Microorganisms They are every where Many live in or on our body and - PDF document

Infection Prevention Boot Camp I for the Novice January 16 ‐ 17, 2020 Infection Preventionist Microbiology Microorganisms They are every where Many live in or on our body and don’t cause disease unless they get into a sterile place Definitions • Normal Flora - microbes that are normally present in a particular environment and are found in most people, most of the time • Pathogen - an organism that is causing disease • Colonization – when a microbe is present but no disease • Contaminant – microorganism is present due to poor handling or poor specimen acquisition. Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 1

Infection Prevention Boot Camp I for the Novice January 16 ‐ 17, 2020 Infection Preventionist COLONIZATION Colonization VS Infection Definitions Colonization Growth and Multiplication without Disease Infection Clinical or subclinical response 3 Major Types for Discussion  Bacteria  Viruses  Fungi  Parasites  Prions Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 2

Infection Prevention Boot Camp I for the Novice January 16 ‐ 17, 2020 Infection Preventionist Bacteria  Free Living  Single celled  Multiply by replication and cellular division  Cell contains DNA, ribosomes, membrane and a cell wall  Some may have additional components The Gram Stain  Helpful for guiding empiric therapy  Distinguishing between gram positive and gram negative  Shapes will help identify the organism Bacterial Gram Stain  Stains the cell wall  Gram positive vs. gram negative bacteria  Visualization of the morphology/shape of the bacteria (cocci or rods)  Visualization of red/white blood cells Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 3

Infection Prevention Boot Camp I for the Novice January 16 ‐ 17, 2020 Infection Preventionist Microbial Morphology RODS COCCI COCCOBACILLI CHAINS CLUSTERS YEASTS Gram negative diplococci Gram Stain & Cell Morphology Gram-positive cocci Gram-negative rods  Escherichia coli  Staphylococcus epidermidis  Klebsiella spp.  Staphylococcus aureus  Enterobacter spp.  Enterococcus spp.  Pseudomonas aeruginosa  Acinetobacter baumannii  Serratia spp. Other stains: Acid Fast Bacillus (AFB) Stain Used to stain Mycobacteria species  Ziehl-Neelsen  Kinyoun  Auramine O  Fluorescent stain http://phil.cdc.gov/phil/sessionexpired.asp Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 4

Infection Prevention Boot Camp I for the Novice January 16 ‐ 17, 2020 Infection Preventionist Other Stains or Microscopy  Wet Prep  KOH, Lactophenyl cotton blue  Direct Exams  Direct Fluorescent Antibody (DFA) http://phil.cdc.gov/phil/details.asp Culture Media  Agar/solid media, Broth, Biphasic http://contactome.com/index.php/Biomarker_Wiki Other identifying methods  Hemolysis  O 2 requirement Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 5

Infection Prevention Boot Camp I for the Novice January 16 ‐ 17, 2020 Infection Preventionist Biochemical Testing  Catalase  Coagulase  Other biochemical tests Rapid Molecular Tests  Have revolutionized the microbiology laboratory!  Growth of the organism not required for detection  Genetic material from the organism is detected  Some tests actually amplify any small amounts of genetic material that may be present in a specimen EIA/ELISA  Can be used to detect either antigen (including toxin) or antibody  Uses an enzyme linked to either an antigen or antibody  After binding to the antigen or antibody, the enzyme can be detected by a color change. Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 6

Infection Prevention Boot Camp I for the Novice January 16 ‐ 17, 2020 Infection Preventionist Nucleic acid amplification tests (NAAT)  Most common is polymerase chain reaction (PCR)  Used to detect antigen (organisms or toxins)  Primers are used for selective amplification of specific regions of DNA Other helpful tests  Urinalysis (UA)  Chest X-ray  Can aid in the diagnosis  Can aid in the of pneumonia diagnosis of a  New or progressive and persistent UTI infiltrates  What to look for  >10 WBCs  Positive Leukocyte Esterase  Positive Nitrate MORE helpful tests 1. What is the blood WBC count? 2. Are there WBCs in the stool? 3. Elevated ESR (erythrocyte sedimentation rate), CRP (C- reactive protein), Or lactate? 4. Protein and glucose levels in the CSF? 5. Gross description of the specimen by the Lab  Blood in the stool, cloudy CSF, etc. Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 7

