be enhanced by the use of an informatics continuum. In the future, diagnostic data will be gathered on a continuous basis: - Ubiquitously in the home to establish wellness routines and to forecast the onset of disease. - Following the appearance of chronic and acute conditions, then point of care systems will be used to enhance the diagnostic process. Once professional medical intervention is necessary, then esoteric testing will be performed in the Core Laboratory. - The data continuum will be autoverified and interpreted automatically, where possible, and then only the more difficult cases will be sent to medical professionals. The electronic medical record is the gathering point for all the medical information. Not only is the electronic medical record a storage location (much like a patient chart), but it is also a point where data interpretation can be enhanced by the juxtaposition of so many diagnostic measures. It is essential that the laboratory embraces the notion that it can play a major role in creating and maintaining the diagnostic knowledge engine that drives much of the electronic medical record. Thus the laboratory will become an essential partner in clinical care.
  • Automation can add value to what we currently think of as our end product, a lab test result. Automation can provide faster turnaround time, improved accuracy, precision and safety. Information value can be enhanced by auto-validation of the results and also by providing the physician with trending information. If properly reported in context with the patients current health condition, lab results can encourage healthy lifestyle changes and ultimately the selection of appropriate therapeutics.
  • However, significant gains can be made in terms of sample processing simply by adopting new labeling methods. Bar coding at the point of phlebotomy is still only practiced by less than 50% of hospitals. Becton Dickenson has had their bar coding system on the market for many years that allows bedside bar code scanning and printing, and assures proper label placement. In the future we will use 2D bar codes which will be easier to read, and allow greater data densities than one dimensional codes. Ultimately, the radio frequency ID chip will be attached to every tube once the price drops to less than 5 cents a label.
  • Of the 166 separate steps associated with getting a specimen into the laboratory, there is a technology that can improve the process. Automation can provide just in time supplies to the phlebotomy process, improved labeling of the specimen to assure rapid transportation to the appropriate analytical system using mobile robots or automated pneumatic tube systems. Pre-analytical processors can automatically complete most of the accessioning and pre-analytical processing steps. Instruments designed to operate with automation systems can rapidly sample the specimen and release it for further processing. Intelligent test reporting can be implemented at the end of an efficient workflow process using autoverification, and automated test expansion (for example, repeat, reflex, and add-on testing). Finally, process control software systems can monitor and optimize every step in the process to make sure the result is accurate, timely, and is posted securely to the electronic medical record.
  • Process control allows more sophisticated management of the laboratory process. Automation is responsible for: Sample quality assessment at the beginning of the process Optimized specimen routing and scheduling Intelligent reporting Information management includes the: Accessioning process Specimen tracking Data logging and reporting Quality control documentation
  • Automation in microbiology

    1. 1. AUTOMATION IN MICROBIOLOGY ( for blood cultures ) Dr.T.V.Rao MD
    2. 2. Beginning of Microbiology <ul><li>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 </li></ul>
    3. 3. Knowledge explosion in Microbiology <ul><li>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. </li></ul>
    4. 4. Rapid Methods are Emerging <ul><li>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. </li></ul>
    5. 5. Changing perceptions , <ul><li>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. </li></ul>
    6. 6. Man has Evolved So also the Microbes, so the need for Automation
