ID Unit Three Review General

Basic Virology…

Influenza Virology:

• RNA based virus 

• A and B sub types 

• Main Antigens: 

  • Hemagglutinin

  • Neuraminidase 

SARS-CoV-2 Virology 

• RNA virus 

• Main antigen = spike protein 

Antigenic Drift vs Shift

Antigenic Drift = small change, antibodies to similar virus less effective 

Antigenic Shift = large change

• No immunity in community 

• May result in epidemic/pandemic 

Flu Vaccine Considerations/Precautions…

1. 6 months to 8 years old: needs 2 doses for first influenza vaccine 

2. Egg allergy NOT anaphylaxis = no special precautions 

3. Egg allergy WITH anaphylaxis = must receive in hospital or doctors office NOT IN PHARAMCY

Signs and Symptons: Influenza 

• Sx onset: 1-4 days 

• Duration: 3-7 days 

• Contagiousness…

  • Starts 1 DAY before symptoms 

  • Most contagious in first 3-4 days 

  • Contagiousness abates with symptoms 

Signs and Symptoms: COVID-19

• Sx onset: 2-5 days

• Duration: highly variable 3-7 days

• Contagiousness…

  • Starts 2-3 DAYS before symptoms 

  • Most contagious 1 day before symptoms 

People at High Risk Flu/COVID-19

→ BOTH can result in severe illness and complications 

• Older adults > 65 years old 

• Complex comorbidiites: asthma, COPD, CKD, DM

• Immunocompromise 

• Pregnancy 

FLU: 

• Young children at higher risk of severe flu 

  • < 2 years old is AT VERY HIGH risk 

COVID-19: 

• Most mortality = older adults

• Longer recovery 

• Higher risk of clot, autoimmune issues 

Flu Approved Treatments:

1. Oseltamivir (Tamiflu) Neuraminidase Inhibitor 

   1. 75 mg PO BID for five days

2. Baloxavir (Xofluza) Endonuclease inhibitor 

   1. One dose = 2 caps 

   2. < 80 kg = 40 mg PO

   3. > 80 kg = 80 mg PO

COVID-19 Approved Treatments:

1. Outpatient…

   1. Nirmatrelvir/ritonavir (Paxlovid) Protease inhibitor 

      1. 300 mg/100 mg 3 tabs BID x 5 days

   2. Molnuiravir

2. Inpatient…

   1. Remdesivir (IV) Nuceloside analog chain terminator 

   2. Dexamethasone adjunctive

Flu Benefit of Treatment…

Most benefit if taken < 2 days of Signs and Symptoms

• Decreased hospitalization

COVID-19 Benefit of Treatment…

Most benefit within 5-10 days of signs and symptoms  

Who Should Get Antivirals?

1. High Priority

   1. Hospitalized patients 

   2. Severe or progressive diseases 

   3. Childrens < 2 years old 

   4. Adults => 65 years old 

   5. Pregnant women 

2. Consider Tx

   1. Outpatients with household contacts at risk 

   2. Outpatients with onset =< 2 days prior 

COVID-19 and Immunomodulators…

Used for patients who require O2 as a RESULT of COVID

• Extensive oxygen requirements: high-flow nasal cannula, CPAP, BiPAP

• Mechanical ventilation or ECMO (extracorporeal membrane oxygenation) 

  • Receive an immunomodulator with dexamethasone

• Baricitinib (PO) preferred

  • Tocilizumab (IV) alternative 

• USE BOTH Baricitinib and Tocilizumab for patients on ventilator or ECMO

Paxlovid (Nirmatrelvir/Ritonavir) Drug Interactions 

→ Ritonavir component (PK enhancer) 

• Strong CYP 3A4 and P-gp inhibitor 

• Antiarrhyhmic and anticonvulsant

Flu Special Population Tx

• Pediatrics 

  • Oseltamivir suspension age ≥ 0 years 

  • Baloxovir suspension age ≥ 25 years

• Pregnancy = Oseltamivir (tamiflu preferred) 

COVID-19 Special Population Tx

• Pediatrics

  • Remdesivir if ≥ 4 weeks old 

  • Paxlovid if ≥ 12 years old 

• Pregnancy: Remdesivir or Paxlovid 

Chemoprophylaxis…Flu/COVID

1. Influenza

   1. Oseltamivir for the entire flu season 

2. COVID-19

   1. For patients ≥ 12 with moderate to severe immunocompromised…

      1. Pemibivart

Sinusitis: Differentiating between viral and bacteria infection 

Viral Sinusitis: 5-10 days

• Systemic symptoms (fevers, myalgias) last only for 1-2 days

• Purulent nasal discharge 

Bacterial Sinusitis: Persistent symptoms > 10 days

• Severe symptom onset fast 

  • Higher fever on onset temp > 39ºC plus purulent discharge 

• Double sickening: initial improvement, followed by sudden worsening 5-6 days later

