ID Flashcards
Name 3 gram negative cocci
- Neisseria meningitidis
- Neisseria gonorrheae
- Moraxella spp,
Name 2 spore forming gram positive rods
- Bacillus sp.
- Clostridium sp.
Name 2 non-spore forming gram positive rods
- Corynebacterium sp.
- Listeria sp.
Name 2 anaerobic gram positive bacilli
- Cutibacterium
- Actinomyces
Name 4 lactose fermenting gram negative bacilli
- E. Coli
- Klebsiella sp.
- Enterobacter sp.
- Proteus sp.
*“gut bugs”
Name 2 non-lactose fermenting gram negative bacilli
- Pseudomonas
- Stenophotomonas
Name 2 anaerobic gram negative bacilli
- Bacteroides
- Fusobacterium
Name 3 spirochetes
- Treponema sp.
- Leptospirosis
- Borrelia
Name 2 yeasts
- Candida
- Cryptococcus
Name a mould
Aspergillus
Name 3 dimorphic fungi
- Blastomycosis
- Histoplasmosis
- Coccidiomycosis
List the HECK-Yes (SPICE-HAM) Organisms
What is special with these organisms and what antibiotics should be used in infections involving them
- Hafnia
- Enterobacter
- Citrobacter
- Klebsiella aerogenes
- Yersinia enterocolitica
- Seratia
- Providencia
- Indole postitive proteus
- Acinetobacter
- Morganella
Inducible amp-c resistance, must be treated with a carbapenem, TMP-SMX, FQ, AG
List 2 ESBL producing organisms. What antibiotics can be used to target them
- E. Coli
- Klebsiella
- Carbapenems
- TMP-SMX
- FQ
- AG
What antimicrobials can be considered in CPE producing organisms
- Colistin
- AG
- Tigecycline
- Possibly FQ or TMP-SMX if lucky
What antimicrobials can be considered to treat MRSA
- Vancomycin
- Doxycycline
- TMOP-SMX
- Clindamycin
- Linezolid
- Daptomycin
- Ceftobiprole
What antimicrobials can be considered to treat pseudomonas
- Pip-tazo
- Ceftazidime
- Cefepime
- Carbapenems (not ertapenem)
- Ciprofloxacin
- AG
- Azetronam
- Colistin
- Tigecycline
- Ceftazidime-avibactam
- ceftolozame-tazobactam
What antimicrobials can be considered to treat enterococcus
- Ampicillin (if S)
- Vanco (not VRE)
- Linezolid
- Daptomycin
Name symptoms associated with meningitis
- Predminantly headache, neck stiffness and fever
- altered LOC late in the course
Name symptoms associated with encephalitis
- Predominantly altered LOC and fevers
- Can get seizures and focal neurological signs
Name 3 signs that, if all absent, rule out meningitis (99%)
- Fever
- Neck stiffness
- Altered mental status
What physical exam sign has the highest sensitivity for meningitis
Jolt accentuation
What 2 physical exam signs are the most specific for meningitis
Kernig’s and Brudzinski’s
What are symptoms of basal skull meningitis
- Regular meningitis symptoms plus:
- CN palsies
- long tract signs
What organisms are known to cause basal skull meningitis?
- Tb
- Listeria
- Cryptococcus
- Syphilis
- Lyme
What are the most common pathogens in meningitis and what antibiotics should be used empirically

What should be the empiric coverage for meningitis in the case of a penicillin allergy?
Vancomycin + Moxifloxacin +/- TMP-SMX(if need to cover listeria)
Describe an approach to investigating suspected meningitis

Other than a positive culture, what would you expect to find on an LP in the case of bacterial meningitis, viral meningitis, TB meningitis and fungal meningitis?

When looking at glucose, protein, WBC, PMN on an LP ad well as the ratio of CSF:blood glucose, which thresholds are 99% specific for bacterial meningitis?
- Glucose <1.9
- Protein >2.2
- WBC>2000
- PMNs>1180
- CSF:blood glucose <0.23
If an LP is performed 2 days after the start of antibiotics, what values can you still rely on and what values may have already corrected on your LP results
- Biochemistry and cell count minimally affected
- Culture yield decreased
For how long should bacterial meningitis be treated
- Depends on the bacteria
- S. Pneumoniae: 10-14 days
- N. Meningitidis: 7 days
- L. Monocytogenes: 21 days
- No pathogen found:
- Depends on clinical context
- Consult ID
When should Dexamethasone be given for meningitis
- Before or with first dose of antibiotics
- Usually give 10mg IV q6h x 4 days
- Stop if CSF non-turbid, low cell count, non-pneumococcal by culture
* DO NOT START IF ANTIBIOTICS HAVE ALREADY BEEN GIVEN
Who should get N. Meningitidis chemoprophylaxis
- Close contacts of N. Meningitidis meningitis cases as defined:
- Household contacts
- Persons Sharing sleeping arangements
- Persons who have direct nose/mouth contamination with oral/nasal secretions
-
Healthcare workers who have had intense unprotected (no mask) contact
- Intubating
- resuscitating
- closely examining nasopharynx
- Airline passengers sitting immediately on either side of the case when total time on aircraft >8hours
Within how many days should you give N. Meningitidois chemoprophylaxis
10 days
What agents can be used for N. Meningitidis chemoprophylaxis?
- Ciprofloxacin 500mg po x1 (increasing resistance!)
- Ceftriaxone 250 mg IM x1
- Rifampin 600mg PO BID x 2 days
Who should get N. Meningitidis immunoprophylaxis?
- Household contacts of a case of invasive menigococcal disease (IMD)
- Persons sharing sleeping arrangements with a case of IMD
- Persons who have direct nose/mouth contamination with oral/nasal secretions of a case with IMD
- Children and staff in contact with a case of IMD in childcare or nursery school facilities
What agents can be used for N. Meningitidis immunoprophylaxis
- Depends on serotype of index case and age/underlying conditions of contact
- Men-C-ACYW
- 4CMenB
What is the diagnostic workup for suspected endocarditis?
- 2 sets of blood cultures prior to antibiotics
- Initial TTE for everyone
- TEE if indicated (class 1):
- non-diagnostic TTE
- suspected IE complications
- intracardiac leads
- TEE if indicated (class 1):
Who can be considered for a stepdown to oral antibiotics after initial IV antibiotics in IE?
- Patients with left-sided endocarditis caused by streptococcus, E. Faecalis, S. Aureus or CNST:
- Deemed stable by multidisciplinary team
- TEE MUST be done prior to switch and show no paravalvular infection
- Frequent and appropriate follow-up can be assured by the care team
- A follow-up TEE can be preformed 1-3 days before the completion of the antibiotic course
List the Duke criteria for diagnosis of IE
-
Major
- Microbiological evidence
- Typical organisms: S. Aureus, Viridans group strep, S. gallolyticus (prev. bovis), Enterococcus, HACEK group
- 2 cultures >12hrs apart or 3 cultures > 1hr appart
- OR 1 blood culture demonstrating Coxiella brunetii OR Coxiella anti-phase 1 IgG > 1:800
- Endocardial involvement
- Oscillating valvular/prosthetic mass
- Valvular abscess
- Dehiscence of prosthetic valve
- New valvular regurgitation
- Microbiological evidence
-
Minor
-
Predisposition
- Heart defect
- Prosthetic valve
- IVDU
- Fever
- Temp >38
- Vascular phenomenon
- Arterial emboli
- septic pulmonary infarcts
- Mycotic aneurysms
- IC hemorrhage
- Conjunctival hemorrhage
- Janeway lesions
- Immunological phenomenon
- GN
- Osler nodes
- Roth spots
- Positive RF
- Microbiological evidence
- blood culture not meeting major criterion
-
Predisposition
What is necessary for a diagnosis of IE
-
Definite IE
- Positive vegetations on culture or histiopathology
- 2 major criteria
- 1 major + 3 minor criteria
- 5 minor criterria
-
Possible IE
- 1 major + 1 minor criteria
- 3 minor criteria
What antibiotics should be used to treat native valve IE caused by MSSA
Cloxacillin or cefazolin
What antibiotics should be used to treat native valve IE caused by MRSA or CNST
Vancomycin
*Most CNST are beta lactam resistant. If susceptible can treat like MSSA
What antibiotics should be used to treat native valve IE caused by Viridans group strep or S. Gallolyticus
Pen G or ceftriaxone
*If higher MIC to PNC levels, consider adding an aminoglycoside
What antibiotics should be used to treat native valve IE caused by E. Faecalis
Ampicillin + gentamycin
OR
Ampicillin + ceftriaxone
What antibiotics should be used to treat native valve IE caused by E. Faecium
Vancomycin + gentamycin
What antibiotics should be used to treat native valve IE caused by HACEK group bacteria
Ceftriaxone
What antibiotics should be used to treat prosthetic valve IE caused by MSSA
Cloxacillin OR cefazolin
AND
Rifampin
AND
Gentamicin
What antibiotics should be used to treat prosthetic valve IE caused by MRSA or CNST
Vancomycin
AND
Rifampin
AND
gentamicin
*Most CNST are beta lactam resistant. If susceptible can treat like MSSA
What antibiotics should be used to treat prosthetic valve IE caused by viridans group streop or S. Gallolyticus?
Pen G OR ceftriaxone
What antibiotics should be used to treat prosthetic valve IE caused by E. Faecalis
Ampicillin + Gentamicin
OR
Ampicillin + Ceftriaxone
What antibiotics should be used to treat prosthetic valve IE caused by E. Faecium
Vancomycin + Gentamicin
What antibiotics should be used to treat prosthetic valve IE caused by HACEK bacteria
Ceftriaxone
for how long should IE be treated?
4-6 weeks
Longer for increasing beta-lactam resistance, S. Aureus, prosthetic valve
List the HACEK organisms
- Haemophilus
- Aggregatibacter
- Cardiobacterium
- Eikenella
- Kingella
List the class 1 indications for early surgery in IE
Early surgery: during initial hospitalisation before full treatment course of antibiotics
- Decisions about surgery should be made by a “multidisciplinary heart valve team” of cardiologists, CV surgeons, and ID specialists
- Valve dysfunction with signs or symptoms of heart failure
- Left sided IE caused by S. Aureus, fungi or highly resistant organisms
- Heart block, annular/aortic root abscess, destructive penetrating lesions
- Persistant bacteremia or fever > 5d after starting appropriate ABx
- Complete removal of implantable electronic cardiac device systems in patients with definite IE
List the class 1 indications for delayed surgery in IE?
- prosthetic valves: relapsing infection
- Defined as new fever/bacteremia after a complete course of appropriate antibiotics and interval sterile blood cultures. No other source or portal of infection
*In patients with recurrent endocarditis in the setting of continued IVDU, consultation with addiction medicine before repeat surgical intervention is considered
List the class II surgical indications in endocarditis
- Early surgery is reasonable in those with recurrent emboli and persistent vegetation despite appropriate antimicrobial therapy
- Early surgery may be considered in patients with native left-sided endocarditis with mobile vegetation >10mm with or without embolic phenomenon. Especially if it’s on the anterior MV leaflet
- Early (as opposed to late) surgery in patients who have had a minor (no extensive neuro deficits) embolic stroke without ICH, in patients with an indication for IE surgery
- Consider delay surgery >4 weeks in HD stable patients after a major ischemic or hemorrhagic stroke
When should IE prophylaxis be considered?

