Microbiology 🦠 Flashcards
What is the genus mycobacterium composed of?
Around 100 species.
What are the most familiar species of mycobacterium?
The most familiar species are Mycobacterium tuberculosis (M. tuberculosis), the causative agent of tuberculosis (TB) and Mycobacterium leprae (M. leprae), the causative agent of leprosy.
What are mycobacterium classified into?
- Members of M. tuberculosis complex:
- Cause tuberculosis in different hosts.
- Examples: M. tuberculosis, M. bovis. - Non-tuberculous Mycobacteria (Atypical Mycobacteria)
- Example: Mycobacterium avium complex (MAC). - M.leprea: The causative agent of leprosy.
What are the characteristics of nontuberculous mycobacteria?
- Less pathogenic species.
- Not transmitted from human to human (acquired from natural sources).
- Cause infections in immune-compromised patients.
- Resistant to the usual anti-tuberculosis drugs.
- Wide range of diseases: Pulmonary disease that resembles TB, Cervical lymphadenitis, Granulomatus skin lesions & soft tissue infections.
What are the properties (key characters) of mycobacteria?
- The cell wall contains extremely high lipid content (40-60 %), which is responsible for their staining and cultural characters.
- Acid fastness (Acid-fast bacilli). “Not decolorized by acids”
- Slow growth rate.
What is the morphology of mycobacteria?
- Straight or slightly curved rods.
- Occurring singly, in pairs, or small clumps.
- Non-motile, Non-spore forming, Non-capsulated.
- Acid & alcohol fast.
- Not stained by Gram.
What are the cultural characters of mycobacteria and what is responsible for it?
- Strict aerobe.
- 5 - 10% CO2, enhances growth.
- Optimum temperature is 37 °C.
- Very slow grower (may require 2-8 weeks to get visual colonies).
- No growth on ordinary media.
What are the media used to grow mycobacteria?
Egg-based media:
➢ Lowenstein-Jensen medium.
“Selective medium to isolate TB from contaminated specimens”
➢ Dorest egg medium.
Agar-based media:
➢ Middle brook’s medium.
What is the Reservoir and the source of mycobacterium tuberculosis?
Humans are the only reservoir and source for M. tuberculosis.
What is the mode of transmission of mycobacterium tuberculosis?
Mode of transmission: inhalation of infectious airborne droplets.
- M. bovis causes TB in cows, and is transmitted to humans by ingestion of raw “not sterealizd” milk leading to extra pulmonary TB. “GIT TB”
What is the virulence mechanism of mycobacterium tuberculosis?
The basis for M. tuberculosis virulence is largely unknown
- M. tuberculosis doesn’t produce any toxin.
- Main determinant of virulence is the capability for intracellular growth in alveolar macrophages. “Replicate in phagosome as they prevent the action of lysosomes”
- Main pathology in infected tissue is primarily due to immune response of host rather than any virulence factor produced by it.
What are the risk factors for TB?
- Small rooms & rooms with poor ventilation.
- Steroids, chemotherapy, malignancies, malnutrition.
- HIV (one of the most important risk factors): Patients with TB should be tested for HIV & those with HIV should be tested periodically for TB. HIV reactivates latent TB infection, makes disease more serious, renders treatment ineffective. “TB is related to HIV”
What are the clinical syndromes of TB?
A. Pulmonary TB: Affects the lower respiratory system.
Characterized by: (WSAF FC)
➢ Chronic productive cough up to coughing bloody sputum,
➢ Low-grade fever,
➢ Weight loss, “mild”
➢ Night sweats,
➢ Appetite loss
➢ Fatigue.
B. Extra pulmonary TB: due to spread of bacilli through circulation during initial stage of multiplication e.g. Renal TB, Gastrointestinal TB, TB meningitis.
What is a laboratory diagnosis for mycobacterium tuberculosis?
- Specimen Collection
- Direct smear
- Culture
- Rapid culture method (BACTEC System)
- Intradermal skin test (Tuberculin test)
- Recent methods for diagnosis
How are specimen for mycobacterium tuberculosis collected?
- Sputum, bronchial or gastric washings (Gastric washings are especially used for young children).
- At least 3 morning samples of sputum are required for diagnosis. “ for 3 successive days”
What are the stains used for mycobacterium tuberculosis?
Ziehl-Neelsen (Z-N) stain and Fluorochrome stain.
What color does mycobacterium tuberculosis give with Zein Nelson stain?
Bacilli appear pink in a contrasting blue background
What color does mycobacterium tuberculosis give With fluorochrome stain?
Bacilli appear as bright yellow on dark background
What are the advantages and disadvantages of direct smear?
- Advantages: Rapid, Cheap, Simple.
