Microbiology - Medically important microbes Flashcards

(54 cards)

1
Q

Outline the classification scheme for gram positive cocci

A

Gram positive rods

Gram positive cocci:

  • Catalase positive GPC in clusters - Staphylococcus sp.
  • Catalase negative GPC in chains - Streptococci and Enterococcus
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2
Q

S. aureus

List types of infections

A

Infections:

  • Skin/ soft tissue
  • Abscesses
  • Native or prosthetic joint septic arthritis
  • Osteomyelitis
  • Pneumonia
  • Infective endocarditis
  • Endovascular infection
  • Surgical site infection

Toxin-mediated:

  • Food poisoning by staphylococcal enterotoxin
  • Toxic shock syndrome
  • Scalded skin syndrome
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3
Q

4 subtypes of S. aureus with varying antibiotics resistance

List the antibiotics resistance

A

MSSA: Sensitive to most B-lactams

HA- MRSA: Resistant to B-lactams and others e.g. clindamycin

CA- MRSA (may carry PVL toxin for necrotizing infection): Resistant to B-lactams, less resistant to non-B-lactams e.g. clindamycin

VISA/ VRSA: Immediate or full resistance to glycopeptides

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4
Q

Antibiotics of choice for MSSA, MRSA, VRSA

A

MSSA: Cloxacillin

HA- MRSA: Vancomycin, Linezolid, Daptomycin, Ceftaroline

CA-MRSA: Vancomycin, Linezolid, Daptomycin, Ceftaroline + any susceptible antibiotics

VISA/VRSA: Linezolid, Daptomycin, Ceftaroline

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5
Q

Function of coagulase test for gram positive cocci?

A

Catalase positive GPC in clusters:

  • Coagulase positive = S. aureus
  • Coagulase negative = Staphylococci spp.
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6
Q

Coagulase negative staphylococcus

  • Nature source of bacteria
  • Infections
  • Collection method
A

Natural skin commensals, benign

Exceptions:

  • Genuine infection of prosthesis
  • S. saprophyticus = UTI
  • S. lugdunensis = Virulent
  • S. epidermidis = prosthesis/ catheter-related infection

Collection:
Take at least two sets of blood culture if GPC in clusters
Single blood culture isolate may be contamination due to improper blood taking technique

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7
Q

Alpha hemolytic streptococci

Types of infection caused by Strep. pneumoniae

A

Streptococcus pneumoniae

Pneumonia 
Meningitis 
Otitis media 
Sinusitis 
Septicaemia
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8
Q

List 5 medically important alpha-hemolytic streptococci

List infections these cause

A
  1. Streptococcus pneumoniae: pneumonia, meningitis, otitis media, sinusitis, speticaemia
  2. Viridans streptococci- infective endocarditis, dental carries, oral infections
  3. Streptococcus anginosus/ S. milleri - Abscess formation in abdominal, pelvic cavities
  4. Streptococcus bovis - bacteremia, IE, GI malignancies (CRC)
  5. Streptococcus suis - meningitis, bacteremia
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9
Q

Which alpha-hemolytic streptococcus is related to colorectal cancer and IE

A

Strep. bovis

Major biotype in HK is type 2, associated with cholangitis
Biotype 1 is associated with IE and CRC

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10
Q

Beta-hemolytic streptococci

S. pyogenes infections

A

S. pyogenes (GAS in Lancefield grouping)

  • Local skin Infections: impetigo, cellulitis, necrotizing fasciitis
  • Respiratory: pneumonia, pharyngitis
  • Systemic infections: Toxic shock syndrome, Scarlet fever, lymphadenitis
  • Post-infectious syndrome: PSGN, acute rheumatic fever
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11
Q

Outline scheme for differentiating Catalase negative GPC/ Streptococci spp.

A

First: Alpha/ Gamma hemolysis or Beta hemolysis pattern

Alpha/ Gamma group:

  • Optochin susceptible and bile soluble, PYR +ve and VP -ve = Streptococcus pneumoniae
  • Optochin resistant and bile Insoluble = Viridans streptococci, Strep. bovis and Enterococci

Beta groups:
- Lancefield grouping, Bacitracin susceptibility, Biochemical reactions
GAS = Strep. pyogenes
GBS (Bacitracin resistant, CAMP _ve, Hippurate hydrolysis +ve) = Strep. agalactiae
GCS or GGS = Strep. dysgalactiae
Streptococcus anginosus group/ Strep. milleri

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12
Q

Virulent mechanisms of group A strep.

