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JC WCS > Microbiology JC087: Classification Of Microbes > Flashcards

Microbiology JC087: Classification Of Microbes Flashcards

1
Q

How to classify life

A
  1. Physical characteristics (Phenotypic classification):
    - **Morphology
    - Colour
    - Nutritional requirements
    - **    Biochemical reactions
    - ***Antigenicity and Serotyping (protein composition)
  2. Genetic differences (Genotypic classification):
    - DNA-DNA hybridisation
    - Sequence of particular genes
    - Whole genome sequencing
  3. Practical clinical medical classification
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2
Q

Medically important microbes

A

Prokaryotes
1. Bacteria

ALL medically important prokaryotes are Bacteria

  • single called organisms ***without a nucleus
  • **chromosomal and **plasmid DNA
  • multiply by binary fission
  • typically <5um in size

Eukaryotes

  1. Fungi
  2. Parasites
  3. Viruses
  4. Prions
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3
Q

Bacterial phyla

A 
Most bacteria are NOT medically important
Important ones:
- Actinobacteria
- Bacteroidetes / Chlorobi group
- Chlamydiae / Verrucomicrobia group
- Firmicutes (gram +ve bacteria)
- Fusobacteria
- Proteobacteria (purple bacteria and relatives)
- Spirochaetes
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4
Q

Gram smear

A

Most important, Basis of classification of bacteria

Crystal violet —> Iodine —> Alcohol / Acetone wash —> Safranin (counter stain)
Purple —> Brown —> Pink —> Ready!

Gram +ve: retain purple colour even after washing
Gram -ve: no more colour after washing —> stained by Safranin (red / pink)

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5
Q

***Classification of bacteria

A

Gram +ve / -ve / unstainable by Gram stain

Rods / Cocci / Coccobacilli (in-between)
1. Gram +ve cocci (GPC):
- Catalase +ve (in Clusters —> Staphylococci)
—> Coagulase +ve (Staph. aureus)
—> Coagulase -ve (Staphylococci, many species, commensals mostly)

  • Catalase -ve (in Chains —> Streptococci)
    —> Streptococcus (α-haemolytic / γ-haemolytic / β-haemolytic)
    —> Enterococcus

(No Gram -ve cocci in Chains / Clusters!!!)
(Anaerobic GPC are insignificant)

  1. Gram +ve rods (GPR):
    - Aerobic
    —> Bacillius spp.
    —> Corynebacterium spp.
    —> Listeria monocytogenes
    —> Nocardia, Rhodococcus (modified acid fast)
    —> Mycobacteria (acid fast)
    ——> Mycobacterium TB complex
    ——> Non-tuberculosis mycobacteria (NTM)
  • Anaerobic
    —> Spore forming (Clostridium spp.)
    —> Non-spore forming
  1. Gram -ve cocci (GNC)
    - Moraxella catarrhalis
    - Neisseria gonorrheae
    - Neisseria meningitidis
  2. Gram -ve rods (GNR)
    - Aerobes / Facultative anaerobes
    —> Enterobacteriaceae
    —> Vibrionaceae and Other genera
    —> Non-fermenters
    ——> Pseudomonas aeruginosa
    ——> Acinetobacter baumannii
    ——> Stenotrophomonas maltophlia
    ——> Burkholderia cepacia complex
—> Others
——> Haemophilus influenzae
——> Legionella pneumophila
——> Campylobacter spp.
——> Helicobacter pylori
——> Brucella spp.
——> HACEK group (Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella)
  • Anaerobes
    —> Oral flora (Fusobacterium spp.)
    —> Gut flora (Bacteroides fragilis)
  1. “Unculturable” bacteria
    - Spirochaetes
    —> Treponema pallidum (Syphilis)
    —> Borrelia recurrentis (Relapsing fever)
    —> Borrelia burgdorferi (Lyme disease)
    —> Leptospira (Leptospirosis)
    - Mycoplasma and Ureaplasma
    - Chlamydia and Chlamydophila
    - Coxiella burnetii (Q fever)
    - Bartonella quintana (trench fever) and B. henselae (cat-scratch disease)
    - Rickettsia spp. and Orientia tsutsugamushi: typhus, spotted fever
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6
Q

