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S.N Microbiology > Clinical Microbiology > Flashcards

Clinical Microbiology Flashcards

1
Q

Skin infections (a few examples) - Gram (+)

A 
Staphylococcus Aureus
Streptococcus Pyogenes
Bacillus Anthracis and Bacillus Cereus
Corynebacterium Diphtheriae
Peptostreptococci and Enterococci
Erysipelothrix Rhusiopathiae
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2
Q

Skin infections (a few examples) - Gram (-)

A 
Escherichia Coli
Neisseria Meningitidis 
Proteus sp.
Pseudomonas Aeruginosa
Francisella Tularensis
Yersinia Pestis
Treponema Carateum and Treponema Pertenue
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3
Q

Wounds infections (a few examples) - Gram (+)

A

Staphylococcus Aureus
Streptococcus Pyogenes
Enterococci and Peptostreptococci
Clostridium Tetani and Clostridium Perfringens

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4
Q

Wounds infections (a few examples) - Gram (-)

A 
Escherichia Coli
Proteus 
Klebsiella 
Pseudomonas Aeruginosa
Pasteurella sp.
Bacteroides sp..
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5
Q

Bacteria causing endogenous and mixed abdominal infections (a few examples):

A

Aerobic and Facultative bacteria
Escherichia Coli
Enterococci
α-haemolytic streptococci

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6
Q

Bacteria causing endogenous and mixed abdominal infections (a few examples):

A

Obligate Anaerobic Bacteria
Bacteroidaceae
Anaerobic Cocci

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7
Q

Bacteria causing Peritonitis (a few examples):

A

S. Pneumoniae (Children)
Group A Streptococci
Bacteroids

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8
Q

Infections causing Cholecystitis and Cholangitis (a few examples):

A

Pseudomonas aeruginosa
Clostridium perfringens
Actinomyces sp
Fungi: Candida Albicans

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9
Q

Diagnosis of Infectious Peritonitis:

A

Sampling form: Peritoneal fluid (lavage), Blood, Pus, Gall.

Detection: Gram staining, aerobic and anaerobic bacteria, cultivation, antibiogram

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10
Q

Diagnosis of Infectious Cholecystitis:

A

Sample from: Gall (invasive techniques E.g. duodenal sonda) High Contamination→Quantitative cultivation: Germ number 105/ml means infection.
Detection: Gram staining, aerobic and anaerobic bacteria, cultivation, antibiogram

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11
Q

Diagnosis of Infectious Cholangitis:

A

Sample from: Blood, Liver biopsy, Gall (with percutan-transhepatic choledochus (PTC) or from duodenum zonda)
Detection: Gram staining, aerobic and anaerobic bacteria, cultivation, antibiogram

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12
Q

Abdominal Infections:

Surgical Therapy for appendicitis needs and Prophylaxis :

A

Appendectomy - in surgical prophylaxis Metronidazole

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13
Q

Abdominal Infections:

Medical Therapy for Complications such as perforation or long lasting cystic obstruction and appendicitis needs

A

Combination: Lactamase- stabilising penicillins or 2. - 3. Generation cephalosporins or fluoroquinolon, together with Metronidazole or Aminoglycoside

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14
Q

Bacteria causing ophthalmic infections (a few examples) - Gram (+):

A

Staphylococcus Aureus
Streptococcus Pyogenes
Streptococcus Pneumoniae

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15
Q

Bacteria causing ophthalmic infections (a few examples) - Gram (-):

A 
Chlamydia Trachomatis
Neisseria Gonorrhoeae
Haemophilus Influenzae and Haemophilus Aegyptius
Pseudomonas Aeruginosa
Moraxella Lacunata
Enterobacteriaceae
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16
Q

Viruses causing ophthalmic infections (a few examples):

A 
Coxsackie Virus
Adenovirus
Herpes Simplex Virus (HSV1)
Cytomegalovirus
Varicella Zoster Virus (HHV3)
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17
Q

Bacteria causing air-borne upper respiratory tract infections (a few examples) - Gram (+):
(Pharyngitis, tonsillitis, otitis, epiglotitis, sinusitis)

A 
Streptococcus Pyogenes
Streptococcus Pneumoniae
Staphylococcus Aureus
Streptococcus B, C, G
Arcanobacterium
Corynebacterium Haemolyticum
Enterococci and Peptostreptococci
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18
Q

Bacteria causing air-borne Upper Respiratory Tract infections (a few examples) - Gram (-):
(Pharyngitis, tonsillitis, otitis, epiglottitis, sinusitis)

A 
Haemophilus Influenzae
Neisseria Meningitidis
Klebsiella sp.
Pseudomonas Aeruginosa
Acinetobacter sp.
Neisseria gonorrhoeae
Moraxella catarrhalis
Bacteroidaceae and Enterobacteriaceae
(Treponema Vincentii Complex)
Chlamydia Trachomatis D-K
Chlamydia Pneumoniae
Xanthomonas Maltophilia
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19
Q

Diagnosis of agents causing air-borne upper respiratory tract infections:

A
  • Sputum specimens (and Blood) are cultured for bacteria, fungi and viruses.
  • Enzyme-linked immunoassay methods can be used for detections of microbial antigens as well as antibodies.
  • Detection of nucleotide fragments specific for the microbial antigen in question by DNA probe or polymerase chain reaction can offer a rapid diagnosis.
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20
Q

Diagnosis of agents causing air-borne upper respiratory tract infections:
Culture of nasal washings is usually sufficient in _____ with bronchiolitis.

A

Bacterial Diagnosis of agents causing air-borne upper respiratory tract infections:
Culture of nasal washings is usually sufficient in infants with bronchiolitis.

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21
Q

Diagnosis of agents causing air-borne upper respiratory tract infections:
_________ staining technique can be used for legionellosis.

A

Diagnosis of agents causing air-borne upper respiratory tract infections:
Fluorescent staining technique can be used for legionellosis.

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22
Q

Treatment of agents causing air-borne upper respiratory tract infections:

A

Symptomatic treatment is used for most viral infections. Bacterial pneumonias are treated with antibacterials.

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23
Q

Prevention of agents causing air-borne upper respiratory tract infections:

A

A Polysaccharide vaccine against 23 serotypes of Streptococcus pneumoniae is recommended for Individuals at high risk.

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24
Q

Viruses causing air-borne Respiratory Tract infections (a few examples):
(Pharyngitis, tonsillitis, otitis, epiglottitis, sinusitis and Pneumonia)

