Preparing for Evolving Clinical Objectives Microbiology...
Transcript of Preparing for Evolving Clinical Objectives Microbiology...
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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 Labplates, tubes, biochemicals, microscopes
Circa 1980
Do You Remember? A walk down Memory Lane with phenotypic, biochemical tests
Welcome to 2018 Microbiology: Rise of the Machinesdo you recognize any of these instruments currently used in our laboratory?
Copan WASP automated plater
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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 detectionNot perfect; has trouble distinguishing genetically similar organisms (ie, S. pneumoniae and
S.mitis group)
PNA FISH technologyFluorescent 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: “The Three Amigos”Turnaround time is 4‐ 6 hours
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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 high-throughput DNA sequencing technologies. Millions or billions of DNA strands can be sequenced in parallel, yielding substantially more throughput and minimizing the need for the fragment-cloning methods that are often used in Sanger sequencing of genomes.”
• (https://www.nature.com/subjects/next-generation-sequencing)
Here’s the process:Acknowledgement to Heather Miller, MHS, M(ASCP)
Library Prep
Sequencing
Bioinfomatics
Sample Processing
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.
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Rise of Technology in Microbiology
• Improves timeliness and accuracy of patient results
• 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
Some labs have embraced Total Microbiology Automation
Work up cultures on line, even from home in your pjs!
What’s Coming Next?On the Horizon:
Advances in Antimicrobial Susceptibility Testingresults 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 60‐90 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?
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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
• Prepare students for a meaningful, educational clinical laboratory experience (and future career) during rotations
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 10‐12 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!
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 SkillsWhat 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 IssuesWhat 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 ([email protected]) 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
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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 Lab100+ 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
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Sample Schedule
Johns Hopkins Hospital MLS Microbiology rotation, 12‐15 daysMonday Tuesday Wednesday Thursday Friday
1 Arrive 9:00 am
Orientation
HIPAA Lab/hospital tours
Lab safety
Gram stain review
Basic bacteriology
review/sample unknowns
2 Specimen processing
area
ID sample unknowns
ID rounds
3 Mycology lab 4 Virology/ HIV lab
Review blood parasites
smears
Plate rounds
5 AFB Lab
6 Wounds/body
fluids/anaerobes
7 Molecular Epidemiology
Lab
ID rounds
Phoenix/ MALDI TOF
benches
8 Respiratory and Cystic
Fibrosis cultures
9 Urine cultures
Plate rounds
Review respiratory cultures
if desired
(Day 2)
10 Blood cultures
Fellow didactic session
Review urine cultures if
desired (day 2)
11
Start independent
unknowns
12 Special micro (antibiotics)
Lab
ID rounds
Unknowns
13 Stools (BD Max)
Microbiology presentation and
lunch
Unknowns
14 GLC/sequencing
Plate rounds
Review gram stains and CDs
Unknowns
15 Complete unknowns and
quizzes
Lab practical
Gram stain competency
Final evaluation
Structuring a Great Microbiology Rotation: What Works for Us
• Independent activities alternate with bench experience:
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)
2. smear reviews (practice gram stain and blood parasite interpretation)
3. Student manual with flowcharts and culture guidelines; educational CDs, flashcards, review books available
MYCOBACTERIOLOGYWhich 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 30-32 degrees C:• a. Mycobacterium tuberculosis• b. Mycobacterium avium- intracellulare (MAI)• c. Mycobacterium marinum• d. Mycobacterium xenopi•
4. ID unknowns from 6‐8 cultures by classicmethods:
‐‐ 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
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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 Rotationsfrom 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 permissionOther images and cartoons obtained from Google