    7. 7. Beginning of Automation <ul><li>The field started around mid-1960s and with the development of a variety of miniaturized microbiological techniques developed </li></ul><ul><li>Streamlining workflow maintains consistency but allows microbiologists to devote more time to operations that require their unique skills and experience </li></ul>
    8. 8. Hospital Acquired Infection a threat to Medical Profession- needs faster methods to Identify. <ul><li>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. </li></ul>
    9. 9. The Clinicians need Quicker Results <ul><li>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. </li></ul>
    10. 10. Automation enters into several areas in Microbiology <ul><li>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. </li></ul>
    11. 11. Automation reduces errors and innovative <ul><li>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. </li></ul>
    12. 12. Lesser Manpower More volume of work <ul><li>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. </li></ul>
    13. 13. Desired Objectives in Automation <ul><li>Reexamination of laboratory functional steps </li></ul><ul><ul><li>Phlebotomy </li></ul></ul><ul><ul><li>Sample labeling </li></ul></ul><ul><ul><li>Transportation </li></ul></ul><ul><ul><li>Pre-, peri-, and post-analytical processing </li></ul></ul><ul><li>Laboratory automation for improved efficiency and error reduction </li></ul><ul><li>Create an informatics continuum </li></ul><ul><ul><li>Process Control vs. LIS function </li></ul></ul><ul><ul><li>Auto-verified and auto-interpreted data </li></ul></ul><ul><li>Predictive genomics and the passive home monitoring paradigm </li></ul>
    14. 14. Adding Value to Lab Tests Through Automation <ul><li>Lab Test </li></ul><ul><ul><li>Faster TOT </li></ul></ul><ul><ul><li>Accuracy, Precision, Safety </li></ul></ul><ul><li>Add information value </li></ul><ul><ul><li>Auto validation </li></ul></ul><ul><ul><li>Trending </li></ul></ul><ul><li>Effecting change using lab results </li></ul><ul><ul><li>Lifestyle changes </li></ul></ul><ul><ul><li>Selection of therapeutics </li></ul></ul>Lab Test Auto validation Trending Life Style Adjustments Appropriate Therapeutics
    15. 15. Every Body is a Learner to New Technologies, Enthusiasm Makes Difference
    16. 16. Blood culturing most important and live saving Investigation Needs optimal Methods for Diagnosis of Blood Borne Pathogens
    17. 17. Why Blood Culture <ul><li>Physician can find source of infection </li></ul><ul><li>Physician can initiate life-saving support measures </li></ul><ul><li>Physician can start targeted antibiotic therapy </li></ul>
    18. 18. What is a Blood Culture? <ul><li>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. </li></ul>
    19. 19. Need for Blood Culture? <ul><li>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.” </li></ul><ul><li>- L. Barth Reller, Clin. Infect. Diseases, 1996 </li></ul>
    20. 20. Proof in Blood borne Infection <ul><li>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. </li></ul>
    21. 21. Blood culture is a Important a Diagnostic tool in Infectious diseases <ul><li>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. </li></ul>
    22. 22. What are We doing Now is not optimal – Needs Rapid Methods <ul><li>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 </li></ul>
    23. 23. Optimal Methods of Blood Collection makes difference <ul><li>The physicians consent with filled in request with details for culturing the Blood </li></ul><ul><li>Gloves will be worn in accordance with standard precautions.. </li></ul><ul><li>Appropriate verification of the patient's identity, by means of an armband or area specific procedure, will occur before the specimen collection. </li></ul><ul><li>Cultures should be drawn before administration of antibiotics, if possible. </li></ul><ul><li>If at all possible, blood cultures should not be drawn from lines, but should be drawn only via venepuncture </li></ul>
    24. 24. PHLEBOTOMY TRAINING PROGRAMS <ul><li>WHO? </li></ul><ul><li>WHAT? </li></ul><ul><li>WHERE? </li></ul>
    25. 25. NEW CATEGORY OF LAB PERSONNEL <ul><li>Phlebotomist </li></ul><ul><li>Defined as a person who collects blood for clinical laboratory test or examination purposes </li></ul>
