Microbiology Unit 4 Test

Specimen Collection:

1. Importance of specimen collection

2. Performance

3. “Clean Catch” samples

4. Sputum samples

Transport:

5. What should be done to ensure correct transport?

1. The lab can only identify the correct pathogen if the specimen is collected properly. Poor collection can lead to contamination, false-negative results, or growth of normal flora instead of the pathogen.

2. Collection must be performed using aseptic technique. Specific procedures are used to prevent contamination of a specimen with microorganisms from the environment or the collector.

• Examples include using sterile swabs, sterile collection containers, proper hand hygiene, and avoiding touching sterile surfaces prior to collection.

3. “Clean catch” samples are typically URINE. They are used to reduce contamination from skin and normal flora. PTs are instructed to clean the area, begin urinating, and collect the middle portion (midstream) of urine.

4. Sputum samples should be collected by deep coughing into a sterile container (not saliva). A good, appropriately collected specimen from the res. tract, is thick sputum with the presence of WBC. A poorly collected specimen contains mostly saliva and many squamous epithelial cells.

5. Specimens should be labeled correctly, reach the lab quickly, and be stored appropriately if transport is delayed.

• Some organisms require special transport media. ← Neisseria gonorrhoeae, since it dies quickly outside the body.

Diagnostic Testing Methods:

1. Phenotypic Methods

• Advantages/ Disadvantages

• Biochemical Tests

• Coagulase Test

2. Genotypic Methods

• RT-PCR

• Microarrays

2. Immunologic Methods

1. Methods identify organisms by their observable characteristics (appearance and behavior, such as enzymatic activity). Includes Gram stain, colony morphology, biochemical tests, hemolysis, catalase, and coagulase testing. These methods provide rapid preliminary information.

• Ask “What does the organism look like or do?”

- Advantages/ Disadvantages- Inexpensive and widely available / requires growth, which can take several days in some cases (some organisms do not grow well).

• Biochemical tests: Used to identify bacteria by the enzymes they produce or chemicals they metabolize. Include catalase, coagulase, oxidase, indole, urease, citrate, and lactose fermentation.

• Coagulase Test- Classified as a biochemical test (detects the enzyme coagulase, which clots plasma); is used to distinguish Staphylococcus aureus from CoNS (coagulase-negative staphylococcus).

2. Methods identify organisms using DNA or RNA (organisms’ genetic material). Includes PCR, RT-PCR, DNA probes, and whole-genome sequencing.

• PCR amplifies DNA so even small amounts become detectable. It provides rapid diagnosis without culture.

-RT-PCR (reverse transcriptase PCR) detects viral RNA (used for RNA viruses). ← SARS-CoV-2, Influenza, and RSV.

-Microarrays (genotypic method)- Has thousands of DNA probes on 1 chip and can identify many pathogens simultaneously.

3. Methods detect antigen or antibody using antigen-antibody reactions (serological analysis). Includes ELISA, latex agglutination, rapid antigen tests, fluorescent antibody testing, etc.

• In this method, we use antibodies to find the organism. We can use serology testing to find antibodies in the serum. This is used to determine if the patient has a current or previous infection, and their immune status.

• Detects antigen (foreign substance recognized by the immune system such as a bacterial toxin or capsule) or antibody (protein produced by B lymphocytes that specifically binds to an antigen).

Antibody-Based Testing (connects to immunologic):

1. What are antibodies specific to?

2. High Specificity

3. Sensitivity

Antibody Titer:

4. What is it?

PCR vs. Antigen Tests:

5. PCR

6. Antigen Tests

7. Difference between RT-PCR and Antigen Tests

1. Antibodies are specific to a single epitope.

2. Antigen-based testing should have High Specificity. This means the test can correctly identify PT without the disease. A high-specificity test will have a low false-positive rate. They are good confirmatory tests.

3. Sensitivity refers to the ability of a test to correctly identify PT who have the disease (detect even small quantities of antibody or antigens). A high-sensitivity test will have a low false-negative rate and is good for screening.

