Clinical Micro Review and Course Introduction 2024 PDF

Pathophysiology and Therapeutics of Infectious Diseases P325 Jason C. Gallagher, Pharm.D., FCCP, FIDP, FIDSA, BCPS Clinical Professor  How We Learn Environment Lecture,...

Pathophysiology and Therapeutics of Infectious Diseases P325 Jason C. Gallagher, Pharm.D., FCCP, FIDP, FIDSA, BCPS Clinical Professor  How We Learn Environment Lecture, Reading, EXPOSURE Attendance Paying attention (!) Feels familiar Working Feels challenging and comfortable Memory and discomforting (Thinking) Memorizing facts Learning the “whys” Reading lectures repeatedly Completing cases No practice Active studying/learning Long Term Forgetting Memory (perhaps after the exam) (Knowledge for rotations and your career) 2 Adapted from: Willingham DT. American Educator 2009;3:4-14 a  My Expectations What is expected of you: – To learn the material because of your commitment to patient care – To want to know why things are done, not just memorize that they are – To participate and ask questions by whatever mechanism you are most comfortable – To prepare for class by doing the required reading – To provide constructive feedback on the course 3  You Can Expect What you can expect of me: – To do my best to help you learn the material – To be fair and consistent in grading – To answer “Why do we care about this?” at any time. – To answer questions posted to discussion board within 24- 48 hours (excepting weekends) – To post lecture material ~1 week in advance – To provide optional homework cases and other material to help you learn the material 4  We Will Use Poll Everywhere in this Course… Often Why? – To answer clinical cases in class – To assess the effectiveness of my teaching – To evaluate understanding of material 5  Dosing Guide Know how to use it, don’t memorize Question – Patient with UTI and CrCl of ~35 mL/min – what is the dose of aztreonam? Correct answer: 1 gm q12h Incorrect answers: 2 gm q8h, 2 gm q12h, 1 gm q8-12h This will be provided as an attachment on all exams 6 a 7 Syllabus Review 8 Clinical Microbiology Review Jason C. Gallagher, PharmD, FCCP, FIDP, FIDSA, BCPS Clinical Professor  Objectives At the end of the lecture, the student should be able to: Describe normal human flora and their impact on antibiotic therapy Describe the basic characteristics of many common bacterial pathogens Interpret basic Gram stain results 10  General Approach to Infectious Diseases Suspect infection Culture suspected sites EMPIRIC THERAPY for likely pathogens Stain sample Identification Susceptibilities Gallagher JC, MacDougall CM. Antibiotics 11 Simplified 5th ed. Jones & Bartlett 2023. DEFINITIVE THERAPY It’s best not to think of it as competition 12  It’s best not to think of it as competition Variable Microbes Humans Factor Number on earth 5 x 1031 6 x 109 ~1022 Mass (metric tons) 5 x 1016 3 x 108 ~108 Generation time 30 min 30 years ~5 x 105 Time on earth (years) 3.5 x 109 4 x 106 103 13 Adapted from: Spellberg B et al. CID 2008;46:155-64.  Our microbiota is very specialized 14 Image from: Jawetz, Melwick, and Adelberg’s Medical Microbiology, 26th ed. McGraw-Hill. 2013. The Gram Stain https://en.wikipedia.org/wiki/Gram_staining#/ 15 media/File:Gram_Stain_Procedure.png Sputum Gram Stain #1 16 Sputum Gram Stain #2 17  Gram-positive cocci Anaerobes Aerobes Peptococcus Peptostreptococcus Clusters Pairs/Chains Catalase + Catalase - Staphylococcus Streptococcus/Enterococcus Coagulase + Coagulase - α-hemolysis β -hemolysis γ-hemolysis S. aureus S. epidermidis S. saprophyticus S. capitis S. hominis E. faecalis S. pneumoniae E. faecium viridans strep S. pyogenes S. agalactiae 18 a  Staphylococci S. aureus Flora of nares, axillae Can be highly pathogenic Cause bacteremia, endocarditis, PNA, toxic shock, etc S. epidermidis Normal flora of skin, mucous membranes Occasional pathogen 19 Image courtesy of Susan D. Caston, University of Pennsylvania.  Staphylococci Coagulase Test Differentiates Species No longer done in many labs, but “coagulase negative staphylococci” is still a common term 20 Streptococcal Hemolysis Patterns Help Differentiate Species 21  Alpha-hemolytic streptococci Viridans streptococci Normal mouth flora Oral infections, endocarditis S. pneumoniae Encapsulated, virulent Transiently reside in upper respiratory tract Upper and lower resp. tract infections, meningitis 22 Image: http://textbookofbacteriology.net/S.pneumoniae.html  Beta-hemolytic streptococci S. pyogenes (GAS) SSSIs, pharyngitis May prolifically produce toxins S. agalactiae (GBS) Human GI flora Neonatal sepsis 23  Non-hemolytic streptococci Enterococci Normal GI flora Opportunistic Hearty E. faecalis More common and virulent E. faecium Usually vancomycin-R Difficult to treat 24 Image: Wikimedia Commons  Clinical Importance of Gram Stain Results 1. 33-year-old man with a 3. 76-year-old woman in large abscess on the right the ICU receiving thigh vancomycin Gram stain: GPC-clusters Blood culture: non- hemolytic GPC-chains 2. 45-year-old woman with 4. 