What ABx regimen should be given for endocarditis prophylaxis when such intervention is indicated?
- Amoxicillin 2g PO x1
- If NPO give 2g IV or IM or cefazolin/ceftriaxone 1g IV/IM
- If PNC allergy: Cephalexin 2g PO OR azithromycin 500mg PO OR doxycycline 100mg PO
- NPO + PNC allergy: Cefazolin/Ceftriaxone 1g IM/IV
How is pneumonia diagnosed?
Clinical (Fever, productive cough, SOB, consolidation) + Radiographic findings (CXR infiltrate)
What criterias can be used to decide who should be hospitalised in pneumonia?
- PSI/PORT (prefered by IDSA/ATS 2019)
- CRB-65
List the CRB 65 criteria
- Confusion
- RR>30
- SBP<90 or DBP<60
- Age ≥ 65
if 0-1 treat as outpatient
if ≥2 admit to hospital
Give the IDSA/ATS criteria to define severe CAP
- Minor criteria
- RR>30
- PaO2/FiO2 ≤250
- Multilobar infiltrates
- Confusion/disorientation
- Uremia (BUN>20)
- Leukopenia (WBC<4)
- Thrombocytopenia (plt<100)
- Hypothermia (T<36)
- Hypotension requiring aggressive fluid resuscitation
- Major criteria
- Septic shock with need for vasopressors
- Respiratory failure requiring mechanical ventilation
What are common pathogens in CAP
- S. Pneumoniae
- H. Influenzae
- M. Pneumoniae
- C. Pneumoniae
- Respiratory viruses
- Influeza
- Parainfluenza
- RSV
- rhinovirus
- adenovirus
- coronaviruses
- Legionella pneumophila (severe disease)
What pathogens should also be considered in patients with pneumonia who have multiple comorbidities, antibiotic exposure or hospital exposures?
- Gram negatives
- Klebsiella pneumoniae
- Pseudomonas
- S. Aureus inc. MRSA
In which patients should sputum cultures be obtained in the context of CAP?
- inpatients with severe CAP
- intubated patients
- Patients being treated empirically for MRSA or pseudomonas
What other investigations (other than CXR, basic blood work, sputum cultures, and blood cultures) should be considered in patients with CAP and in what setting should they be considered?
- Pneumococcal + Legionella Ag +/- lower tract legionella NAAT
- In severe CAP or when indicated by epidemiological factors such as an outbreak
- Rapid influenza NAAT + COVID test when these viruses are circulating
*Do not send procalcitonin
What are the outpatient treatment options for CAP?
- Healthy outpatients
- Amoxicillin 1g TID (preferred)
- Doxycycline 100mg BID
- Azithromycin 500mg PO x1 then 250mg PO BID only in areas with low pneumococcal resistance
- Not in most of Canada
- Patients with comorbidities (chronic heart, lung, liver, renal, DM, alcoholism, malignancy, asplenia)
- Amox-clav or cephalosporin (cefpodoxime, cefuroxime) plus macrolide or doxycycline
- Respiratory fluoroquinolone (moxi, levo)
- adds additional coverage for H. Flu and moraxella catarrhalis as well as coverage for S. aureus and gram negatives
What are the inpatient treatment options for CAP?
- Non-ICU with no risk factors for MRSA or pseudomonas
- Beta lactam (CTx, amp-sulbactam, cefotaxime, ceftaroline) plus macrolide
- Doxy is a third line option if unable to give other options
- Respiratory fluoroquinolones (levo, moxi)
- * Insufficient evidence for omadacycline
- Beta lactam (CTx, amp-sulbactam, cefotaxime, ceftaroline) plus macrolide
- ICU without risk factors for MRSA or pseudomonas
- Beta-lactam plus macrolide
- Beta lactam plu__s respiratory fluoroquinolone
- Some evidence for decreased death with beta-lactam + macrolide
- Aspiration pneumonia
- Don’t add empiric anaerobe coverage unless empyema or abscess present
When should MRSA be covered in CAP and what agents can be used
- Based on local risk factors
- Use Vancomycin or Linezolid
- Daptomycin can’t be used in respiratory infections as it is inactivated by surfactans
When should pseudomonas be covered in CAP and with what agents?
- Based on locally validated risk factors
- Use:
- Piptazo
- Cefepime
- ceftazidime
- azetronam
- meropenem
In admitted patients with CAP, when can a transition to PO antibiotics be considered
When the patient is hemodynamically stable, improving, tolerating PO intake and absorbing from GI tract
For how long should CAP be treated
- 5 days in well selected patients
- Afebrile x48hrs
- ≤1 sign of CAP clinical instability (HR>100, RR>24, SBP<90, PaO2<90%, can tolerate PO, normal mental status)
- Otherwise 10 days
When should steroids be considered in CAP
Only in refractory shock
How should influenza pneumonia be treated
- Oseltamivir if Sx <48hrs and hospitalized
- COnsider treating bacterial superinfection
What are the pathogens involved in HAP/VAP
- S. Pneumoniae
- MSSA
- H. Influenzae
- GNB including pseudomonas
How is HAP/VAP diagnosed
Based on clinical gestalt + sputum/ETT/blood cultures
*CPIS score NOT recommended by IDSA
List the risk factors for MDR VAP and HAP
- RF for MDR VAP
- Prior IV ABx use within 90 days
- septic shock at time of VAP
- ARDS preceding VAP
- ≥ 5 days hospitalization prior to VAP
- Acute renal replacement therapy prior to VAP onset
- RF for MDR HAP
- Priorr IV ABx use within 90 days
- RF for MRSA HAP/VAP
- Prior IV ABx use within 90 days
- RF for MDR Pseudomonas VAP/HAP
- Prior IV ABx use within 90 days
How should HAP/VAP be treated empirically?

In which patients should stool cultures be sent for Salmonella, Shigella, Campylobacter, yersinia and STEC
- Diarrhea and:
- Fever
- Bloody or mucoid stools
- Severe abdo pain
- Sepsis
In which patients presenting with diarrhea should you send C. Difficile testing
- Recent antibiotics
- Persons who work in healthcare, LTC, prison
- Compatible syndrome
- IBD flare
In what patients with diarrhea should blood cultures be sent?
- Immunocompromise
- Sepsis
- Suspicion of enteric fever
In what patients with diarrhea should stool samples be sent for Ova and parasites?
- Diarrhea ≥ 14 days
- Immunocompromise
- Travel
How can you increase the yield of stool Ovo and parasite testing?
Order daily x 3 days
Which patients with bloody diarrhea should get empiric antibiotic treatment?
- Sick immunocompetent patients with bacillary dysentery (frequent scant bloody stools, abdo pain, tenesmus, fevers), suggestive of shigella
- Recent travel with high fevers (>38.5) and/or sepsis
- Sick immunocompromised patients
What empiric antibiotic should be used when treating patients with bloody diarrhea? (empiric)

What is the first choice and alternative choice antibiotic to treat campylobacter diarrhea
First choice: Azithromycin
Alternative choice: Ciprofloxacin
What is the first choice and alternative choice antibiotic to treat S. enterica typhi and paratyphi diarrhea?
First line: ceftriaxone OR ciprofloxacin
Alternatives: Ampicillin OR TMP-SMX OR azithromycin
What is the first choice and alternative choice antibiotic to treat Shigella diarrhea
First line: Azithromycin OR ciprofloxacin OR ceftriaxone
Alternative: TMP-SMX OR ampicillin
What is the first choice and alternative choice antibiotic to treat Vibrio cholerae diarrhea
First line: Doxycycline
Alternative: Ciprofloxacin, Azithromycin, ceftriaxone
What is the first choice and alternative choice antibiotic to treat Yersinia enterocolitica diarrhea
First line: TMP-SMX
Alternative: cefotaxime, ciprofloxacin
What is the first choice and alternative choice antibiotic to treat STEC diarrhea
No ABx, risk of HUS
How is testing performed for C. Diff
- Stool toxin testing:
- EIA for GDH, toxin
- NAAT PCR for toxin
- Pseudomembranes on colonoscopy
Describe the clinical findings of CDiff
Unexplained new-onset ≥3 unformed stools in 24 hours
List the criteria for severe C. Diff
- WBC ≥ 15 OR Serum creatinine 1.5 x pre-morbid levels
- Age > 65, immunosuppression, T>38, albumin <30
List the findings in fulminant C. diff
- Sepsis
- Shock
- Illeus
- perforation
- toxic megacolon (colon dilation > 6cm)
How is the first episode of C. Diff treated
- STOP unnessessary antibiotics
- Stop PPI if not needed

Why is fidaxomicin superior to Vancomycin?
Less recurrence!
They have similar efficacy at treating the initial C.Diff infection
What are the risk factors for C. Diff recurrence?
- Recurrent CDI in the last 6 months
- Age >65
- immunocompromised
- Severe CDI on presentation
How is recurrent C. Diff treated?

