Objectives. Preparing for Evolving Clinical Microbiology Rotations February 23, /12/2018

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1 Preparing for Evolving Clinical Microbiology Rotations February 23, 2018 Paula C. Mister, MS, MT, SM (ASCP)CM Educational Coordinator, Clinical Microbiology Johns Hopkins Hospital Objectives Develop an awareness of current and potential future technology used in medical microbiology laboratories Describe ways to prepare MLT and MLS students for clinical rotations in evolving microbiology labs Use creative ideas while working with clinical sites to plan student microbiology rotations for creating great learning experiences Share ideas, questions, and tips with the group! Traditional Microbiology Lab plates, tubes, biochemicals, microscopes Circa 1980 Do You Remember? A walk down Memory Lane with phenotypic, biochemical tests Welcome to 2018 Microbiology: Rise of the Machines do you recognize any of these instruments currently used in our laboratory? Copan WASP automated plater 1

2 LEFT: Bactec FX(BD) continuous blood culture monitoring system RIGHT: Phoenix (BD) antimicrobial susceptibility testing for bacteria and yeast MALDI TOF (mass spec ID) A card of up to 96 organisms is identified within 15 minutes Direct Detection of Organisms from Blood Verigene (Nanosphere) can identify some organisms directly from positive blood bottles within 4 hours by nucleic acid analysis (sequence, structure, expression), give limited genetic resistance information (ie, meca gene for MRSA), and be used for enteric pathogen and respiratory virus detection Not perfect; has trouble distinguishing genetically similar organisms (ie, S. pneumoniae and S.mitis group) PNA FISH technology Fluorescent in situ hybridization BD MAX, a real time PCR instrument, is used at JHH for enteric pathogens tests for Salmonella, Shigella, Camplylobacter, E coli 0157:H7 and other Shiga toxin organisms, Yersinia, Vibrio, Plesiomonas, C. diff, and 3 parasites: Giardia, Cryptosporidium and Entamoeba histolytica directly from a single stool specimen within a few hours NAAT (Nucleic Acid testing) for STIs: Gonorrhea, Chlamydia and Trichomonas: Turnaround time is 4 6 hours The Three Amigos 2

3 LEFT: Architect (Abbott): PCR HIV testing RIGHT: QIA Symphony: PCR Viral testing Rapid Detection of Resistance: meca in MRSA from a single colony Immunochromatogenic test detects PBP2a protein, which meca gene in MRSA produces, in 5 minutes directly from a colony on a culture plate Rapid Antigen tests (L) and Chromagars(R) used for screening And.Next Generation Sequencing (NGS) Next-generation sequencing refers to non-sanger-based highthroughput DNA sequencing technologies. Millions or billions of DNA strands can be sequenced in parallel, yielding substantially more throughput and minimizing the need for the fragmentcloning methods that are often used in Sanger sequencing of genomes. ( Here s the process: Acknowledgement to Heather Miller, MHS, M(ASCP) Sample Processing Library Prep Sequencing Bioinfomatics Nucleic Acid Extraction NGS: Why are we doing this? 50% of encephalitis cases do not have a known causative agent. Up to 70% of untreated meningitis is fatal, 20% of survivors have permanent sequelae Infections may be cause by virus, bacteria, fungi, or parasites Diagnosis is often both expensive and invasive; unbiased metagenomics can look for all pathogens with one test. 3

4 Rise of Technology in Microbiology Improves timeliness and accuracy of patient results Some labs have embraced Total Microbiology Automation Work up cultures on line, even from home in your pjs! Initial cost of instrumentation pays for itself: more sensitive in many cases (eg, Shigella and some parasite diagnosis has increased with BD Max PCR) faster diagnosis and targeted treatment shorter hospital stays less incidence of nosocomial infection reduction of patient suffering and (possibly) death What s Coming Next? On the Horizon: Advances in Antimicrobial Susceptibility Testing results available in a few hours for common pathogens Time elapsed microscopy: photography of bacterial colonies growing at incubation temperature for a period of time, with and without particular antibiotics added to the colonies Measurement of light scattered at a particular angle by a suspension of bacteria with and without antibiotic added, after incubation of minutes, can determine if an antibiotic is effectively inhibiting the growth of bacteria Measurement of microbial weight over time: miniscule differences in the weight of bacterial colonies over a prescribed length of time to determine if growth has continued or been inhibited by addition of antibiotic So does this mean TSI = RIP? Maybe. Maybe not entirely, just yet. Most current labs are a mix of the old and the new. (And we need back up methods if technology goes down) The Challenge: How do we get students ready for this paradigm shift? 4