Staphylococcus aureus

A

Infections

  1. ***Skin / Soft tissue infections
  2. Abscesses
  3. Native / Prosthetic joint septic arthritis
  4. Osteomyelitis
  5. ***Pneumonia
  6. ***Infective endocarditis (native / prosthetic valves)
  7. Endovascular infections
  8. Surgical site infections

Toxin mediated diseases:

  1. ***Food poisoning in Staphylococcal enterotoxin
  2. ***Toxic shock syndrome
  3. ***Scalded skin syndrome
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7
Q

Further classification of S. aureus: Antibiotic resistance

A

MSSA (Methicillin-sensitive SA)

  • ***sensitive to most β-lactams
  • **Cloxacillin (anti-staphylococcal penicillin) / 1st gen Cephalosporin / **Augmentin
  • X Penicillin / Ampicillin

HA-MRSA

  • resistant to β-lactams, other agents e.g. Clindamycin
  • ***Vancomycin / Linezolid / Daptomycin / Ceftaroline (5th gen)
  • carriage common in old age home residents and after prolonged hospitalisation

CA-MRSA

  • resistant to β-lactams
  • often less resistant to non-β-lactams e.g. ***Clindamycin
  • ***Vancomycin / Linezolid / Daptomycin / Ceftaroline (5th gen) + Any susceptible antiobiotics
  • may carry PVL toxin (↑ pathogenicity)

VISA / VRSA (Vancomycin-resistant)

  • intermediate to full resistance to Glycopeptides
  • ***Linezolid / Daptomycin / Ceftaroline (5th gen) etc.
  • very rare
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8
Q

Coagulase -ve Staphylococcus (CNS)

A
  • usually benign commensals of skin
  • single blood culture isolates of CNS usually represent contamination of blood culture due to improper collection technique
  • exceptions:
    1. **S. saprophyticus: UTI
    2. S. lugdunensis: Virulent organism
    3. **    S. epidermidis: Prosthesis / Catheter-associated (propensity to form ***biofilm)
  • Genuine infection should be considered when CNS are isolated from blood cultures / sterile site specimens of patients with ***prostheses

Tip: Whenever has GPC in clusters in blood culture —> Always repeat ***>=2 sets of blood culture before making any changes in antibiotics

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9
Q

Streptococcus

A

Classified according to Haemolysis pattern

- β-Haemolytic —> Lancefield grouping

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10
Q

Streptococcus pneumoniae

A
  • aka ***Pneumococcus
  • α-haemolytic
  • optochin susceptible, bile soluble
  • causes more than **Pneumonia: **Meningitis, Septicaemia, ***Otitis media, Sinusitis
  • usually easy to treat, but emergence of PRSP (penicillin-resistant) strains
  • ***vaccination included in universal programme (but does not cover all serotypes well e.g. serotype 3)
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11
Q

Other important α- / γ-haemolytic Streptococci

A
  1. Viridans streptococci (α-haemolytic)
    - group of related **oral streptococci
    - dental caries, **    infective endocarditis
  2. S. anginosus (S. milleri)
    - ***abscess formation (brain, lung, parapharyngeal, intraabdominal, liver)
  3. S. bovis
    - now known as: gallolyticus, infantarius, pasteurianus
    - bacteraemia, endocarditis etc.
    - associated with underlying GI malignancy (screen for CRC)
  4. S. suis
    - ***meningitis, bacteraemia in HK
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12
Q

β-haemolytic Streptococci

A
  1. S. pyogenes (Group A strept)
    - infections: **pharyngitis, **scarlet fever, **impetigo, celluitis, necrotising fasciitis
    - **    toxic shock syndrome
    - ***post-infectious syndromes: acute rheumatic fever, PSGN
  2. S. agalactiae (Group B strept)
    - **neonatal sepsis / meningitis, **peripartum infections
    - invasive in elderly / immunocompromised
  3. S. dysgalactiae (Group C / G strept)
    - skin / soft tissue infections