How are intra-abdominal infections managed?
- Source control!
- Percutaneous>laparoscopic
- If <3cm, can forgo source control initially
- Empiric antibiotics
- CA-no previous hospitalisations
- Ceftriaxone + Flagyl OR Cipro + flagyl
- Healthcare associated or critically ill
- Pseudomonas coverage: Pip-tazo, meropenem, ceftazidime or cipro AND metronidazole
- Add enterococcal coverage (vanco) if immunocompromised. post-op or recurrent or if valvular heart disease/intravascular prosthesis
- Consider targetted antifungal coverage in severe or nosocolilal IAI if candida isolated from intraabdomional or blood cultures
- In other cases no mortality benefit
- CA-no previous hospitalisations
How long should antibiotics be continued for intraabdominal infections?
If source control is achieved: 3-5 days (STOP-it trial)
What are the criteria for a complicated UTI?
- Hemodynamically unstable
- Male
- Pregnancy
- Indwelling Foley catheter, instrumentation
- Functional or anatomic anomalies
- Urinary tract obstruction
How is a UTI diagnosed?
CLinically, supported by UA and culture
What are the first line empiric treatment options for cystitis?
- Nitrofurantoin 100 BID x5 days
- Avoid if concerns for pyelo
- Septra DS 1 tab BID x 3 days
- Avoid if recently used or in pregnancy
- Fosfomycin 3g x1
- Avoid if concerns for pyelo
- Covers ESBLs
JAMA 2018: Nitrofurantoin superior to fosfomycin
What are the second-line empiric treatment options for cystitis?
- Fluoroquinolones (Levo or cipro)
- Beta lactams
What are the first line empiric treatment options for pyelonaphritis?
- IV beta lactam (prefered in pregnancy) x7-14 days
- Fluoroquinolones (if resistance rates are low) x 5-7 days
What organisms usually cause prostatitis
- E. Coli
- Pseudomonas
- Enterococcus
When should proatatitis be treated
- If symptomatic
- Do not treat if asymptomatic unless
- elevated PSA
- planning for Bx
- infertility
What are the symptoms of acute prostatitis?
- Fever
- intense local pain
- sepsis
What should be obtained before giving empiric antibiotics if there is suspicion for acute proatatits?
UA+culture
What is the empiric antimicrobial treatment for acute prostatitis?
- If well
- Fluoroquinolone
- If unwell
- Fluoroquinolone
- 3rd gen cephalosporin
- Pip-tazo
How long should acute prostatitis be treated for?
2-4 weeks
What are the symptoms of chronic prostatitis
- May or may not be symptomatic
- If they are symptomatic, the symptoms are the same as acute prostatitis
- Fever
- Local pain
- Sepsis
What antibiotics should be used to treat chronic prostatitis?
Fluoroquinolones or pathogen directed therapy
For how long should chronic prostatitis be treated?
- If using a fluoroquinolone: 4-6 weeks
- If using any other ABx: 8-12 weeks
What are the bacteria that tend to cause post-partum endometritis?
- Group B strep
- enterococci
- S. Aureus
- anaerobic GPC
- E. Coli
- Gardnerella
- Bacteroides
(polymicrobial)
What are the symptoms of post-partum endometritis?
- Fever
- Uterine tenderness
- Bleeding
- Foul-smelling lochia
Why do we worry about post-partum endometritis
It can progress to sepsis
What should you assess for once you diagnose post-partum endometritis?
- Retained products of conception
- abscesses
What empiric antibiotics can be used to treat post-partum endometritits?
- Clindamycin + Aminoglycoside(Add ampicillin or vancomycin if suspected enterococcus)
- Stepdown to oral once deferveses
- No good evidence on duration
What are the indications to treat asymptomatic bacteriuria?
For how many days should you treat for each indication
- Pregnancy
- Treat for 4-7 days
- Invasive urological procedures
- Treat for 1-2 days
- Areas of limited evidence
- First month after renal transplant
- High risk neutropenia (ANC<0.1 for ≥ 7 days)
What is the incubation period for gonorrhea?
2-7 days
What symptoms can be associated with gonorrhea?
- Can be asymptomatic
- Rectal and pharyngial infections more likely to ba asymptomatic
- Purulent discharge
- pelvic pain
- proctitis
- pyuria
- dysuria
- epididymitis
What symptoms can be associated with Chlamydia?
- Can be asymptomatic
- Rectal and pharyngial infections more likely to ba asymptomatic
- Purulent discharge
- pelvic pain
- proctitis
- pyuria
- dysuria
- epididymitis
How is gonorrhea diagnosed?
- NAAT /culture as indicated
- Urine
- Cervical
- rectal
- Pharyngeal
- Add blood, joint pustule swab for disseminated
*cultures are generally preferred for sensitivity testing
How is gonorrhea treated
- Ceftriaxone 500mg IM x1
- Alternatives:
- Gentamycin 240mg IM x1 AND Azithromycin 2g PO x1 OR cefixime 800mg PO x1
- Doxy x 7 days if chlamydia not excluded
Name possible complications of gonorrhea and chlamydia
- In males
- Urethral strictures with fistula
- epididymitis (chlamydia>gonorrhea)
- Infertility (rare)
- In females
- PID
- infertility
- ectopic pregnancy
- Fitz-Hugh-Curtis syndrome
- In both
- Re-infection
- reactive arthritis
- DGI: arthritis
- dermatitis
- endocarditis
- meningitis (more common in pregnant women, or MSM)
- Increased risk of HIV
What is the incubation period of chlamydia?
2-6 weeks
What percentage of chlamydia and gonorrhea infected patients are asymptomatic
50% Gono
70% chlam
How is chlamydia diagnosed?
Urine, cervical, vaginal, rectal, pharyngeal NAAT
How is chlamydia treated?
Doxycycline 100mg PO x 7 days
Azithro 1g PO x1 is an alternative
How should patients be counciled regarding sexual activity after a diagnosis of chlamydia or gonorrhea?
Abstinence x7days and until partner is treated
How is chlamydia treated differently in pregnancy?
Doxy is contraindicated 2nd and 3rd trimester of pregnancy
What criterias define treatment failure in chlamydia or gonorrhea?
- Positive gram stain >72hrs after treatment
- Positive culture >72hrs after treatment
- Posiitve NAAT 2-3 weeks after treatment
***Reinfection is more common that Tx failure
Which are the indications to perform a test of cure after treatment of chlamydia or gonorrhea?
- All gonococcal infections, especially if suspected Tx failure/drug resistance, alternative Rx, pregnancy, pre-puberty or pharyngeal infection
- Chlamydia in pregnancy (4 weeks post Tx)
- Chlamydia Tx with ongoing symptoms, alternative regimen, suboptimal adherence
What are the indications for repeat testing (3 months later) after chlamydia or gonorrhea infection?
All individuals
What are the clinical manifestations of primary syphilis
Painless chancre and regional LN
How long after initial syphilis infection can primary syphilis last?
1st 3 weeks after infection
What are the manifestations of secondary syphilis?
- Fever
- Malaise
- Rash
- Alopecia
- uveitis
- meningitis
- LN
- herpatitis
- arthralgias
- condyloma lata
How long after initial syphilis infection can secondary syphilis last?
6 months
What timeframe differentiates early latent syphilis from late latent syphilis?
Early (<1 year since infection)
Late (>1 year or unknown duration)
What are the manifestations of latent syphilis
None
simply have positive serology
What are the manifestations of tertiary syphilis?
- Cardiovascular
- Aortitis
- Gummatous
- Late neurosyphilis
- Tabes dorsalis
- General paresis
What is the treatment for primary, secondary and early latent syphilis?
Pen G 2.4 mU IM x1
Alternatives (really use penG if you can!):
Doxycycline 100 mg PO x 14 days
Tetracycline 500mg po QID x 14 days
Ceftriaxone 1g IV /IM x 10 days
What is the treatment for late latent, unknown duration or tertiary syphilis?
Pen G 2.4 mU IM Weekly x 3
Alternative (Use pen G when possible)
Doxycycline 100 mg PO BID x 14 days
Tetracycline 500 mg QID PO x 14 days
What is the treatment for neurosyphils?
- Aqueous penicliiin 4mU q4h IV x 14 days
No alternatives, desensitize if allergy to PNC
What are the treponemal tests
- Immunoassay
- TPPA
- FTA-ABS
What are the non-treponemal tests?
- VDRL
- RPR
What is the difference between treponemal and non-treponemal tests?
- Treponemal
- Specific antibody against Treponema Pallidum
- Persists for life
- Non-treponemal
- non-specific antibody released during infection
Interpret the various combinations of negative and positive Screening CIMA, confirmatory RPR and confirmatory TPPA tests

