Microbiology Flashcards
What are the TORCH infections?
Toxoplasmosis Other: syphilis, HIV, HBV, VZV Rubella CMV HSV
What are the signs + symptoms of toxoplasmosis in neonates?
- Chorioretinitis
- Cerebral calcification -> Low IQ, seizures
- Microcephaly
- Deafness
What are the signs + symptoms of congenital rubella syndrome?
- Cataracts + other eye things (microophthalmia, retinopathy)
- Deafness
- Cardiac disease (PDA most common)
- Growth retardation, low IQ
- Blueberry muffin rash (due to extramedullary haematopoiesis)
How can HSV affect the neonate?
- Eyes/skin
- Encephalitis
- Disseminated infection eg. hepatitis, pneumonitis
Primary HSV at which gestation has the highest risk for the baby?
- 1st trimester infection is bad as can recur later on
- 3rd trimester, esp around delivery has high risk of transmission
Define neonatal infection (and early onset, late onset)
Infection in the first 6 weeks of life (adjusted for prematurity)
- Early onset: within 48 hours
- Late onset: >48 hours
Why is prematurity associated with a high rate of infection?
- Less barriers to pathogen entry
- No/low maternal Ig
- Iatrogenic causes (indwelling lines)
Which organisms are common causes of early onset neonatal infection? What are some types of infection?
- GBS, Listeria, E coli
- Sepsis, pneumonia, meningitis
Which organisms are common causes of late onset neonatal infection?
Staphylococcus aureus + coagulase -ve staph, Enterococcus, Klebsiella
Describe the features of GBS organisms
- Gram +ve cocci
- Catalase -ve
- B haemolytic
- Lancefield Group B
A 2 day old baby is brought to A&E with a fever, lethargy and poor feeding. The blood culture is positive for Listeria. What other investigations are needed?
LP. This is necessary when there are positive blood cultures of GBS, Listeria, and E coli
What is the first line antibiotic treatment for early onset neonatal sepsis?
Benzylpenicillin + gentamicin, amoxicillin if Listeria present
Name some common childhood infections
- Usually viral eg. RSV, EBV, CMV, HSV, VZV
- URTI very common
- UTIs common
- Also bacterial pneumonia eg. Strep pneumonia and Haemophilus influenzae
Which organisms commonly cause bacterial meningitis in children?
In all children:
- Neisseria meningitidis (esp Men B)
- Streptococcus pneumoniae
- Haemophilus influenzae
In neonates: also GBS, E coli, Listeria
Describe the characteristics of Streptococcus pneumoniae
- Gram +ve diplococci in chains
- A haemolytic
- Optochin sensitive
Which medium is best for culturing Haemophilus influenzae?
Chocolate agar
What type of vaccine against pneumococcus is given to children?
Conjugated vaccine. This is effective in children under 2 years of age. Name is Prevenar
What are the common pathogens causing respiratory infection in children? What are the treatments?
- Viruses!!! eg. RSV. Usually conservative
- Streptococcus pneumoniae: amoxicillin
- Mycoplasma pneumoniae (in older children): azithromycin
Describe the presentation of mycoplasma pneumoniae
- Outbreaks occur every 3-4 years
- Asymptomatic or non-specific: fever, dry cough, headache, myalgia
- Can also have haemolysis or neurological features
What are the haematological features of mycoplasma pneumoniae infection?
- IgM antibodies to the I antigen on RBCs
- Cold agglutination
Describe some features of HIV infection in children (vertically acquired)
- Chronic parotid swelling
- Recurrent/chronic molluscum
- Lymphadenopathy
- Dental + oral problems: caries, gingivitis, thrush
- Encephalopathy
- Shingles
- Failure to thrive
What are the risk factors for HIV transmission during pregnancy?
- New infection (viraemia)
- HCV coinfection
- Vaginal delivery
- Breastfeeding
- Placental infection/inflammation eg. malaria
How can we prevent vertical HIV transmission?
- Reduce rates of HIV in mothers pre-pregnancy (contraception, treatment)
- Prevent malaria infection
- C section if high viral load (>50 copies/ml)
- No breastfeeding unless high rate of childhood mortality due to diarrhoeal disease
- Triple ARVs during pregnancy and breastfeeding
- ART to neonates for 4-6 weeks
What is IRIS (in the context of HIV)?