A

Invasion and spread through tissue via Streptokinase, Hyaluronidase

Systemic toxin: Streptolysin O, superantigen and other Streptococcal pyrogenic exotoxins

Anti-phagocytosis and adhere to epithelial cells/ mucosa : M protein, capsule

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13
Q

Scarlet fever

  • Presentation
A

Rash:

  • Facial flushing with peri-oral pallor
  • Diffuse, centrifugally spreading rash over face and upper chest
  • Blanchable

Strawberry tongue

Eosinophilia

Preceding pharyngitis or any GAS infection

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14
Q

Diagnostic criteria of Streptococcal toxic shock syndrome

Treatment options

A

Lab: Isolation of Group A Streptococcus

Clinical: 
- Hypotension 
- Multiorgan involvement with at least 2 of 
Renal impairment 
Coagulopathy 
Liver involvement 
ARDS 
Generalized, erythematous macular rash 
Soft tissue necrosis

Tx: Penicillin + Clindamycin or linezolid

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15
Q

Diagnostic criteria for acute rheumatic fever

A
Jone's criteria 
Major: 
- Carditis 
- Arthritis 
- Sydenham's chorea 
- Subcutaneous nodules 
- Erythema marginatum 

Minor:

  • Fever
  • Arthralgia
  • High ESR or CRP
  • Long PR interval

Supportive:

  • High Anti-streptolysin O titer (ASO)
  • Positive throat culture for GAS

Dx: 2 major or 1 major + 2 minor

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16
Q

Treatment of acute rheumatic fever

A

Penicillin x 10 days
Anti-inflammatory: Aspirin, Corticosteroids
Surgery for mitral valve involvement

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17
Q

S. agalactiae infections

Biochemical tests

A

S. agalactiae (GBS in Lancefield grouping)&raquo_space;> Raw fish!
Major infections: Meningitis, Pneumonia, Sepsis, Skin, Septic arthritis, Osteomyelitis, Female genital tract infections

  • Neonatal sepsis, meningitis, peripartum infections , pneumonia
  • Pregnant women: UTI, genital tract infection, placenta infection, post-partum sepsis
  • Elderly/ immunocompromised: skin infection, septic arthritis, osteomyelitis, pneumonia, endocarditis, meningitis, sepsis

Bacitracin resistant
CAMP positive
Hippurate hydrolysis positive

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18
Q

S. dysgalactiae Infections

Biochemical tests

A

Infections: Very similar to S. agalactiae
Same as S. agalactiae: Meningitis, Pneumonia, Sepsis, Skin infection, Septic arthritis, Osteomyelitis
Add-on: Pharyngitis, PSGN, Endocarditis
No pregnancy/ female genital infections

Lancefield group C/G
Bacitracin resistant
PYR -ve
VP -ve

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19
Q

S. anginosus/ S. milleri

Infections
Biochemical tests

A

Abscess formation
- Dental, brain, liver, pelvic, lung, empyema
Endocarditis
Bacteremia in neutropenic patients - ARDS, Toxic shock

Bacitracin resistant
PYR -ve 
VP +ve
Alpha/ Gamma hemolysis 
Lancefield non-groupable 

(Caramel smell)

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20
Q

Viridans streptococci

Source of bacteria
Types of infections

A

Common oral flora

Infections:
Dental carries
Infective Endocarditis

Bacteremia in neutropenic patients
Meningitis
Pneuomonia

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21
Q

Enterococci

Examples
Lancefield grouping and special biochemical tests, growth environment
Types of infections

A

Example: E. faecium and E. faecalis

Lancefield group D
Grows in 6.5% NaCl and 40% bile salt (similar to gut environment)
PYR +ve, Hydrolyzes bile esculin

Normal gut flora, causes mainly opportunistic infections

-Catheter-associated UTI, Line sepsis
-Endocarditis
- Component of polymicrobial intra-abdominal/ biliary infections

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22
Q

Outline the classification scheme for gram positive rods

A

Aerobic GPR: BCLNM

  • Bacillus
  • Corynebacterium
  • Listeria monocytogenes
  • Norcardia, Rhodococcus
  • Mycobacteria: MTB complex and non-tuberculosis mycobacteria

Anaerobic GPR:

  • Spore forming: Clostridium spp.
  • Non-spore forming
23
Q

Bacillus spp.

List examples and types of infection
Source of bacteria

A

Widely distributed in environment

B. anthracis = anthrax
B. cereus = Food poisoning
(rice products)

Bacillus in blood culture is most likely contamination

24
Q

Listeria monocytogenes

Source of bacteria
Types of infections
Antibiotic resistance
Tx

A

Source: Milk, Chicken and poultry products

Infections:

  • Neonatal meningitis and pregnancy infections
  • CNS infections in elderly/ immunocompromised
  • Resistant to cephalosporins, sensitive to ampicillin

Tx: Ampicillin, (ceftriaxone)