A 
Rhinovirus
Coronavirus
Influenza and Parainfluenza Virus
Adenovirus
Respiratory Syncytial Virus
Epstein-Barr Virus
Cytomegalovirus
Herpes Simplex Virus
Coxsackie Virus
Measles Virus
Varicella Zoster Virus
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25
A Common Fungi that colonize that Upper respiratory Tract and possibly causing Pharyngitis:
Candida Albicans
26
Normal flora of the oral cavity: Anaerobic Bacteria (a few examples)
Peptostreptococcus Veillonella Actinomyces Fusobacterium
27
Normal flora of the oral cavity: Aerobic Bacteria (a few examples)
Streptococcus Haemophilus Neisseria
28
Normal flora of the oral cavity: Parasites (a few examples)
Entamoeba | Trichomonas
29
Infective agents causing Esophagitis (Could be Iatrogenic):
Candida Albicans Cytomegalovirus Herpes Simplex Virus
30
Normal flora of the Stomach: Bacteria (a few examples)
Lactobacillus Casei Streptococcus spp. Helicobacter Pylori
31
Normal flora of the Small Intestine: Bacteria (Most are) Anaerobes (a few examples)
Peptostreptococcus Porphyromonas Prevotella
32
Agents causing Infection of Small Intestine (Could be Iatrogenic):
Salmonella Typhi and Salmonella Enteritidis | Campylobacter Jejuni
33
Normal flora of the Colon: Bacteria (a few examples)
``` Bifidobacterium Eubacterium Bacteroides Fragilis Enterococcus Escherichia Coli ```
34
Agents causing Infection of Colon (Could be Iatrogenic):
``` Bacteroides Fragilis VRE Pseudomonas Aeruginosa Clostridium Difficile EHEC Shigella Dysenteriae Entamoeba Histolytica ```
35
Normal flora of the Colon: Fungi (a few examples)
Candida Spp.
36
Normal flora of the Colon: Parasites (a few examples)
``` Blastocystis Chilomastix Endolimax Entamoeba Iodamoeba Trichomonas ```
37
Which Bacteria is able to synthesize Vitamin K and Biotin in the Colon? (For Extra Knowledge, Just one Example)
Escherichia Coli
38
Bacterial Pathogens of the faecal-oral route causing Bloody Diarrhea (a few examples):
``` Shigella EHEC Yersinia Enterocolitica Salmonella Campylobacter jejuni Aeromonas spc. Vibrio parahaemolyticus ```
39
Bacterial Pathogens of the faecal-oral route causing Watery Diarrhea (a few examples):
``` Shigella Vibrio Cholera ETEC, EIEC, EPEC Clostridium perfringens Clostridium difficile ```
40
Bacterial Pathogens of the faecal-oral route causing Typhoid fever (a few examples):
``` Salmonella Typhi Salmonella Paratyphi A, B Yersinia Enterocolitica Yersinia Pseudotuberculosis Campylobacter Fetus ```
41
Viral Pathogens of the faecal-oral route causing Diarrhea (a few examples):
``` Rotavirus Caliciviridae Flavivirus Orthomyxovirus Crimean-Congo Virus HHV-7 ```
42
Protozoal Pathogens of the faecal-oral route causing Diarrhea (a few examples):
``` Entamoeba Histolytica Balantidium Coli Giardia Lamblia Cryptosporidium Blastocystis hominis ```
43
Helminth Pathogens of the faecal-oral route causing Diarrhea (a few examples):
Strongyloides Stercoralis
44
Normal Flora of the Anterior Urethra and Vagina - (a few examples):
``` Lactobacillus Casei Streptococcus spp. Staphylococcus Epidermidis Staphylococcus Saprophyticus Candida Albicans Ureaplasma spp. ```
45
The Most Important Microbial pathogens of the urinary tract :
``` Escherichia Coli Staphylococcus Saprophyticus Candida Albicans Neisseria Gonorrhoeae Chlamydia Trachomatis Ureaplasma spp. ```
46
Causative agents of Arthropod-borne Bacterial infections - (a few examples):
``` Rickettsia Prowazekii Rickettsia Rickettsii Coxiella Burnetii Francisella Tularensis Borrelia Burgdorferi Yersinia Pestis ```
47
Causative agents of Arthropod-borne Viral infections - (a few examples):
Togavirus (Alphavirus) Flaviviruses (Dengue, Yellow Fever, West Nile) Reovirus (Coltivirus ) Bunyaviruses (California Encephalitis +Rift Valley Fever)
48
Bacterial pathogens of food-poisoning and toxico-infections - Contaminated Milk (a few examples):
Salmonella Spp. Campylobacter Jejuni Yersinia Enterocolitica Mycobacteria Tuberculosis
49
Bacterial pathogens of food-poisoning and toxico-infections - Contaminated Meat (a few examples):
Clostridium Perfringens EHEC and EPEC Campylobacter Jejuni Yersinia Enterocolitica
50
Bacterial pathogens of food-poisoning and toxico-infections - Contaminated Rice (a few examples):
Bacillus Cereus
51
Bacterial pathogens of food-poisoning and toxico-infections - Contaminated Water (a few examples):
ETEC, EPEC and EIEC | Vibrio Cholerae
52
Zoonotic infections of Bacterial Origin (a few examples):
``` Anthrax: Bacillus Anthracis Typhus: Rickettsia Prowazekii Lyme disease: Borrelia Burgdorferi, Afzelii and Ganiri Leprosy: Mycobacterium Leprae Bubonic plague: Yersinia Pestis Q-Fever: Coxiella Burnetii Rabbit Fever: Francisella Tularensis Brucellosis: B. Suis, B. Melitensis, B. Abortus, B. Canis ```
53
Zoonotic infections of Viral Origin (a few examples):
``` Bird Flu: Influenza A virus Rabies: Rhabdovirus Lassa Virus Hantavirus Cardiovirus ```
54
Zoonotic infections of Parasitic Origin (a few examples):
Chagas disease: Trypanosoma Cruzi Toxoplasmosis: Toxoplasma gondii Leishmaniasis: Leishmania Sleeping Sickness: Trypanosoma Brucei Gambiense
55
Zoonotic infections of Prion Origin (a few examples):
Mad Cow Disease/Creutzfeldt-Jakob disease (vCJD)
56
Most important bacteria causing Meningitis - Gram(+) (a few examples):
Streptococcus Pneumoniae Streptococcus Agalactiae Staphylococcus Aureus Listeria Monocytogenes
57
Most important bacteria causing Meningitis - Gram(-) (a few examples):
``` Neisseria Meningitidis Haemophilus Influenzae Escherichia Coli Pseudomonas Aeruginosa Proteus ```
58
Most important bacteria causing Meningitis - Gram Intermediate (a few examples):
Mycobacterium Tuberculosis | Leptospira Interrogans
59
Most important bacteria causing Encephalitis - Gram(+) (a few examples):
Listeria Monocytogenes
60
Most important bacteria causing Encephalitis - Gram(-) (a few examples):
Borrelia Burgdorferi
61
Most important bacteria causing Encephalitis - Gram Intermediate (a few examples):
Rickettsia Prowazekii | Chlamydia Psittaci
62
What is the classical diagnostic triad of symptoms for Meningitis?
1) Nuchal rigidity 2) Sudden High fever 3) Altered Mental status
63
What type of Meningitis is presented along with rapidly-spreading petechial rash?
"Meningococcal" Meningitis (i.e. meningitis caused by the bacteria Neisseria meningitidis)
64
Meningitis - Sample taking? What is Checked?
CSF is examined for WBCs, RBCs, protein content and glucose level.
65
How can we tell based on the CSF-WBC what type (Bacterial/Viral) of Meningitis ?
The type of white blood cell predominantly present predicts whether meningitis is due to bacterial or viral infection. (Lymphocytes = Viral and Neutrophills =Bacteria)
66
How can we tell based on the CSF-Glucose what type (Bacterial/Viral) of Meningitis ?
Bacterial: CSF glucose to serum glucose ratio is < 0.4 . Viral: CSF glucose to serum glucose ratio is 1~
67
Apart from CSF-Glucose and CSF-WBC, What other more specific diagnostic Lab test are possible for Meningitis?
Microbiological culture, Latex agglutination, PCR (Especially after antibiotics), Limulus lysate test for Gram Negative (Endotoxin Sensitive).
68
Meningitis - Principles of Treatment and Initial Response
Medical Emergency: Empiric antibiotics even before LP. Prednisone (corticosteroid) reduces rates of mortality, severe hearing loss and neurological sequelae.
69
Bacteria causing Pneumonia - Gram(+) (a few examples):
``` Streptococcus pneumoniae Staphylococcus aureus Peptostreptococcus sp. Streptococcus pyogenes Enterococcus sp. Actinomyces sp. Nocardia sp. Bacillus anthracis ```
70
Bacteria causing Pneumonia - Gram(-) (a few examples):
``` Haemophilus influenzae Bacteroidaceae Legionella sp. Klebsiella pneumoniae Enterobacteriaceae Pseudomonas aeruginosa Moraxella catarrhalis Francisella tularensis Yersinia pestis. ```
71
Bacteria causing Pneumonia - Gram Intermediate (a few examples):
``` Mycoplasma pneumoniae Chlamydia Pneumoniae Chlamydia Psittaci Coxiella burnetii Mycobacterium sp. ```
72
Bacteria causing Whooping cough: (a few examples):
Bordetella Pertussis | Bordatella Parapertussis
73
Bacteria causing Tuberculosis: (a few examples):
Mycobacterium Tuberculosis Mycobacterium Bovis Mycobacterium Africanum
74
Diagnostic Measures of Lower Respiratory Tract Bacterial Infections:
Sample from secretions of pus. | Microscopy, Culture, Serology, PCR.
75
Bacterial exotoxins and the Related diseases: | Superantigens of S. Aureus and S. Pyogenes
``` Toxic shock syndrome: Superantigens bridge the MHC class II protein on antigen presenting cells with the T cell receptor on the surface of T cells with a particular Vβ chain ```
76
Bacterial exotoxins and the Related diseases: | Heat labile toxin of E.coli
Gastroenteritis: Bind and activate guanylate cyclase, which leads to ↑cGMP. This leads to the loss of electrolytes and water from intestinal cells.
77
Bacterial exotoxins and the Related diseases: | Anthrax toxins of Bacillus anthracis
Anthrax: | EF + PA: increase in target cell cAMP level, localized edema; LF + PA: death of target cells and experimental animals
78
Bacterial exotoxins and the Related diseases: | Bordetella adenylate cyclase and Pertussis
Lymphocytosis and Bronchial Cell Death: | Increase in target cell cAMP level
79
Bacterial exotoxins and the Related diseases: | Botulinum toxin of Clostridium botulinum
Flaccid paralysis: | Decrease in peripheral, presynaptic acetylcholine release
80
Bacterial exotoxins and the Related diseases: | Cholera toxin of Vibrio cholerae
Cholera - Secretory Diarrhea: | Activation of adenylate cyclase, increase in cAMP level
81
Bacterial exotoxins and the Related diseases: | Diphtheria toxin of Corynebacterium Diphtheriae
Diphtheria - Pharyngeal Pseudomembranes: | Inhibition of protein synthesis
82
Bacterial exotoxins and the Related diseases: | Pseudomonas exotoxin A of Pseudomonas aeruginosa
Similar to Diphtheria - Pharyngeal Pseudomembranes: | Inhibition of protein synthesis
83
Bacterial exotoxins and the Related diseases: | Shiga toxin of Shigella Dysenteriae
Shigellosis: | Inhibition of protein synthesis and Cell Death
84
Bacterial exotoxins and the Related diseases: | Tetanus toxin of Clostridium tetani
Tetanus, Opisthotonus: | Decrease in neurotransmitter release from inhibitory neurons, spastic paralysis
85
Septic shock - Microbiologic Diagnosis
Diagnosis is made by culturing local infections thought to be the source of microbemia and by culturing the blood.
86
Septic shock - Prevention and Treatment
Treatment consists of high-dose intravenous broad-spectrum antimicrobial agents, intravenous fluids, supplemental oxygen therapy, mechanical ventilation, hemodialysis, and transfusions of blood products and clotting factors, as needed.
87
Endocarditis - Microbiologic Diagnosis
Infective endocarditis is diagnosed through blood cultures
88
Endocarditis - Prevention
Antimicrobial prophylaxis is administered to patients with defective heart valves who are undergoing dental and other procedures known to produce bacteremia.
89
Endocarditis - Treatment
Prolonged intravenous treatment with bactericidal antibiotics to eradicate bacteria within the protective clot. Surgical replacement of infected valves may be required to cure prosthetic valve infections.
90
Blood cultures - Initial Importance in Diagnosis
Most clinical laboratories will give a preliminary report of a negative culture if no growth is detected after 4 days of incubation. A final negative report is made if there is no growth after 7 days of incubation.
91
Blood cultures - What should be done if the patient has received antimicrobial agents before sampling?
The Clinical Laboratory can add penicillinase to remove β-lactam antibiotics, use an antimicrobial removal device or special resin bottle to remove or inactivate the antimicrobial agent, or prolong blood incubation for 2 weeks to improve the chances of obtaining a positive culture.
92
Blood cultures - What should be done If infective endocarditis is suspected?
Blood culture bottles should be incubated for 2 weeks to allow growth of slow-growing or fastidious microorganisms.
93
Blood cultures - What should be done If fungemia is suspected?
Special media and techniques are used to grow fungi
94
Blood cultures - What should be done If central venous catheter infection is suspected?
Blood should be drawn both from the line and from a peripheral vein, and the results of quantitative cultures compared. If the catheter blood culture has a 10-fold greater count than the peripheral blood culture or has more than 100 CFU/ml, the catheter is probably infected.
95
Serum Procalcitonin is a definite indication of a _______ Infection.
Serum Procalcitonin is a definite indication of a Bacterial Infection.
96
Serum Leukocytosis and CRP elevation is an initial indication of an _______ .
Serum Leukocytosis and CRP elevation is an initial indication of an Infection
97
In case of Transient Bacteremia blood sample should be taken from the patient at :
The beginning of the fever
98
In case of Continuous Bacteremia blood sample should be taken from the patient at :
Blood can be taken at any time
99
How blood should be taken for Blood culture from an Adult?
10-20 ml
100
How blood should be taken for Blood culture from an child?
1-2 ml
101
How many times do we need to sample blood for blood cultures? and from which vessels?
3 Times and from the Peripheral Veins
102
What pathogens require a special Blood culture mixtures?
Fungi and Mycobacteria
103
Liquid media for Anaerobic culture - Methods of Environment Production for Anaerobes
Before inoculation, O2 is eliminated from media by means of boiling. After inoculation, media are sealed by means of sterile wax or Vaseline.
104
Gas-pack jar (Compartment) - Methods of Environment Production for Anaerobes
Cultivation of Anaerobic microbes by - Placing a Gas Pack in the Jar that releases H2 and CO2, a Catalyst in the cell produces Water from O2 and H2 thus ultimately eliminating the Oxygen in the sealed Jar.
105
Anaerostate (Compartment) - Methods of Environment Production for Anaerobes
Cultivation of Anaerobic microbes by - Air Expulsion by Pressure Cylinder, Air Aspiration and Filling or Anaerocult that produces the Correct Gas mixture.
106
Biological method - Fortner-technique: Environment Production for Anaerobes
Growing Anaerobes and Aerobes together on Blood agar - Anaerobe over consume the Oxygen allowing for an Anaerobic environment for the other Anaerobe.
107
Chemical method - Liquid media for Anaerobic culture
Thioglycolate broth allows for reduction of Oxygen to water in the tube. Aerobes will culture the top of the liquid (Contact with air) anaerobe the bottom.
108
Types of metabolism preformed by aerobic and anaerobic bacteria?
Aerobic bacteria - Respiration | Anaerobic bacteria - Fermentation
109
Enterally acquired Parasitic infections - Indirect (fecal-oral) - give a few examples:
``` Entamoeba Histolytica Giardia lamblia Enterobius vermicularis Balantidium coli Ascaris lumbricoides Toxocara spp. Trichuris trichiura ```
110
Enterally acquired Parasitic infections - direct (venereal) - give a few examples:
Entamoeba Histolytica
111
Enterally acquired Parasitic infections - Contaminated Meat - give a few examples:
Taenia saginata Taenia solium Diphyllobothrium latum (Fish)
112
Enterally acquired Parasitic infections - Contaminated Eggs - give a few examples:
Echinococcus granulosus and multilocularis | Hymenolepis nana
113
What are the Microscopical Diagnostic Measures for Enterally acquired Parasitic infections?
Wet mount Permanent stains Stool concentrates
114
What are the Serologic Diagnostic Measures for Enterally acquired Parasitic infections?
ELISA: Antibody response or Antigen detection
115
What are the Nucleic acid hybridization Diagnostic Measures for Enterally acquired Parasitic infections?
Restriction Endonuclease and PCR
116
What are the Unique options for Diagnosis of Enterally acquired Parasitic infections?
Animal inoculation and Culture
117
Causative agents associated with arthropod-borne Parasitic infections - Protozoa (few examples):
``` Plasmodium spp: Anopheles mosquito Toxoplasma gondii: Fecal-oral route, carnivorism Leishmania species: Phlebotomus sandfly Trypanosoma cruzi: Reduviid bug Trypanosoma brucei: Tsetse fly ```
118
Causative agents associated with arthropod-borne Parasitic infections - Helminths (few examples):
Wuchereria bancrofti: Mosquito Loa loa: Chrysops fly Onchocerca volvulus: Simulium black fly Dirofilaria immitis: Mosquito
119
Plasmodium spp - Diagnostic Procedure
Blood Sample Microscopic examination (Giemsa stain) or acridine orange fluorescent stain: ●Thin film ●Thick film