- Disadvantages: Low sensitivity in addition to being non specific
What is the definitive method to detect and identify Tuberculosis?
Culture
What are the disadvantages of direct smear? “In details”
• Low sensitivity: (at least 5,000 – 10,000 bacilli/ml
sample should be present to have +ve smear).
• Non specific: (Other AFB are similar to M. tuberclosis in stained smear).
What should happen to all positive and negative direct stand smear samples?
They should be cultured
What are the steps of culture of mycobacterium tuberculosis?
- Sputum is inoculated on selective medium (Lowenstein-Jensen), as it contains normal bacterial flora.
- Cultures are incubated in appropriate conditions (see culture Charaters) and are examined weekly for 2-8 weeks (Slow-growing bacillus).
What are the advantages and disadvantages of culture of mycobacterium tuberculosis?
Advantages:
1. Highly sensitive & specific.
2. Useful for identification and susceptibility testing to antituberculous drugs.
Disadvantage:
long period of incubation (2-8 weeks) to get visual colonies.
What is rapid culture method and what time does it take? (BACTEC System)
- M. tuberculosis multiplies in broth media containing radio-labeled palmitic acid (sole carbon source) and release radio-labeled CO2.
- As M. tuberculosis multiplies, it utilizes the palmitic acid and release radio-labeled CO2.
- Growth can be detected in 9-16 days. “2 weeks”
What is the principle of intradermal skin (tuberculin test)?
- This test measures the patient’s cell mediated immune response (CMI) to bacterial Ag (tuberculoprotein) in a type IV hypersensetivity reaction.
- Intradermal injection (ID) of PPD (purified protein derivative) into a previously infected hypersensitive person results in the delayed (48-72 hr) appearance of an induration of ≥10 mm.
What is the value of tuberculin test in diagnosis?
- Positive reaction means previous exposure to M. tuberculosis (active/past infection). It carries no implication about the activity of the infection.
- Negative reaction means that this person has not been infected with M. tuberculosis (susceptible to infection). “And should be vaccinated”
- The value of tuberculin reaction to diagnose active infection is restricted to children <5 years, but in adults is of value only if negative to exclude infection.
- Recent conversion of the tuberculin reaction from negative to positive needs clinical attention.
What are the disadvantages of tuberculin test?
- False positive and False negative results.
What are the recent methods for diagnosis of mycobacterium tuberculosis?
A. Hybridization (DNA probe) and Nucleic Acid Amplification Tests (PCR, GeneXpert): Useful for direct detection of Mycobacterial genes in clinical specimen in ≤ 24hrs.
B. Chromatography: A technology that extracts fatty acids from the mycobacterial cell wall and analyze them.
C. QuantiFERON test: “Like tuberculin” ‘In vitro’ assay test of interferon-Gamma which is a component of CMI response to M. tuberculosis.
What are the characteristics of the recent methods for diagnosis of TB?
Rapid, specific & sensitive methods.
How to prevent and control TB?
- Adequate nutrition .
- Good housing.
- Health education.
What is the only licensed vaccine to prevent the development of active TB disease?
BCG Vaccine
What is BCG vaccine?
- Live attenuated vaccine prepared from attenuated strain of M. bovis (Bacillus of Calmette and Guerin) by repeated subculture on glycerol-potato-bile medium.
“Mycobacterium tuberculosis was cultured for 250 times over 13 years to give weak TB due to malnutrition”
Administration of BCG vaccine.
- Vaccine is given by ID injection to all infants in the first year of life & to tuberculin negative adults.
- Following vaccination, a tuberculin-negative individual → positive reactor (tuberculin conversion) after ~6 weeks.
What are the virus causes of respiratory tract infections?
▪ Myxoviridae family
- Orthomyxoviridae.. Include one genus :
✓ Influenza virus - Paramyxoviridae…Include 3 genera:
✓ Paramyxovirus (parainfluenza viruses and mumps virus);
✓ Pneumovirus (respiratory syncytial virus);
✓ Morbillivirus (measles virus).
▪ Coronaviridae family: Corona virus
▪ Adenoviridae family: Adenovirus
▪ Picornaviridaefamily: Human rhinoviruses
What is the morphology of influenza virus?
- Influenza virus particles are highly pleomorphic, 80-120 nm in diameter., The genome consists of Segmented (-) sense, s/s RNA in 8 segments (7 in Influenza C).
” - sense means can’t act directly as mRNA”
- The outer surface of the particle consists of a lipid envelope from which project prominent glycoprotein spikes of two types:
a) Haemagglutinin (HA).
b) Neuraminidase (NA). - The inner side of the envelope is lined by matrix protein (MP).