25
Corynebacterium Example Type of infection Presentation Source of bacteria
**Respiratory and cutaneous diphtheria** infection Sore throat with **grey pseudo-membrane in oropharynx** **Cervical lymphadenopathy**, toxin-mediated **cardiac and neurological complications** Source: Skin, oral mucosal commensals, mostly cause opportunistic infections
26
Nocardia and Rhodococcus - Type of infection - Biochemical test
Infection: Opportunistic infection, chronic in immunocompromised pt. Test: Weakly/ **Modified acid-fast** Nocardia: **Pulmonary abscess, CNS abscess and cutaneous nocardiosis** (Lung and brain abscess > think Nocardia) Rhodococcus: **Pneumonia, lymphadenopathy, wound infections** (Zoonotic)
27
List anaerobic gram positive rods and related infections
Spore-forming; Clostridium spp. - **C. perfringens**: gas gangrene, food poisoning, biliary sepsis - **C. tetani**: tetanus - **C. botulinum**: Botulism - **C. difficile**: Pseudomembranous colitis, Antibiotics associated diarrhea Non-spore forming: **Actinomyces** - **GI and genital tract** colonizer - **Pelvic (IUCD use), abdominal, cervicofacial actinomycosis** - Infection across tissue planes, invasive
28
Outline classification scheme for Gram negative bacteria
Gram negative **rods** - **Anaerobes**: oral flora - **Fusobacterium**; Gut flora - **bacteroides** - **Aerobes/ facultative anaerobes**: **Enterobacteriaceae, Vibrionaceae, Non-fermenters** - Other Aerobes: e.g. H.influenzae, Legionella pneumophilia, Campylobacter, H. pylori, HACEK group, brucella Gram negative **cocci** - **Neisseria - Moraxella catarrhalis**
29
Enterobacterales List examples under this group
Think inflammatory gastroenteritis: **E. coli** Klebsiella **Proteus Enterobacter** Citrobacter Morganella Serratia **Salmonella Shigella Yersinia** ```
30
Enterobacterales Types of infections
UTI **Inflammatory Diarrhoea** syndromes: E.coli, Non-typhoidal salmonella, shigella Specific syndromes: **Bacillary dysentry (Shigella), Typhoid fever (Salmonella typhi/ paratyphi)**
31
Enterobacterales Antibiotics resistant subtypes
**ESBL-producers** = resistant to B-lactams except carbapenems, so use carbepenems! **CPE (Carbapenemase-producing Enterobacteriaceae)** = Resistant to carbapenems
32
Vibrionaceae Examples and related infections Biochemical tests
Vibrio: - V. cholerae: Cholera epidemics (O1, O139); Watery diarrhea (Non-O1, Non-O139) - V. vulnificus: Necrotizing fasciitis - V. parahaemolyticus: Food poisoning Aeromonas Plesiomonas Tests: Glucose fermenters, oxidase positive
33
List non-fermenters and related infections
Most are environmental **- Pseudomonas aeruginosa - Acinetobacter baumannii** - Stenotrophomonas maltophilia - Burkholderia cepacia complex **Nosocomial infections: pneumonia, wound infections, prosthesis-related** Chronic infection e.g. P. aeruginosa, Burkholderia spp. in cystic fibrosis pt. Burkholderia pseudomallei = cause of severe community-acquired pneumonia and bacteremia
34
Anaerobic gram negative rods Source of bacteria Type of infection 2 examples
Normal flora in oral cavity and GIT Causes polymicrobial infections and abscess - **Fusobacterium spp.: Lemierre's disease (IJV thrombophlebitis**; - high fever with acute neck pain), **Brain abscess** - **Bacteroides fragilis**: GI colonizer, complicated **intra-abdominal infections**
35
Gram negative cocci Examples and related infections
36
List bacteria that are unculturable/ unstainable by gram smear
1. **Spirochaetes:** - **Treponema pallidum (Syphilis)** - Borrelia recurrentis (recurring fever) - Borrelia burgdorferi (Lyme disease) - **Leptospira (Leptospirosis)** 2. **Mycoplasma and Ureaplasma** 3. **Chlamydia and Chlamydophilia (STD)** 4. **Coxiella burnetii (Q fever)** 5. **Bartonella** quintana (Trench fever) and B. henselae (Cat-scratch disease) 6. **Rickettsia spp. and Orientia tsutsugamushi**: Typhus, spotted mountain fever
37
Fungi Classification and examples
Yeast - unicellular - Candida - Cryptococcus - Trichophyton - Malassezia Mould - Pro-mycelial - Dermatophytes - Aspergillus - Zygomycetes - Fusarium Dimorphic fungi Pneumocystis jiroveci
38
Candida spp Type of infection Examples according to sensitivity to Azoles