120
Leishmania Donovani- Diagnostic Procedure
Bone Marrow Aspirate Microscopic examination (Giemsa stain), Culture, Serology (antibody).
121
Trichinella spiralis and Trypanosoma cruzi- Diagnostic Procedure
Muscle Biopsy Muscle Microscopic examination (permanent stains) and Serology
122
Onchocerca volvulus and also Leishmania Braziliensis and Tropica - Diagnostic Procedure
Scrapings and Skin snip Biopsy Microscopic examination with Wet mount or Permanent stains
123
Pathogens of the air-borne viral infections - Give a few examples
``` Coronavirus Paramyxoviruses Influenza viruses Picornaviruses Rhinoviruses Adenovirus Varicella-zoster virus B19 virus (Parvovirus) Polyomavirus ```
124
Pathogens of the enterally acquired viral infections, Specific for infants - Give a few examples
* Rotavirus A * Adenovirus 40, 41 * Coxsackie A24 virus
125
Pathogens of the enterally acquired viral infections, General Population - Give a few examples
* Norwalk virus * Calicivirus * Astrovirus * Rotavirus B (outbreaks in China) * Reovirus * HAV * HEV
126
Viruses infecting the small intestine causes damage to the epithelial lining and the absorptive villi, the result is :
Malabsorption of Water and an Electrolyte Imbalance
127
Although enteroviruses (picornaviruses) are spread by the fecal-oral route, they usually cause only mild or no gastrointestinal symptoms. Instead, these viruses establish a _______ , spread to other target organs, and then cause clinical disease.
Although enteroviruses (picornaviruses) are spread by the fecal-oral route, they usually cause only mild or no gastrointestinal symptoms. Instead, these viruses establish a VIREMIA , spread to other target organs, and then cause clinical disease.
128
Most important Fungi causing Meningitis (a few examples):
``` Candida Albicans Cryptococcus Neoformans Aspergillus Fumigatus Coccidioides Immitis Histoplasma Capsulatum ```
129
Most important Fungi causing Brain Abscesses (a few examples):
``` Candida Albicans Cryptococcus Neoformans Aspergillus Fumigatus Coccidioides Immitis Blastomyces dermatitidis Zygomycetes - Mucor ```
130
Most important Viruses causing Meningitis (a few examples):
``` Enteroviruses (Echo-, Coxsackie- and Polioviruses) Herpes simplex virus 2 Human T-Lymphotropic Virus Mumps virus Lymphocytic choriomeningitis virus (Flavi-) West Nile Virus ```
131
Most important Viruses causing Paralysis (a few examples):
Poliovirus Enteroviruses 70 and 71 Coxsackie A7 virus (Flavi-) West Nile Virus
132
Most important Viruses causing Encephalitis (a few examples):
``` Herpes simplex virus 1 Varicella-zoster virus Rabies virus Coxsackie A and B viruses Polioviruses (Flavi-) West Nile Virus ```
133
Most important Viruses causing Postinfectious Encephalitis - Immune Mediated and Long term Complications (a few examples):
``` Measles virus - SSPE JC virus - Progressive Multifocal Leukoencephalopathy Mumps virus Rubella virus Varicella-zoster virus Influenza viruses ```
134
Most important Bacteria causing Endocarditis -(a few examples):
``` Staphylococcus Aureus - Acute Viridans streptococci - Subacute Streptococcus Bovis - Colon Cancer Staphylococcus Epidermidis - Prosthetic Valves Corynebacterium Diphtheriae Bartonella Henselae Enterococci ```
135
Most important Fungi causing Endocarditis -(a few examples):
Candida Albicans Histoplasma Capsulatum Aspergillus Fumigatus
136
Most important Viruses causing Endocarditis -(a few examples):
Coxsackievirus group B Human Herpes Virus 6 Parvovirus B19
137
Most important Parasites causing Heart Diseases -(a few examples):
Trypanosoma cruzi (Chagas) Echinococcus multilocularis Echinococcus granulosus
138
Fungi causing Pneumonia - (a few examples):
``` Candida Albicans Aspergillus Fumigatus and Aspergillus Flavus Pneumocystis jirovecii Histoplasma Capsulatum Blastomyces Dermatitidis Paracoccidioides Brasiliensis Coccidioides Immitis Cryptococcus Neoformans ```
139
Fungi causing Bronchitis- (a few examples):
Aspergillus Fumigatus and Aspergillus Flavus | Cryptococcus Neoformans
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Parasites causing Lung Abscesses - (a few examples):
Entamoeba Histolytica | Paragonimus Westermani
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Parasites causing Lung Nodules - (a few examples):
Echinococcus Multilocularis | Echinococcus Granulosus
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Parasites causing Pneumonitis - (a few examples):
Ascaris Lumbricoides Toxocara Canis Strongyloides Stercoralis Paragonimus Westermani
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Microbes causing pre- and perinatal infections in the fetus/newborn: Bacteria
``` Chlamydia Trachomatis Listeria Monocytogenes Mycobacterium Tuberculosis Group B Streptococci Treponema Pallidum ```
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Microbes causing pre- and perinatal infections in the fetus/newborn: Viral
``` Cytomegalovirus Zika Virus Rubella Virus Herpes Simplex Virus Human Immunodeficiency Virus Hepatitis B Virus Hepatitis A Virus Coxsackie B Virus Parvovirus - B19 ```
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Microbes causing pre- and perinatal infections in the fetus/newborn: Fungi
``` Malassezia Furfur Pneumocystis Jirovecii Candida Albicans (and Candida Parapsilosis) Aspergillus Fumigatus Zygomycetes - Mucor ```
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Microbes causing pre- and perinatal infections in the fetus/newborn: Parasites
Toxoplasma Gondii Plasmodium spp. Trichomonas Vaginalis
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Microbes causing Malformations, Developmental Abnormalities and Spontaneous Abortion - PREnatal:
``` Toxoplasma Gondii Listeria Monocytogenes Parvovirus B19 Rubella Cytomegalovirus (#1 Mental Retardation by Infection) Human Immunodeficiency Virus Ureaplasma spp. Treponema Pallidum ```
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Microbes causing Malformations/Developmental Abnormalities - POSTnatal and NEOnatal:
``` Human Immunodeficiency Virus Cytomegalovirus Herpes Simplex Virus Hepatitis B virus Coxsackie B Virus Echovirus ```
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What are the 6 Childhood infections characterised by exanthems?
1st - Measles, Exanthema: Koplik Spots 2nd - S.Pyogenes, Scarlet Fever: Erythematous Rash 3rd - Rubella: Pin-Points Exanthema 5th - Parvovirus B19: Erythema infectiosum 6th - Roseola (HHV 6+7): Exanthema Subitum VZV (HHV3) - Chickenpox ("Non-Classical Exanthema")
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Sexually Transmitted Infection- Gram Positive Bacteria:
Streptococcus Agalactiae | Gardnerella Vaginalis
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Sexually Transmitted Infection - Gram Negative Bacteria:
Neisseria gonorrhoeae Haemophilus ducreyi Calymmatobacterium Granulomatis
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Sexually Transmitted Infection - Gram Intermediate Bacteria:
``` Treponema Pallidum Chlamydia Trachomatis L 1-3 Chlamydia Trachomatis D-K Ureaplasma Urealyticum Mycoplasma Hominis. ```
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Sexually Transmitted Infection - Viruses:
``` Human Papillomavirus - 6, 11, 16, 18, 31, 33 Herpes simplex virus - Mostly HSV 2 Cytomegalovirus Hepatitis Viruses: B, C and D Human Immunodeficiency Virus Human T-cell Lymphotropic Virus 1 ```
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Sexually Transmitted Infection - Protozoa:
Trichomonas Vaginalis Entamoeba histolytica (Oral-Anal Sex) Giardia lamblia (Oral-Anal Sex) Cryptosporidium (Oral-Anal Sex)
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What serological tests can help with Initial Screening of HIV?
ELISA Latex Agglutination Rapid Oral Antibody Test
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What lab tests can help to Confirm Initial Screening of HIV?
Western blot analysis | Immunofluorescence
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What lab tests can help with Detection and Quantitation of HIV in Blood?
Virion RNA RT-PCR (Detection Only) | Real Time RT-PCR
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What is the early marker of infection with HIV?
p24 Antigen