4. The highest dilution of serum that still contains detectable antibody. A higher titer means that more antibody is present.

• Higher titer (e.g. 1:200) = higher antibody concentration = stronger immune response. Ex- 1:1000 is a higher antibody concentration than 1:60.

5. PCR detects DNA or RNA. It is very sensitive and can detect low numbers of organisms. It can identify infections earlier on, but testing is more expensive and takes longer.

6. Antigen tests detect pathogen proteins. It is an easy and rapid test to perform but it is less sensitive.

7. An RT-PCR detects viral RNA- it is more sensitive and can detect low viral loads. Antigen tests are faster but less sensitive.

Matching Review:

1. PCR

2. Biochemical Tests

3. Microarray

4. Serotyping

Line of Defense:

5. What is the body’s 1st line of defense?

6. Broken skin

Skin Lesions:

7. Macules

8. Papules

9. Pustules

10. Vesicles

11. Exanthem

1. PCR- Polymerase chain reaction; uses a technique that amplifies segments of DNA for testing. Using denaturation, primers, and heat-resistant DNA polymerase, the number can be increased several million-fold. Genotypic method.

2. Biochemical Tests- Used to identify bacteria by the enzymes they produce or chemicals they metabolize. Phenotypic method.

3. Has thousands of DNA probes on 1 chip and can identify many pathogens simultaneously. High-throughput. Genotypic method.

4. Serotyping- A lab method used to classify and identify microorganisms into serotypes based on antigens found on cell surfaces.

5. The skin is the body’s 1st line of defense.

• Normal skin flora is usually harmless and beneficial. ← Ex: Staphylococcus epidermidis, Corynebacterium spp., and Cutibacterium acnes

6. Broken skin greatly increases the risk of infection.

7. Macules- A flat discoloration. Ex- freckle or measles rash.

8. Papules- A small, raised, and solid lesion. Ex- wart.

9. Pustules- Raised lesion filled with pus. Ex- acne.

10. Vesicles- A small fluid-filled blister. Ex- Chickenpox or Herpes Simplex.

11. Exanthem- A widespread rash that is usually associated with viral infections. Ex- Measles and Rubella.

Common Diseases:

1. Rubella

2. Ringworm

3. Impetigo

4. Cellulitis

5. Shingles

6. Leishmaniasis

7. Smallpox

Clinical Scenarios to Know:

8. Tree Branch Wound

9. Unilateral Facial Rash

10. “Slapped Cheek” Rash

1. Rubella- known as German measles, produces a mild fever with a fine pink rash. It is a big concern in pregnant women as it can cause congenital rubella syndrome.

2. Ringworm- a dermatophyte fungal infection. There are different types, such as Tinea pedis (athlete's foot). Ringworm is a ring-shaped lesion with a central clearing. It is NOT caused by a worm!

3. Impetigo- skin disease caused by S. aureus or S. pyogenes, respectively. Characteristics include a honey-colored crust, that is highly contagious and common in children.

4. Cellulitis- an infection of the deeper skin layers; usually caused by S. aureus or S. pyogenes. It can spread rapidly and is often red, warm, swollen, and painful.

5. Shingles- caused by Herpes Zoster, occurs after childhood chickenpox and is caused by reactivation of the Varicella Zoster virus. It produces a painful vesicular rash.

6. Leishmaniasis- caused by a protozoan parasite and is transmitted by a sandfly (female). Chronic skin ulcers are produced.

7. Smallpox- is caused by the Variola virus and forms deep pustules that are all in the same stage of development. Declared eradicated in 1980, and vaccination is no longer routine.

8. Tree Branch Wound- Think Sporothrix schenckii (sporotrichosis or Rose Gardener’s); fungal, contracted through cuts from thorns, splinters, contaminated plant matter.