Tip: β-haemolytic streptococci are ***sensitive to penicillin

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13
Q

Enterococcus

A
  • **Normal gut flora, mainly **opportunistic infections (e.g. GI perforation, biliary sepsis, underlying catheter)
  • E. faecium, E. faecalis most common

Diseases:
- **catheter associated UTI, **endocarditis, component of polymicrobial ***intra-abdominal / biliary infections, line sepsis

  • ***Resistant to many antiobiotics e.g. Cephalosporins
  • VRE: Vancomycin resistant enterococcus (usually E. faecium) may need Daptomycin / ***Linezolid / Tigecycline
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14
Q

Gram +ve Rods (GPR)

A

Aerobic

  1. Bacillius spp.
  2. Listeria monocytogenes
  3. Corynebacterium spp.
  4. Nocardia, Rhodococcus (modified acid fast)
  5. Mycobacteria (acid fast, have gram +ve cell wall but may not stain with Gram stain)
    - Mycobacterium TB complex
    - Non-tuberculosis mycobacteria (NTM)

Anaerobic

  1. ***Clostridium (Spore forming)
  2. Actinomyces (Non-spore forming)
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15
Q
  1. Bacillus
A
  • widely distributed in environment e.g. ***soil
  • B. anthracis: anthrax (炭疽)
  • B. cereus: food poisoning (most commonly seen) / bloodstream infection
  • Bacillus in blood cultures is most often a contaminant
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16
Q
  1. Listeria monocytogenes
A
  • association with milk + chicken
  • Neonatal ***meningitis + infections in pregnancy
  • ***CNS infections in elderly / immunocompromised
  • **resistant to Cephalosporin, **sensitive to Ampicillin

Tip: Consider adding ***Ampicillin for Listeria coverage on top of Ceftriaxone if encounter high-risk patients (pregnant women) with meningitis

17
Q
  1. Corynebacterium
A

Corynebacterium diphtheriae

  • respiratory diphtheria + cutaneous diphtheria
  • rare in HK due to vaccination
  • sore throat with adherent grey ***pseudo-membrane in oropharynx
  • diphtheria toxin
  • **cervical lymphadenopathy, **toxin-mediated cardiac / neurological complications

Other Coryneforms

  • usually opportunistic pathogens
  • skin and oral mucosal commensals
  • contaminants in clinical specimens (beware in immunocompromised / repeated isolates in specimens)
18
Q
  1. Nocardia and Rhodococcus
A
  • opportunistic pathogens causing chronic infections in very ***immunocompromised patients
  • weakly acid-fast (need modified acid-fast stain)
  • form filaments / hyphae

Nocardia:
- pulmonary, CNS, cutaneous nocardiosis

Rhodococcus:

  • zoonotic organism
  • presentation: pneumonia, lymphadenopathy, wound infections etc.
19
Q
  1. Mycobacterium
A
  • Acid-fast bacilli
  • Gram +ve cell structure but do not retain Gram stain well
  • NOT all AFB is TB
  • NOT all Mycobacteria are TB

Mycobacterium tuberculosis
- Endemic + Important disease in HK

20
Q

Non-tuberculous mycobacterium (NTM)

A

aka Atypical mycobacteria / MOTT

Most are **environmental bacteria, **opportunistic human pathogens
- elderly, smoking, underlying lung disease (cystic fibrosis, bronchiectasis)

  1. M. marinum
    - **skin / soft tissue infection among **fishermen (e.g. tenosynovitis, cutaneous ulcers)
  2. M. avium-intercellulare
    - lung disease (***Lady Windermere’s syndrome)
    - disseminated infection in AIDS patients
  3. M. leprae
    - causative agent of ***leprosy
    - cutaneous +/- neuronal involvement
  4. M. abscessus / chelonae
    - fast growing mycobacteria
    - various opportunistic infections

Tip: must find a specialist to manage

21
Q

Anaerobic Gram +ve Rods (GPR)