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What Immunological studies values are expected to be low in HIV infection?
The absolute number of CD4 lymphocytes and the ratio of helper to inducer lymphocytes (CD4:CD8 ratio) are low in HIV.
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Microbes causing opportunistic infections related to AIDS - Protozoa:
Toxoplasma Gondii (Brain) Cryptosporidiosis with diarrhea Isosporiasis with diarrhea
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Microbes causing opportunistic infections related to AIDS - Fungal:
``` Candida Albicans- Esophagus, Trachea, and Lungs Pneumocystis Jiroveci - Pneumonia Cryptococcus Neoformans (extrapulmonary) Histoplasma Capsulatum (disseminated) Coccidioides Immitis (disseminated) ```
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Microbes causing opportunistic infections related to AIDS - Viral:
Cytomegalovirus Herpes simplex virus JC Virus (Progressive multifocal leukoencephalopathy) Epstein-Barr virus (Hairy leukoplakia)
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Microbes causing opportunistic infections related to AIDS - Bacterial:
Mycobacterium Avium-complex (disseminated) Mycobacterium Tuberculosis (disseminated) Bartonella Henselae Nocardia Asteroides
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Which Hepatitis viruses are transmitted in a Feco-Oral manner?
Hepatitis A Virus | Hepatitis E Virus
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Which Hepatitis viruses are transmitted in a Parenteral and Sexuall manner?
Hepatitis B Virus Hepatitis C Virus Hepatitis D Virus
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Structure and Family of Hepatitis A Virus
Picornavirus; capsid, RNA
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Structure and Family of Hepatitis B Virus
Hepadnavirus; envelope, DNA
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Structure and Family of Hepatitis C Virus
Flavivirus; envelope, RNA
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Structure and Family of Hepatitis D Virus
VIROID-like; envelope, circular RNA
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Structure and Family of Hepatitis E Virus
Norovirus; capsid, RNA
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Hepatitis A Virus - Diagnosis:
Anti-HAV IgM - ELISA or RIA.
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Hepatitis B Virus - Diagnosis: "SpECiES"/"SECES" mnemonic by order of appearance
``` HBsAg -Active disease; 1st marker HBeAg- infectivity; 2nd marker Anti-HBc Ab; Window Period Anti-HBe Ab; Low infectivity Anti-HBs Ab; Immunized/Recoverd ```
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Hepatitis C Virus - Diagnosis:
ELISA - anti-HCV Antibody RT-PCR Branched-chain DNA
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Hepatitis D Virus - Diagnosis:
Delta Antigen; RT-PCR | Anti-HDV Antibody - ELISA or RIA
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Hepatitis E Virus and Hepatitis G Virus - Diagnosis:
RT-PCR
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Use of laboratory animals in the medical microbiology - What animal was used to form the Smallpox Vaccine?
Cows- Edward Jenner's cowpox vaccine
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Use of laboratory animals in the medical microbiology - What are Embronated eggs used for?
Growing Viruses
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Use of laboratory animals in the medical microbiology - What infections are Armadillos associated with?
Armadillos- Mycobacterium Leprae (Leprosy)
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Use of laboratory animals in the medical microbiology - What Rabbit Testes used for?
Growing Treponema Pallidum (Syphilis)
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Use of laboratory animals in the medical microbiology - What is Römer Test?
Corynebacterium Diphtheria Culture from Löffler medium is injected into Guinea pigs, one of which received anti-toxin.
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Use of laboratory animals in the medical microbiology - What are sheep used for?
Blood in several cultures
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Use of laboratory animals in the medical microbiology - What are Horses used for?
Immunoglobulins serum additions
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What are the basic rules for using the Bottle cultures in the appropriate way?
- NO IV for collection of samples | - 2 Samples must be taken from different anatomical positions
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Samples for detection of Microbes
Serum CSF Urine Bronchoalveolar Lavage
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What type of Serology Test is described below? - Bacterial Colony is fixed to a plate and covered with matrix fluid leading to Ionization. - Applying a laser beam allow for ionizing particles (mostly ribosomal) to separate from Sample-Matrix - Electromagnetic field propels the charged particles and time of flight analysis shows the Mass spectrum which is bacteria specific!
Matrix-Assisted laser desorption Ionization time of flight | MALDI-TOF
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Rules and regulations of the collection, Storage and Transport of Infectious Materials: Transportation to the laboratory. Urine sample transport- long delays before inoculation can result in the growth of : .....
Urine sample transport- long delays before inoculation can result in the growth of clinically insignificant bacterial contaminants in the specimen.
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Rules and regulations of the collection, Storage and Transport of Infectious Materials: Transportation to the laboratory. All specimens should be ______
All specimens should be labelled.
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Rules and regulations of the collection, Storage and Transport of Infectious Materials: Transportation to the laboratory. Clinicians should provide the laboratory with ______ ________.
Clinicians should provide the laboratory with diagnostic questions.
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Rules and regulations of the collection, Storage and Transport of Infectious Materials: Transportation to the laboratory. Rapid transport- S.pneumoniae, N. gonorrhoeae are fastidious: .....
Rapid transport- S.pneumoniae, N. gonorrhoeae are fastidious- may not survive temperature extremes or drying.
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Rules and regulations of the collection, Storage and Transport of Infectious Materials: Specimens should be collected in clean, sterile containers - Examples:
- cotton swab, Dacron swab, syringe/catheter aspiration - sufficient material for both culture and Gram stain - transport medium (Stuart medium) - transport culture medium (Uricult Plus)
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Rules and regulations of the collection, Storage and Transport of Infectious Materials: Specimens should be collected in a manner that: .....
Specimens should be collected in a manner that minimizes contamination by resident bacterial flora
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Rules and regulations of the collection, Storage and Transport of Infectious Materials: The clinician should obtain specimens before : .....
The clinician should obtain specimens before initiating or changing antibiotic therapy.
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Phage typing- Examples for Diagnosed Microbes
Strains of : S.Aureus, Salmonella Spp and Listeria Monocytogenes.
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Phage Typing
Describes the strains of different bacteria - Epidimiological. Hospital Departments check ups. Phage could attack the specific Bacteria strain -Infecting Doctor and Carrying Patient would have same result.
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Preparation of Lawn Culture - Purpose
Uniform Growth: - Antibiotic Susceptibility - Bacteriophage Typing - Antigen Preparation for Vaccine
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What type of Serology Test is described below? - A culture is grown on an agar and dried - A grid is drawn on the base of the petri dish to mark out different regions - Inoculation of the grid is done by a different phage. - Susceptible phage regions are will show a circular clearing where the bacteria are lysed - Differentiation!