Sinusitis Bacterial Pathogens…

1. S. pneuomoniae 

2. H. flu

3. M. catarhallis 

4. S. pyogenes

5. Staph aureus

Sinusitis…IF patient is B-lactam allergic:

• Adults: Levofloxacin, Moxifloxacin, Doxycycline 

• Peds: Cefpodoxime/Cefixime + Clindamycin, Levoflox (?)

Sinusitis…Risk of Resistance of failed therapy OR recent amox/clav use prior

• Adults: High dose amox/clav first, Levofloxacin, Moxifloxacin

• Peds: High dose amox/clav, Cefpodoxime/Cefixime + Clindamycin

Sinusitis…Hospitalized Patient

• Adults: ampicillin-sulbactam IV coverage

  • Ceftriaxone/Cefotaxime, Levofloxacin/Moxifloxacin

• Peds: ampicillin-sulbactam

  • Ceftriaxone/Cefotaxime, Levofloxacin/Moxifloxacin

Pharyngitis

“Strep Throat”

→ vast majority caused by viruses 

→ most COMMON bacterial pathogen = Strep. pyogenes (Strep A) 

Diagnosis of Bacterial Pharyngitis 

• Patchy exudates on tonsils 

• Suddent onset

• Fever 

• Nausea/Vomiting/Abdominal Pain 

• Tonsil Inflammation 

Diagnosis of Viral Pharyngitis 

• Conjuctivitus 

• Cough

• Hoarsness 

• Diarrhea

Antimicrobial Tx for Pharyngitis…Strep Throat

• First line = penicillin or amoxicillin

• If B-lactam allergy 

  • Non-anaphylaxis reaction: 1st gen cephalospore (cephalexin, cefadroxil) 

  • Anaphylaxis reaction: clindamycin, clarithromycin, or azithromycin 

Treatment Duration = 10 days (EXCEPT azithromycin = 5 days)

Severe Complications of Upper Resp. Infection Pharyngitis

1. Rheumatic Fever: may be result of induction of autoimmune reaction 

2. Post-streptococcal Glomerulonephritis; immune mediated renal injury (quicker onset than rheumatic fever) 

Role of Antimicrobial Therapy…Upper Resp. Infection Pharyngitis

Shorten symptoms duration, reduce transmission, avoid more serious complications

• Acute rheumatic fever 

• Post streptococcal glomerulonephritis 

• Abscess development 

• Acute otitis media 

Acute Otitis Media: ear infection

Signs and Symptoms: 

• Ear pain (tugging/holding/rubbing ear) recent onset < 48 hours 

• Drainage

• Hearing loss 

• Fever 

• Evaluation of tympanic membrane 

SEVERE Acute Otitis Media

• Moderate to severe otalgia (ear pain) 

• Otalgia > 48 hours 

• Temperature Fever > 39ºC

Antibiotics vs. Watch and Wait Approach for Acute Otitis Media

• Non-severe 

  • > 24 months old = watch and wait regardless of unilateral/bilateral 

  • < 24 months and younger…

    • Bilateral: antibiotic treatment 10 days

    • Unilateral: watch and wait

• Severe presentation = antibiotic treatment 10 days

If no improvement within 48-72 hours 

→ start antibiotics 

Acute Otitis Media Antibiotic Treatment 

→ first line: amoxicillin IF NO USE OF AMOX in past 30 days

• If amox use in past 30 days = amoxicillin-clavulanate

Options for pen allergy:

• PO: cefdinir, cefuroxime, cefpodoxime 

• IM/IV: Ceftriaxone

Acute Otitis Media Treatment Duration

1. Patients < 2 years old OR with severe symptoms = 10 days therapy 

2. Patients > 2 years old AND with mild/moderate symptoms = 7 day course 

   1. Watch and wait patients 

Classification of UTI

Uncomplicated UTI:

• Localized to bladder → signs and symptoms are localized to bladder

Complicated UTI:

• Infections extending beyond the bladder

  • Systemic signs/symptoms 

  • Pyelonephritis 

  • Catherizaton 

• Systemic Signs/Symptoms include:

  • Fever

  • Chills/Rigors/Hypotension 

  • Flank Pain

  • Costovertebral angle tenderness

UTI Pathogens…

1. Uncomplicated UTI/cystitis → E.coli

2. Complicated UTI → E.coli

Both: gram-negatives 

• Other Enterobacterales (KEEPs), Enterococcus species 

• Pseudomonas aeruginosa in critically ill patients 

Local vs Systemic UTI Sx…

Local Urinary Signs and Symptoms…

• Dysuria 

• Urinary frequency 

• Urgency 

• Suprapubic pain 

Systemic Urinary Signs and Symptoms…

• Fever

• Mental status changes (confusion, lethargy)

Urinalysis and UTI…

1. Elevated WBC in urine = UTI present 

   1. If absent of WBC = means NO uti 

   2. Not reliable for catheterized patients 

2. Leukocyte esterase 

   1. Surrogate for presence of WBC

3. Nitrites 

   1. Metabolic byproduct of gram-negative bacteria 

Urine Culture

used to guide antibiotic therapy 

→ MUST BE TAKEN BEFORE initiation of antibiotics 

• Identifies: pathogen, quantity, susceptibilities 

Who do we treat for asymptomatic bacteriuria?

1. Pregnany women: reduces the risk of pyelonephritis

2. Patients undergoing traumatic genitourinary procedures associated with mucosal bleeding

Uncomplicated UTI (Cystitis)...first line treatments

→ first line treatments: Nitrofurantoin, Fosfomycin

TMP/SMX (Bactrim) for uncomplicated UTIs…

• Duration = 3 days 

• Major DD with warfarin 

• Lower risk of resistant bacteria being resistant to other drug classes

Nitrofurantoin (Macrobid)

→ only used for uncomplicated UTIs

Duration = 5 days

• Do NOT use in Pyelonephritis 

• Do NOT use if CrCl < 30 mL/min

Fosfomycin (Monurol)

Duration = 1 dose ONLY

• Oral form not indicated for pyelonephritis  

Acute Cystitis IDSA guideline recs

(uncomplicated UTIs)

1. Nitrofurantoin 5 days 

2. Bactrim 3 days

3. Fosfomycin single dose

Other agents…

• B-lactam (oral) 5-7 duration if top three cannot be used

  • amox/clav, cefdinir, cephalexin

• Fluoroquinolones 3 day duration (last line)

  • Ciprofloxacin, levofloxacin

IDSA recs for complicated UTI: OUTPATIENT…

• Outpatient and FQ resistance < 10%

  • Ciprofloxacin for 7 days 

  • Levofloxacin for 5 days 

• Outpatient AND bactrim susceptible

  • Bactrim (TMP/SMX) for 14 days

IDSA recs for complicated UTI: INPATIENT…

• Empiric IV…7 day course

  • 3rd/4th gen Cephalosporin (ceftriaxone, cefepime)

  • pip/tazo

  • Carbapenem

  • Fluoroquinolone 

  • Aminoglycoside

Durations of Treatment for Complicated UTIs

• Levoflox - 5 days IV/PO

• Ciprofllox - 7 days IV/PO

• IV B-lactam - 7 days 

• Initial IV Tx - 7 days 

• TMP/SMX - 7 days IV/PO

Duration of Catheter Associated UTI TX…

• Prompt clinical response = 7 days 

• Delated clinical response = 10-14 days 

• NOT severely ill = Levo for 5 days

• Women < 65, no upper UTI symptoms, catheter has been removed = 3 days

Catheter Associated UTI Symptoms

systemic signs/symptoms 

• fever/rigors

• Altered mental status 

• Flank pain 

Remove catherer if possible and replace, need to culture urine from NEW catherer 

What is community acquired MRSA?