A
  1. Clostridium (Spore forming)
    - C. perfringens: **gas gangrene, food poisoning, biliary sepsis
    - C. tetani: tetanus
    - C. botulinum: **    botulism
    - **C. difficile: **pseudomembranous colitis
  2. Actinomyces (Non-spore forming)
    - GI / Genital tract coloniser causing pulmonary / **pelvic / abdominal / cervicofacial actinomycosis
    - infection crossing tissue planes (mucosal disruption)
    - **    pelvic actinomycosis associated with IUCD use
    - treatment requires ***prolonged courses of antibiotics
22
Q

Gram -ve bacteria

A

Gram -ve Cocci

  1. Neisseria
  2. Moraxella catarrhalis
Gram -ve Rods
Aerobes / Facultative anaerobes
1. Enterobacteriaceae
2. Vibrionaceae and Other genera
3. Non-fermenters
4. Others
- Haemophilus influenzae
- Legionella pneumophila
- Campylobacter spp.
- Helicobacter pylori
- Brucella spp.
- HACEK group (Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella)

(Strict) Anaerobes

  1. Oral flora (Fusobacterium spp.)
  2. Gut flora (Bacteroides fragilis)
23
Q
  1. Enterobacteriaceae
A

Large group of pathogens

Commensals

  1. E. coli
  2. Klebsiella
  3. Proteus
  4. Enterobacter
  5. Citrobacter
  6. Morganella
  7. Serratia

Not commensal, spread from person-to-person

  1. Salmonella (Typhi / Non-Typhi)
  2. Shigella
  3. Yersinia

Disease associations similar:

  • ***GI infections
  • ***UTI
  • ***Wound infections (esp. nosocomial)
  • ***Abdominal infections
  • ***Diarrheal syndromes

Specific syndromes:
- Bacillary dysentery (Shigella)
- ***Typhoid fever (Salmonella Typhi / Paratyphi)
(Non-Typhoid Salmonellosis: diarrheal symptoms)

Antibiotics resistance:

  • ***ESBL-producers: Resistant to β-lactams except Carbapenems
  • ***CPE (Carbapenemase producing Enterobacteriaceae)

Tip: Documented severe infection due to ESBL +ve Enterobacteriaceae —> ***Carbapenem is the antibiotic of choice

24
Q
  1. Vibrionaceae and Other genera
A
  1. Vibrio
    - **V. cholerae: Cholera epidemics (O1, O139)
    - Non-O1, Non-O139 V. cholerae: Diarrhoea
    - **    V. vulnificus: necrotising fasciitis (食肉菌感染)
    - V. parahaemolyticus: food poisoning
  2. Aeromonas
  3. Plesiomonas
    - most of the time self-limiting GE
25
Q
  1. Non-fermenters
A
  • GNR not fermenting glucose / other sugars
  • Most are ***environmental bacteria found in healthcare settings

Medically important examples:

  • ***Pseudomonas aeruginosa
  • Acinetobacter baumannii
  • Stenotrophomonas maltophlia
  • ***Burkholderia cepacia complex

Mainly ***nosocomial infections:

  1. ***Pneumonia
  2. Wound infections
  3. Prosthesis-associated
    - ***Foley catheter, Tracheostomy, Endotracheal intubation, Central line infections
  4. Chronic infections
    - P. aeruginosa and Burkholderia spp. in cystic fibrosis patients
  • Have good ability to pick up resistance, can be ***highly resistant to antibiotics e.g. PRPA, MRAB

Tip: Burkholderia pseudomallei is a cause of severe CAP and Bacteraemia in HK

26
Q
  1. Other important Gram -ve Rods
A
  1. Haemophilus influenzae
    - severe sepsis, meningitis, ***epiglottitis (Hib) —> vaccine preventable
    - sinusitis, otitis media (non-typeable Hi) —> no vaccine
  2. Legionella pneumophila
    - ***CAP
  3. Campylobacter spp.
    - ***GE
  4. Helicobacter pylori
    - **gastric ulcer, **Ca stomach
  5. Brucella spp.
    - febrile illness
  6. HACEK group (Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella)
    - fastidious organism
    - rare cause of ***infective endocarditis
27
Q