What are the indications for PNC desensitization in syphilis patients
- Neurosyphilis
- Pregnancy
- Late latent or latent of unknown duration syphilis
- Tertiary syphilis
What are the indications to get an LP in syphilis?
- Neuro, occular or auditory symptoms or signs
- HIV and neuro symptoms or signs
- HIV and RPR ≥ 1:32
- HIV and CD4 < 350
- Previously treated syphilis and failed to achieve adequate serological response to treatment (i.e. four fold drop in RPR)
What should be considered in persistant PID, urethritis or cervicitis
Especially if initial gono-chlam comes back negative after empiric Tx
- Retreat once for usual pathogens
- Remember, risk of reinfection>risk of Tx failure)
- Consider mycoplasma genitalium or T. Vaginalis
- Test available for mycoplasma henitalium at national microbiology lab in Winnipeg
- Treat with moxifloxacin x7-14 days depending on extent of infection
What is the organism responsible for chancroid?
H. Ducreyi
What are the symptoms and signs of chancroid
- Painfull ulcer with granulomatous base that bleeds
- Painfull inguinal LN
What is the treatment for chancroid?
Azithromycin 1g PO x1
CTx 250 mg IM x1
Cipro 500 mg PO BID x3days
What is the organism causing LGV
Chlamydia. Serovars L1-L3 more invasive
What are the symptoms of LGV
- Painfull LN
- Hemorrhagic proctitis
How is LGV treated
Doxycycline 100 mg PO BID x21 days and treat partners
What are the symptoms of genital HSV?
Painfull vesicles/ulcers with prodrome
What can be used to treat genital HSV
- Acyclovir
- Valacyclovir
- Famcyclovir
What can be used to treat anogenital warts
- HPV vaccine for prevention
- For treatment
- Spontaneous resolution
- consider imiquimod or cryotherapy
What are the symptoms of trichomonas vaginalis
- Vaginal pH >4.5
- Neg Whiff
- yellow frothy discharge
- strawberry cervix
How is trichomonas vaginalis treated?
- Metronidazole
- 2g PO x1
- OR 500 mg po x 7 days
- Treat partners
What are the symptoms and diagnostic tests for vulvovaginal candidiasis?
- Vagina pH < 4.5
- Neg whiff
- wet mount with 10% KOH budding yeast
How is vulvovaginal candidiasis treated?
- clotrimazole or miconazole cream
- fluconazole 150mg PO x1
What are the symptoms and diagnostic tests for bacterial vaginosis?
- Vaginal pH >4.5
- pos whiff
- clue cells on gram stain
- fishy odor
How is bacterial vaginosis treated?
- Metrronidazole 500mg PO BID x 7 days or 5g application PV x 5 days
Name 4 purulent skin and soft tissue infections
- Folliculitis
- Infection of hair follicle
- Furuncle
- Infection of hair follicle extending into the dermis and sc tissue
- Carbuncle
- coalescence of several infected follicles
- Abscess
- collection of pus within the dermis + sc tissue
Name 4 non-purulent skin and soft tissue infections and their most common infectious etiologies
- Impetigo
- S. Aureus
- Erysipela
- GAS
- Cellulitis
- GAS
- Necrotizing fasciitis
- Depends on type
How should purulent SSTIs be managed
I&D and C&S should be performed

How should non-purulent SSTIs be managed?
Treat predisposing trauma, tinea pedis, xerosis, lymphedema, etc…
Consider MRSA coverage if cellulitis is associated with penetrating trauma, evidence of MRSA infection elsewhere, nasal colonisation with MRSA or IVDU
If severely immunosuppressed, consider pip-taz vanco or mero-vanco

When should prophylactic antibiotics be considered to prevent recurrent cellulitis and which agent should be used?
- Consider if ≥3 episodes of cellulitis a year despite controlling other risk factors
- Use penicillin or an equivalent beta lactam (amoxicillin, cephalexin)
What should be done in patients with lymphedema and recurrent cellulitis?
COmpression
What symptoms suggest nec. fasc.
- Erythema with
- systemic toxicity
- gangrene/anesthesia
- hard induration
- hemorrhagic bullae
- pain out of proportion
- Pain extending beyond erythema
How is necrotizing fasciitis treated emipically?
- Emergent surgical inspection/debridement
- Consult surgery urgently
- Empiric antibiotics
- Piptazo + Vanco + Clindamycin
- Consider IVIG if shock or pre-operative
What are the organisms associated with each type of nec. fasc and how are they treated

Who gets type 1 nec. fasc.
- Usually younger patients
- following minor trauma
- they can have DM/PAD/IVDU
Who gets type 2 nec. fasc.?
- Older patients
- DM
- pelvic wounds
What is associated with clostridium induced nec. fasc.
- Trauma
- colon Ca
What is associated with vibrio vulnificus nec. fasc.
- Saltwater exposure
- Underlying liver disease
- seafood ingestion
What is associated with Aeromonas hydrophila induced Nec. Fasc.
Freshwater exposure, injury
What bacteria cause toxic shock syndrome?
- GAS
- S. aureus
What are the diagnostic criteria for toxic shock syndrome?
- Hypotension (SBP<90) AND
- Isolation of GAS for normally sterile site AND
- At least 2 of:
- Renal impairment (Cr >177)
- Coagulopathy (plt<100 or DIC)
- Liver function abnormalities (ALT/AST/bili 2x ULN)
- ARDS
- Generalized erythematous macular rash that can desquamate
How is toxic shock syndrome managed?
- Contact + droplet precautions
- Volume resuscitation
- Surgery (esp. if necrotizing SSTI suspected)
- ABx
- Beta lactams + clindamycin
- IVIG – Limited evidence, can be considered if severe infection
- Hyperbaric O2 – efficacy unknown
- Chemoprophylaxis – cephalexin x 10 days (clinda if allergy)
What microbiology is classically associated with diabetes
- Polymicrobial infections
- Often pseudomonas and anaerobes
What SSTI microbiology is classically associated with water exposure?
- Vibrio vulnificus (salt water)
- Aeromonas spp (fresh water)
- M. Marinum (fish tank exposures)
- M. Fortuitum (hot tub exposure)
What SSTI microbiology is classically associated with rose gardens?
sporothrix schenckii
What SSTI microbiology is classically associated with meat, butchers and veterinarians?
Erysipelothrix rhusiopathiae
What SSTI microbiology is classically associated with ecthyma gangrenous, malignant/invasive otitis external, hot tub folliculitis, and green nail syndrome?
Pseudomonas
What SSTI microbiology is classically associated with herpetic whitlow and eczema herpeticum?
HSV-1 and HSV-2
What SSTI microbiology is classically associated with umbilicated lesions, HIV, subacute meningitis and increased LP opening pressure?
Cryptococcus neoformans
What SSTI microbiology is classically associated with burrows, pruritus and visible tracts in web spaces?
Scabies
What SSTI microbiology is classically associated with HIV+ patients with white plaques on lateral aspects of the tongue that don’t scrape off?
Oral hairy leukoplakia (EBV)
What SSTI microbiology is classically associated with black eschar in nasal mucosa or palate of diabetic patients?
Mucormycosis (Rhizopus spp.)
How does osteomyelitis develop (pathophysiology). Which pathophysiological mechanism is more likely to cause monomicrobial infections and which is most likely to cause polymicrobial infections?
- Hematogenous spread
- More common in children
- In adults, commonly causes vertebral OM
- Monomicrobial
- Contiguous spread
- From SSTI, trauma, surgery
- Polymicrobial
Differentiate neuropathic, arterial and venous foot ulcers
- Neuropathic
- Pressure points
- punched-out appearance
- deep ulcer
- minimal pain
- warm dry foot
- Arterial
- Lateral malleolous
- Dry and punctate
- Decreased pulses
- Cold-dry foot
- Venous
- Medial malleolous
- Irregular margins
- Shallow depth
- mildly painfull
- venous stasis dermatitis/lipodermatosclerosis
What are signs that a foot ulcer is infected
- Pain in a chronic wound (LR 11-20)
- Foul odor (LR 1-3)
- Purulence, exudate, erythema, warmth edema (LR<1)
What is the most likely microbiological etiology of osteomyelitis in patients with the following risk factors:
- All patients
- Foreign body, prosthetic infections
- Nosocomia
- DM
- immunocompromise

What clinical findings have the highest +LR and -LR for OM of the lower extremities in patients with diabetes?
Presence or absence of ulceration does not modify probability of disease

What is the gold standard for diagnosis of lower extremity OM in diabetic patients?
-
Bone biopsy and culture
- Superficial swab cultures do not reliably predict bone microorganisms or diagnose infection
What are the most commonly involved organisms in native vertebral OM?
- S. Aureus (most common)
- Beta hemolytic strep
- GNB
- Less common
- Tb
- Brucella
- Fungi
List risk factors for native vertebral OM
- Elderly
- immunocompromised
- IVDU
- Patients with PICCs/Ports
What are the signs and symptoms of native vertebral OM?
- New/worstening back pain in the context of suggestive blood work
- Fever in 45% of patients
How can a diagnosis of native vertebral OM be posed? What is the workup
- Biopsy
- Blood cultures (50% pos. if S. Aureus)
- ESR, CRP (sens 94-100%)
- MRI (sens. 97%, spec. 93%)
When might a biopsy not be required when diagnosing native vertebral OM
- If S.Aureus bacteremia in last 3 months
How is native vertebral OM treated?
- If no sepsis/neuro compromise, hold ABX until Bx results
- If empiric ABx must be used : Ceftriaxone + vanco
- Treat for 6 weeks
- Surgery if
- Neuro deficits
- spinal cord compression
- progression/recurrence despite appropriate ABx
How should native vertebral OM be followed after ABx started?
- Monitor clinically and repeat inflamatory markers
- repeat MRI only if poor clinical response after ABx
How should a possible prosthetic joint infection be worked up in patients with suggestive symptoms
- Make a microbiological diagnosis
- Withhold ABx if stable clinically
- perform arthrocentesis
What is the surgical management of prosthetic joint infections (i.e when do you change the prosthesis and when do you debride)?