Infection Prevention Boot Camp I for the Novice January 16 ‐ 17, 2020 Infection Preventionist Quiz #1 1. Types of bacterial shapes a. pathogen 2. Gram stain results b. positive or negative 3. Organism that causes c. cocci or bacilli disease 4. Presence of organism does d. PCR not necessarily indicate disease 5. Most common nucleic acid e. colonization amplification test Gram Positive Bacteria Staphylococcus species Streptococcus species Enterococcus species Clostridium species Staphylococcus  Gram positive cocci in clusters  Two major species (but many more species exist)  Staphylococcus aureus  Staphylococcus epidermidis (Coagulase negative Staph) Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 8

Infection Prevention Boot Camp I for the Novice January 16 ‐ 17, 2020 Infection Preventionist Staphylococcus aureus • Pathogenic but can be a colonizer Public Health Image Library • Carrier state common (20-50%)  Formerly hospital associated; now common in the community • Transmission via direct/indirect contact • Forms biofilm Staphylococcus epidermidis (aka Coagulase negative Staph) Normal skin flora Forms biofilm Transmission • Contaminated surfaces such as needleless connectors Prevention • Hand hygiene/gloves • Aseptic technique for vascular access and site/line care Enterococcus • 2 species of clinical relevance E.faecalis, E.faecium • Normally found in the GI tract. •The organism can cause UTI, wound infections, intra- abdominal/pelvic wounds, and endocarditis. Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 9

Infection Prevention Boot Camp I for the Novice January 16 ‐ 17, 2020 Infection Preventionist Streptococcus Streptococcus pneumoniae • Normal flora in some people • Also pathogenic causing pneumonia, sepsis, meningitis. Streptococcus pyogenes • Beta hemolytic. • Associated with necrotizing fasciitis, Strep throat Clostridium – anaerobic spore forming gram positive rod • Anaerobic spore forming gram positive rod • Cause of colitis & pseudomembranous enterocolitis • Associated with antibiotic use • Difficult to grow in lab • Spore producer • Exotoxin production Gram Negative Bacteria Enterobacteriacae Non-enterics Escherichia coli Moraxella catarrahalis Klebsiella pneumoniae Neisseria meningitidis Enterobacter cloacae Legionella pneumophilia Proteus species Haemophilus influenzae Stenotrophmonas maltophilia Acinetobacter baumannii Pseudomonas aeruginosa Serratia marcescens Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 10

Infection Prevention Boot Camp I for the Novice January 16 ‐ 17, 2020 Infection Preventionist Enterobacteriacae Escherichia coli • Normal flora in the GI tract • Common cause of UTI, sepsis and Intra-abdominal infections. Klebsiella pneumoniae • Normal GI flora • Common cause of pneumonia, UTI, wound infections. Enterobacter cloacae • Normal flora of the GI • Common in the environment. • Common cause of UTI, wound infections, bacteremia and pneumonia. Gram Negative Bacteria Proteus mirabilis • Genus responsible for 90% of all Proteus infections which include pneumonia, wounds, urinary tract infection, and sepsis Stenotrophomonas maltophilia • Common inhabitant of water, soil and plants • Isolated from Cystic Fibrosis patients Gram Negative Bacteria Pseudomonas aeruginosa • Associated with biofilm formation and antibiotic resistance. Serratia marcescens Implicated in outbreaks following pooling of multi- dose medication vials as well as contamination in manufacturing of shampoo-related products. Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 11

Infection Prevention Boot Camp I for the Novice January 16 ‐ 17, 2020 Infection Preventionist Gram Negative Bacteria Acinetobacter baumannii • Commonly isolated from sputum, UTI, wounds, and septicemia. • Can be a highly resistant pathogen. Non-enteric Gram Negative Bacteria Haemophilus influenzae • normally found in the upper respiratory tract Legionella pneumophila • not transmitted person-person Non-enteric Gram Negative Bacteria Moraxella catarrhalis • Gram negative, aerobic, diplococcus. • Seen often in COPD patients Neisseria meningitidis • Gram negative diplococci, • Transient flora of the Oropharynx. Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 12