9. Unilateral Facial Rash- Think Shingles. A unilateral facial rash following a dermatome (specific area of skin supplied by a single spinal or cranial nerve) is most commonly Shingles. It stops abruptly at the body’s midline.

10. “Slapped Cheek” Rash- Think Parvovirus B19, Erythema infectiosum (Fifth Disease); the eyes have natural defenses to protect them from infection

The Nervous System:

1. What does it include and what is it shielded by?

Meningitis:

2. What is it?

3. Symptoms

4. Most serious acute bacterial

5. Neonatal meningitis

6. Diagnosis

1. Brain and spinal cord; shielded by the skull, vertebrae, meninges, CSF, and the blood-brain barrier.

• Because of these defenses, infections are relatively uncommon, but when they do occur, they can progress rapidly and cause permanent neurological damage or even death. Early recognition and treatment are critical!

2. Inflammation of the meninges (outer to inner- dura mater, arachnoid mater, pia mater), which is the protective membrane that surrounds the brain and spinal cord. MEDICAL EMERGENCY!

• The meninges swell inside of a space that cannot expand (skull)→ Pressure builds up, damaging brain tissue → Permanent injury can occur very quickly (so if suspected, antibiotics are started prior to the return of the culture results)

3. Severe headache, fever, neck stiffness, photophobia, nausea/vomiting, confusion, and altered mental status.

4. Most serious acute bacterial- Neisseria meningitidis (associated with college dorms). It is spread by close contact and respiratory droplets. Can be prevented with meningococcal vaccines.

5. Neonatal meningitis- Streptococcus agalactiae (Group B Strep). This is spread by the mom carrying Group B Strep normally. When the baby passes through the birth canal, the bacteria can enter the bloodstream and travel to the meninges.

• Pregnant women are screened around 35-37 weeks and + mothers receive IV penicillin during labor.

6. Diagnosis- Lumbar puncture; sample CSF directly. Many tests can be performed on these samples, but appearance, cell count, glucose, protein, Gram stain, and culture results are key players.

• PCR is often used on the sample for rapid diagnosis.

Common Diseases:

1. Rubella

2. Ringworm

3. Impetigo

4. Cellulitis

5. Shingles

6. Leishmaniasis

7. Smallpox

Clinical Scenarios to Know:

8. Tree Branch Wound

9. Unilateral Facial Rash

10. “Slapped Cheek” Rash

1. Rubella- known as German measles, produces a mild fever with a fine pink rash. It is a big concern in pregnant women as it can cause congenital rubella syndrome.

2. Ringworm- a dermatophyte fungal infection. There are different types, such as Tinea pedis (athlete's foot). Ringworm is a ring-shaped lesion with a central clearing. It is NOT caused by a worm!

3. Impetigo- skin disease caused by S. aureus or S. pyogenes, respectively. Characteristics include a honey-colored crust, that is highly contagious and common in children.

4. Cellulitis- an infection of the deeper skin layers; usually caused by S. aureus or S. pyogenes. It can spread rapidly and is often red, warm, swollen, and painful.

5. Shingles- caused by Herpes Zoster, occurs after childhood chickenpox and is caused by reactivation of the Varicella Zoster virus. It produces a painful vesicular rash.

6. Leishmaniasis- caused by a protozoan parasite and is transmitted by a sandfly (female). Chronic skin ulcers are produced.

7. Smallpox- is caused by the Variola virus and forms deep pustules that are all in the same stage of development. Declared eradicated in 1980, and vaccination is no longer routine.

8. Tree Branch Wound- Think Sporothrix schenckii (sporotrichosis or Rose Gardener’s); fungal, contracted through cuts from thorns, splinters, contaminated plant matter.

9. Unilateral Facial Rash- Think Shingles. A unilateral facial rash following a dermatome (specific area of skin supplied by a single spinal or cranial nerve) is most commonly Shingles. It stops abruptly at the body’s midline.

