Clinical Microbiology: Flashcards
Important Bacterial and Viral causes of Community-Acquired Pneumonia by Age:
What are the risk factors of the typical organisms causing Community-Acquired Pneumonia?
Alcoholism is a risk factor of which pathogen to cause Community-Acquired Pneumonia:
Klebsiella Pneumonia and Oral Anaerobes
COPD is a risk factor of which pathogen to cause Community-Acquired Pneumonia:
Hemophilus Influenza
Which pathogen is associated with an increased risk of causing Community-Acquired Pneumonia in individuals with cystic fibrosis?
Pseudomonas aeruginosa
Which pathogen is associated with an increased risk of causing Community-Acquired Pneumonia in individuals with influenza virus infection or post influenza virus infection?
Staphylococcus Aureus
In individuals with history of bird exposure, particularly parrots, which pathogen poses a high risk of causing Community-Acquired Pneumonia?
Chlamydophila psittaci
Which virus is associated with Squamous cell laryngeal carcinoma and Squamous cell pharyngeal cancer:
🔸Human papillomavirus (HPV)
Low-risk subtypes: HPV 1, 2, 6 and 11
High-risk subtypes: HPV 16, 18, 31, and 33
JC Virus can cause:
🔸 Progressive Multifocal Leukoencephalopathy (PML)
The JC virus (JCV) is a type of human polyomavirus that was discovered in 1971. It is named after the initials of the patient, John Cunningham, from whom the virus was first isolated. The JC virus is a small, non-enveloped DNA virus that belongs to the Polyomaviridae family.
In the general population, the JC virus is quite common, with studies indicating that up to 70-90% of adults have been exposed to the virus at some point in their lives. After initial infection, the JC virus usually establishes a latent (inactive) infection in the kidneys and other sites, such as the bone marrow and lymphoid tissue.
In individuals with a healthy immune system, the JC virus typically remains dormant and does not cause any noticeable symptoms or complications. However, in people with weakened immune systems, such as those with HIV/AIDS, organ transplant recipients, or individuals with certain autoimmune conditions, the JC virus can become reactivated and cause significant health problems.
The most notable complication associated with JC virus reactivation is progressive multifocal leukoencephalopathy (PML).
- JC Virus Reactivation:
In individuals with HIV infection, the immune system is compromised, leading to a decreased ability to control viral infections. When the immune system is weakened, the JC virus can reactivate and start replicating in the brain. - Progressive Multifocal Leukoencephalopathy (PML):
PML is a rare but severe neurological condition caused by the JC virus. It primarily affects the white matter of the brain, leading to the destruction of myelin, the protective covering of nerve cells. As a result, individuals with PML can experience a range of neurological symptoms. - Clinical Presentation:
The symptoms of PML can vary depending on the areas of the brain affected. Common signs and symptoms may include:
- Changes in vision, such as blurred vision or loss of visual acuity.
- Difficulty with coordination, balance, and walking.
- Weakness or paralysis on one side of the body.
- Cognitive and behavioral changes, including confusion, memory loss, and personality changes.
- Speech problems.
- Seizures.
- Headache. - Diagnosis:
The diagnosis of PML involves a combination of clinical evaluation and diagnostic tests:
- Neurological Examination: A thorough neurological examination is performed to assess the individual’s symptoms and signs.
- Magnetic Resonance Imaging (MRI): An MRI scan of the brain is typically conducted to detect characteristic white matter lesions that are indicative of PML.
- JC Virus DNA Testing: Cerebrospinal fluid (CSF) samples may be collected and tested for the presence of JC virus DNA using a technique called polymerase chain reaction (PCR). - Management:
There is no specific antiviral treatment for PML, and the main focus is on managing the underlying HIV infection and supporting the individual’s immune system. This may involve the following:
- Antiretroviral Therapy (ART): Effective ART helps to restore the immune system function and control HIV replication, which can slow down the progression of PML.
- Immune Reconstitution Inflammatory Syndrome (IRIS): In some cases, as the immune system starts to recover with ART, an exaggerated inflammatory response can occur, which is known as IRIS. Treatment may involve medications to manage this immune response.
- Supportive Care: Symptomatic treatment is provided to manage specific symptoms and improve the individual’s quality of life. This may include physical therapy, speech therapy, and medications to control seizures or manage pain.
Explain Fifth Disease:
Fifth disease, also known as Erythema Infectiosum:
🔸Epidemiology:
Fifth disease is most commonly seen in children, particularly between the ages of 5 and 15 years. Outbreaks of the infection are more common during the winter and spring months. Adults can also be affected, especially those who are in close contact with infected children or have compromised immune systems.
Peak Incidence: 5 to 15 years old
🔸Transmission:
Parvovirus B19, the causative agent of Fifth disease, is primarily transmitted through respiratory droplets. It spreads from person to person through coughing, sneezing, or close contact with an infected individual. The virus can also be transmitted vertically from an infected mother to the fetus during pregnancy.