What are the empiric antibiotics of choice in prosthetic joint infections and for how long should a patient be treated
IV or high dose oral ABx for 4-6 weeks
Empirically: Vanco + CTx
Name 7 steps in the management of a new diagnosis of HIV
- Stage the HIV infection
- Confirm the positive test
- CD4 count
- Viral load
- Genotype (assess for resistance)
- Tropism testing (CCRS)
- Assess for opportunistic infections
- Treat if present
- Prophylaxis based on CD4 count
- Assess for co infections
- TB: TST/IGRA, CXR
- Serologies
- CMV
- toxoplasma
- Hepatitis B/C
- STIs and sexual health
- Syphilis
- Gono/chlam
- pap-test (cervical +/- anal)
- Immunizations
- Hepatitis A if at risk
- Hepatitis B
- Annual influenza
- COVID
- HPV
- PCV-13 then PPV-23 eight weeks later
- Hib, meningiococcus
- caution with live vaccines if CD4<200
- Assess general health
- CBC, lytes, Cr, PO4
- Non-fasting lipids, glucs
- UA, beta-HCG
- Initiate ARV
- Drug safety screening
- HLA-B5701 (ABC hypersensitivity)
- G6PD
- Start ASAP and council on side effects
- Drug safety screening
- Follow-up and councilling
- Prognosis
- Safe sex
- HIV in pregnancy
- Duty to disclose
What are the symptoms and signs of early HIV infection. Which ones have the highest +LR and -LR
- Fever
- Nausea
- emesis
- weight loss
- arthralgias/myalgias
- pharyngitis
- oral ulcers
- rash
- LADP

Which patients with HIV should be getting ARV?
- All individuals with HIV who are ready for treatment. No waiting period
What are the recommended initial treatments for HIV
- 2 NRTIs PLUS INSTI OR NNRTI OR PI
- bictegravir/tenofovir alafenamide/emtricitabine
- Dolutegravir plus:
- Tenofovir alafenamide/emtricitabine
- Tenofovir disoproxil fumarate/emtricitabine
- Tenofovir disoproxil fumarate/lamivutide
- Dolutegravir/lamivudine with cavieats
*Tenofovir alafenamide has fewer bone and renal side effects wheras tenofovir disoprooxil fumarate is associated with lower lipid levels and lower costs
Against what agents should prophylaxis be provided in HIV and at what CD4 count thresholds?
- CD4 <200
- PJP prophylaxis
- CD4 <100
- Toxoplasmosis
- CD4 <50
- MAC (no longer recomended unless patients are noot on ART or not on fully suppressive ART
What is the preferred agent for PJP prophylaxis? What are the alternatives?
- Prefered
- TMP-SMX 1 DS tab daily
- Alternatives
- TMP-SMX 1 ss tab daily or 1 DS tab M/W/F
- Dapsone
- Atovaquone
- aerosolized pentamidine monthly
What is the preferred agent for Toxoplasmosis prophylaxis? What are the alternatives?
- Preferred
- TMP/SMX 1 DS tab daily
- Alternatives
- TMP/SMX 1 SS tab daily or 1 DS tab M/W/F
- Dapsone + pyrimethamine
- Atovaquone
What is the preferred agent for MAC prophylaxis? What are the alternatives?
- Prefered
- Azithromycin 1200mg weekly
- Clarythromycin 500mg BID
- Alternative
- Rifabutin
What is the preferred and alternative treatment for PJP in HIV patients
- Preferred
- IV TMP SMX
- If PaO2 <70 or A-a gradient >35 (severe PJP)
- Prednisone 40mg PO BID x 5 days then
- Prednisone 20 mg PO BID x 5 days then
- Prednisone 20 mg PO daily x 11 days
- Alternative
- Moderate to severe
- Primaquine + clindamycin IV
- Pentamidine IV
- Mild-moderatge
- Dapsone + TMP
- Primaquine + clindamycin PO
- Atovaquone 750mg PO BID
- Moderate to severe
What is the preferred and alternative treatment for toxoplasmosis in HIV patients
- Preferred
- Sulfadiazine + primethamine(AI) x 6 weeks +/- chronic maintenance if ongoing clinical or radiographic disease
- Not available in Canada
- Sulfadiazine + primethamine(AI) x 6 weeks +/- chronic maintenance if ongoing clinical or radiographic disease
- Alternative
- Primethamine + Clindamycin (AI)
- TMP-SMX (b1)
- Atovaquone +sulfadiazine
- atovaquone + pirymethamine
- Atovaquone
What is the preferred and alternative treatment for MAC in HIV patients
- Preferred
- Clarithromycin + ethambutol OR Azithromycin + ethambutol x 12 months
- Alternative
- COnsider ADDING rifabutin, amikacin, FQ if advanced HIV or severe disease
What antimicrobials should not be used in G6PD deficiency
- Dapone
- Primaquine
What should be added to pyrimethamine to prevent toxicity
Leucovorin
What HIV complications can arise with CD4 counts above 500
- Fever
- Night sweats
- LADP
- headache
- Malaise
- Weight loss
What additional complications can arise in HIV when the CD4 count drops to between 200-500
- Non-invasive candidiasis
- Recurrent mucocutaneous HSV-1, HSV-2, VZV
- Oral hairy leukoplakia (EBV)
- Cutaneous KS (HHV-8)
- Sinusitis, bacterial pneumonia (esp. invasive pneumococcus)
- TB
- Cervical dysplasia, cervical carcinoma in situ
- CVD, stroke, CKD
- Psoriasis, seborrheic dermatitis, bacillary angiomatosis, molluscum contagiosum
- ITP
What additional complications can arise in HIV when the CD4 count drops <200
- HIV associated myelopathy
- Visceral KS
- Endemic fungi
- Coccidiosis
- Histoplasmosis
- Blastomycosis
- Non-endemic fungi
- Aspergillosis
- cryptococcus
- PJP (subacute presentation over 2 weeks)
- NHL>HL, MM, leukemia, anal cancer, liver cancer, cervical cancer, vulvar/vaginal cancer
What additional complications can arise in HIV when the CD4 count drops to between <100
- Toxoplasmosis
- PML (JC virus)
What additional complications can arise in HIV when the CD4 count drops <50
- CMV retinitis, colitis
- MAC
- CNS lymphoma, HAND
When is it safe to get pregnant if you have HIV?
- When on ARV and undetectable viral load\
How should HIV be managed through pregnancy?
- Always continue ARV
- If VL >1000 copies (or unknown) near delivery, give IV Zidovudine and recommend schedules C/S
- If VL is suppressed, no increased risk with vaginal delivery
How should HIV patients be managed in the post partum period?
- If maternal viral load not suppressed at birth, give zidovudine to baby x 6 weeks and nevirapine x 3 doses
- Breastfeeding NOT recommended
Describe the natural history of Tb

How is latent Tb diagnosed
TST or IGRA
What are the particularities of the TST and IGRA?