- Immune reconstitution inflammatory syndrome
- When you treat the HIV, T cell count improves and responds to coexisting infections and creates a huge inflammatory response
- This can cause significant clinical illness
Define pneumonia. How does it present?
Inflammation of the lung alveoli
- Fever, productive cough w/ purulent sputum, SOB, chest pain, severe respiratory distress (hypoxia, cyanosis, tachypnoea)
- Raised WCC and acute phase proteins (CRP)
- Consolidation on CXR
What are some pathogens that commonly cause community acquired pneumonia? HAP?
CAP:
- Streptococcus pneumoniae
- Haemophilus influenzae
- Klebsiella pneumonia
- Atypicals: mycoplasma pneumo, Legionella, Chlamydia, Coxiella
- Children: also viruses eg. RSV, influenzae
HAP:
- Pseudomonas aeruginosa
- Klebsiella pneumonia
- Staphylococcus aureus
What scoring system is used for assessing the severity of pneumonia? Describe.
CURB 65: Confusion (Y/N) Urea >7 Resp rate >30 BP <90 systolic >65
2+: consider admission
2-5: severe pneumonia
Define bronchitis. How does it present?
Inflammation of the medium size airways (bronchi)
-Fever, cough, SOB is important factor, sputum
Which organisms cause bronchitis?
- Viruses common
- Bacteria: Strep pneumo, HiB
Which organisms can cause cavitating lung lesions?
- Staph aureus!
- Klebsiella
- TB
- +/- HiB
Describe the characteristics of haemophilus influenzae
- Gram -ve coccobacillus
- Facultative anaerobe
- Grows best on chocolate agar
- Can produce beta-lactamase
- Commonly infects lungs with pre-existing disease eg. smoking, COPD
Describe the characteristics of legionella pneumoniae infection (transmission, presentation, diagnosis, treatment)
- Transmitted through infected water droplets (consider aircon, pools/hot-tubs, etc)
- Flu-like prodrome, cough and fever
- Multi-organ involvement: confusion, abdo pain + diarrhoea, hyponatraemia, hepatitis
- Diagnosis: urinary antigens
- Treatment: macrolides (erythro, clarithro)
Describe the treatment for atypical pneumonia. Why is this different?
Antibiotics: macrolides + tetracyclines
-Atypicals do not have cell walls, therefore penicillins are ineffective to treat
What medium is Legionella best cultured on?
Buffered charcoal yeast extract
Coxiella usually comes from ___. Chlamydia psitacci comes from ___.
Domesticated farm animals eg. aerosol/milk
Birds
Describe the characteristics of Mycoplasma pneumonia infection (presentation, diagnosis, treatment)
- Usually comes around every 3-4 years in outbreaks, esp. schools/unis
- Dry cough, arthralgia, erythema multiforme
- Cold agglutination test
- Treatment with tetracyclines
A 60 year old woman is treated for pneumonia. Name some causes of failure to improve on treatment
- Empyema
- Wrong cover eg. atypical organism
- Antibiotic resistance
- Immunodeficiency
Describe the presentation of tuberculosis. What is the appearance on CXR? Diagnosis?
- Travel history, high risk area, positive TB contacts
- Prolonged fever, cough, haemoptysis, weight loss, night sweats
- CXR: upper lobe cavitation, lymphadenopathy (Ghon focus= lymph node + primary lesion), miliary TB
- Diagnosis: sputum sample for Ziehl-Neelson stain (AFB appear as red rods), auramine stain, culture for sensitivity
Define hospital acquired pneumonia. What are the common organisms? How should it be diagnosed?
Pneumonia developed >48 hours after admission to hospital. Can include VAPs
- Enterobacteriaciae: E coli, Klebsiella
- S aureus
- Pseudomonas
- Acinetobacter baumanii
Get sputum sample from bronchoalveolar lavage
Describe the presentation of PCP. What is the diagnosis + treatment?
Pneumocystitis jirovecii pneumonia:
-SOB key feature (insidious onset- worsening)
-Dry cough
-Weight loss
-Bat wing shadowing on CXR
Diagnosed with BAL -> immunofluorescence, silver stain (Grocott-Gomori) shows cysts.