24-year-old man with mental status changes H/O IVDU and CSF Gram stain: GPC-pairs bacteremia Blood culture: alpha- hemolytic strep 25 26 27 28 29  Gram-positive bacilli Aerobes Anaerobes Listeria Clostridioides Corynebacterium Propionibacterium Bacillus Lactobacillus 30  Clostridia Spore-forming, obligate anaerobes Clostridioides spp. C. difficile C. perfringens C. septicum C. botulinum C. tetani 31  Gram-negative cocci Cocci Coccobacilli Neisseria meningitidis Haemophilus Neisseria gonorrheae Moraxella Acinetobacter 32 Neisseriae Encapsulated N. gonorrheae STI -> disseminated infection Easily transmitted N. meningitidis Can be normal flora Meningitis outbreaks 33  Gram-negative bacilli Anaerobes Aerobes Bacteroides Fusobacterium Prevotella Glucose nonfermenters Glucose fermenters Acinetobacter^ Enterobacterales Pseudomonads Escherichia* Pseudomonas Klebsiella* Burkholderia Serratia* Stenotrophomonas Enterobacter* Citrobacter* Salmonella ^coccobacilli Shigella *also ferment lactose 34 a  Pseudomonas aeruginosa Opportunistic, drug- resistant GNR Common nosocomial pathogen Often selected for by antibiotic therapy 35 Image courtesy of Susan D. Caston, University of Pennsylvania.  Acinetobacter baumannii “Gram variable coccobacilli” Poorly stained Correctly stained 36 Image courtesy of Susan D. Caston, University of Pennsylvania. Acinetobacter baumannii Not highly pathogenic, but very drug resistant Can be resistant to all antibiotics 37 a  Enterobacterales (order) Enterobacteriaceae (family) Normal GI flora, but can be virulent Escherichia coli Main cause of UTIs Also causes GI and nosocomial infections Klebsiella pneumoniae Rapidly spreading resistant pathogen (pneumonia, UTI nosocomial infections) Enterobacter spp. Drug resistant – can appear falsely susceptible to 3rd gen cephs Salmonella, Shigella spp. Food poisoning 38 Image courtesy of Susan D. Caston, University of Pennsylvania.  Clinical Importance of GNRs in Gram Stain Results 1. 29-year-old woman in 3. 56-year-old man in the emergency room with back ICU receiving pain and fever ampicillin/sulbactam for Urine gram stain: lactose- fermenting GNRs an intra-abdominal infection 2. 81-year-old woman resident Sputum Gram stain: non- of a nursing home with lactose fermenting GNRs mental status changes and incontinence Urine Gram stain: non-lactose- fermenting GNRs 39 40 41 42 Bacteria Identification 43 Bacteria Identification 44 Bacteria Identification 45  Bacteria Identification- MALDI-TOF Murray PR. J Mol Diagn 2012;14:419-23. https://en.wikipedia.org/wiki/Matrix-assisted_laser_desorption/ionization 46 http://www.pharmaceutical-technology.com/contractors/imaging-analysis/anagnostec/anagnostec2.html  Mycobacteria Slow-growing, drug- resistant bacteria Structurally different from “typical” bacteria Do not stain with Gram stain “Acid-fast” organisms 47 CDC.gov  The Kingdom Fungi FUNGI YEASTS DIMORPHIC MOLDS Trichosporon Histoplasma Aspergillus Cryptococcus Coccidioides Fusarium Blastomyces Scedosporium Paracoccidioides Mucorales Penicillium Dematiaceous molds Candida Sporothrix 48  Culture! Blood cultures – Should be 2 sets from 2 different sites – 1 set = 1 aerobic and 1 anaerobic bottle – Potential for contamination with skin flora Perform multiple cultures Urine culture – Should be mid-stream, suprapubic, or via catheter – Presence of large #s of epithelial cells = contamination – UA should always be performed to assess relevance of positive cultures – Catheterized patients are almost always colonized 49  Culture! Lung – Sputum – most common Frequent site of colonization (esp. on ventilator) Look for lots of WBCs, few epithelial cells Low yield in CAP, not routinely recommended – Bronchoalveolar lavage fluid (BAL or BALF) Done via bronchoscopy – less contamination Can quantify cultures 50  Culture! Wound/Skin – Contamination/colonization frequent – Check for presence of WBCs – Not very specific Cultures should be performed BEFORE initiating therapy! 51 Susceptibility Testing Disk Diffusion 52 MIC testing MIC – minimum concentration at which growth is inhibited Property intrinsic to a particular strain/drug combination 53  Susceptibility Testing Tube Dilution and Microdilution 32 16 8 4 2 1 0.5 0.25 Swenson JM et al. J Clin Microbiol 2004;42:5102-8. 54 https://emerypharma.com/biology/minimum-inhibitory-concentration/ Susceptibility Testing E-tests 55  Pharmacodynamics The MIC Concentration (mcg/mL) 0.125 0.25 0.5 1 2 4 8 Minimum inhibitory concentration 2 mcg/mL 56 a  Reading In Vitro Susceptibility Results Susceptible Susceptible, dose-dependent Intermediate Resistant 57  Is It Susceptible? The Lab Compares the MIC to the Breakpoint 1) Organism Isolated: Enterobacter aerogenes 2) Drug tested: Gentamicin 4) Interpretation: Enterobacter aerogenes 2 Drug MIC Result Gentamicin 2 S 3) CLSI Standards for Enterobacteriaceae Drug S I R Gentamicin ≤4 8 ≥16 58 The Breakpoint – Anything higher is bad a Microbiology Lab Reports Date: Day 1 59 Microbiology Lab Reports Date: Day 2 60 Microbiology Lab Reports Date: Day 3 61  The Cumulative Path to ID Knowledge at TUSP Therapeutics P&T of ID Microbiology (3rd year) Principles of ID (1st year) Pharmacology Pathophysiology P&T of ID and Medicinal (3rd year) Chemistry Principles of ID and Patient Care Medicinal Chemistry 2 APPEs (1st year) (4th year)