→ less resistant, produces panton-valentine leukocidin toxin

• TMP/SMX

• Doxycycline

• Clindamycin 

• vancomyin, linezolid

Impetigo

Purulent SSSI…Superficial skin infecion 

Minor skin abrasion, small cuts, insect bites

1. Non-bullous

2. Bullous (purulent)

Impetigo-Pathogens…

1. Bullous

   1. Staphlyococcus aureus 

   2. MAY need MRSA coverage 

2. Non-bullous

   1. S. aureus

   2. Streptococcus pyogenes 

   3. May be a mixed infection 

Treatment for Impetigo and Ecthyma

Empiric therapy should cover both MSSA and streptococci 

Agents: 

1. Cephalexin/Cefadroxil (PO)

   1. Covers MSSA and streptococci

2. Clindamycin (PO)

   1. Covers CA MRSA and Strep. Pyogenes

   2. Good option in penicillin allergic patients 

3. TMP/SMX (PO)

   1. Covers CA MRSA and Strep. Pyogenes

   2. Good option in penicillin allergic patients 

4. Dicloxacillin 

5. Doxycycleine 

6. Mupriocin (topical)

Furuncles and Carbuncles 

Infections of the hair follicle

• Small abscess forms in subcutaneous tissue

• Carbuncles are larger deeper versions of furuncles 

Common pathogens: S. aureus

Cutaneous Abscesses

collections of pus under the dermis 

→ pathogen cause: S. aureus

Treatment of Cutaneous Abscess: 

1. Incision and drainage alone is enough to treat most

2. Systemic treatment should be given if: 

   1. Patient is immunocompromised 

   2. Signs of systemic infection: fever/leukocytosis/tachycardia

   3. Multiple abscesses 

   4. Lack of response to incision and drainage

TREATMENT OF PURULENT SSSIs…

Pyomyositis

infection within a muscle 

• Staph. aureus is most common pathogen 

  • S. pyogenes

  • S. pneumoniae 

  • Gram-negative enteric bacteria

Coverage for Pyomyositis: empiric treatment can be broad

• MRSA coverage needed 

• Gram-negative and anaerobe coverage for:

  • HIV, Diabetes, Cancer, Rheumatological condition

Drainage of abscess is essential  

Cellulitis

occurs when bacteria invade deeper tissues in the skin 

Pathogens: Group A Strep (Strep. pyogenes) is the most common pathogen

Treatment- Cellulitis

need Streptoocci coverage for cellulitis 

TREATMENT DURATION: 5-10 DAYS

1. Cephalexin/cefadroxil (PO) - covers streptococci and MSSA

2. Clindamycin (IV/PO) - covers streptococci and MSSA and CA-MRSA

3. Cefazolin (IV) - covers streptococci and MSSA

4. Dicloxacillin (PO) - covers streptococci and MSSA

5. Amox/Clav

6. Penicillin 

Necrotizing Fasciitis…

Surgical intervention is key 

• Urgent surgery is needed 

Symptoms: 

• Severe systemic symptoms 

• Firm underlying tissues (wooden feel) 

• Discoloration 

• Pain OUT OF PROPORTION with injury 

Necrotizing Fasciitis Pathogens…

Monomicrobial infections

1. Streptococcus pyogenes - most common 

2. Staphylococcus aureus (CA-MRSA)

Necrotizing Fasciitis Empiric Treatment

Should be broad 

MRSA Coverage + Broad Gram-negative anaerobic coverage

• MRSA coverage: vancomycin, daptomycin OR linezolid 

• Gram: negative coverage

  • piperacillin/tazobactam 

  • Carbapenem 

  • Ceftriaxone plus metronidazole 

  • Fluoroquinolone plus metronidazole 

• Add Clindamycin (INHIBITS TOXIN PRODUCTION)

  • Do not have to add if LINEZOLID IS IN REGIMEN 

DO NOT GIVE VANCOMYCIN PLUS PIP/TAZO due to acute kidney injury…

bottom line: linezolid + pip/tazo for NF

NF Empiric Treatment Key:

Vancomycin + 

• Carbapenem

• Ceftriaxone plus metronidazole 

• Fluoroquinolone plus metronidazole 

  • AND Clindamycin 

Daptomycin +

• Pip/tazo 

• Carbapenem

• Ceftriaxone plus metronidazole 

• Fluoroquinolone plus metronidazole 

  • AND Clindamycin 

Linezolid + 

• Pip/tazo 

• Carbapenem

• Ceftriaxone plus metronidazole 

• Fluoroquinolone plus metronidazole

Fournier’s Gangrene

necrotizing infection involving sexual organs 

Pathogens:

• Staph. aureus 

• Pseudomonas aeruginosa

Empiric Treatment needs Pseudomonas coverage)

Bite Wounds…

1. Amox/Clavulanate is first line 

Summary of SSTIs

• Non-puruent SSTIs are typically caused by: group A strep (Strep. pyogenes)

• Purulent SSTIs: Staph. aureus (including MRSA)

• Bite wounds: amoxicillin/clavulante