Phage Typing
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How does Serotyping works? What is the end goal?
Using Slide Agglutination or Latex Agglutination in order to detect a subspecies level antigen type for Epidemiological and Therapeutic reasons.
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Examples where serotyping is could be used for choosing therapy?
1) EHEC - O157:H7 a serotype causing HUS and Hemorrhagic Colitis 2) Serotype B of H. Influenzae can cause Meningitis, Vaccination
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What type of Serology Test is described below? - The whole bacterial genome is digested by restriction enzymes - Specific sites of Cleavage - Large 10k-1M Base pair fragments are pushed in a voltage gradient (Pulsating electric field) gel to be differentiated!
Pulsed-Field Gel Electrophoresis
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What is common for all the serological test listed below? - Western Blot - Tube Agglutination - Complement Fixation Test - Direct ELISA
Demonstration of Antibodies in Serum
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Diagnostic Skin tests: | Dick Test - with positive result
Scarlet Fever - Toxin Injection into skin | Reddening of the skin over 10 millimeters in diameter within 24 hours indicates lack of Immunity.
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What is Schick Test?
Skin test for Diphtheria
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``` Diagnostic Skin tests: Tuberculin test (PPD) - with Positive and False Positive results ```
Purified Protein derivative of TB- Injection into skin. Takes 48-72 hours. Positive - red lesion greater than 15 mm indicates TB infection or previous exposure. False Positive - Lesser reactions indicate infections with other mycobacteria or BCG vaccination passive immunity.
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``` Diagnostic Skin tests: Tuberculin test (PPD) - with False Negative and Negative results ```
Purified Protein derivative of TB- Injection into skin. False Negative -rare, due to AIDS/Steroids/Malnutrition. Negative - 0 mm lesion should be recorded
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Diagnostic test using Antitoxins
ELEK's Test - For C. Diphtheriae Diagnosis
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Which STD causing bacteria are not diagnosed with Serology? How are they diagnosed, Otherwise?
- N.Gonorrhoeae - Chlamydia Trachomatis - Mycoplasma and Ureaplasma * Diagnosis by PCR (Called NAAT in Chlamydia)
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How are STD samples collected? (Instrument)
Cytobrush
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How are Mycoplasma and Ureaplasma are cultured? (STD)
Eaton Agar
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Syphilis - Screening (Aka Non-Specific): Antigen Used Antibody Used
Antigen Used - Cardiolipin from catale's heart | Antibody Used - From damaged cells during early phase, present on cell surface of T.Pallidum
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Syphilis - Screening (Aka Non-Specific): | Wassermann reaction
Complement fixation test: - Negative: Lysed Sheep's RBCs - Positive: RBCs remain intact (Ag-Ab interaction fixate Complement)
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Syphilis - Screening (Aka Non-Specific): | VDRL
Venereal Disease Research Laboratory: | -A drop of Cardiolipin is placed on a slide with a drop of serum for microscopical investigation
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Diagnosis of Syphilis - Specific Methods for Diagnosis: | TPI
T. Pallidum Immobilization test: Living T.Pallidum = Antigen, Complement of Guinea Pigs. If in a mixture with IgGs from Serum there is no locomotion because of a Ab-Ag-Complement reaction this is a Positive result.
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Diagnosis of Syphilis - Specific Methods for Diagnosis: | TPHA
T.Pallidum Haemagglutination test: (Flocculation) | -Aggregation of T. Pallidum sensitized (with Ab) RBCs with exposure to patient serum means Positive result.
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Diagnosis of Syphilis - Specific Methods for Diagnosis: | FTA-ABS
Fluorescent Treponemal Antibodies: - Antigen = Killed T.Pallidum , Second Antibody = Fluorescein labeled Anti-Human Antibodies, First Antibody from Patient Serum! - Positive results: Bright yellow fluorescence upon triple particle Immunocomplex formation.
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What are important intracellular enzymatic reactions products in bacteria? Importance?
Indole, Ammonium, H2S | Detection by indicators and diagnosis
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What is the importance of extracellular enzymes found on bacteria? (Collagenases, haemolysin..)
In vitro - diagnostics In vivo - virulence factors Pharmaceutical - antibiotics
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What Serological Measurement is described here? Antibodies or Ag in vitro are bound to the surface of latex particle or red blood cells so that the binding partner will cause agglutination. Modern, fast technique. The antibodies or the Antigens are in vitro bound to latex particle.
Latex Agglutination - Diagnosis of meningitis Co-Agglutination - S. Aureus Diagnosis (Both are Passive Processes)
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Antibody Titer (Quantitative Tube Agglutination): Definition and Example
A serial dilution is made from patient sera, known antigen solution is added to each tube. The Result Value Corresponds to the highest dilution factor (lowest concentration) that still yields a positive reading. Grubel-Widal reaction - Salmonella typhi.
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What Serological Measurement is described here? Precipitation ring can be seen in the equivalent zone- the zone where the amount of antigen and antibody are equal.Qualitative measurement. Steps: introduce serum into the tube → add ag → disc-shaped zone of precipitation
Ring Precipitation - Liquid phase precipitation
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What Serological Measurement is described here? The precipitation reactions can be visualised by allowing the Ag and the Ab to diffuse towards each other through agar gel - Immunodiffusion.
Semi-solid phase precipitation (agar gel precipitation)
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What Serological Measurement is described here? -Filter paper impregnated with anti-toxin (antibody against bacterial toxin) is placed in agar plate. - Bacterial strains to be tested are placed onto the surface of the plate at right angles to the paper strip. - Antitoxin diffuses from the filter paper into the agar-gel, binds to the toxin produced by the bacteria. - A fine precipitation line is formed in the equivalence zone.
ELEK’s test - Diphtheria Toxin detection
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Complement Fixation test (for Antibody detection) | Which bacterial antibodies are diagnosed with it?
- Mycoplasma Pneumoniae - Chlamydophila Pneumoniae - Chlamydia Psittaci
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Latex Agglutination- Examples for Diagnosed Microbes
Bacterial Antigens of : S. Agalactiae, S. Pneumoniae, H. Influenzae B, N. Meningitidis. Primarily from CSF specimens.
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Serotype
a group of closely related microorganisms distinguished by characteristic set of antigens.
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Blood culture bottles: | Importance
- Bacteriemia increases the mortality rate by 40+% | - Collecting the blood specimens efficiently is essential for diagnosis and treatment
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Indications for Blood culture ( Try to remember at least 5)
- Bacteremia - Septicemia - Shock - Unexplained fever of several days - Chills and fever in patients (Infectious patients) - Debilitating patients - Following body piercing with signs of infection