    26. 26. Principles for Collection <ul><li>Gloves will be worn in accordance with standard precautions. </li></ul><ul><li>• A physician’s order must be obtained for specimen collection. </li></ul><ul><li>• Appropriate verification of the patient's identity, by means of an armband or area specific procedure, will occur before the specimen collection. </li></ul><ul><li>• Cultures should be drawn before administration of antibiotics, if possible. </li></ul><ul><li>• If at all possible, blood cultures should note drawn from lines, but should be drawn viavenipuncture. </li></ul>
    27. 27. Materials <ul><li>Chlorhexidine swabs (1-2 packages) </li></ul><ul><li>Alcohol swabs </li></ul><ul><li>Blood culture bottles (2 bottles per set) </li></ul><ul><li>2 syringes (adult: 20 cc, paediatric: 5 cc) </li></ul><ul><li>2 needles (adult: 22 gauge or preferably larger butterfly or standard needle; pediatric: 25 or 23 gauge butterfly or standard needle) </li></ul><ul><li>Gloves (sterile &nonsterile) </li></ul><ul><li>Tourniquet </li></ul><ul><li>Sterile gauze pad </li></ul><ul><li>Adhesive strip or tape </li></ul><ul><li>Self-sticking patient labels </li></ul><ul><li>Plastic zip lock specimen bags </li></ul>
    28. 28. Steps 1 – 3, Check, Explain, Wash <ul><li>1.Identify the patient by checking the arm band or area-specific procedure. </li></ul><ul><li>2.Explain the procedure to the patient. </li></ul><ul><li>3.Wash hands with soap and water with friction for 15 seconds or use alcohol based hand rub </li></ul>
    29. 29. Step 4 –Prep Cap <ul><li>Prep the rubber cap of the blood culture bottles with an alcohol pad in a circular motion. Allow the alcohol to dry. </li></ul>
    30. 30. Step 5 -Prep the Puncture Site <ul><li>Prep the puncture site with Chlorhexidine: </li></ul><ul><ul><li>• Using aseptic technique, remove the applicator from its package. </li></ul></ul><ul><ul><li>• Holding the applicator downward, gently squeeze the wings to release the solution. </li></ul></ul><ul><ul><li>• Scrub with a back & forth motion using friction for 30 seconds on dry skin or 2 minutes on wet skin. </li></ul></ul><ul><li>• Do not wipe the site after cleansing the skin with Chlorhexidine. </li></ul>
    31. 31. Step 6 -Gloves <ul><li>Apply gloves: </li></ul><ul><li>If palpation of site prior </li></ul><ul><li>to puncture is </li></ul><ul><li>anticipated, wear sterile </li></ul><ul><li>gloves. </li></ul><ul><li>If palpation of site prior to puncture is not anticipated, wear nonsterile gloves. </li></ul>
    32. 32. Step 8 -Mix <ul><li>Gently rotate the bottles to mix the blood & the broth (do not shake vigorously). </li></ul>
    33. 33. Step 9 and 10 (Label) <ul><li>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. </li></ul><ul><li>Send the blood cultures to the Clinical Microbiology receiving area as soon as possible. </li></ul>
    34. 34. Step 11 <ul><li>11.Document the following in the medical record Date & time specimen obtained </li></ul><ul><li>– Site of specimen collection </li></ul><ul><li>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 </li></ul>
    35. 35. Techniques of Paediatric Collections Tourniquet Application <ul><li>Need to maximize chances of successful collection </li></ul><ul><li>Remember that the vein is still developing and might need to rely on firm tightness </li></ul><ul><li>Ideally, tourniquet should not be kept on for more than one minute </li></ul><ul><li>If possible, apply heat </li></ul><ul><li>If using a hand, consider a bucket of warm water </li></ul>
    36. 36. Techniques of Paediatric Collections Insertion Principles <ul><li>Cantilevering of elbow </li></ul><ul><li>The option factor: </li></ul><ul><li>-Choose your options of direction before insertion </li></ul><ul><li>-Minimize the odds of unnecessary “digging” </li></ul><ul><li>Avoid plunging the needle right up to the hilt </li></ul><ul><li>Often, a drawback does the trick </li></ul><ul><li>If vacutainer is slowing down, replace with a syringe </li></ul>
    37. 37. Self Protection A few ways to make sure your role in the collection process is carried out with efficiency, orderliness and safety
    38. 38. The Contaminated Blood Culture <ul><li>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. </li></ul><ul><li>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. </li></ul>
    39. 39. Sample Labeling Efficiencies <ul><li>Bar coding at the point-of-phlebotomy </li></ul><ul><li>2D vs. 1D bar codes </li></ul><ul><ul><li>Reduce the number of computer interfaces </li></ul></ul><ul><ul><li>Self directing specimens </li></ul></ul>B-D id