🔸Incubation Period:
The incubation period for Parvovirus B19 infection is typically 4-14 days, with an average of 10 days. This means that symptoms may appear within this timeframe after exposure to the virus.
🔸Clinical Presentation:
Fifth disease typically begins with a prodromal phase characterized by mild symptoms such as low-grade fever, headache, fatigue, and malaise. After a few days, the characteristic rash appears. It starts with a “slapped cheek” appearance, with bright red erythema on both cheeks, giving the face a flushed appearance. This is followed by a lacy, reticular rash on the trunk and extremities. The rash can be itchy but is usually not painful. The rash tends to fade over time, but it may reappear with heat, exercise, or sun exposure.
▪️Stage 1: Mild Symptoms
🔺Prodromal phase: characterized by mild symptoms such as low-grade fever, headache, fatigue, and malaise.
▪️Stage 2: Exanthem or Rash
It starts 2-5 days after the Mild or Prodromal Phase
The Rash first starts in the face with Slapped cheek rash and then extends to the trunk and extremities.
🔺Slapped-Cheek Rash: This rash involves the face with diffuse redness of the face with peri-oral sparing. 🔺Rash spread to Trunk and Extremities: Maculopapular rash, may be associated with pruritis in 50% of cases, fades after 7-10 days. Becomes more pronounced after exposure to sunlight or heat.
🔸Diagnosis:
All age groups may have transient normocytic anemia as Parvovirus B19 can affect the RBCs.
▪️Diagnosis in Immunocompetent Children:
🔺Clinical Diagnosis - Slapped Cheek rash
▪️Diagnosis in Immunocompetent Adults:
🔺If diagnosis is unclear we can do serology testing:
- IgM antibody
Appears within ∼ 10 days of initial exposure, indicating acute illness
Remains positive for 2–3 months - IgG antibody
Appears approx. 2 weeks following infection
Remains positive for life
▪️Diagnosis in Immunocompromised:
🔺Initial diagnostic test: viral DNA testing such as PCR of blood or bone marrow
🔺Adjunctive diagnostic test: serologic antibody testing
🔸Management:
In most cases, Fifth disease is a self-limiting condition that resolves on its own without specific treatment. Symptomatic management may include rest, hydration, and over-the-counter pain relievers to alleviate any discomfort.
Treatment is not necessary in most cases, as the disease is often self-limited
Analgesics and nonsteroidal anti‑inflammatory drugs (NSAIDs)
Short course of low‑dose prednisone for parvovirus B19‑associated arthritis
🔸Complications:
Fifth disease is generally a mild illness with a low risk of complications. However, certain populations, such as individuals with underlying immune deficiencies or pregnant women, may be at a higher risk of complications. In pregnant women, Parvovirus B19 infection can lead to fetal complications, including hydrops fetalis, as mentioned earlier.
Describe this picture, and what is the causative organism of this:
Slapped Cheek rash seen in Fifth disease
Caused by Parvovirus B19
Classification of Enveloped DNA Viruses:
Classification of Non-Enveloped DNA Viruses:
Explain Respiratory Syncytial Virus (RSV) and it’s course of Pathogenesis:
Respiratory Syncytial Virus (RSV) is a common viral infection that primarily affects the respiratory tract, particularly in young children. Let’s explore the details of RSV:
🔸Epidemiology:
RSV is a highly prevalent respiratory virus, and almost all individuals have had an RSV infection by the age of 2. Reinfection can occur throughout life due to the presence of different strains and waning immunity over time. This highlights the importance of continued preventive measures, especially in high-risk populations.
RSV infection can cause significant morbidity and mortality, particularly in young children and older adults. In young children, RSV is a leading cause of hospitalization, primarily due to bronchiolitis, which is the inflammation and obstruction of the small airways in the lungs. RSV bronchiolitis can lead to respiratory distress, difficulty breathing, and in severe cases, may require intensive care and mechanical ventilation. In older adults, RSV infection can also lead to severe respiratory illness, especially in those with underlying health conditions.
▪️RSV is the most common cause of hospitalization, bronchiolitis, and pneumonia in infants.
🔸Clinical Presentation:
- Symptoms of Nonspecific Viral Illness:
- Lethargy or fatigue: RSV infection can cause a general feeling of tiredness or lack of energy.
- Irritability: Infants and young children with RSV infection may become more irritable or fussy than usual.
- Decreased appetite: RSV infection can lead to a decreased desire to eat or drink.
- Fever: Fever is a common symptom of RSV infection, although not all individuals will experience it. The fever is usually mild to moderate in nature. - Symptoms of Upper Respiratory Tract Infection:
- Rhinorrhea: RSV infection can cause a runny nose, with the nasal discharge often being thick and copious in infants.
