Antibiotics are pharmaceuticals used in the treatment and prevention of bacterial infections. There exist many types, with varying degrees of antimicrobial coverage. Given their essential role in health care, it is imperative that clinicians are well-versed in the appropriate selection and duration of specific antibiotics for specific infections, as failure to do so can result in increasing antibiotic resistance and multi-drug resistant organisms. On this page, this broad topic will be broken down by relevant body systems, with common infectious organisms, and appropriate respective antibiotic choices.

Respiratory Edit

Pneumonia (see separate Pneumonia page for further details) Edit

Common pathogens Edit

  1. Streptococcus pneumoniae
  2. Klebsiella pneumoniae
  3. Haemophilus influenzae
  4. Legionella pneumophila
  5. Mycoplasma pneumoniae
  6. Mycobacterium tuberculosis*
  7. Mycobacterium avium complex*
  8. Pneumocystis jirovecii*

Antibiotic regime Edit

A general approach to all community acquired pneumonias (CAP) should, at minimum, include coverage for atypicals.

Generally, in an uncomplicated CAP case in a patient with NO risk factors (healthy, no lung disease, not a smoker):

First line choices:


  • azithomycin 500mg loading dose on day 1, then 250mg po daily for subsequent days
  • clarithromycin 500mg po bid


  • Doxycycline 100mg po bid


  • Amoxicillin 500mg po tid (or 90mg/kg split tid or bid) - preferred first line agent in pediatric population due to liquid formulation.

Second line choices (or for pneumonia refractory to above treatment):


  • Cefuroxime 500mg po bid (in combination with a macrolide or doxycycline to cover atypicals)
  • Amoxicillin-clavulanate 500/125mg po bid*


  • Moxifloxacin 400mg po daily
  • Levofloxacin 750mg po daily

Duration: a 5 day course is generally sufficient. If no resolution, or worsening of symptoms by 5 days, consider switching agents.

Hospital acquired pneumonia

First line regimes:

  • Ceftriaxone 1g IV + Azithromycin 500mg IV daily
  • Levofloxavin 750mg IV/PO daily
  • Piperacillin-Tazobactam 3.375g IV daily*
  • Imipenem-cilastin 500mg IV q12h

* Pip/Tazo will cover Pseudomonas, and should be considered in patients who develop a pneumonia after recently having been on a ventilator. Another option for pseudomonal coverage in lower respiratory tract infections is ceftazidime 1-2g IV q8h. Pseudomonal coverage will be discussed in further detail below.

Skin and bone Edit

Cellulitis, osteomyelitis, septic arthritis Edit

Common organisms:

  1. Staphylococcal species
  2. Streptococcal species
  3. Methicillin-resistant staphylococcus aureus
  4. Anaerobic species, eg Clostridium, Bacteroides, Peptostreptoccus (in necrotic tissue)

Antibiotic regime Edit

As noted above, skin and bone infections often involve similar organisms (most typically, skin flora).

In an uncomplicated cellulitis, a course of a first generation cephalosporin is usually sufficient.

First line:

  • Cephalexin (Keflex) 500mg po QID x 7-10 days*

Second line:

  • Clindamycin 300mg po QID
  • Cloxacillin 500mg po QID

*Duration will depend on responsiveness of the infected area to treatment, and should last until all evidence of infection is gone.

Severe Cellulitis:

  • Cefazolin (Ancef) 1-2g IV q8h
  • Ceftriaxone 1g IV 24h
  • Clindamycin 600mg IV q8h


  • Cefazolin 2g IV q8h


Community acquired:

  • Clindamycin 400mg po QID
  • Septra DS 2 tabs po BID

Hospital acquired/severe infections:

  • Vancomycin 1-1.5g IV q12h
  • Linezolid* 600mg IV q12h
  • Daptomycin*
  • Tigecycline*

*Recommend consultation with ID specialist

Animal Bites

  • Amoxicillin-clavulanate 500-875mg po TID for 7-14 days

Second line:

  • Doxycycline 100mg po BID first day, then 100mg po daily for 7-14 days
  • Ceftriaxone 1-2g IM/IV q24h x 7-14 days

Lyme Disease

First line:

  • Amoxicillin 500mg po TID x 14-21 days
  • Doxycycline 100mg po BID x 14-21 days

Second line:

  • Cefuroxime 500mg po BID x 14-21 days

Third line:

  • Ceftriaxone IV 2g q24h x 14-21 days

Gastrointestinal Edit

Intra-abdominal infections Edit

Any intra-abdominal infection should include broad spectrum coverage for Gram negative bacteria as well as anaerobes. A fluoroquinolone or a third generation cephalosporin in combination with metronidazole is usually a fairly good starting regime.