Treat with Septrin (co-trimoxazole)
Respiratory tract infections
HIV is a RF for:
Neutropenia is a RF for:
Splenectomy is a RF for:
- HIV: TB, PCP, cryptococcus neoformans
- Neutropenia: fungal (Aspergillus)
- Splenectomy: encapsulated bacteria (S. pneumo, HiB, NMen)
Describe the antibiotic treatment of CAPs and HAPs
CAPs:
- Mild/mod: target Gram +ves eg. amoxicillin or macrolide if allergic for 5-7 days
- Mod-severe: cover gram+ves and atypicals with amoxicillin + macrolide (co amox + clarithro) for 2-3 weeks
HAPs: cover everything including good gram-ve
- 1st: ciprofloxacin +/- vancomycin
- 2nd line: Tazocin (pip + tazobactam) + vanc.
Which GI infections are notifiable?
- Campylobacter
- Salmonella
- Shigella
- Cholera
- Norovirus
- Listeria
- E coli O157
What are the different groups of presentations of GI infection? Broadly speaking what is the pathophysiology of each? What organisms cause each type?
- Febrile diarrhoeal (Inflammatory diarrhoea): caused by exudative inflammation of the bowel. Campylobacter, Shigella, non-typhoid Salmonella, EIEC
- Non-febrile diarrhoeal (Secretory diarrhoea): caused by toxins + dehydration. Cholera, ETEC, EPEC, EHEC
- Febrile, non-diarrhoeal (Enteric fever): caused by interstitial inflammation. Typhoid Salmonella, Yersinia, Brucella
Describe the pathophysiology of Cholera infection
- Cholera toxin causes chloride channels to open, causing water to move into the bowel lumen
- Causes ricewater stools and rapid dehydration
Name some pathogens that cause rapid-onset diarrhoeal illness
- Staph aureus
- Bacillus cereus
- Salmonella
Describe the characteristics of Staphylococcus aureus
- Gram +ve cocci in clusters/tetrads
- Coagulase +ve, catalase +ve
- Forms yellow colonies on blood agar
- Protein A is the main virulence factor
Describe the diarrhoeal illness caused by Staph aureus
- Produces enterotoxin that causes rapid-onset secretory diarrhoea and vomiting
- Self-limiting, lasts about 1 day
- Supportive treatment only
Describe the characteristics of Bacillus cereus and the infection it causes.
- Gram +ve rod, forms spores
- Typically occurs after eating reheated rice
- Produces toxins (heat stable emetic toxin, heat labile diarrhoeal toxin) that causes food poisoning eg. rapid-onset secretory diarrhoea and vomiting
- Self limiting
Name the types of Clostridium and describe the GI infections they cause (transmission, presentation, treatment).
- Gram +ve rods
- Botulinim: produces botulinum toxin -> descending paralysis. Found in cans, honey, formula powder. Treat with antitoxin.
- Perfringens: causes food poisoning from reheated meat. Rapid-onset secretory diarrhoea + cramps.
- Difficile: causes pseudomembranous colitis. After antibiotics treatment (HAI) with 3 C’s: cipro, cephalosporin, clindamycin. Treat with metronidazole +/- vanc, stop causative antibiotics.
What are the 3 antibiotics that commonly cause C difficile?
Ciprofloxacin
Clindamycin
Cephalosporins
Describe the characteristics of Listeria and GI infection with Listeria. What is the treatment?
- Gram +ve V/L shaped rod
- B haemolytic
- Aesculin +ve, tumbling motility
- Found in refrigerated food, unpasteurised cheese
- Causes inflammatory diarrhoea: watery diarrhoea, cramps, fever, vomiting, headache
- Treatment: ampicillin/amoxicillin, ceftriaxone
Describe the characteristics of Enterobacteria. What are the different types that cause GI infection?
- Facultative anaerobes
- Glucose/lactose fermenters
- Oxidase negative
Mainly E coli species
-ETEC: toxigenic, causes travellers diarrhoea. Heat labile toxin (stimulates adenyl cyclase) and heat stable (stim guanyl cyclase). Acts on jejunum + ileum
-EIEC: invasive. Dysentery.
-EPEC: paediatric
-EHEC: haemorrhagic. Has verotoxin. O157:H7 can can HUS
Avoid antibiotic treatment. Supportive management
Describe the characteristics of Salmonella and the infections they cause.