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Eosin-Methylene-Blue medium (EMB) - What happens when a lactose fermenting bacteria is introduced? Describe the Process
Lactose Fermentation → pH ↓→ eosin loses its color→ The blue color remains→ the bacteria incorporate it→ the colony is BLUE in color (Klebsiella Pneumoniae). *E.Coli → Metallic Green!
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Eosin-Methylene-Blue medium (EMB) - What happens when a non lactose fermenting bacteria is introduced? Describe the Process
No Lactose Fermentation → pH same→ Pink color is enhanced (Salmonella Typhi).
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What type of Serology Test is described below? 1. Premade -Antigens are affixed to the vessel Surface 2. Patient serum added and Ab-Ag binding occurs 3. Enzyme-Conjugated Anti-Human Antibody (E) is added 4. After binding of E to Ab a substrate added is converted to Chromophore - Spectrophotometric Analysis is done.
Direct ELISA - Antibody Detection
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What type of Serology Test is described below? 1. Premade -Antibody are affixed to the vessel Surface 2. Antigen specimen added and Ab-Ag binding occurs 3. Second Premade -Enzyme-Conjugated Anti-Human Antibody (E) is added (Ab-Ag-E complex) 4. After binding of E to Ag a substrate added is converted to Chromophore - Spectrophotometric Analysis is done.
Indirect ELISA - Soluble Antigen Detection
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What type of Serology Test is described below? 1. Proteins are separated by SDS-PAGE 2. Proteins are blotted into nitrocellulose paper 3. Incubation with antigen-specific antibody or patient sera (1Ab) 4. Incubation with enzyme-conjugated anti human sera sera (2Ab) 5. Enzyme conversion of substrate identifies the antigen.
Western Blot
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What is common for all the serological test listed below? - Real-time PCR - Nucleic Acid Hybridization - Immunofluorescence assays - Indirect ELISA - Latex Agglutination
Direct Detection of Pathogen (Antigen)
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FITC - Definition
Fluorescein Isothiocyanate - Molecule covalently attached to Antibodies allowing for Direct and Indirect Immunofluorescence.
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How does Direct Immunofluorescence work?
Checking the presence of the Antigen by confirming its attachment to FITC-labeled Antibody.
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How does Indirect Immunofluorescence work?
Checking the presence of the Antigen by attachment to a Primary Antibody that will be afterwards confirmed by binding to a Second type FITC-labeled Antibody/ies.
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ELISA- Definition | Give an example in Microbiology
Enzyme Linked Immunosorbent Assays B. Anthracis detection by Anti-PA (Protective Antigen, Indirect) T. Pallidum detection by Recombinant Antigen (Direct)
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Diarrhea -Biochemical Tests:
- Clinically: Bloody/Watery and Onset - Selective Culture Media: EMB, Brilliant-green, McConkey - Serology Methods using stool as a sample; Toxins/Bacterial Antigens
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Determination of MIC - Disc diffusion test
1)Preparation of lawn culture (Flooded Equal Bacterial Growth Solid Media) 2)Placing paper discs covered with antimicrobial drug 3)37°C overnight 4)Measuring the diameter of the zone of inhibition around the discs
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Complement Fixation test | Indirect Method - presence of specific Ab is checked
Ag-Ab complex causes Complement aggregation preventing lysis of the Sheep RBCs by MAC : Lysed RBCs - NEGATIVE No Lysis, RBCs Intact - POSITIVE
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MALDI-TOF
Matrix assisted laser desorption/Ionization, Time of Flight Culturing and using the machine to identify by Ionization of the bacterial lysed biochemical components. Very efficient.
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Motility test Medium, how does it enable detection?
Semisolid Material suspension with straight line stab - Turbidity after incubation means bacteria moved away and growed.
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Determination of MIC - Punching test
1) Preparation of lawn culture (Flooded Equal Bacterial Growth Solid Media) 2) Making several holes on the surface ("punch") and Pipetting Standard dilution of each Ab drug into them. 3) 37°C overnight 4) Measuring the diameter of the zone of inhibition
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TORCHES test - when is it done ?
Before or in the First Trimester of the Pregnancy
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Determination of MIC - Agar plate dilution test
1) Various concentrations of antibiotic are incorporated in a series of plates and Agar solidify them 2) Equal amount of bacteria into each Agar 3) Incubation Overnight at 37 C 4) MIC will be the Highest dilution tube that's transparent!
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TORCH - mnemonic
``` Toxoplasma Other - Syphilis,VZV, S. Agalactiae Rubella CMV Herpes ```
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MIC - Minimal inhibitory concentration | Methods of Determination: (3)
Micro and Macro Dilution Agar Dilution E-Test
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Determination of MIC - Microdilution test | Equal amount of bacteria into each
1) Sequential dilution:96-well polystyrene microtiter plate | 2) MIC will be the Highest dilution tube that's transparent!
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LAL test
Atlantic horseshoe crab blood aggregates in presence of Lipid A - Detection of Pathogens
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India Ink and Quellung test are 2 Important tests that help in visualization of _________ bacteria.
India Ink and Quellung test are 2 Important tests that help in visualization of Encapsulated bacteria.
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Determination of MIC - E –test
Placing a plastic strip impregnated with the concentration gradient of the certain antibiotic on a Lawn Culture. From the scale you can read the MIC numerically. MIC = number where the elliptic zone crosses the plastic strip.
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How can we study of the resistance of microbes to antimicrobial agents?
Determination of MIC: E –test, Microdilution test, Agar plate dilution test....
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Which bacteria is detected by Slide agglutination ? How does it work? Qualitative or Quantitative ?
E. Coli Serotypes Detection, E.g. O157:H7 Latex agglutination of the released antigen Qualitative: Y/N (15 tests instead of 100 method)
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Neisser Staining: Microscopic Image
Rods with Club ends (Purple) and Yellow Body | חצופים בקלאב הוטל ה"סוף הסגול " העיקר גוף צהוב
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Capsule Stain: Preparation process and Purpose לקחתי קפסולה אחי בהודו משהו שלילי אחי משהו דארק סלייד אחי. תשמע התחממתי אז נוסע לפושקין דקה לשים קצת מים ושמן, השקעה אחי.
- Drop of India Ink spread with other slide - Heat fix - Fuchsine for 1 minute - Water rinse and Oil Immersion for observation
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Materials for Gram staining
Crystal Violet with sodium oxalate Potassium-Iodide (Lugol Solution) Ethanol Safranin
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3 examples for Bacteria that are not identified with gram stain in labs?
Mycobacteria - mycolic acid do not absorbs gram stain. Mycoplasma - lack cell wall Spirochaetes - too thin wall
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Flagella stains material | "Titanic Flagella"
Tannic Acid
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Ziehl-Neelsen Staining (Acid Fast): Preparation process and Purpose נילסן אכל קבבול בפושקין התעצבן שלוש פעמים אז שפכו עליו מים והקיא את כל ה96% אלכוהול נהיה חיוור אז שמו לו מטלית כחול
- Carbol-Fuchsin (Mycolic acid binds) - Heat 3 times and Wash with water - Decolorization with 96% alcohol - Counter stain with Methylene Blue