How are virus strains classified? ”influenza”
- Is done on the basis of antigenicity of nucleoprotien “in RNA” (NP) and matrix protien (MP) into three main groups A, B and C.
- Influenza A is classified into subtypes according to HA (16) and NA (9). “GP spikes”
What is antigenic shift and how common is it?
• This refers to major dramatic changes in the H and/or N proteins, which occurs when a cell is infected with two genetically distinct influenza virus……Undergoes reassortment
• Every 10-20 years and involves change in subtype
In which type of influenza does antigenic shift occur?
Type A
What is the definition of antigenic drift and how common is it?
- This refers to minor antigenic changes in the H and N protein that occur each year.
- Does not involve a change in the viral subtype.
In which type of influenza does antigenic drift occur?
A & B
Which of antigenic shift or antigenic drift cause pandemics and epidemics?
Antigenic shift
What is the source of influenza?
human beings .
How is influenza spread?
- rapid via respiratory droplets, Rapid spread leads to epidemics.
What is the incubation period of influenza?
- short (1-3 days). Rapid spread leads to epidemics.
What are the symptoms of infection with influenza?
- is characterized by fever “39 or above”, myalgia “pain in ,muscles”, headache and pharyngitis.There is usually no coryza ( no runny nose)
What are the complications of infection with influenza?
- Pneumonia caused by influenza virus itself.
- Pneumonia caused by bacteria “Secondary to viral infection” : S. aureus, Haemophilus influenza, or Stept. pneumoniae.
- Other viral super-infection, e.g. Adenovirus..
How is influenza diagnosed?
• Samples: Respiratory secretions, by aspirate, gargle or nasal washings used for:
a) Rapid examination of cells by IF for antigen detection.
b) Inoculation of cell cultures (or eggs).
• Serology: By detection of antibodies in the serum by haemagglutination inhibition (HAI).
• Molecular Techniques: By RT-PCR
How is influenza treated?
Several anti-influenza drugs exist.
• Amantadine and Rimantadine are active against influenza A (but not B viruses).
• Zanamivir by inhalation and oseltamivir (Tamiflu) orally: inhibit viral neuraminidase which is present in both influenza A and B viruses and is necessary for viral release from the infected cell.
What are the vaccines for influenza and what are their characteristics?
• Formaline inactivated vaccine:
✓ Produced by virus growth in embryonated egg.
✓ The vaccine is given IM once for adults every year (annually)
✓ For children it may be given twice 4 weeks apart according to the age.
• Much interest in other types of vaccine, especially: genetically engineered/subunits and Live attenuated vaccine (LAV).
What is avian influenza and what is it characterized by?
• Avian influenza is an infectious disease of birds caused by type A strains of the influenza virus.
• Highly pathogenic avian influenza is characterized a mortality that can approach 100% of the infected birds.
What are avian flu strains that can be transmitted from birds to human?
H5N1 and H7N9
What are the symptoms of infection with pathogenic strains of avian flu to humans?
• Infection is transmitted form birds to human but no Human to Human transmission is documented.
• Stomach upset and diarrhea may occur with avian influenza.
Is there a vaccine for avian flu?
• There is no vaccine for humans but bird vaccination is available.
What is swine flu and does it affect humans?
• Type A influenza of pigs and does not normally infect humans.
What are the variants of swine flu that infect humans and when did they appear?
• However, in 2009 a new H1N1 swine flu variant appeared with the ability to infect humans.
• In 2011, another swine flu strain (H3N2) appeared.
What does the subfamily Paramyxoviridae contain?
- This sub-family contains parainfluenza viruses (1, 2, 3 and 4), measles virus, mumps virus and respiratory syncytial virus (RSV).
What is the morphology of paramyxoviruses?
• Paramyxoviruses are composed of one piece of ssRNA, a helical nucleocapsid, and an outer lipoprotein envelope.
• The envelope is covered with spikes, which contain haemagglutinin, neuraminidase, and a fusion protein that causes cell fusion (form large multinucleate giant cells)
What do paramyxoviruses infect?
- Usually occur in (early) childhood, however, re-infections do occur in adulthood, but disease is sub-clinical or very minor.
How are paramyxoviruses spread?
- By droplets from the nose and mouth to fairly close contacts.
What do para influenza viruses cause?
• Cause acute laryngo-tracheo-bronchitis in children.
• Can cause pneumonia. “Complication”
How are para influenza viruses diagnosed?
• Detection of the viral RNA by RT-PCR.
• Detection of the viral antigens or antibodies by EIA and IF.
• Virus isolation: on cell culture and detection of cytopathic effects.
How are para influenza viruses treated?
• No specific treatment is available.
• No specific vaccine is available.