Who should be tested for latent Tb?
- As a general rule: Patients with a high probability of infection or significant risk factors for reactivation and low risk of treatment toxicity and high probability of treatment completion:
- Contacts of an active case of pulmonary Tb
- Immigrants from countries with a high Tb incidence
- Travelers to countries with high Tb incidence
- Indigenous communities
- People who inject drugs
- Homeless
- Health care workers
- Residents of LTC facilities or correctional facilities
How is a TST interpreted
- 0-4mm
- Negative
- 5-10 mm
- Positive if:
- HIV
- Contact with positive case within past 2 years
- Presence of fibronodular disease on CXR
- Organ transplant
- TNF alpha inhibitor user
- Patients on immunosuppressive drugs
- ESRD
- Positive if:
- >10 mm
- Positive in all situations
How is latent Tb managed?
- Rule out active disease
- Balance the risks of reactivation and the risk of treatment adverse events
- If treating, then
- Prefered
- Isoniazid daily x 9 months
- Alternative
- Isoniazid daily x 6 months
- isoniazid + rifampin daily x 3 months
- * new evidence for rifampin x 4 months, not in guidelines
- Prefered
What is the treatment for active Tb
- Caveats
- EMB can be stopped early if fully susceptible isolate
- Supplement INH with vitamin B6 to prevent peripheral neuropathy
- Steroids in Tb Meningitis or pericardial disease (not in newer guidelines)
- Consider prolonged treatment if persistent cavity, culture positive at 2 months CNS or bone disease

What are the side effects of isoniazid?
- Common
- Rash
- hepatitis
- neuropathy
- Unusual but important
- CNS toxicity
- Anemia
What are the side effects of rifampin?
- Common
- Drug interactions
- rash
- hepatitis
- Uncommon but impoortant
- Hepatitis
- Flu-like illness
- Neutropenia
- thrombocytopenia
What are the side effects of pyrazinamide?
- Common
- Hepatitis
- Rash
- arthralgias
- Rare but important
- Gout
What are the side effects of ethambutol?
- Common
- Eye toxicity
- Rare but important
- rash
Rash and hepatitis are side effects of most anti Tb drugs. List Tb drugs in RIPE in the order of most to least likely to cause both of these side effects

How should active Tb be managed in pregnancy?
- In pregnancy risk to the foetus from active Tb>risk from Rx
- In pregnancy INH, RIF, EMB are safe
- WHO recommends the use of PZA in pregnancy
- Some uncertanties about safety but no reports of teratogenic effects
- Give in women with extensive disease or in patients who cannot tolerate other first line drugs
When should Latent TB be treated in pregnancy?
- Close contact of TB case
- Otherwise, wait until after delivery
Who should get an HIV test after a diagnosis of Tb
Everyone
Which HIV patients with latent Tb should be treated for latent Tb
Everyone, high risk of reactivation!
When should ART be started in patients with HIV and Tb
- CD4<50: within 2 weeks
- CD4 >50: Within 8 weeks
- Pregnancy: ASAP regardless of CD4
- In the presence of Tb meningitis: defer 8 weeks given increased risk of IRIS, especially if low CD4 count
What should be given to patients at high risk of Tb-IRIS
Preemptive predisone
What is the new prefered treatment for latent Tb in HIV+ patients?
- Isoniazid + Pyridoxine x 6-9 months
What are the diagnostic criteria non-tuberculous mycobacteria lung disease
- Clinical AND
- pulmonary or systemic symptoms
- Radiological PLUS
- Nodular or cavitary lesion on CXR
- Bronchiectasis on CT
- one of:
- 2 or more sputum positive for same species NTM
- 1 BAL/bronch culture positive for NTM
- Biopsy with mycobacterial histology (AFB/Granuloma) and positive culture
How are NTM pulmonary infections treated
- Discussion around clinical factors, infecting species and patient priorities
- Ideally treat based on succeptibilities
- Minimum 3 drug regimen
- Macrolide
- ethambutol
- +/-rifampicin
- +/-aminoglycoside
No empiric treatment
Name 4 species of NTM
- Mycobacterium avium ocmplex
- mycobacterium Kansaii
- Mycobacterim Xenopi
- Mycobacterium abscessus
what questions should you ask a patient with fever after travel
- pre travel
- PMHx, meds
- pre-travel consultation?
- Vaccines?
- malaria prophylaxis?
- travel
- purpose (greatest risk = VFR)
- travel itinerary
- Type of accommodation (urban or rural)
- Insect precautions
- Individual exposures
- raw meat, seafood, street food, unclean water, unpasteurized dairy products
- Freshwater exposure
- Visits on farms, slaughterhouses, funerals, hospitals
- Animal bites or scratches, insect or arthropod bites, hiking/caving
- Body fluid exposure (tattoo, sexual activity)
- Medical care overseas
- Post-travel
- Timing of fevers/clinical symptoms
- Short incubation period:
- Malaria, dengue, chikungunya, travelers diarrhea, viral URTI, influenza
- Long incubation period
- Malaria, TB, hepatitis, HIV, enteric fever, due to salmonella spp.
- Short incubation period:
- Pattern of fever
- Daily: malaria, traveller’s diarrhea, viral RTI, enteric fever
- Biphasic: Malaria, Dengue
- Relapsing: Malaria, enteric fever
- Timing of fevers/clinical symptoms
What is the main DDx for fever in returned travelers?
- Infectious – Travel-related
- MALARIA
- Typhoid/enteric fever
- Dengue, Chikungunya, Zika
- Viral hepatitis
- Rickettsiae, Brucellosis, Leptospirosis, Q-Fever, Ebola
- STIs, acute HIV
- Infectious – Non travel related
- UTI
- CAP
- mono
- Meningitis
- C. Diff.
- influenza
- COVID-19
- Non-infectious
- VTE
- Drug fevers
- illicit drugs
What are the initial investigations that should and can be sent in patients with fevers returning from travel?
- CBC+diff, peripheral smear
- Electrolytes, Cr, urea, glucose
- ALT, ALP, AST, bili, INR/PTT
- Blood cultures x2, urine culture
- CXR
- Malaria x3 (over 24hrs)
- RDT
Consider
- Stool C&S, stool O&P, C. difficile
- Dengue, chikungunya, zika, PCR or serology
- hepatitis serology
- HIV, STI screen
- NP swab for viral PCR
How is malaria diagnosed?
- Thick and thin blood smear x3 over 24hrs separated by at least 6hrs
- Thick smear: Looks for parasites
- Thin smear: Identifies parasitemia (%) and speciation
- Rapid detection test
- Seperate tests for P. falciparum and others
- Highest sensitivity for falciparum
Name the 6 species of malaria
- P. Falciparum
- P. Ovale
- P. vivax
- P. Malariae
- P. Knowlesi
- P. Simiun
What is unique to P. Vivax and Ovale
Can present years later due to hypnozoites in the liver
Name the severity criteria for malaria
- Essentially any end-organ damage:
- Neurological: Confusion, prostration (severe weakness), seizures
- Respiratory: ARDS, pulmonary edema
- Hematological: DIC, Jaundice, hemoglobinuria. Black water fever
- Severe anemia (Hb<50)
- Hypoglycemia (glucose<2.2)
- Acidosis (pH<7.25, HCO3 <15)
- Renal impairment (Cr >265)
- Lactic acidosis
- Hyperparasitemia
- ≥ 5% for non-immune adults
- ≥ 10% for semi-immune adults
How is falciparum malaria managed
- Uncomplicated
- From chloroquine sensitive area: Chloroquine
- From chloroquine resistant area:
- Atovaquone-proguanil
- Quinine+doxycycline
- Quinine + clindamycin
- Complicated
- IV artesunate x 48hrs then:
- PO atovaquone proguanil
- Doxycycline
- Clindamycin
- IV artesunate x 48hrs then:
How is non-falciparum malaria managed?
- Uncomplicated
- Chloroquine sensitive area (most): Chloroquine
- Chloroquine resistant area
- Atovaquone-proguanil
- Quinine + doxycycline
- Complicated (unusual for non-falciparum)
- IV artesunate x 48hrs then:
- PO atovaquone proguanil
- Doxycycline
- Clindamycin
- IV artesunate x 48hrs then:
Describe the areas of the world with chloroquine sensitive/resistant malaria
Sensitive=grey areas on map

What agents can be used for malaria chemoprophylaxis?
- Chloroquine in sensitive areas
- Atovaquone proguanil
- Doxycycline
- Mefoquine
- primaquine
Which forms of malaria chemoprophylaxis are safe in pregnancy?
- Chloroquine
- Mefloquine
- Atovaquone proguanil has insuficient data regarding use in pregnancy
What clinical findings have the highest +LR and -LR for malaria

What is the incubation period of dengue?
<2 weeks
What are the clinical features of Dengue
- Fever
- Maculopapular rash
- retro-orbital pain
- myalgias (“break bone fevers”)
- Cytopenias
What is the treatment for Dengue?
- Supportive care
- avoid NSAIDS
What is the incubation period of Zika?
- <2 weeks
What are the clinical features of Zika virus?
- 75% are asymptomatic
- Fever
- Rash
- arthralgias
- myalgias
- conjunctivitis
- HA
- retro-orbital pain
- Association with GBS
- If caught in the first trimester, association with congenital Zika:
- Microcephaly
- intracranial calcifications
- renal and hearing abnormalities
- Arthrigryposis
How is Zika virus treated?
Supportive care
What is the incubation period for chikungunya
< 2 weeks
What are the clinical findings in chikungunya?
- Fever
- Polyarthralgias (usually arthritis)
- Lymphopenia
- Maculopapular rash
What is the treatment for chikungunya
Supportive care
What is the etiological agent for typhoid?
Salmonella Typhi/paratyphi
What is the incubation period for typhoid?
5-21 days
What are the clinical features in Typhoid?
- Fever
- Flu-like illness
- salmon colored spots
- constipation
- abdo pain
- relative bradycardia
How is typhoid treated?
- IV ceftriaxone
- IV cipro
- Azithromycin
* increasing FQ resistance in SE asia
From what type of exposure can a person get Leptospirosis?
- Animal waste
- Soil, water exposure
What is the incubation period for Leptospirosis
2-26 days (average 10 days)`
What are the clincal features of Leptospirosis?
- Fever
- Myalgias
- HA
- Conjunctivitis
- Hypokalemia
- Cytopenias
- sterile pyuria
- Rarely in severe disease
- Jaundice + Renal failure (weil’s disease)
- ARDS
- Pulmonary hemorrhage
How is leptospirosis treated?
- Mild disease
- Doxycycline
- Azithromycin
- Severe disease
- CTx
- Penicillin
- doxycycline
What finding on a CBC increases suspicion for nematodes in returned travelers?
- Eosinophilia
How is the diagnosis of nematode diseases posed?
- Stool/urine/sputum(strogyloides) microscopy (Ova and parasites)
- +/- serology (positive for life)
Where can one get Strongyloides stercoralis?
Soils in Africa, South America, Asia
How does strongyloides stercorales manifest in immunocompromised patients
- Disseminated disease
- Polymicrobial GNB bacteremia
- GNB meningitis
How is strongyloides stercoralis treated?
Ivermectin
How can one get schistosomia?
Contact with water (water/snail host) in troopical/sub-tropical areas
What are the manifestations of Schistosoma
- Chronic infection
- Can predispose to liver and bladder Ca
How is Schistosoma treated?
Praziquantel
How is taenia solium treated?
Neurocysticercosis: albendazole +/- praziquantel +/- steroids
How can one get Taenia Solium
By eating infected/uncooked meat (taeniasis) or eggs (neurocysticercosis)
How might one get trichinella spiralis?
From eating undercooked wild animal meat (bear/pork)
List symptoms of trichinella spiralis
- GI symptoms
- Muscle pains (cysts)
How is Trichinella spiralis treated?
Albendazole/mebendazole
How is COVID 19 transmitted?
Droplets
Aerosols in AGMP
What is the incubation period of COVID 19?
2-14 days (average 5-6 days)
What are the clinical features of COVID 19?
- Fever
- Cough
- SOB
- fatigue
- anosmia
- GI Sx
- anorexia
How is COVID 19 diagnosed?
RT-PCR
Highest sensitivity with LRT specimen
Rapid antigen available
Listt risk factors for severe COVID 19 infections