5 Educator Responsibilities to Students Teach basic concepts of microbiology Teach basic manual skills needed in the laboratory Prepare students for the ASCP and other board exams Prepare students for employment in a professional laboratory environment AND KUDOS to the Educators: You Do a Great Job Johns Hopkins Hospital (Baltimore, MD) is currently the clinical affiliate for one MLT and 6 MLS programs, as well as a histotechnology program JHH Microbiology takes 3 4 MLT and MLS students/year on rotations The vast majority of rotating students say they are extremely or very well prepared for rotations in microbiology and ASCP exam Great quality and preparation of students on rotation we hire a lot of them! Prepare students for a meaningful, educational clinical laboratory experience (and future career) during rotations Basic Microbiology Concepts: What Are We Looking For in the Clinical Setting? Microbiology is more than bacteria: don t forget fungi, parasites, viruses I know, there s no time, and the ASCP exam is all about bacteria. Real life isn t: Students will see testing methods for other organisms Recognition/knowledge of: distinct, common organisms (classic Staph aureus, Proteus, Pseudomonas) typical microbiota vs potential pathogens expected by body site contamination and mixed cultures hemolysis patterns quick, presumptive tests for ID ( indole for E. coli, oxidase for Pseudomonas) Basic Microbiology Lab Skills What Are We Looking For in the Clinical Setting? Plate streaking for isolation PLEASE. Students are perpetually weak in this skill. Gram stain performance and interpretation also generally weak. Skills for molecular testing: pipetting, sterile technique, instrument operation, maintenance and troubleshooting. These will never go away. Knowledge of the importance of QC standards and performance Organizational, problem solving skills: follow a flow chart/procedure; accurately label plates and tubes, record results; make informed decisions, try to resolve discrepancies. Students need to show effort, not necessarily ability. Comments from Students: Addressing the Issues What could have better prepared you for your microbiology rotation? More background knowledge of parasitology, mycology and virology from multiple students, multiple programs before coming to the rotation Possible solution: One credit on line or self study course; with power points and required questions Does anyone do this already? How is it working out? Comments from Students: Addressing the Issues Exposure to, or knowledge of, newer technology It was a happy, awesome surprise to see cool new instruments and what they do, but would have been nice to have a heads up first Create brief presentation of current technology, with attached websites or videos showing principle and operation; if no class time, make it an assignment with required questions Karen Stephan (kstephan@ccbcmd.edu) of CCBC MLT program created a terrific introductory power point (now online and interactive!) on current technology in microbiology labs Educator, educate thyself: Visit clinical sites; check out the operation of new technology Film a virtual tour or arrange a field trip for students 5

6 Comments from Students: Addressing the Issues Better understanding of susceptibility patterns Very confusing at the bench; also had a couple of related questions on the ASCP exam Possible solution: integrate common susceptibility patterns during bacteriology lectures Ex. Discussion of ESBL, carbapenamase producing organisms during gram negative rods; common resistances in non fermenters; resistance genes in gram positives (ie, meca in S. aureus, van a and b in Enterococcus) Comments from Students: Addressing the Issues Molecular testing, methods and techniques Growing career path, great job prospects; need more exposure and promotion Some solutions: Practice and grade streaking, gram staining and reading, pipetting, sterile technique; if low on resources, ask local labs/hospitals to donate expired media and reagents Create basic power point demonstrating important molecular techniques and how they are currently used Ask clinical sites if a molecular tech could talk about the job, show demos or results of in house testing while students are on rotation (often not possible to provide hands on student experience) How many programs do this already? JHH Microbiology Lab 100+ employees, 20,000+ tests per month, 3 shifts JHH Microbiology Lab: Advantages for Rotators Expert faculty, knowledgeable techs; a dedicated educational coordinator Educational opportunities: rounds, lectures, luncheons always include students Diverse, international staff and patient population unusual, interesting organisms often encountered Both cutting edge technology and old methodologies available for many tests (ie, we have $$$$ ) Full service AFB, mycology, virology, molecular, bacteriology and susceptibility testing; some parasitology, epidemiological tests and sequencing; very few sendouts JHH Microbiology Lab: Disadvantages Large, sprawling, older facility in depressed, inner city neighborhood Heavy workload, busy lab, fast pace can be overwhelming and intimidating Generally friendly staff may be stressed Students need to remember that patient care comes first. Often many rotators in the lab at one time; less one on one attention (? advantage for students) Ideas for Structuring a Great Microbiology Rotation: What Works for Us 15 day maximum Microbiology rotation: no exceptions ***No specific number of clinical rotation days required, per Mark Spence, NAACLS staff program coordinator Student sees everything we have to offer: observe/participate at different bench each day, sometimes 2: student can return to a bench later if desired Student is with each teaching technologist for a half day prevent tech burnout Student attends all educational rounds and lectures; students are included in all staff activities: CE, volunteer and teaching opportunities, luncheons, Lab Week events Student performs student level practical and gram stain competency on last day 6

