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

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

Nov 17, 2023 248 likes •439 views

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 dont cause disease unless they get into a sterile place

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Infection Prevention Boot Camp I for the Novice Infection Preventionist January 16‐17, 2020 Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 1

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.

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Infection Prevention Boot Camp I for the Novice Infection Preventionist January 16‐17, 2020 Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 2

COLONIZATION Colonization

VS

Infection Definitions

Colonization Infection Growth and Multiplication without Disease Clinical or subclinical response

3 Major Types for Discussion

 Bacteria  Viruses  Fungi  Parasites  Prions

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Infection Prevention Boot Camp I for the Novice Infection Preventionist January 16‐17, 2020 Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 3

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

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Infection Prevention Boot Camp I for the Novice Infection Preventionist January 16‐17, 2020 Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 4

Microbial Morphology

RODS COCCI COCCOBACILLI CHAINS CLUSTERS YEASTS Gram negative diplococci

Gram Stain & Cell Morphology

Gram-positive cocci 

Staphylococcus epidermidis  Staphylococcus aureus  Enterococcus spp.

Gram-negative rods 

Escherichia coli  Klebsiella spp.  Enterobacter 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

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Infection Prevention Boot Camp I for the Novice Infection Preventionist January 16‐17, 2020 Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 5

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  O2 requirement

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Infection Prevention Boot Camp I for the Novice Infection Preventionist January 16‐17, 2020 Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 6

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.

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Infection Prevention Boot Camp I for the Novice Infection Preventionist January 16‐17, 2020 Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 7

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)

 Can aid in the

diagnosis of a UTI

 What to look for

 >10 WBCs  Positive

Leukocyte Esterase

 Positive Nitrate

Chest X-ray 

Can aid in the diagnosis

  • f pneumonia

 New or progressive and persistent infiltrates

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.

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Infection Prevention Boot Camp I for the Novice Infection Preventionist January 16‐17, 2020 Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 8

Quiz #1

  • 1. Types of bacterial shapes
  • a. pathogen
  • 2. Gram stain results
  • b. positive or negative
  • 3. Organism that causes

disease

  • c. cocci or bacilli
  • 4. Presence of organism does

not necessarily indicate disease

  • d. PCR
  • 5. Most common nucleic acid

amplification test

  • e. colonization

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)

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Infection Prevention Boot Camp I for the Novice Infection Preventionist January 16‐17, 2020 Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 9

Staphylococcus aureus

  • Pathogenic but can be a colonizer
  • Carrier state common (20-50%)

 Formerly hospital associated; now common in

the community

  • Transmission via direct/indirect contact
  • Forms biofilm

Public Health Image Library

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.

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Infection Prevention Boot Camp I for the Novice Infection Preventionist January 16‐17, 2020 Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 10

Streptococcus pneumoniae

  • Normal flora in some people
  • Also pathogenic causing pneumonia, sepsis,

meningitis. Streptococcus pyogenes

  • Beta hemolytic.
  • Associated with necrotizing fasciitis, Strep

throat

Streptococcus

  • Anaerobic spore forming gram positive rod
  • Cause of colitis & pseudomembranous

enterocolitis

  • Associated with antibiotic use
  • Difficult to grow in lab
  • Spore producer
  • Exotoxin production

Clostridium – anaerobic spore forming gram positive rod

Gram Negative Bacteria

Enterobacteriacae

Escherichia coli Klebsiella pneumoniae Enterobacter cloacae Proteus species Stenotrophmonas maltophilia Pseudomonas aeruginosa Serratia marcescens

Non-enterics

Moraxella catarrahalis Neisseria meningitidis Legionella pneumophilia Haemophilus influenzae Acinetobacter baumannii

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Infection Prevention Boot Camp I for the Novice Infection Preventionist January 16‐17, 2020 Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 11

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.

Enterobacteriacae

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.

Gram Negative Bacteria

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Infection Prevention Boot Camp I for the Novice Infection Preventionist January 16‐17, 2020 Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 12

Acinetobacter baumannii

  • Commonly isolated from sputum, UTI,

wounds, and septicemia.

  • Can be a highly resistant pathogen.