What are the side effects of viral vector-based COVID vaccines?
- Common vaccine side effects
- VTE (VITT)
- capillary leak syndrome
- GBS
- anaphylaxis
What are the side-effects of COVID 19 mRNA vaccines?
- Myocarditis/pericarditis
- Bell’s palsy
- Anaphylaxis
Who should get a booster shot of the COVID-19 vaccine?
- Should be offered at least 6 months after primary series
- Adults > 50
- Adults living in LTC or other settings that provide congregate care for seniors
- Recipients of a viral vector vaccine only series
- Adults from or in first nation communities
- Frontline healthcare workers regardless of interval from initial series
- Can be considered in other adults 18-49
- Adults with moderate to severe immunocompromise
- Active cancer treatment
- Transplant recipients
- CAR-T or HSCT in last 2 years
- Advanced untreated HIV
- immunosuppressive meidications
List therapies that can be used in COVID 19 and when they should be used
- Dexamethasone 6mg PO/IV x 10 days
- If requiring O2, hospitalized, intubated
- Remdesevir 200mg IV x1 then 100mg IV x4 days
- If needing O2 but not intubated
- Tocilizumab
- If requiring O2/intubation with systemic inflammation (CRP>75) and worstening despite 24-48hrs of steroids
- Casirivimab+imdevimab and sotrovimab
- Consider in certain population
- Mild-moderate COVID 19 in adults and adolescents at high risk for progression to hospitalisation and death
- Within 10 days of positive test
- Mild-moderate COVID 19 in adults and adolescents at high risk for progression to hospitalisation and death
- Consider in certain population
- VTE prophylaxis
- More in heme deck
- Antibiotics
- Do not start empirically
- Not recomended
- Colchicine, IFN, Vit D
- Recomended against
- Hydroxychloroquine, Ivermectin, lopinavir/ritonavir
Where is Zika virus endemic?
- Most of carribean and south america
- Africa
- South east asia
How is Zika transmitted?
- Primarily through mosquito bites “day biters”
- Reports of transmission via sexual intercourse or blood donations
How is zika virus diagnosed
- Molecular testing
- Within 2 weeks of symptom onset
- Confirmatory plaque reduction neutralization test
- Acute and convalescent serologies
- Carefull: cross reactions, lack of specificity
- Order >10 days after symptom onset
Who should get tested for Zika?
- Relevant exposure and:
- Symptomatic patient within 3 days of arriving or 14 days of departing a high risk area
- Symptomatic pregnant women
What is the incubation period of Ebola?
8-12 days usually (2-21 day range theoretically)
What are the symptoms of Ebola?
- Fevers
- Myalgias
- GI Sx
- Anorexia
- Bleeding <20%
What should be the isolation protocol for patients with Ebola?
Droplet/contact and call IPAC vs impermeable neck to toe with N95 and face shield
How is Ebola diagnosed?
- Viral cultures
- NAAT
- viral antigen testing
- Serology from appropriate sites
How is Ebola treated?
- Supportive care, essential procedures only
- Don’t forget to rule out malaria
What is the case fatality rate of Ebola?
60%
What is the incubation period of Measles
14 days
What are the symptoms of measles
- Fever
- Cough
- Coryza
- conjunctivitis
- Koplik spots
- rash (centrifugal)
How should patients with measles be isolated?
- Airborne precautions
Who should be contact traced after a diagnosis of measles?
- Contacts 4 days before and after onset of rash
How is measles diagnosed
PCR of pharynx, NP, urine
Serology possible but can be false negative early
List possible complications of measles
- Pneumonia
- Encephalitis
- subacute sclerosing pancreatitis
What should be used for post-exposure prooophylaxis in measles
- MMR vaccine
- Immunoglobulins
*based on time from exposure
Describe the testing for lyme disease

In what condition can you diagnose Lyme disease without serology?
In the presence of erythema migrans = clinical diagnosis
What are the manifestations of CNS lyme disease
- meningitis
- radiculoneuritis
- mononeuritis multiplex
- CN palsy
- Spinal cord inflamation
How is CNS lyme disease diagnosed
Serum antibody testing (not with PCR or culture of CSF!)
What should be considered in Lyme patients with persistent fevers on antibiotics
COnsider co-onfections (Babesia, anaplasma)
How should Lyme disease be treated?

What is the definition of Fever of Unknown origin?
To >38.3 over 3 weeks with 1 week investigations
What is the DDx of FUO?
- Infection
- Intra-abdominal abscess (30%)
- IE
- Sinusitis
- TB
- CMV
- EBV
- HIV
- Inflammatory (25%)
- GCA
- Still’s disease
- IBD
- Malignancy (15%)
- Lymphoma
- RCC
- CRC
- leukemia
- Drugs/misc (10%)
- VTE
- Antimicrobials
- NSAIDs
- Allopurinol
- Anti-epileptics
- Idiopathic (25%)
What are the first line investigations that should be sent in the context of FUO?
- Hx & PE. Comprehensive fever diary
- CBC + Differential + blood film
- Lytes Cr,
- LDH, TSH, CK, LFTs, SPEP
- Blood cultures, urine C&S
- HIV, CMV IgM, Hepatitis serologies
- CXR, Abdo U/S
- ANA, ANCA, RF
- Consider EBV, monospot, q-fever serologies in right setting
What second line investigations/steps should be undertaken if the first line investigations don’t lead to any diagnosis?
- in this order
- Discontinue non-essential medications, institute fever diary
- CT abdomen
- Nuclear imaging
- TTE and duke criteria
- Doppler U/S bilaterally – lower extremities (R/O DVT)
- Temporal artery biopsy (IF ESR>50, patient>50)
- Liver biopsy
*Empiric trials of ABx or steroids rarely establish a diagnosis. Discouraged
What workup should be sent before starting long-term corticosteroids?
- TST/IGRA:
- If planning Prednisone>15mg for >4 weeks AND > 1 other Tb risk factor
- RF: close contact, recent immigration, high risk work/life exposure
- If planning Prednisone>15mg for >4 weeks AND > 1 other Tb risk factor
- Hepatitis B
- If prednisone >7.5 mg
- PJP
- Consider prophylaxis if pred >20mg for >4-8 weeks
- Strongyloides
- Screen with serology +/- stool O&P if any immunosuppression and lived (or extended travel) to endemic areas
Which cancer patients on chemotherapy should get antimicrobial prophylaxis?
- Prophylaxis with ciprofloxacin in those at high risk for FN or prolonged profound neutropenia (ANC<0.1 for >7 days)
- Antifungal (oral triazole or echinocandin) if prolonged and profound neutropenia such as in AML/MDS, HSCT. Not in solid tumors
- TMP-SMX in chemo with PJP risk >3.5% (e.g. prednisone ≥20mg for >1 month)
- Patients who are HSV + undergoing allo-HSCT or leukemia induction should get prophylactic acyclovir
- NRTI if high risk of hep B reactivation
- Yearly flu vaccine
- Avoid environments with high concentrations of fungal spores
How should Healthcare-associated ventriculitis and meningitis be managed?
- Complete removal of infected CSF shunt/hardware and replacement with external drain
- Empiric ABx:
- Vanco + (ceftazidime OR Meropenem)
- Add rifampin if staph isolate
- Intraventricular ABx if no response to systemic ABx
- Vanco + (ceftazidime OR Meropenem)
- Repeat CSF cultures to confirm negative growth
- After the end of treatment:
- 10-14 days post last + culture for gram positives
- 21 days post last + culture for gram negatives
- After the end of treatment:
- Reimplantation of new shunt once repeat CSF culture negative for 7-10 days
When should a line infection be suspected?
- Fever + line: Dx should be considered
- Get peripheral + line cultures
How are line infections treated?
- Remove line if possible
- ALWAYS for S. aureus and candida or with complicated infection (IE, OM, thrombophlebitis)
- Directed therapy x 7 days
- Minimum 14 days if S. Aureus or candida
How are surgical infections managed
- Superficial
- Treat as cellulitis
- deep or organ space
- Drainage +/- ABx
How are catheter associated UTIs managed?
- Only get culture if patient symptomatic
- If Sx and + culture, treat for 7 days
- Remove/change catheter if possible
List prevention strategies for VAP
- Avoid intubation if possible (lol)
- Use NIPPV if possible
- Keep head of bed at 30-45 degrees
- Daily oral care with chlorhexidine
- Daily sedation vacation and assessment of readiness to extubate
- Facilitate early mobilisation
List prevention strategies for central line associated infections
- Subclavian ≥ Jugular > femoral
- Use maximal sterile barrier precautions and sterile full body drapes when inserting CVCs
- Clean skin with chlorhexidine before inserting line
- chlorhexidine bathing
- Use sterile gauze or transparent, semi-permeable dressing to cover catheter site
- Daily assessment of wether CVC is needed
List prevention strategies for catheter-associated UTIs
- Hand hygiene; insert catheter using aseptic technique and sterile equipment
- Use smallest possible catheter
- Maintain sterile, continuously closed drainage system
- keep collection bag below the level of the bladder
- Empty collection bag regularly
- Daily discussion of indication for catheter
- Avoid unnecessary re-insertion
List the sensitivity profiles of the various species of Candia