  • Ceftriaxone 1g IV q24h + Metronidazole 500mg IV/PO q8h
  • Ciprofloxacin 400mg IV/500mg PO q8h + Metronidazole 500mg IV/PO q8h

Clostridium difficile Edit

  • Metronidazole 500mg PO q8h
  • Vancomycin 125mg po bid (to start, and uptitrate dose/frequency as necessary).

Helicobacter pylori Edit

Combination therapy with a PPI BID

  • Amoxicillin 1000mg po BID + Clarithromycin 500mg po BID x 1 week
  • Metronidazole 500mg po BID + Clarithromycin 500mg po BID x 1 week
  • (Second line)
    • PPI BID + Metronidazole* 500mg po BID + Amoxicillin 1000mg po BID
    • *Levofloxacin 500mg po daily can be substituted for metronidazole in treatment-refractory H. pylori

Genitourinary Edit

Common organisms infecting the genitourinary tract Edit

  • Escherida coli
  • Klebsiella species
  • Enterococcus species
  • Proteus species
  • Serratia species
  • Pseudomonas species
  • Actinobacter species
  • Citrobacter species
  • Enterobacter species
  • Staph saprophyticus

Simple cystitis (Also see UTI page) Edit

First line options

  • Septra DS 1 tab po bid x 3 days
  • Macrobid (Nitrofurantoin) 100mg po bid x 5 days

Second line options

  • Amoxicillin 500mg po TID x 7 days
  • Ciprofloxacin 250mg po BID x 3 days (should be reserved, if possible, for Pseudomonas)

Third line options

  • Cephalexin (Keflex) 250-500mg po QID x 7 days
  • Levofloxacin 250mg po daily x 3 days

Recurrent cystitis should have the duration of treatment extended to 7-10 days.

Complicated UTI or Pyelonephritis Edit

First line options for mild-moderate infection

  • Septra 1 tab po bid x 7-14 days (depending on severity of symptoms)\
  • Macrobid 100mg po bid x 7-14 days
  • Ciprofloxacin 500mg po bid x 7-14 days
  • Levofloxacin 500mg po daily x 10 days or 750mg po x 5 days

Second line options for mild-moderate symptoms

  • Amoxicillin/clavulanate 500mg po TID or 875mg po BID x 7-14 days

First line therapy options for severe infection (parenteral therapy)

  • Ampicillin 1g q6h IV + Gentamicin 4-7mg/kg q24h IV
  • Ampicillin 1g q6h IV + Tobramycin 4-7mg/kg q24h IV

Second line therapy options for severe infection

  • Ceftriaxone 1-2g IV q24h
  • Ciprofloxacin 200-400mg IV q12h
  • Levofloxacin 250mg IV q24h
  • PIp/Tazo 3.375g IV q6h

Third line

  • Meropenem 500-1000mg IV q8h
  • Ceftazidime 1-2g IV q8h

Duration of treatment should be 10-14 days

Prostatitis Edit

Acute Edit

  • Septra DS 1 tab po bid x 4-6 weeks
  • Ciprofloxacin 500mg po bid x 4-6 weeks
  • Levofloxacin 500mg po daily x 4-6 weeks

Chronic Edit

Chronic prostatitis is a fairly uncommon and very difficult disorder to diagnose and treat. Generally, first-line agents are fluoroquinolones, such as ciprofloxacin 500mg po bid or levofloxacin 500mg po daily, for a duration of 4-6 weeks. For patients who cannot tolerate fluoroquinolones (prolonged QTc, myasthegia gravis, etc), Septra DS 1 tab po bid is a reasonable alternative, also to be maintained for 4-6 weeks.

CNS Edit

Bacterial meningitis Edit

  • Ceftriaxone 2g IV q12h x 48h then q24h + Vancomycin 1g IV q12h + Ampicillin 2g IV q6h for a total of 2 weeks