- Acute otitis media: Up to 60% of children with RSV infection may develop acute otitis media, which is an infection of the middle ear. This can present with symptoms such as ear pain, fever, and irritability. - Symptoms of Lower Respiratory Tract Infection:
- Cough: A persistent cough is a common symptom of RSV infection in patients of all ages.
- Tachypnea: RSV infection can lead to rapid breathing, known as tachypnea.
- Rales, wheezes, crackles: These abnormal lung sounds may be heard upon auscultation of the chest. Rales are crackling sounds, wheezes are high-pitched whistling sounds, and crackles are intermittent clicking or rattling sounds.
In Young Children:
- Clinical features of bronchiolitis: RSV infection commonly causes bronchiolitis in infants and young children. Bronchiolitis is characterized by inflammation and narrowing of the small airways in the lungs, resulting in wheezing, difficulty breathing, and respiratory distress.
- Clinical features of pediatric pneumonia: In some cases, RSV infection in young children can progress to pneumonia, which may present with symptoms such as fever, cough, rapid breathing, and signs of respiratory distress.
In Older Children and Adults:
- Clinical features of acute bronchitis: RSV infection in older children and adults may manifest as acute bronchitis, which is characterized by cough, production of sputum, and chest discomfort.
- Clinical features of pneumonia: RSV infection can also lead to pneumonia in older children and adults, with symptoms such as fever, cough, shortness of breath, and signs of pneumonia on clinical examination.
▪️Signs of Severe RSV Infection:
In severe cases of RSV infection, certain signs may indicate respiratory distress or severe illness:
- Signs of respiratory distress: These can include increased work of breathing, such as rapid or labored breathing, retractions (visible inward movement of the chest wall during inhalation), and nasal flaring.
- Hypoxemia: Severe RSV infection may lead to low oxygen levels in the blood, known as hypoxemia.
- Apnea: Episodes of temporary cessation of breathing, known as apnea.
🔸Transmission:
RSV is highly contagious and spreads through respiratory droplets when an infected person coughs or sneezes. It can also be transmitted through direct contact with surfaces contaminated by the virus. RSV is most prevalent during the fall, winter, and spring seasons.
▪️Incubation Period: 2-8 days
🔸Risk Factors:
▪️Risk factors for severe RSV infection in Children:
Age < 6 months: This is considered the single most important risk factor for severe RSV infection in children. Infants under 6 months of age have a higher risk of developing severe lower respiratory tract infection due to their immature immune systems and smaller airways.
Preterm birth, especially if associated with chronic lung disease of prematurity
Congenital heart disease
Immunocompromised states
Neuromuscular disorders that affect the ability to clear airway secretions
Childcare Attendance: Children who attend daycare or are in close contact with other children have a higher risk of RSV infection due to increased exposure to the virus.
Exposure to Tobacco Smoke: Secondhand smoke exposure can impair the respiratory defenses and increase the risk of severe RSV infection in children
▪️Risk factors for severe RSV infection in Adults:
Older age: ≥ 60 years (especially ≥ 75 years)
Chronic lung diseases: COPD, asthma
Cardiac diseases: congestive heart failure, coronary artery disease
Neurologic disorders: cerebrovascular disease, neuromuscular conditions
Diabetes mellitus
Chronic kidney disease
Liver disease
Hematologic disorders
Immunocompromised state
🔸RSV Virulence Factors:
▪️Fusion (F) Protein: The F protein is responsible for viral entry into host cells. It facilitates the fusion of viral and host cell membranes, allowing the virus to enter and infect respiratory epithelial cells. The F protein is a major target for neutralizing antibodies and plays a crucial role in RSV pathogenesis.
▪️Attachment (G) Protein: The G protein is involved in viral attachment to host cells. Although it is not essential for infection, it enhances viral infectivity and contributes to viral replication. The G protein also helps the virus evade the host immune response by interfering with the production of neutralizing antibodies. Glycoprotein G allows the virus to attach to respiratory epithelial cells; its ability to frequently mutate helps the virus evade the host immunity and permits reinfections throughout an individual’s life.
▪️RNA Polymerase: RSV encodes an RNA-dependent RNA polymerase that is crucial for viral replication and transcription of viral genes. This enzyme is essential for the production of viral RNA and proteins necessary for viral replication and assembly.
▪️Nonstructural Proteins: RSV produces nonstructural proteins, such as NS1 and NS2, which play a role in inhibiting the host immune response. These proteins interfere with the production of interferons, which are important antiviral molecules produced by the host cells to limit viral replication.
▪️Interferon Antagonism: RSV has developed mechanisms to counteract the host interferon response, which is a crucial defense mechanism against viral infections. The virus inhibits the production of interferons and interferon-stimulated genes, allowing it to replicate and spread within the host respiratory tract.