List risk factors for Candidemia
- Use of broad spectrum antibiotics
- ICU admission
- CVC
- TPN
- Neutropenia
- Immunosupressive agents
- Intra-abdominal surgical procedures
- Necrotizing pancreatitis
- Candida colonization in 3 sites
How is Candidemia treated?
- IF stable, no recent azole exposure: Fluconazole
- IF unstable, neutropenic or recent azole exposure: Echinocandin
- Pregnancy: Amphotericin B
- CNS infections: Amphotericin B +/- flucytosine
*Consult ophthalmology to R/O endophtalmitis
*remove CVC
*Treat for 2 weeks after 1st negative BC
*Consider TTE if persistent candidemia. R/O IE
What are 4 syndromes associated with aspergillus infections?
- ABPA/Allergic rhinosinusitis
- Aspergiloma
- Chronic cavitary pulmonary aspergilosis
- Invasive aspergilosis
What is ABPA and what are its clinical/lab findings
- Hyper-sensitivity response to Aspergillus antigens/precipitants
- Presents with Asthma-like Sx, brown sputum, eosinophilia, bronchiectasis, elevated IgE
What is an aspergilloma
- Mycetoma that forms within a pre-existant cavity
- “Fungus ball”
What is Chronic cavitary pulmonary aspergillosis and what are its clinical/lab findings
- Progression of aspergilloma in pre-existing structural lung disease (most commonly COPD)
- Weight loss, Worsening cough +/- hemoptysis
What is invasive aspergillosis and how is it diagnosed
- Opportunistic infection seen in neutropenia/cellular immunocompromise
- Diagnosis using:
- CT chest
- indirect tests (Serum/sputum galactomannan)
- Direct tests (fungal culture or pathology)
How is ABPA treated?
- Steroids/anti-IgE +/- itraconazole (anti-fungal controversial)
How are aspergillomas treated
- Single lesion: surgical resection +/- antifungals
- Multiple lesions: Antifungals x6 months
How is chronic cavitary pulmonary aspergillosis treated?
Antifungals x 6 months
How is invasive aspergillosis treated
Voriconazole ≥ 6 weeks or longer
Where is blastomycosis endemic?
Border of the great lakes (incl. northern Ontario)
Southeastern/central USA
St. Lawrence river valley
What are the symptoms of Blastomycosis?
Pneumonia
Skin/joint infections
How is blastomycosis diagnosed?
- Fungal cultures
- PCR
- Pathology
- Serum/urine antigen
How is blastomycosis treated?
- Mild to moderate: Itrraconazole
- Severe: Amphotericin B
- Treat for 6-12 months or 3 months after complete resolution
Where is Histoplasma endemic?
St. Lawrence and Ohio rivers
What are the clinical manifestations of Histoplasmosis?
- Self limited PNA
- TB mimicker
How is Histoplasmosis diagnosed?
- Fungal culture
- PCR
- Pathology
- Urine antigen
How is histoplasmosis treated?
- Mild: no Tx
- Moderate: Itraconazole
- Severe: Amphotericin B
Treat for 12 weeks
Where is Coccidioides endemic
- Valley fever
- New mexico
- Arizona
- Mexico
- Central America
In which patients should we suspect Coccidiodomycosis?
- Returned travelers with PNA, meningitis
How is coccidiodomycosis diagnosed?
- Fungal culture
- Path
- antigen test
- LP if meningitis symptoms
How is coccidiodomycosis treated?
Only treat if symptomatic
Itraconazole
List aerosol generating medical procedures
- Intubation/extubation, manual ventilation
- Open endotracheal/deep succison
- CPR (*not chest compressions but airway manipulations)
- Bronchoscopy and BAL
- Tracheostomy/laryngoscopy
- Sputum induction
- Nebulized therapy (not MDI)
- HFNC
- NIPPV
- Some dental procedures
- Drilling
- U/S scaling
What isolation precautions need to be taken in the following diseases, for how long:
- Tb
- Disseminated VZV
- Primary or disseminated, extensive varicella
- Measles
- COVID-19
- Mumps
- Meningococcus
- VHF inc. ebola

What isolation precautions need to be taken in the following diseases, for how long:
- Invasive GAS (TSS/NF/PNA/meningitis)
- C. Difficile
- Disseminated/primary extensive HSV
- Diphteria (pharyngeal)
- Influenza
- Norovirus
- Scabies
- Antibiotic resistant organisms

Which patients should get prophylactic or pre-emptive antibiotics antibiotics after a bite?
- Immunocompromised
- Asplenic
- Advanced liver disease
- Pre-existing or resultant edema of affected area
- Moderate to severe injury (especially to hand or face)
- Penetrating injuries to periosteum or joint capsule
What is the microbioology of animal bites
- Pasteurella multocida
- Capnocytophagia Canimorsus
- Staph
- strep
- anaerobes
What empiric antibiotic regimens can be considered following an animal bite?
- Clavulin
- 2nd or 3rd generation cephalosporin + metronidazole
- Moxifloxacin
- Doxy + clinda
What empiric antibiotic regimens can be considered following a human bite?
- Clavulin
- 2nd or 3rd generation cephalosporin + metronidazole
- Moxifloxacin
- Doxy + clinda
What is the microbiology of human bites?
- Eikenella corrodens
- Strep
- S. Aureus
- Anaerobes
Who should get a tetanos shot and/or immunoglobulins after wound management

In which patients with bite wounds should you give rabies post-exposure prophylaxis?
- If exposure to rabies is considered likely
- Ask about animal species, type of exposure, circumstance, behavior and vaccination status of the animal, domestic vs stray animal, provoked vs unprovoked attack, location and severity of the bite
- Make sure to immediately clean and flush the bite for 15 min
- Call public health for assistance in risk management
What should be given for rabies post-exposure prophylaxis
RabIg + vaccination
If prior vaccination, no need to give RabIg
What tests should be sent following a bloodborne pathogen exposure?

How much time does it take before an HIV, HCV and HBV test become positive after an exposure?

What is the risk of transmission from percutaneous exposure to HIV, HCV and HBV
- HIV: 0.23-1.3%
- HBV: 6-30%
- HCV: 3-10%
What post-exposure prophylaxis should be offered after HIV exposure?
Truvada + Dolutegavir (or raltegravir) x 28 days within 72 hrs of exposure
What post-exposure prophylaxis should be offered after HBV exposure
- Immune Anti HBs>10: No further management
- Non-immune (non-vaccinated or Anti HBs<10) or unknown: Vaccine series +/- HBIG
What post-exposure prophylaxis should be offered to patients following hep-c exposure
None. Repeat testing in 4-6 months
Which vaccines should be given to adults, and at what age

Which adult patients should get a Hib vaccine
- Asplenia/hyposplenism
- HIV
- Malignant hematological disorders
- PID
- Solid organ transplant
- Cochlear implants
Which adult patients should get a meningococcal vaccine?
- Asplenia/hyposplenism
- HIV
- Complement deficiency
- Travelers to “meningitis belt” (subsaharan africa)
- Pilgrims to hajj
- military personnel
- lab workers
- close contacts to a case
Which adult patients should get the pneu-c-13 followed by pneu-P-23 8 weeks later (pneumococcal vaccine). with single re-immunisation with pneu-p-23 5 years after?
- Asplenia/hyposplenism
- Sickle cell disease
- hemoglobinopathies
- HIV
- nephrotic syndrome
- solid organ transplant
- leukemia
- lymphoma
- immunisupressed
- complement deficiencies
Which adult patients should get 1 dose of pneu-p-23 then a second one 5 years later?
- Age > 65
- Chronic CSF leak
- Chronic cardiac/pulmonary disease
- DM
- CKD
- CLD
- EtOH
- smokers
- homeless persons
- LTC
- IVDU
How should patients be managed when there is a suspicion for influenza? (who should be tested and treated empirically)

For how many days should Oseltamivir treatment be given
5 days, longer if immunocompromised, severe PNA, ARDS
When should patients with influenza be treated for bacterial coinfection?
- Initial severe disease
- Failure to improve
- Biphasic response