    40. 40. Technological Improvements for All Steps in the Diagnostic Process Just in Time Supplies Reporting Analysis Transportation Accessioning Biorepository Recording Process Control Pre-analytical Analytical and Automation Automated Phlebotomy Trays RFID Mobile Robot Storage 2D-Codes Instruments Designed for Automation EMR
    41. 41. What is a Blood Culture? <ul><li>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. </li></ul>
    42. 42. Blood & Body Fluid Cultures <ul><li>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. </li></ul><ul><li>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. </li></ul><ul><li>Delayed transport does not compromise results. </li></ul><ul><li>The instrument is capable of recovering significantly more organisms that resin. </li></ul>
    43. 43. BacT/AlerT 3D culture system <ul><li>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.. </li></ul>
    44. 44. Principles in BacT/AlerT 3D culture system <ul><li>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. </li></ul>
    45. 45. You are guided by Computerized Systems <ul><li>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 </li></ul>
    46. 46. bioMérieux BacT/ALERT® 3D <ul><li>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. </li></ul>
    47. 47. Principles of functioning of BacT alert Monitors <ul><li>Microorganisms multiply in the media, generating CO2. As CO2 increases, the sensor in the bottle turns a lighter colour. </li></ul><ul><li>Measuring reflected light, the BacT/ALERT 3D monitors and detects color changes in the sensor. </li></ul><ul><li>Algorithms analyze the data to determine positivity, and the laboratory is notified immediately with visual and audible alarms . </li></ul>
    48. 48. Automation becomes more complex
    49. 49. Automation becomes need of the Hour <ul><li>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.. </li></ul>
    50. 50. Automation improves quality of services <ul><li>Overall, laboratories transitioning from conventional to automated processes find that technologists and microbiologists are more open to innovation and improved quality. </li></ul>
    51. 51. Industry flourishes too.. <ul><li>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. </li></ul>
    52. 52. Advantages of automation <ul><li>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. </li></ul>
    53. 53. Automation increases efficacy and eliminates individual variations <ul><li>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 </li></ul>
    54. 54. Automation is Advantageous <ul><li>Include the elimination of subjective variability, </li></ul><ul><li>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. </li></ul>
    55. 55. Automation combined with Laboratory Information management <ul><li>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 </li></ul>
    56. 56. Workflow Management <ul><li>DATA </li></ul><ul><li>Accessioning </li></ul><ul><li>Specimen tracking </li></ul><ul><li>Data logging and reporting </li></ul><ul><li>Quality control documentation </li></ul><ul><li>PROCESS MANAGEMENT </li></ul><ul><li>Sample quality assessment </li></ul><ul><li>Optimal routing and scheduling </li></ul><ul><li>Intelligent reporting </li></ul>Automation Data Process Control Information
    57. 57. Bar coding, robotics and computers <ul><li>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. </li></ul>
    58. 58. Bar coding replacing the Manual reading – Reduces errors <ul><li>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. </li></ul>
    59. 59. Kiestra's BarcodA <ul><li>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. </li></ul>
    60. 60. Bar-coding helps in tracing the errors <ul><li>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. </li></ul>
    61. 61. Quality replacing Quantitity <ul><li>Quality issues are becom in g in creas in gly 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 cont in u in g quality of our service. Mov in g towards a quality -assured system is not easy, requir in g a meticulous attention to detail in all areas of a laboratory's work in g and organization. </li></ul>
    62. 62. Automation gained the Universal acceptance <ul><li>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. </li></ul>
    63. 63. Created by Dr.T.V.Rao MD for “e” learning Programme Email [email_address]