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Antimicrobial and Clinical Microbiology Guidebook © 2010

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Antimicrobial and Clinical Microbiology Guidebook © 2010 TABLE OF CONTENTS Introduction 2 Contacts 2 Clinical Microbiology Organism Identification Flowcharts 3 Key phrases in microbiology 5 Bacteriology 5 Susceptibility Testing 5 Interpretation of Reports 10 Specimen Requirements 11 Timing of Reports 11 Urinalysis and Urine Culture 12 Stool Cultures 12 Blood Cultures 13 Respiratory Cultures 14 Mycobacteriology 14 Virology 15 Mycology 17 Parasitology 17 Interpretation of Viral Diagnostic Tests 19 Antimicrobial Formulary 23 Antimicrobial Costs 25 Antimicrobial Concepts and Tips 27 Antimicrobial Restrictions and Utilization Guidelines 33 Antimicrobial Clinical Practice Guidelines Antibiotic lock therapy 35 Ethanol lock therapy 36 Clinical pathway for Clostridium difficile infection 39 Community-acquired pneumonia in adults 42 Nosocomial pneumonia in adults 47 Invasive Candidiasis 50 Prophylaxis in surgery 57 Sepsis in adults 60 Skin and Soft Tissue Infections 63 Renal Dosage Adjustment Guidelines for Antimicrobials 71 Antimicrobial Therapeutic Interchanges 87 Antimicrobial IV to PO Conversion Protocols 91 Antimicrobial Drug-Food Interaction Chart 93 Infection Control Contact information 99 Isolation precautions 99 Isolation precaution quick reference 100 Removing a patient from isolation 101 Guidelines for prevention of central venous catheter-related infections 101 Guidelines for prevention of nosocomial pneumonia 102 Guidelines for prevention of surgical site infections 102 Guidelines for prevention of urinary tract infections 102 Bloodborne pathogen exposure 103 Reportable diseases 103 1 ANTIMICROBIAL AND CLINICAL MICROBIOLOGY GUIDEBOOK © 2010 INTRODUCTION This is the Second Edition of the Antimicrobial and Clinical Microbiology Guidebook at The Nebraska Medical Center. The development of this guidebook has been a joint effort of the Antimicrobial Stewardship Program (ASP), the Microbiology Department, the Infectious Disease section, and the Department of Healthcare Epidemiology. The purpose of the booklet is to optimize antimicrobial usage and patient outcomes for infectious disease-related issues. We hope that the information in this booklet will be useful in the provision of best practices to patients at The Nebraska Medical Center. Every effort has been made to ensure that the information included is complete, accurate, and up to date; however this booklet does not serve as a substitute for clinical judgement or consultation with experts in Infectious Diseases. Application of the information contained herein to each clinical situation is the responsibility of the practitioner. The content in the booklet can be found online at http://www.nebraskamed.com/asp. CONTRIBUTING AUTHORS (alphabetical) Amy Armbrust, MS, MT(ASCP) Gerald A.Capraro, Ph.D. Paul D. Fey, Ph.D. Jodi Garrett, MT(ASCP)SM Alan E. Gross, Pharm.D., BCPS Elizabeth D. Hermsen, Pharm.D., M.B.A., BCPS-ID Steve Hinrichs, M.D. Peter C. Iwen, Ph.D. Jan Keuchel, RN Jessica C. Njoku, Pharm.D., BCPS Mark Rupp, M.D. Kathy Talmon, MT(ASCP)SM Kate Tyner, RN Trevor C. VanSchooneveld, M.D. CONTACTS The Antimicrobial Stewardship Program Trevor C. VanSchooneveld, M.D. 559-8376/888-3680 [email protected] Mark E. Rupp, M.D. 559-5276/888-2417 [email protected] Alan Gross, Pharm.D., BCPS 559-4149/888-0349 [email protected] Microbiology Laboratory 552-2090 Steve Hinrichs, M.D. 559-8301/231-6900 Paul Fey, PhD. 559-2122 Kendall Bryant, Ph.D., Clinical Microbiology Fellow 552-2090 Infectious Diseases 559-8650 (This number can be called for infectious disease consult services, or the person on call may be paged.) 2 Organism Identification Flowcharts Common Clinically Significant Gram BACILLI COCCI Positive Microorganism Flowchart Anaerobic Aerobic Anaerobic Aerobic Sporeformers: Non-sporeformers: Peptostreptococcus spp. Clostridium spp. Propionibacterium spp. Catalase test Eubacterium spp. Bifidobacterium spp. (-) (+) Actinomyces spp.* Streptococcus spp. Staphylococcus spp. Mobiluncus spp. Coagulase test Hemolytic Properties on Blood Agar (-) (+) Beta hemolysis Alpha hemolysis Gamma hemolysis S. epidermidis S. aureus (complete; clear) (partial; green) (none) S. saprophyticus Bile esculin test (+) S. hemolyticus PYR test (-) (+) Sporeformers: Non-sporeformers: Group A Bacillus spp. Listeria monocytogenes CAMP test Growth in 6.5% NaCl S. pyogenes Erysipelothrix spp. (+) (-) or PYR test Optochin test & Corynebacterium spp. Group B Bile solubility test Lactobacillus spp. S. agalactiae (-) (+) Nocardia spp.