- Gram -ve rods
- Non-lactose fermenters
- H2S producers (form black colonies)
- Culture on TSI agar, XLD agar, Selenite F broth
- Have different antigens to differentiate types including O (cell wall), H (flagellar), Vi (capsule)
Typhi/paratyphi: cause enteric fever. Multiply in Peyer’s patches -> fever, constipation, splenomegaly, rose spots, anaemia. Positive blood cultures. Treat with cef/cipro
Enteritides: causes inflammatory diarrhoea (no blood). From poultry, eggs, meat. Self limiting, supportive treatment.
Describe the characteristics of Shigella and the infection it causes.
- Gram -ve rods
- Non-lactose fermenters (as opposed to E coli)
- Non-motile, non-H2S producing
- Also has antigens: O (cell wall), polysaccharide (A-D, best for differentiating)
- Shigella flexneri affects MSMs
- Most effective bacterial enteric pathogen (low number infective dose)
- Causes dysentery w/ blood and mucus, produces Shiga toxin.
- Do not give antibiotics
Describe the characteristics of Vibrios and the infections they cause
-Gram -ve, comma shaped
-Late lactose fermenter
-Oxidase +ve
Cholera: O1 group causes epidemics, non-O1 small outbreaks usually from contaminated shellfish. Cause ricewater stools from toxin production.
Parahaemolyticus: from raw seafood. Self limiting diarrhoea for 3 days.
Vulnificus: causes cellulitis from shellfish cuts. VERY bad in HIV +ve -> fatal sepsis.
Describe the characteristics of Campylobacter and the infection it causes
- Gram -ve, comma shaped
- Microaerophilic
- Oxidase +ve
- From contaminated food/water. Causes inflammatory diarrhoea, self limiting but can last long time. Treat with azithromycin if immunocompromised.
- Associated with Guillain-Barre and reactive arthritis
Describe the characteristics of Yersinia and the infection it causes
- Gram -ve
- Non-lactose fermenter
- Likes cold environments
- Causes enterocolitis (febrile non-diarrhoea), mesenteric adenitis
Describe infection with Entamoeba histolytica
- Protozoa: trophozoite/cyst, 4 nuclei
- Flask-shaped ulcers in colon
- Causes diarrhoea, wind, tenesmus, weight loss, RUQ pain (abscess)
- Do stool microscopy (wet mount)
- Treatment: metronidazole +/- paromomycin
Describe Giardia infection
- Protozoa, pear-shaped trophozoite.
- 2 nuclei, 4 flagella, suction disk
- Attaches to the duodenum and causes malabsorption -> bad smelling diarrhoea, cramping, lots of wind
- Dx: stool microscopy, string test (swallow string and pull back up)
- Treatment: metronidazole
Kinyoun acid fast stain identifies:
Cryptosporidium parvum
Causes severe diarrhoea in immunocompromised
Name the viruses that commonly cause diarrhoea. What are the characteristics of each?
- Norovirus: highly contagious. Diarrhoea and vomiting.
- Rotavirus: affects children. Secretory diarrhoea, with 2x infection leading to immunity
- Poliovirus, enterovirus, Hep A, adenovirus
What vaccines against pathogens causing GI infections exist?
- Rotavirus (routine vaccination)
- Cholera
- Salmonella typhi
- Campylobacter
Name some bacteria that commonly cause UTI and describe their features
- E coli: Most common. Adhere with p fimbriae
- Proteus: associated with struvite stones
- Staphylococcus saprophyticus: young women
- Klebsiella, Pseudomonas: associated with structural abnormalities and recurrent UTI
Name some risk factors for UTI. What is the presentation?
RFs: sex, female, catheter, elderly, incontinent, structural abnormalities
Presentation: dysuria, frequency, urgency, nocturia, smelly/cloudy urine, fever, flank pain, rigors, sepsis, confusion, incontinence
How is UTI formally diagnosed?
> 10 ^5 cfu/ml is diagnostic of infection/bacteriuria
+ symptoms -> UTI
In practice: symptoms + positive urine dip -> treat
What is sterile pyuria? What are some causes?
- Presence of white cells in urine but no growth (MC&S)
- Caused by STI, stones, tumours, TB
Describe the culture part of a urine MC&S
- Use chromogenic agar -> specific colours depending on the organism
- Pink: E coli
- Blue: other coliforms
What is a common antibiotic regime used in pyelonephritis
- Broad spectrum PO/IV antibiotics
- Co-amoxiclav +/- gentamicin
What are the different sites of antibiotic action?