10. “Slapped Cheek” Rash- Think Parvovirus B19, Erythema infectiosum (Fifth Disease); the eyes have natural defenses to protect them from infection

Arboviruses:

1. What are they? Examples.

Creutzfeldt-Jakob Disease:

2. What is it? What is it caused by?

• What is present?

• Symptoms

• Transmission & Treatment

• Importance in healthcare

1. Arthropod-borne viruses- Viruses borne by insects; for example, mosquitoes and ticks both transmit viruses. Examples include West Nile virus, Eastern Equine Encephalitis, St. Louis Encephalitis, and Zika virus.

• Arbo = arthropod-borne

2. CJD is a prion disease. The prion is an abnormal protein that causes every normal protein around it to fold incorrectly. This chain reaction slowly destroys the brain (spongiform damages- holes of brain).

• There are no bacteria, viruses, or fungi present. ONLY an abnormal protein called a prion.

• Symptoms- altered behavior, dementia, memory loss, etc. PT experience uncontrollable muscle contractions until death, which usually occurs within 1 year of diagnosis.

• Humans contract the disease by ingesting contaminated meat. There is no treatment for CJD aka “Mad Cow Disease.”

• Healthcare providers should be aware of the possibility of CJD in PT when surgical procedures are performed, since it can be transmitted through contaminated surgical equipment. Prions are resistant to normal sterilization and disinfection procedures.

Cardiovascular and Lymphatic System:

1. Microorganisms and Blood

2. Lymphatic System Function

Terminology:

3. Viremia

4. Septicemia

5. Bacteremia

6. Sepsis

7. Blood Cultures

1. Normally blood is sterile! Unlike the skin, mouth, or intestines, microorganisms should never be freely circulating in the bloodstream.

• Access to blood allows microorganisms to spread rapidly throughout the body, causing widespread inflammation, organ damage, and death.

2. Serves as one of the body’s “filtration systems,” helping immune cells recognize and destroy pathogens before they become systemic.

3. Viremia- The presence of viruses in the bloodstream. Ex- HIV, Measles

4. Septicemia- Used to describe microorganisms multiplying in the bloodstream and causing illness.

5. Bacteremia- The presence of bacteria in the bloodstream. It could be temporary, but could lead to more serious infections if not cleared.

6. Sepsis- Normally, inflammation helps fight infection. In sepsis, the immune response becomes widespread and uncontrolled. Instead of helping, it begins damaging the PT’s own organs. So both the bacteria and the body’s overwhelming immune response cause damage.

7. Blood cultures are used to identify microorganisms causing bloodstream infections. They should always be collected before antibiotics when possible.

Ebola Virus Disease

1. What is it?

HIV Case Study: Suzanne

2. What does HIV target?\

3. Transmission (Horizontal and Vertical)

4. Prevention

5. HIV vs AIDS

Diseases and Transmission:

6. Tularemia

7. Plague

8. Subacute endocarditis

9. Cat Scratch Disease

1. Ebola Virus Disease is a hemorrhagic fever transmitted by bodily fluids that damages blood vessels.

• There are also nonhemorrhagic fever diseases that produce fever without widespread bleeding (infectious mononucleosis, HIV, Lyme Disease, and Cat Scratch Disease).

2. HIV attacks the CD4 Helper T cells. These cells help coordinate the immune response. When enough cells are lost, the immune system begins failing.

3. Horizontal transmission refers to person-to-person (sexual contact, needle sharing, blood products- rare today). Vertical transmission refers to parent-to-child (pregnancy, birth, breastfeeding).

4. Condoms, PrEP (pre-exposure prophylaxis), needle safety, screening blood donors, maternal antiviral therapy.

5. HIV is the virus, and AIDS is an advanced disease that results years after immune destruction.

6. Tularemia is caused by Francisella tularensis and transmitted by rabbits, ticks, and deer flies. “Rabbit Fever".”

7. Plague is caused by Yersinia pestis. The vector is fleas carried by rodents. It causes buboes, which are swollen lymph nodes.