Anaerobes

A
  • normal flora in oral cavity, GI
  • part of polymicrobial infections, abscesses

Medically important:

  1. Fusobacterium spp.
    - Oral flora
    - ***Lemierre’s disease (IJV thrombophlebitis) (Parapharyngeal abscess)
    - Brain abscess
  2. Bacteroides fragilis (Gram -ve rods)
    - Gut flora
    - GI tract coloniser often found in complicated ***intra-abdominal infections
    - ↑ antimicrobial resistance
28
Q

Gram -ve Cocci

A
  1. Moraxella catarrhalis
    - oral commensal
    - acute bacterial **sinusitis, **otitis media, implicated in ***COPD exacerbation
  2. Neisseria gonorrheae
    - Gonorrhea
    - **genital and extragenital manifestations
    - **    Tenosynovitis arthritis dermatitis syndrome, **Fitz Hugh Curtis syndrome, **Pelvic inflammatory disease, Gonococcal ophthalmia neonatorum, rarely Gonococcal endocarditis
  3. Neisseria meningitidis
    - Meningococcemia
    - Meningitis
    - ***vaccine preventable
29
Q

“Unculturable” bacteria

A

Cannot use Gram stain to classify

  1. Spirochaetes
    - Treponema pallidum (Syphilis)
    - Borrelia recurrentis (Relapsing fever)
    - Borrelia burgdorferi (    Lyme disease)
    - Leptospira (***Leptospirosis)
  2. Mycoplasma and Ureaplasma
    - **lack of cell wall
    - **    mycoplasma pneumonia (most common pneumonia in children)
    - mycoplasma genitalium
  3. Chlamydia and Chlamydophila
    - ***STI, pneumonia
  4. Coxiella burnetii (Q fever)
    - zoonotic infection
  5. Bartonella quintana (trench fever) and B. henselae (cat-scratch disease)
  6. Rickettsia spp. and Orientia tsutsugamushi: typhus, spotted fever
30
Q

***Fungi classification

A
  1. Yeast
    - Candida
    - Cryptococcus neoformans, Cryptococcus gattii
    - Trichosporon spp.
    - Malassezia
  2. Mould
    - Dermatophytes
    —> Trichophyton spp.
    —> Microsporum spp.
    —> Epidermophyton floccosum
  • Aspergillus
    —> A. fumigatus
    —> A. flavus
    —> A. niger
  • Zygomycetes
    —> Rhizopus spp.
    —> Mucor
  • Fusarium
    —> F. solani
    —> F. oxysporum
  • Acremonium
  • Penicillium
  1. Dimorphic fungi
    - Sporothrix schenckii
    - Coccidiodes immitis
    - Paracoccidioides brasiliensis
    - Blastomyces dermatitidis
    - Histoplasma capsulatum
    - Penicillium marneffei
  2. Pneumocystis jiroveci (PCP)
31
Q
  1. Yeasts
A
  1. Candida
    - **mucosal candidiasis
    - systemic infections in immunocompromised / intensive care patients
    —> **    C. albicans
    —> C. parapsilosis
    —> C. krusei
    —> C. glabrata
    —> C. auris (very drug resistant)
  2. Cryptococcus neoformans, Cryptococcus gattii
    - opportunistic ***meningitis
    - systemic infections in immunocompromised patients
  3. Trichosporon spp.
    - piedra
    - systemic infections in immunocompromised patients
  4. Malassezia
    - pityriasis versicolor
32
Q
  1. Moulds
A

Mostly seen in post-chemo patients, immunocompromised patients etc.

