Microbiology JC087: Classification Of Microbes

Question 1

How to classify life

Answer 1

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

Question 2

Medically important microbes

Answer 2

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

2. Fungi
3. Parasites
4. Viruses
5. Prions

Question 3

Bacterial phyla

Answer 3

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

Question 4

Gram smear

Answer 4

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)

Question 5

***Classification of bacteria

Answer 5

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)

2. 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

3. Gram -ve cocci (GNC)
   - Moraxella catarrhalis
   - Neisseria gonorrheae
   - Neisseria meningitidis
4. 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)

5. “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

Question 6

Staphylococcus aureus

Answer 6

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

Question 7

Further classification of S. aureus: Antibiotic resistance

Answer 7

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

Question 8

Coagulase -ve Staphylococcus (CNS)

Answer 8

• 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

Question 9

Streptococcus

Answer 9

Classified according to Haemolysis pattern

- β-Haemolytic —> Lancefield grouping

Question 10

Streptococcus pneumoniae

Answer 10

• 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)

Question 11

Other important α- / γ-haemolytic Streptococci

Answer 11

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

Question 12

β-haemolytic Streptococci

Answer 12

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

Question 13

Enterococcus

Answer 13

• **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

Question 14

Gram +ve Rods (GPR)

Answer 14

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)

Question 15

1. Bacillus

Answer 15

• 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

Question 16

2. Listeria monocytogenes

Answer 16

• 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

Question 17

3. Corynebacterium

Answer 17

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)

Question 18

4. Nocardia and Rhodococcus

Answer 18

• 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.

Question 19

5. Mycobacterium

Answer 19

• 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

Question 20

Non-tuberculous mycobacterium (NTM)

Answer 20

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

Question 21

Anaerobic Gram +ve Rods (GPR)

Answer 21

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

Question 22

Gram -ve bacteria

Answer 22

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)

Question 23

1. Enterobacteriaceae

Answer 23

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

8. Salmonella (Typhi / Non-Typhi)
9. Shigella
10. 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

Question 24

2. Vibrionaceae and Other genera

Answer 24

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

Question 25

3. Non-fermenters

Answer 25

• 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

Question 26

4. Other important Gram -ve Rods

Answer 26

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

Question 27

Anaerobes

Answer 27

• 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

Question 28

Gram -ve Cocci

Answer 28

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

Question 29

“Unculturable” bacteria

Answer 29

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

Question 30

***Fungi classification

Answer 30

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

3. Dimorphic fungi
   - Sporothrix schenckii
   - Coccidiodes immitis
   - Paracoccidioides brasiliensis
   - Blastomyces dermatitidis
   - Histoplasma capsulatum
   - Penicillium marneffei
4. Pneumocystis jiroveci (PCP)

Question 31

1. Yeasts

Answer 31

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

Question 32

2. Moulds

Answer 32

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

Question 33

3. Dimorphic fungi

Answer 33

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

Question 34

Fungal diseases

Answer 34

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

Question 35

Parasites

Answer 35

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)

3. Ectoparasites
   - ***Sarcoptes scabiei
   - Lice, fleas

Question 36

Virology

Answer 36

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

Question 37

Respiratory tract infection

Answer 37

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

Question 38

Viral meningoencephalitis/ encephalopathy

Answer 38

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

Question 39

Viral GE

Answer 39

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