**Mucosal candidiasis, Thrush, systemic infection in immunocompromised and ICU pt.** Azole sensitive: - **C. albicans** - C. parapsilosis Azole resistant: - **C. krusei** - C. glabrata - C. auris
39
Types of infection caused by crytococcus, trichosporon, malassezia
**All yeasts cause opportunistic infections in immunocompromised** Cryptococcus: opportunistic meningitis, opportunistic pneumonia, systemic infections in immunocompromised Trichosporon spp: piedra, systemic infection in immunocompromised Malassezia: pityriasis versicolor, systemic infection
40
Moulds List examples and types of infection
**Dermatophytes: Tinea pedis, Tinea cruris, Tinea corporis, Onychomycosis** - Trichophyton spp. - Microsporum spp. - Epidermophyton floccosum Severe **systemic infections in immunocompromised**: **Aspergillus**: - A. fumigatus - A. falvus - A. niger Zygomycetes: Rhizopus spp. Mucor **Fusarium**: F. solani, F. oxysporum
41
Examples of dimorphic fungi
Sporothrix schenckii Blastomyces dermatitidis Histoplasma capsulatum **Penicillium marneffei**
42
Examples of fungal disease according to skin layers
Superficial mycoses: Tinea, Onychomycosis (thrush), Cutaneous candidiasis, Pityriasis verisolor Subcutaneous mycoses: mycetoma (gardener) Deep mycoses
43
3 classes of parasites and examples
44
List viruses with high propensity to cause lower respiratory tract illness
Decreasing propensity to cause LRTI Rhinovirus/ Enterovirus Coronavirus Parainfluenza (CROUP or bronchoiolitis)
45
List viruses that cause URTI
``` Bocavirus Adenovirus Influenza A,B (URTI or bronchiolitis) Enterovirus D68 Rhinovirus ```
46
Viruses that cause hepatitis
Hepatitis A virus, HBV, HCV, HDV, HEV cytomegalovirus (immunocompromised), primary EBV (also causes infectious mononucleosis), primary HHV-6 (human herpesvirus), adenovirus, enterovirus
47
Viruses that cause gastroenteritis
**Rotavirus** (children, vaccine-preventable), **Norovirus** (any age group), **Sapovirus, Adenovirus, Astrovirus** Others: Hepatitis A virus, CMV, Coronavirus, HIV, Influenza, Torovirus, Aichi virus, Picobirnavirus, Bocavirus
48
Viruses that cause meningoencephalitis/ encephalopathy
**Herpes simplex virus (HSV) and Other herpesviruses**: Primary EBV, Primary CMV, Primary HHV-6 **Varicella zoster virus (VZV)** **Exanthematous disease viruses**: Measles (but mainly cough, rash), rubella, parvovirus B19  **Japanese encephalitis** (JE), Animal contact: Rabies, Herpes B, LCMV, Hendra, Nipah  **Enterovirus**  **Influenza-associated encephalopathy**: Influenza, adenoviruses
49
First-line investigation for viral meningoencephalitis
```  Brain scans (CT/MRI)  Lumbar puncture  PCR for specific viral pathogens  Antibodies against specific viral pathogens  Electroencephalogram ```
50
Viruses that cause myocarditis
```  Adenovirus  Enterovirus  HSV/ VZV  Cytomegalovirus  Influenza ```
51
4 viral rashes
Chickenpox:  Varicella zoster virus: reactivation as herpes zoester/ shingles Measles Rubella Enterovirus Parvovirus B19: ‘slapped cheek rash’, ‘fifth disease' HHV-6: Roseola infantum
52
Arboviruses Examples and related infections
 Japanese encephalitis (JE): meningoencephalitis  Dengue (登革熱): hemorrhagic fever if severe  Zika (Zika infection during pregnancy - microcephaly)  West Nile virus: meningoencephalitis  Yellow Fever virus
53
Major cancers associated with viral infections
Nasopharyngeal carcinoma, lymphoma: Epstein-Barr virus (EBV) Hepatocellular carcinoma: Hepatitis B virus (HBV), HCV ``` Cervical cancer, anal cancer, oropharyngeal cancer: Human papillomavirus (HPV), high-risk genotypes (16, 18) ```
54
Transmissible spongiform encephalopathies Pathogenesis Causative pathogen Types
proteinaceous infectious particle (no DNA or RNA):  Autocatalytic conversion of normal prion protein to abnormally folded prion protein: Chain reaction: PrPC >> PrPSc  Accumulation of abnormal prion protein causes spongiform changes and vacuolation in the brain (looks like cheese) >> fatal, no effective treatment Types of TSE: - Sporadic CJD (sCJD) - Variant CJD (vCJD):Transmission of BSE (bovine spongiform encephalopathy) agent from cows to humans (consumption of beef) - Iatrogenic CJD (iCJD): prion exposure due to surgical procedures and blood transfusion (vCJD) - Genetic CJD (gCJD)