How is mumps virus transmitted?
Spread by the respiratory route.
What is the incubation period of mumps virus?
- has a relatively long incubation of about 21 days.
What is the clinical picture of mumps virus?
- It causes inflammation of the salivary glands, classically the parotid and submaxillary glands.
What are the complications of mumps virus?
1) Aseptic (viral) meningitis
2) Mumps meningoencephalitis: is rarer but a more serious development.
3)Orchitis: can occur, more often after puberty, unilateral or bilateral, but is rarely followed by infertility. “Only if bilateral”
4) Other glandular tissue is very occasionally involved e.g. pancreatitis, oophoritis or thyroiditis.
How is mumps virus diagnosed?
• Isolation of the virus from saliva, CSF “in case of meningitis” or urine by culture on monkey kidney cells.
• Serologically: Confirmed Diagnosis by positive IgM antibodies by using CF, HI and ELISA.
How is mumps virus prevented?
- Live attenuated virus vaccine given in MMR vaccine.
which virus is considered as one of the most infectious disease is known?
Measles
How is measles virus transmitted?
Transmission is by respiratory route (airborne). The virus can also infect via the eye and multiply in the conjunctivae.
What is the incubation period of measles virus?
10-12 day
What is the clinical picture of infection was measles virus?
- Prodromal “initial” phase is characterized by fever, dry cough,
sore throat, conjunctivitis, and Koplik’s spots (raised red spots with white centers in the mouth). After few days, the characteristic red, maculopapular rash starts on the head and then spreads to body. “Behind the ear”
What are the complications of infection with measles virus?
1) Bronchopneumonia and otitis media
2) Encephalitis occurs in ~1:2000 cases.
3) Subacute sclerosing pan encephalitis: It is a chronic infection in which the virus multiplies in the brain resulting in neurodegenerative disease. “Characteristic”
How is measles virus diagnosed?
- Measles is easy to diagnose clinically. Laboratory diagnosis is rarely needed.
How is measles virus prevented?
- Trivalent live attenuated vaccine (MMR) is usually given by sub cutaneous injection. It is given at 12 – 15 months age. A single dose of the MMR vaccine gives around 90% protection against measles and mumps and 95-99% against rubella.
How is measles virus treated?
• No specific drugs.
• Symptomatic treatment only.
What is the Characteristic thing about the morphology of respiratory syncytial virus?
- RSV resembles the other members of Paramyxoviruses morphologically, but it has no haemagglutinin or neuraminidase
“Even though it belongs to Paramyxoviridae”
What is the prime cause of bronchiolitis? “in children”
RSV
What is the common disease that is linked to RSV?
- RSV may be linked to epidemics of asthma and has been identified as an exacerbating factor in other diseases
What is the morphology of coronavirus?
- Coronaviruses are single stranded RNA enveloped viruses. They are named for the crown-like spikes on their surface.
What is the frequency of mutation of coronavirus and is this usual for an RNA virus with unsegmented Genome?
• Coronaviruses exhibit a high frequency of mutation. “New strains”
• This is unusual for an RNA virus with a nonsegmented genome and may contribute to the evolution of new virus strains.
What are the coronaviruses that can infect human?
• Seven coronaviruses that can infect human were identified till now and among them:
✓ SARS-CoV, the coronavirus that causes severe acute respiratory syndrome (SARS).
✓ Middle East respiratory syndrome coronavirus (MERS-CoV) “Saudi SARS”
✓ SARS-CoV-2, the virus causing the current pandemic of COVID- 19
How is coronavirus transmitted?
• Coughing and sneezing:(droplet vs air-borne)
“Air-borne transmission happens in special circumstances like in medical actions in the hospital”
• Close personal contact, such as touching or shaking hands.
• Coronaviruses are zoonotic, meaning they are transmitted between animals and people
What is the clinical picture of infection by COVID-19?
• Patients with confirmed COVID-19 infection have reportedly had mild to severe respiratory illness with symptoms of: *Fever *cough *shortness of breath….
• Symptoms of COVID-19 may appear in as few as 2 days or as long as 14 after exposure.
How is coronavirus diagnosed?
• Nose and throat swabs are the best specimens for detecting common human coronaviruses. Serological testing requires collection of blood specimens.
How is COVID-19 diagnosed?
✓ Specific laboratory tests include (RT-PCR) and serology for detection of specific antibodies
✓ Non specific laboratory tests include detection of elevated CRP, serum ferritin, LDH and D-dimmer. CBC shows lymphopenia.
✓ Radiological diagnosis of pneumonia: chest X-ray and CT
How is coronavirus treated?
• There are no specific treatments for illnesses caused by human coronaviruses.