Cell well
Ribosome/protein synthesis
DNA/RNA synthesis
Other
What are some different antibiotics that inhibit cell wall synthesis? Name some examples of each
Beta lactams: penicillins, cephalosporins, carbapenems
Glycopeptides: vancomycin, teicoplanin
How do beta lactams work? Are they bactericidal or bacteriostatic?
Inhibit transpeptidase PBP (penicillin binding protein), prevent crosslinking of peptidoglycan -> weak cell wall
Bactericidal- only works on rapidly dividing bacteria
Which bacteria are sensitive to beta lactams and glycopeptides and why?
Mostly Gram +ve, some have broader action against gram -ve. They have an outer peptidoglycan cell wall compared to gram -ves which have peptidoglycan within the 2 membranes.
Not effective on Chlamydia, Mycoplasma- no peptido.
If a patient is allergic to penicillin, which other antibiotics may they be allergic to?
5% chance of allergy to cephalosporins, carbapenems- because they have the same beta-lactam ring.
What are some different penicillins, and which bacteria are they effective for?
Penicillin: gram+ve except beta-lactamase
Amoxicillin: broad spectrum- gram +ve, Enterococcus, gram -ve. Not beta-lactamase
Flucloxacillin: gram +ve including beta-lactamase
Piperacillin: broad spectrum. Also Pseudomonas.
Which additional agents can be given with beta-lactams to increase their efficacy? What do they do?
Clavulanic acid and Tazobactam eg. Co-amoxiclav, Tazocin
-Inhibit beta-lactamase, increase susceptibility
Increase coverage to broad-spectrum including anaerobes and beta-lactamases
What are some types of cephalosporins and which bacteria are they effective for and not effective for?
Cefalexin: UTIs
Cefuroxime: similar to co-amoxiclav eg. gram +
Ceftriaxone (3rd gen): Broad spectrum- gram+ and gram -
Ceftazidime: good for Pseudomonas
Not for anaerobes or ESBL (eg E coli)
What are some types of carbopenems and which bacteria are they effective for?
Meropenem
Ertapenem
Broad spectrum: gram +, gram -, ESBLs
What are some glycopeptides, which bacteria are they effective against and why?
Vancomycin, teicoplanin
Active against gram + because can’t cross gram - outer membrane
Especially for MRSA
Name some classes of antibiotics that inhibit protein synthesis and give examples
Aminoglycosides: gentamicin, amikacin Macrolides: erythromycin, azithromycin Tetracyclines: doxycycline Chloramphenicol Oxazolidinones: linezolid
Describe the MoA of aminoglycosides. Which bacteria are they effective against?
Bind to the 30S ribosome subunit and inhibit protein synthesis.
Broad spectrum: esp gram - and Pseudomonas. Synergistic with beta-lactams
Describe the MoA of tetracyclines. Which bacteria are they effective against?
Bind to the 30S subunit and inhibit protein synthesis.
Intracellular pathogens eg. chlamydia, mycoplasma. Not very good for gram -
Describe the MoA of macrolides. Which bacteria are they effective against?
Bind to 50S subunit and inhibit protein synthesis.
Mild Staph/strep infection, Legionella, mycoplasma
Describe the MoA of chloramphenicol. Which bacteria is it effective against?
Bind to 50S subunit and inhibit protein synthesis.
Broad spectrum but only really used as eye drops for conjunctivitis because aplastic anaemia + grey baby syndrome
Describe the MoA of oxazolidinones. Which bacteria are they effective against?
Bind to the 23S of 50S ribosome subunit.
Gram + cover including MRSA and VRE, not gram -
Name some classes of antibiotics that inhibit DNA synthesis and give examples
Fluoroquinolones: ciprofloxacin, levofloxacin
Nitroimidazoles: metronidazole
Describe the MoA of fluoroquinolones. Which bacteria are they effective against?
Inhibits DNA gyrase.
Broad spectrum especially gram - and Pseudomonas. Levo is good for gram +
eg. UTIs, atypical pneumonia
Describe the MoA of nitroimidazoles. Which bacteria are they effective against?
Cause DNA strand breakage in anaerobic conditions
Good for anaerobes and protozoa eg. BV, Giardia