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Neisser Staining: Preparation process and Purpose | ניסר לו איזה תירס עם וולט וחצי כדי לעבוד על כלי-סידן ובלוטין
- Stain fixed smear of Corynebacteria with mixture of N.1 and N.2 (2:1 ratio) - Water Wash - Chrysoidine dye then Dry with blotting paper - Detection of Volutin Granules
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Meningitis - Brudzinski Sign
Neck flexion may cause flexion of the legs
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Meningitis - Kernig Sign
Limitations in leg extension when knee flexed
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ID50/LD50/TCID50 Measurements Gave a value around 1 -10^2 Germs. What does it mean?
High Virulence since this is a Low Germ count that causes 50% of Hosts/Cultures to have a pathologic conditions (Infection/Death/Damage).
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LD50
A Quantitative Determinant of Virulence | Lethal Dose - Number of Germs causing death in 50% of Hosts.
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Definition of Pathogenicity
Ability of an organism to cause harm to its host. Represents a genetic component of the organism. It is manifested through its Virulence and Host interaction.
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ID50/LD50/TCID50 Measurements Gave a value more than 10^5 Germs. What does it mean?
Low Virulence since this is a High Germ count that causes 50% of Hosts/Cultures to have a pathologic conditions (Infection/Death/Damage).
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TCID50
A Quantitative Determinant of Virulence | Tissue Culture Infecting Dose - Number of Germs damaging 50% of Cultures.
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Definition of Virulence
Degree of pathology caused by the organism. | depends on its Virulence factors : Structural as cell wall or Capsule and Biochemical as Exotoxin or Endotoxin.
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ID50
A Quantitative Determinant of Virulence | Infective Dose - Number of Germs inducing disease in 50% of Hosts.
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Potential Biological weapons in Microbiology: Give | a few Bacterial examples
``` Bacillus Anthracis Yersinia pestis Francisella Tularensis Brucella Suis Coxiella Burnetii ```
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Potential Biological weapons in Microbiology: Give | a few Viral examples
Poxvirus Ebolavirus Rift Valley fever virus (Bunyaviridae) Yellow Fever Virus
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Potential Biological weapons in Microbiology: Give | a few Fungal examples
Coccidioides Immitis
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Parasites causing ophthalmic infections (a few examples):
``` Onchocerca volvulus (River Blindness) Loa Loa (aka African Eye Worm) Acanthamoeba Keratitis Trypanosoma Cruzi (Romaña sign) Toxoplasma Gondii (Chorioretinitis) Toxocara Canis and Cati (Ocular Larva Migrans) ```
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Lab Algorithm - DDX Options for: | Gram (+)→ Bacilli → Aerobic
Listeria Monocytogenes Bacillus Anthracis and Bacillus Cereus Corynebacterium Diphtheriae
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Lab Algorithm - DDX Options for: | Gram (+)→ Bacilli → Anaerobic
Clostridia: Tetani / Botulinum /Perfringens / Difficile | Cutibacterium Acne
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Lab Algorithm - DDX Options for: | Gram (+)→ Cocci→ Catalase (+) →Coagulase (+)
Staphylococcus Aureus
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Lab Algorithm - DDX Options for: | Gram (+)→ Cocci→ Catalase (+) → Coagulase (-) → Novobiocin Sensitive
Staphylococcus Epidermidis
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Lab Algorithm - DDX Options for: | Gram (+)→ Cocci→ Catalase (+) → Coagulase (-) → Novobiocin Resistant
Staphylococcus Saprophyticus
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Lab Algorithm - DDX Options for: | Gram (+)→ Cocci→ Catalase (-) → β Hemolytic →Bacitracin Sensitive
Group A, Streptococcus Pyogenes
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Lab Algorithm - DDX Options for: | Gram (+)→ Cocci→ Catalase (-) → β Hemolytic →Bacitracin Resistant
Group B, Streptococcus Agalactiae
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Lab Algorithm - DDX Options for: | Gram (+)→ Cocci→ Catalase (-) → α Hemolytic →Optochin Sensitive
Streptococcus Pneumoniae
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Lab Algorithm - DDX Options for: | Gram (+)→ Cocci→ Catalase (-) → α Hemolytic →Optochin Resistant
Viridans Streptococci: Mutans / Mitis / Sanguinis
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Lab Algorithm - DDX Options for: | Gram (+)→ Cocci→ Catalase (-) → γ Hemolytic →6.5% NaCl Sensitive
Streptococcus Bovis
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Lab Algorithm - DDX Options for: | Gram (+)→ Cocci→ Catalase (-) → γ Hemolytic →6.5% NaCl Resistant
Enterococci: Faecium / Faecalis | could be α hemolytic sometimes
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Lab Algorithm - DDX Options for: | Gram (-)→ Coccobacilli
``` Haemophilus influenzae Bordetella Pertussis Pasteurella Multocida Brucella Suis Francisella Tularensis Acinetobacter Baumannii ```
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Lab Algorithm - DDX Options for: | Gram (-) → Diplococci → Not Maltose Fermenting
Neisseria Gonorrhoeae | Moraxella Catarrhalis
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Lab Algorithm - DDX Options for: | Gram (-) → Diplococci → Maltose Fermenting
Neisseria Meningitidis
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Lab Algorithm - DDX Options for: | Gram (-) → Oxidase (+)→ Grows in 42°C
Campylobacter Jejuni
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Lab Algorithm - DDX Options for: | Gram (-) → Oxidase (+)→ Grows in Alkaline Media
Vibrio Cholerae
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Lab Algorithm - DDX Options for: | Gram (-) → Oxidase (+)→ Urease(+)
Helicobacter Pylori
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Lab Algorithm - DDX Options for: | Gram (-) → Bacilli → Fermenting Lactose Fast
Klebsiella Pneumoniae Escherichia Coli Enterobacter Cloacae
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Lab Algorithm - DDX Options for: | Gram (-) → Bacilli → Fermenting Lactose Slow
Serratia Marcescens
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Lab Algorithm - DDX Options for: | Gram (-) → Bacilli →Not Fermenting Lactose →Oxidase(+)
Pseudomonas Aeruginosa
293
Lab Algorithm - DDX Options for: | Gram (-) → Bacilli →Not Fermenting Lactose →H2S(+)
Salmonellae: Typhi / Paratyphi / Enterica | Proteus Mirabilis
294
Lab Algorithm - DDX Options for: | Gram (-) → Bacilli →Not Fermenting Lactose →H2S(-)
Shigella Dysenteriae | Yersinia Pestis / Yersinia Enterocolitica
295
Lab Algorithm - DDX Options for: | Imaging → Lung Lesion → Cavitary / Ring-like
``` Mycobacterium Tuberculosis Staphylococcus Aureus Streptococcus Pneumoniae Aspergillus Fumigatus Klebsiella Pneumoniae Pneumocystis JiroveciI Nocardia Asteroides ```
296
Lab Algorithm - DDX Options for: | Imaging → Lung Lesion → Atypical Pneumonia → Zoonotic
Francisella Tularensis Coxiella Burnetii Chlamydia Psittaci
297
Lab Algorithm - DDX Options for: | Imaging → Lung Lesion → Atypical Pneumonia → Non-Zoonotic
Chlamydia Pneumoniae Mycoplasma Pneumoniae Legionella Pneumophila
298
What are the Oncogenic Microbes? Which Cancers?
Helicobacter Pylori - Gastric Carcinoma and MALToma Epstein-Barr Virus - Burkitt and Hodgkin Lymphoma Human Papillomavirus - Cervical Carcinoma Human T-Lymphotropic Virus 1 - Adult T-Lymphoma Hepatitis C+B Virus - Hepatocellular carcinoma Human Herpesvirus 8 - Kaposi sarcoma Schistosoma Haematobium - Sq. Bladder Cancer Clonorchis Sinensis - GB Carcinoima
299
Which Bacteria and Viruses have Antigenic Variation Capabilities? (Give a few examples)
``` Neisseria Gonorrhoeae Neisseria Meningitidis Borrelia Burgdorferi Flaviviruses: HCV, Dengue, West nile.. Orthomyxoviruses (Influenza) HIV1 ```
300
Which Parasites have Antigenic Variation Capabilities? (Give a few examples)
Trypanosoma Brucei | Plasmodium Falciparum

S.N Microbiology (16 decks)

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