🔸Diagnosis:
Routine diagnostic testing for RSV is not usually done, but it can be considered depending on the clinical features. The decision to perform diagnostic testing may be considered by the presence of risk factors for severe RSV infection or the need for hospital admission and infection control measures.
- Additional Studies for Severe Illness: In cases of severe RSV infection, additional studies may be obtained to assess the severity of the illness. These studies can include arterial blood gas (ABG) analysis, respiratory viral panel, and chest x-ray. These tests help evaluate the respiratory status and assist in determining the appropriate management and treatment plan.
- Confirmatory Testing for RSV: If indicated based on clinical suspicion, confirmatory testing for RSV can be performed using various methods:
- Nucleic Acid Amplification Test (reverse transcription PCR): This is the preferred diagnostic method for RSV detection in respiratory tract samples.
- Rapid Antigen Detection Test: This test is primarily used in young children and provides quick results but may have slightly lower sensitivity compared to nucleic acid amplification tests.
- Viral Culture: Although rarely used due to its longer turnaround time, viral culture can also be used to identify RSV.
▪️Chest X-ray Findings: Chest X-ray is not routinely indicated in the diagnosis of RSV infection. However, in cases where a chest X-ray is obtained, it may show nonspecific findings such as peribronchial thickening and pulmonary hyperinflation. These findings are not specific to RSV infection but can be seen in bronchiolitis or pneumonia caused by RSV or other pathogens.
🔸Management:
Management of RSV infection focuses on supportive care to alleviate symptoms and prevent complications. This may include ensuring proper hydration, encouraging rest, using saline nasal drops to relieve nasal congestion, and providing fever-reducing medications if necessary. In severe cases, hospitalization may be required for close monitoring and respiratory support.
▪️Supportive Care:
Cool mist humidifier or steamy showers
Antipyretics for fever and/or discomfort
Encourage adequate fluid intake; if unable to tolerate oral fluids, provide NG/IV fluids.
Gentle nasal suctioning in infants
▪️Pharmacotherapy:
Infants and young children: inhaled ribavirin
🔸Prevention:
Preventing RSV infection is crucial, especially in high-risk individuals. Measures for prevention include frequent handwashing, avoiding close contact with sick individuals, covering the mouth and nose while coughing or sneezing, and disinfecting surfaces regularly. Additionally, for certain high-risk populations, a monthly injection of a monoclonal antibody called palivizumab may be recommended during RSV season for prophylaxis.
🔸Complications:
In infants and young children, RSV infection can lead to more severe respiratory symptoms, such as difficulty breathing, decreased appetite, and dehydration. It may also cause secondary bacterial infections, such as ear infections or pneumonia. In high-risk individuals, RSV infection can sometimes be life-threatening.
Respiratory Syncytial Virus (RSV) incubation period _______________.
2-8 days
What are the risk factors for developing Severe Respiratory Syncytial Virus (RSV) Infection in Adults and Children:
▪️Risk factors for severe RSV infection in Children:
- Age < 6 months: This is considered the single most important risk factor for severe RSV infection in children. Infants under 6 months of age have a higher risk of developing severe lower respiratory tract infection due to their immature immune systems and smaller airways.
- Preterm birth, especially if associated with chronic lung disease of prematurity
- Congenital heart disease
- Immunocompromised states
- Neuromuscular disorders that affect the ability to clear airway secretions
- Childcare Attendance: Children who attend daycare or are in close contact with other children have a higher risk of RSV infection due to increased exposure to the virus.
- Exposure to Tobacco Smoke: Secondhand smoke exposure can impair the respiratory defenses and increase the risk of severe RSV infection in children
▪️Risk factors for severe RSV infection in Adults:
- Older age: ≥ 60 years (especially ≥ 75 years)
- Chronic lung diseases: COPD, asthma
- Cardiac diseases: congestive heart failure, coronary artery disease
- Neurologic disorders: cerebrovascular disease, neuromuscular conditions
- Diabetes mellitus
- Chronic kidney disease
- Liver disease
- Hematologic disorders
- Immunocompromised state
What will Respiratory Syncytial Virus (RSV) infection show in Chest X-Ray:
Nonspecific findings such as peribronchial thickening and pulmonary hyperinflation
Respiratory syncytial virus can cause:
- Upper respiratory tract infections
- Bronchiolitis
- Pneumonia
Human metapneumovirus can cause:
- Bronchiolitis
- Pneumonia
Classification of Paramyxoviridae family which is under Enveloped RNA viruses:
Classification of Pneumoviridae family which belongs under Enveloped RNA Viruses:
When is the contagious period of Measles:
Measles is contagious for a period of 4 days before the onset of the characteristic rash (exanthem) and up to 4 days after the rash appears.
Peak incidence of measles:
Below 12 months of age
What is the Gold standard for the diagnosis of Measles:
Serology: Measles-specific IgM antibodies