7 Sample Schedule Johns Hopkins Hospital MLS Microbiology rotation, days Monday Tuesday Wednesday Thursday Friday Structuring a Great Microbiology Rotation: What Works for Us Independent activities alternate with bench experience: 1 Arrive 9:00 am 2 Specimen processing 3 Mycology lab 4 Virology/ HIV lab 5 AFB Lab Orientation HIPAA Lab/hospital tours Lab safety Gram stain review Basic bacteriology review/sample unknowns area ID sample unknowns ID rounds Review blood parasites smears Plate rounds 1. short, multiple choice quizzes after most benches (prompts studying) most questions from ASCP review books; student should know answers from bench experience/ didactic lectures (example, next slide) 6 Wounds/body fluids/anaerobes 11 Start independent unknowns 7 Molecular Epidemiology 8 Respiratory and Cystic 9 Urine cultures 10 Blood cultures Lab Fibrosis cultures Plate rounds Fellow didactic session ID rounds Review respiratory cultures Review urine cultures if Phoenix/ MALDI TOF if desired desired (day 2) benches (Day 2) 12 Special micro (antibiotics) 13 Stools (BD Max) 14 GLC/sequencing 15 Complete unknowns and Lab Microbiology presentation and Plate rounds quizzes ID rounds lunch Review gram stains and CDs Lab practical Unknowns Unknowns Gram stain competency Unknowns Final evaluation 2. smear reviews (practice gram stain and blood parasite interpretation) 3. Student manual with flowcharts and culture guidelines; educational CDs, flashcards, review books available MYCOBACTERIOLOGY Which of the following acid fast organisms is a rapid grower? a. Mycobacterium tuberculosis b. Mycobacterium marinum c. Mycobacterium kansasii d. Mycobacterium fortuitum Which component is NOT used in the digestion/decontamination process for acid fast specimens? a. Hydrochloric acid b. Sodium hydroxide c. Trisodium phosphate d. N-acetyl-L-cysteine A stain used to detect Mycobacterium tuberculosis in sputum is a. Gram stain b. Loeffler s methylene blue c. spore stain d. Kinyoun stain The following mycobacteria require an isolation temperature of degrees C: a. Mycobacterium tuberculosis b. Mycobacterium avium- intracellulare (MAI) c. Mycobacterium marinum d. Mycobacterium xenopi 4. ID unknowns from 6 8 cultures by classic methods: Variety of organisms and body sites given; some mixed cultures Students work independently, or with a partner, for several half days; use flowcharts, traditional tests and written worksheets to document results Often a favorite part of the rotation: can be their own boss Helps evaluate basic skills (ie, streaking, gram staining), organizational and problem solving ability, time management, ability to work as a team with other students or physicians: simulates real life in a micro lab Reinforces knowledge for ASCP exam Not graded per se, but factors into final evaluation and potential as future employee. Example of independent unknown cultures (MLS) (5 days, mostly afternoons) 1 blood K. oxytoca 2 CSF yeast 3 urine E. cloacae, Enterococcus sp. 4 wound S. aureus, S. maltophilia, P. vulgaris 5 sputum S. pneumoniae, M. catarrhalis, strep group C 6 eye H. influenzae 7 stool Yersinia enterocolytica What Students Should Expect From ALL Clinical Sites Safe, professional environment: tour, introductions, safety info on day one Clear daily schedule (student manual is a bonus) provided on day one Mentor/designated technologist to check in with each day Quizzes, practicals, study materials to monitor progress and review material Practical, hands on, or observational bench work with knowledgeable technologists to see available testing on site as much as possible The problem of inconsistency: experiences/facilities vary from site to site (solution open ended objectives?) dedicated coordinator not always available to manage students 7

8 How You Can Help Clinical Preceptors Provide clear, concise, current, generic objectives and/or checklists. The student is responsible for monitoring these objectives, not lab staff. Competency based, psychomotor objectives: do not ask us to review theory with students, rotation is for practical experience Provide clear, concise, simple evaluations taking 5 minutes to complete no calculations should be required by the site. PLEASE. Rotations really should be pass or fail. If rating scale is used: recommend 3 basic levels does not meet, meets, exceeds no numeric value attached Provide independent study materials for students to occupy down time Some Final Thoughts on Rotations from JHH clinical preceptors Think of us as partners with you, the educators; we are working together to transition students to productive laboratory employees We provide a clinical experience not training for students Rotation sites volunteer to take students, receiving no compensation. Please be appreciative and flexible. Clarify professional expectations: students should be on time, engaged, respectful, prepared, and flexible with schedule changes. Patient care comes first and always. Thank You for Your Attention! Acknowledgments: Lorraine Blagg, Christine Hostetter, and Brittney Howard, fellow JHH Education Coordinators, for their additions and suggestions to this presentation Hopkins laboratory personnel photos taken by P. Mister, with permission Other images and cartoons obtained from Google 8