Gram Negative Bacteria

Haemophilus influenzae

  • normally found in the upper respiratory

tract Legionella pneumophila

  • not transmitted person-person

Non-enteric Gram Negative Bacteria

Neisseria meningitidis

  • Gram negative diplococci,
  • Transient flora of the Oropharynx.

Moraxella catarrhalis

  • Gram negative, aerobic, diplococcus.
  • Seen often in COPD patients

Non-enteric Gram Negative Bacteria

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Infection Prevention Boot Camp I for the Novice Infection Preventionist January 16‐17, 2020 Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 13

Interpretation of Susceptibility Test

Ciprofloxacin >=8 R Clindamycin >=8 R Erythromycin >=8 R Gentamycin <=5 S Levofloxacin >=8 R Linezolid 2 S Oxacillin >=4 R Penicillin G >=0.5 R Rifampin <=0.5 S Tetracycline <=1 S Tigecycline <=0.12 S Sulfa/Tri <=10 S Vancomycin <=0.5 S

Anatomy of a Lab Report Wound Culture Report

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Infection Prevention Boot Camp I for the Novice Infection Preventionist January 16‐17, 2020 Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 14

Urine Culture Report Other pathogens…

Mycobacteria Fungi-Yeast and Molds Viruses Prions Mycobacteria “Acid Fast” on staining (AFB)

  • M. Tuberculosis (aka MTb, TB)

“Slow grower” in lab – it may take up to 6 weeks for visible growth on culture

 Some methods of rapid testing for identification

may be used

Cause of HCW exposure due to airborne transmission

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Infection Prevention Boot Camp I for the Novice Infection Preventionist January 16‐17, 2020 Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 15

Mycobacteria

Other species include a group that live in water and soil. The majority are not transmitted person to person

  • Mycobacterium avium-complex (MAC)
  • M. gordoniae
  • M. abscessus
  • M. kansasii

Fungi

Two Broad groups include: 

Yeast

Molds

Available from: URL: ttp://www.cdc.gov/ncidod/EID/vol10no1/03‐0119.htm

Candida albicans

  • Normal GI/skin flora

Frequent issue with

  • Oncology & ICU patients

Fungi

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Infection Prevention Boot Camp I for the Novice Infection Preventionist January 16‐17, 2020 Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 16

Aspergillus

  • Found in soil, outdoor and indoor air.
  • Have been associated with outbreaks related to construction.

Rhizopus

  • Found in soil & environment.
  • Can cause wound infections implicated in
  • utbreak with contaminated dressing supplies.

Fungi

Sarcoptes scabiei

  • Scabies mite
  • Rash mimics many diseases—can be

difficult to diagnose

  • Diagnose by skin scrapings

Parasites

Head louse

Lives on hair

Adult, eggs, nymphs

All visible (very small!)

Do not fly or jump! Pediculosis humanis

Body louse

Lives in clothes, bedding

Adults, eggs, nymphs

All visible (very small!)

Do not fly or jump! Pediculosis capitis

Parasites

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Infection Prevention Boot Camp I for the Novice Infection Preventionist January 16‐17, 2020 Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 17

Viruses

Viruses are obligate intracellular parasites that require living host cells to grow and reproduce

Viruses

Classification of viruses is generally based

  • n:
  • Whether the virus contains DNA or RNA
  • Size and shape
  • Structure of the protein coat
  • Mode of replication

Viruses

Human immunodeficiency virus: retrovirus, causes AIDS, found in blood Influenza virus - cause of the seasonal flu and is spread by droplet transmission

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Infection Prevention Boot Camp I for the Novice Infection Preventionist January 16‐17, 2020 Florida Hospital Association | Mission to Care Hospital Improvement Innovation Network 18

Herpes simplex virus- HSV-1 vs. HSV-2 Cytomegalovirus Epstein-Barr virus Varicella zoster virus

Viruses

Variola (small pox) Vector-borne viruses (WNV) Rhinoviruses Hemorrhagic viruses - Ebola

Rotavirus RSV

Viruses

Prions

Infectious particles with no DNA or RNA present – called ‘rogue’ proteins

  • Creutzfeld-Jakob disease (CJD)
  • CJ variant (Mad cow disease)
  • Kuru
  • Scrapie