8. Subacute endocarditis is caused by bacteria of low pathogenicity, often originating in the oral cavity (alpha-hemolytic streptococci like S. mutans). It’s almost always preceded by damage to the heart valves or abnormal heart valves. Not transmitted by other people or environment, it is the endogenous transfer of normal biota to the bloodstream!

9. Cat Scratch Disease is caused by Bartonella species (B. henselae). It is an infection connected to being clawed or bitten by a cat. It is transmitted among cats by fleas.

Brucellosis:

1. Caused by & Causes…

2. Transmitted from…

Spotted Fever Rickettsioses:

3. Caused by…

4. Notable

5. Symptoms

1. Is caused by Brucella species and causes focal lesions in the liver, spleen, bone marrow, and kidney when in the bloodstream. Causes fluctuating fever (undulant fever).

2. Transmitted from direct contact, airborne, and parenteral (needlesticks).

• Transmitted from infected animals to humans through consuming unpasteurized dairy products, direct contact with infected animal tissue like placenta, blood, birthing fluids, or inhaling airborne bacteria in farms or slaughterhouses. 

3. Caused by Rickettsia sp. (Rickettsia rickettsii) transmitted by hard ticks such as wood ticks, the American dog tick, and the Lone Star tick. 

4. Rash begins on wrists and ankles

5. Symptoms include fever, chills, headache, and muscular pain. A rash appears 2-4 days later before spreading.

Disease and Transmission Matching:

1. Listeria meningitis

2. Infectious mononucleosis

3. Conjunctivitis

4. West Nile Virus

5. Lyme Disease

Why would a sudden outbreak of smallpox be surprising and considered a medical emergency?

1. Listeria meningitis- Ingestion of contaminated dairy products, poultry, meat, and hard-boiled eggs.

• Primary reservoir is water and soil, and secondary sources of infection include animals, plants, and food.

2. Infectious mononucleosis- Direct oral contact and contamination with saliva. Direct, indirect contact, and parenteral.

3. Conjunctivitis- Infection of the conjunctiva of the eye, relatively common. Transmitted by direct and indirect contact.

4. West Nile Virus- Spread by bites of infected mosquitos who pick up virus from infected birds.

5. Lyme Disease- Transmitted by a black-legged tick (deer tick). Causes a bull's-eye rash.

• Caused by Borrelia burgorferi.

This is because the last natural case worldwide was in 1977, and it is a Category A bioterrorism agent. It is highly contagious, and the general public lacks immunity due to smallpox vaccinations being stopped in the US in 1972 (no herd immunity). 

Matching: Signs and Symptoms with Disease:

1. Botulism

2. Impetigo

3. Tinea cruris

4. Infectious mononucleosis

5. Tetanus

1. Botulism- A serious illness caused by the neurotoxin that is produced by Clostridium botulinum. The toxin blocks signals to the muscles, causing flaccid (descending) paralysis (opposite ot tetanus) that can lead to respiratory failure. Common sources include improperly canned foods, contaminated wounds, and honey in infants.

2. Impetigo- A highly contagious superficial bacterial skin infection caused by Staphylococcus aureus or Streptococcus pyogenes. It is common in children and produces honey-colored crusted lesions usually around the nose and mouth.

3. Tinea cruris- AKA jock itch. A fungal infection (dermatophyte/ringworm) that affects the groin, perianal folds, and inner thighs. It thrives in warm, moist environments that cause itchy, red, ring-shaped rash.

4. Infectious mononucleosis- “Mono” or “Kissing disease.” Caused by EBV and spread through saliva. Symptoms include fever, sore throat, swollen llymph nodes, extreme fatigue, and sometimes enlarged spleen.

5. Tetanus- Caused by neurotoxin produced by Clostridium tetani, usually entering through a contaminated wound. The toxin causes painful muscle spasms and spastic paralysis (lockjaw). It is not spread person-to-person and is prevented through vaccination.