  1. Dermatophytes
    - Trichophyton spp.
    - Microsporum spp.
    - Epidermophyton floccosum
    - diseases: Tinea pedis, Tinea cruris, Tinea corporis, Onychomycosis
  2. Aspergillus
    - A. fumigatus
    - A. flavus
    - A. niger
  3. Zygomycetes
    - Rhizopus spp.
    - Mucor
    - seen in severe DKA
  4. Fusarium
    - F. solani
    - F. oxysporum
  5. Acremonium
  6. Penicillium
33
Q
  1. Dimorphic fungi
A

Yeast at body temp, Moulds at room temp

  1. Sporothrix schenckii
  2. Coccidiodes immitis
  3. Paracoccidioides brasiliensis
  4. Blastomyces dermatitidis
  5. Histoplasma capsulatum
  6. ***Penicillium marneffei
34
Q

Fungal diseases

A
  1. Superficial mycoses
    - **Tinea
    - **    Onychomycosis
    - ***Cutaneous candidiasis
    - Pityriasis versicolor
  2. Subcutaneous mycoses
    - ***Mycetoma
  3. ***Deep mycoses
35
Q

Parasites

A
  1. Protozoa (unicellular)
    - **Plasmodium
    - Giardia, **    Entamoeba (GI infection)
    - Naegleria, Acanthamoeba (CNS infection)
    - ***Toxoplasma gondii (self-limiting infection, remain latent and activate during immunosuppression)
  2. Helminths
    - Nematodes (round worms, 線蟲)
    —> intestinal: hookworms
    —> blood and tissue: filariae
  • Trematodes (flukes, 吸蟲)
    —> lung: Paragonimus spp.
    —> liver: **Clonorchis sinensis (Chinese liver fluke —> very common in HK)
    —> intestinal: Fasciolopsis buski
    —> blood: **    Schistosoma spp. (Schistosomiasis)
  • Cestodes (tapeworms, 絛蟲)
    —> intestinal: Taenia solium
    —> tissue: larval stage of cestodes (Taenia solium)
  1. Ectoparasites
    - ***Sarcoptes scabiei
    - Lice, fleas
36
Q

Virology

A

Classified by Viral diagnostic syndromes

  1. Respiratory tract infection
  2. Viral hepatitis
  3. GE
  4. Meningoencephalitis, Myelitis
  5. Myocarditis
  6. Viral exanthems / Arboviruses
  7. Viral haemorrhagic fever
  8. HIV, Viral infections in immunocompromised hosts
  9. Cancer
37
Q

Respiratory tract infection

A

Propensity to cause LRTI (low to high):

  • Bocavirus
  • Rhinovirus / Enterovirus
  • Coronavirus (HKU1, NL63, OC43, 229E)
  • Parainfluenza 1, 2, 3, 4
  • ***RSV, HMPV
  • ***Adenovirus
  • ***Influenza A, B
  • MERS coronavirus
  • COVID-19

But any respiratory virus can cause infection of any part of respiratory tract

38
Q

Viral meningoencephalitis/ encephalopathy

A

Top 5:

  1. ***HSV
  2. ***VZV
  3. ***Enterovirus (Coxsackie virus, ECHO virus, Poliovirus)
  4. ***Japanese encephalitis
  5. Influenza-associated encephalopathy

Others:

  • respiratory viruses: influenza, adenovirus
  • travel: encephalitogenic arbovirus (endemic to areas of travel)
  • animal contact: rabies, herpes B, LCMV, genera, nipah
  • previous residence in uk: variant CJD
  • profound immunosuppression: JC PML, CMV reactivation, HHV-6 encephalitis, HIV encephalopathy, astroviruses etc.
  • other herpesviruses: primary EBV, primary CMV, primary HHV-6
  • exanthematous disease viruses: measles, rubella, parvovirus B19
  • mumps
  • hepatitis E

Diagnosis:

  1. CT / MRI
  2. EEG
  3. ***LP
  4. PCR
  5. Ab against specific viral pathogens
39
Q

Viral GE

A

Top 5:

  1. ***Rotavirus
  2. ***Norovirus
  3. Sapovirus
  4. Adenovirus
  5. Astrovirus
    - spread by direct contact with patients / their environment
    - **watery, **self-limiting diarrhoea
    - complication in infants, immunocompromised patients
    - what kills is the dehydration
    - can cause major outbreaks

Others:

  • CMV
  • coronavirus
  • HIV
  • influenza
  • toro virus
  • hepatitis A virus
  • aichivirus
  • picobirnavirus
  • bocavirus

JC WCS (134 decks)

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