JC87 (Microbiology) - Medically important microbes Flashcards
Outline the classification scheme for gram positive cocci
Gram positive rods
Gram positive cocci:
- Catalase positive GPC in clusters - Staphylococcus sp.
- Catalase negative GPC in chains - Streptococci and Enterococcus
S. aureus
List types of infections
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
4 subtypes of S. aureus with varying antibiotics resistance
List the antibiotics resistance
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
Antibiotics of choice for MSSA, MRSA, VRSA
MSSA: Cloxacillin
HA- MRSA: Vancomycin, Linezolid, Daptomycin, Ceftaroline
CA-MRSA: Vancomycin, Linezolid, Daptomycin, Ceftaroline + any susceptible antibiotics
VISA/VRSA: Linezolid, Daptomycin, Ceftaroline
Function of coagulase test for gram positive cocci?
Catalase positive GPC in clusters:
- Coagulase positive = S. aureus
- Coagulase negative = Staphylococci spp.
Coagulase negative staphylococcus
- Nature source of bacteria
- Infections
- Collection method
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
Alpha hemolytic streptococci
Types of infection caused by Strep. pneumoniae
Streptococcus pneumoniae
Pneumonia Meningitis Otitis media Sinusitis Septicaemia
List 5 medically important alpha-hemolytic streptococci
List infections these cause
- Streptococcus pneumoniae: pneumonia, meningitis, otitis media, sinusitis, speticaemia
- Viridans streptococci- infective endocarditis, dental carries, oral infections
- Streptococcus anginosus/ S. milleri - Abscess formation in abdominal, pelvic cavities
- Streptococcus bovis - bacteremia, IE, GI malignancies (CRC)
- Streptococcus suis - meningitis, bacteremia
Which alpha-hemolytic streptococcus is related to colorectal cancer and IE
Strep. bovis
Major biotype in HK is type 2, associated with cholangitis
Biotype 1 is associated with IE and CRC
Beta-hemolytic streptococci
S. pyogenes infections
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
Outline scheme for differentiating Catalase negative GPC/ Streptococci spp.
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
Virulent mechanisms of group A strep.
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
Scarlet fever
- Presentation
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
Diagnostic criteria of Streptococcal toxic shock syndrome
Treatment options
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
Diagnostic criteria for acute rheumatic fever
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
Treatment of acute rheumatic fever
Penicillin x 10 days
Anti-inflammatory: Aspirin, Corticosteroids
Surgery for mitral valve involvement
S. agalactiae infections
Biochemical tests
S. agalactiae (GBS in Lancefield grouping)»_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
S. dysgalactiae Infections
Biochemical tests
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
S. anginosus/ S. milleri
Infections
Biochemical tests
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)
Viridans streptococci
Source of bacteria
Types of infections
Common oral flora
Infections:
Dental carries
Infective Endocarditis
Bacteremia in neutropenic patients
Meningitis
Pneuomonia
Enterococci
Examples
Lancefield grouping and special biochemical tests, growth environment
Types of infections
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
Outline the classification scheme for gram positive rods
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
Bacillus spp.
List examples and types of infection
Source of bacteria
Widely distributed in environment
B. anthracis = anthrax
B. cereus = Food poisoning (rice products)
Bacillus in blood culture is most likely contamination
Listeria monocytogenes
Source of bacteria
Types of infections
Antibiotic resistance
Tx
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)
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
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)
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
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
Enterobacterales
List examples under this group
Think inflammatory gastroenteritis:
E. coli
Klebsiella
Proteus
Enterobacter
Citrobacter
Morganella
Serratia
Salmonella
Shigella
Yersinia
~~~
Enterobacterales
Types of infections
UTI
Inflammatory Diarrhoea syndromes: E.coli, Non-typhoidal salmonella, shigella
Specific syndromes: Bacillary dysentry (Shigella), Typhoid fever (Salmonella typhi/ paratyphi)
Enterobacterales
Antibiotics resistant subtypes
ESBL-producers = resistant to B-lactams except carbapenems, so use carbepenems!
CPE (Carbapenemase-producing Enterobacteriaceae) = Resistant to carbapenems
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
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
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
Gram negative cocci
Examples and related infections
List bacteria that are unculturable/ unstainable by gram smear
-
Spirochaetes:
- Treponema pallidum (Syphilis)
- Borrelia recurrentis (recurring fever)
- Borrelia burgdorferi (Lyme disease)
- Leptospira (Leptospirosis) - Mycoplasma and Ureaplasma
- Chlamydia and Chlamydophilia (STD)
- Coxiella burnetii (Q fever)
- Bartonella quintana (Trench fever) and B. henselae (Cat-scratch disease)
- Rickettsia spp. and Orientia tsutsugamushi: Typhus, spotted mountain fever
Fungi
Classification and examples
Yeast - unicellular
- Candida
- Cryptococcus
- Trichophyton
- Malassezia
Mould - Pro-mycelial
- Dermatophytes
- Aspergillus
- Zygomycetes
- Fusarium
Dimorphic fungi
Pneumocystis jiroveci
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
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
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
Examples of dimorphic fungi
Sporothrix schenckii
Blastomyces dermatitidis
Histoplasma capsulatum
Penicillium marneffei
Examples of fungal disease according to skin layers
Superficial mycoses: Tinea, Onychomycosis (thrush), Cutaneous candidiasis, Pityriasis verisolor
Subcutaneous mycoses: mycetoma (gardener)
Deep mycoses
3 classes of parasites and examples
List viruses with high propensity to cause lower respiratory tract illness
Decreasing propensity to cause LRTI
Rhinovirus/ Enterovirus
Coronavirus
Parainfluenza (CROUP or bronchoiolitis)
List viruses that cause URTI
Bocavirus Adenovirus Influenza A,B (URTI or bronchiolitis) Enterovirus D68 Rhinovirus
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
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
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
First-line investigation for viral meningoencephalitis
Brain scans (CT/MRI) Lumbar puncture PCR for specific viral pathogens Antibodies against specific viral pathogens Electroencephalogram
Viruses that cause myocarditis
Adenovirus Enterovirus HSV/ VZV Cytomegalovirus Influenza
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
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
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)
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»_space; PrPSc
Accumulation of abnormal prion protein causes spongiform changes and vacuolation in the
brain (looks like cheese)»_space; 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)