* Latex agglutination test; S. bovis Enterococcus *Nocardia spp. and other Other Lancefield groups (formerly known E. faecium Actinomycetes typically show as E. faecalis C, F, G as group D beaded gram-positive rods rather streptococci) (RR) (-) (SS) (+) than demonstrating uniform gram- viridans group positive staining S. pneumoniae streptococci (misc. strep group) 3 Common Clinically Significant Gram Negative Microorganism Flowchart COCCI BACILLI Anaerobic Aerobic Aerobic Veillonella spp. Neisseria meningitidis Anaerobic Neisseria gonorrhoeae Bacteroides spp. Moraxella catarrhalis Prevotella spp. Lactose Fermentation Porphyromonas spp. Fusobacterium spp. (+) (-) Lactose Fermenters Lactose Non-Fermenters Oxidase test Escherichia coli Klebsiella spp. (-) (+) Enterobacter spp. Morganella spp. Pseudomonas aeruginosa Serratia spp. Proteus spp. Pasteurella spp. Citrobacter spp. Providencia spp. Vibrio spp. Aeromonas spp. Salmonella spp. Shigella spp. Plesiomonas spp. OTHER GRAM (-) BACILLI Yersinia spp. (special growth requirements) Haemophilus spp. Stenotrophomonas maltophilia Campylobacter spp. Acinetobacter spp. Legionella pneumophila Bordetella pertussis Brucella spp. Francisella tularensis Helicobacter pylori 4 Key phrases from the Microbiology Laboratory ―Gram positive cocci in clusters‖ may suggest Staphyloccocus species. "Gram positive cocci in pairs and chains" may suggest Streptococcus species or Enterococcus species. ―Gram positive diplococci‖ may suggest Streptococcus pneumoniae. ―Gram negative coccobacilli‖ may suggest Haemophilus species. ―Lactose fermenting Gram negative rods‖ may suggest Enterobacteriaceae. ―Non-lactose fermenting Gram negative rods‖ may suggest non-Enterobacteriaceae. ―Non-lactose fermenting Gram negative rods, oxidase positive‖ may suggest Pseudomonas species. ―Branching Gram positive rods, modified acid fast stain positive‖ may suggest Actinomyces or Nocardia species. ―Acid fast bacilli‖ may suggest Mycobacterium species. ―Budding yeast‖ suggests yeast. "Germ-tube negative yeast" suggests non-albicans Candida yeast (and rules out C. albicans). ―Germ-tube positive yeast‖ is identified as Candida albicans. ―Fungal elements or hyphal elements‖ suggests mold. BACTERIOLOGY Susceptibility Testing Susceptibility testing is an in vitro assay that allows us to predict the likelihood of successfully treating an infection with a particular antimicrobial agent. However, clinical outcome may depend on a variety of factors, such as host immunity or surgical treatment, which are not reflected in laboratory tests. All methods of susceptibility testing are based on diffusion or dilution. A. Semi-Automated Susceptibility Testing Semi-automated antimicrobial susceptibility testing is performed using the Microscan system, which is based on broth microdilution. This system allows the laboratory to rapidly perform identification and susceptibility testing on most common pathogens (e.g. Enterobacteriaceae, Staphylococci, Enterococci, and Pseudomonas aeruginosa). The antibiotics tested vary based upon the Microscan panel used and the antibiotics that are currently on The Nebraska Medical Center hospital formulary. However, the microbiology laboratory reports antibiotics (that are on formulary) from most antibiotic classes that are appropriate for the specific organism tested. For instance, if the laboratory recovers an Escherichia coli isolate from urine, the following results are reported: penicillin, penicillin/ -lactamase inhibitor combination(s), first generation cephalosporin, a cephamycin, multiple expanded-spectrum cephalosporins (including cefepime), a carbapenem, one or two fluoroquinolones, at least two aminoglycosides, trimethoprim-sulfamethoxazole, and nitrofurantoin. The results obtained from the Microscan system are based on the minimum inhibitory concentration (MIC). The MIC is defined as the lowest concentration of antibiotic that completely inhibits growth of the specific organism being tested. For instance, in figure 1, the 5 organism being tested grew in wells containing 0.5, 1.0, 2.0 and 4.0 g/ml of antibiotic. The lowest concentration of antibiotic (MIC) that completely inhibits growth was 8.0 g/ml. Figure 1 MIC=8.0 µg/ml 0.5 µg/ml 1.0 µg/ml 2.0 µg/ml 4.0 µg/ml 8.0 µg/ml 16.0 µg/ml 32.0 µg/ml 64 µg/ml = growth of bacteria in well The MIC is then interpreted (S=susceptible, I=Intermediate, or R=resistant) using CLSI (formerly NCCLS) standards, which are published each year in January. For example, the MIC interpretive standards for ampicillin against E. coli are <8µg/ml=susceptible, 16 µg/ml=intermediate, and ≥32 µg/ml=resistant. These interpretive standards are based on many studies, including clinical, pharmacokinetic/pharmacodynamic, and microbiological studies. It is important to be aware that, although there are many examples of bacteria and antibiotics for which we have CLSI interpretive standards (particularly for the most common pathogens), there are some bacteria for which there are no interpretive standards. Additionally, there are some antibiotics for which there are no interpretive standards. Consultation
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