What are the common causative organisms for infections by body system?

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Common Causative Organisms for Infections by Body System

The most common causative organisms for infections vary significantly by body system, with gram-positive cocci, gram-negative bacilli, and anaerobes predominating in different anatomical locations. Understanding these patterns is essential for appropriate empiric antibiotic selection while awaiting culture results.

Respiratory Tract Infections

Upper Respiratory Tract

  • Pharyngitis/Tonsillitis: Streptococcus pyogenes (Group A Streptococcus) is the predominant bacterial pathogen 1
  • Otitis Media: Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Staphylococcus aureus 2, 1
  • Sinusitis: Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis 1

Lower Respiratory Tract

  • Community-acquired pneumonia: Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis 3, 4
  • Hospital-acquired pneumonia: Pseudomonas aeruginosa, Staphylococcus aureus, and Enterobacteriaceae 4
  • Lung abscess: Anaerobes (including Bacteroides fragilis), Pseudomonas aeruginosa, Staphylococcus aureus 5

Skin and Soft Tissue Infections

  • Cellulitis/Impetigo: Staphylococcus aureus, Streptococcus pyogenes 3, 2
  • Necrotizing fasciitis:
    • Monomicrobial: Group A Streptococcus, Staphylococcus aureus (including MRSA), Vibrio vulnificus, Aeromonas hydrophila 6
    • Polymicrobial: Mixed aerobic-anaerobic bacteria (often originating from gastrointestinal or genitourinary flora) 6
  • Diabetic foot infections: Polymicrobial with gram-positive cocci (especially staphylococci) most common; gram-negative bacilli and anaerobes in chronic infections 6

Urinary Tract Infections

  • Uncomplicated UTI/Cystitis: Escherichia coli (75% of cases), Staphylococcus saprophyticus, Klebsiella pneumoniae 7, 2
  • Complicated UTI: Enterococcus species, Pseudomonas species, Proteus mirabilis, Klebsiella pneumoniae 7, 4
  • Chronic cystitis: Escherichia coli, Enterococcus faecalis, Proteus mirabilis (associated with stone formation), Klebsiella pneumoniae 7

Central Nervous System Infections

  • Bacterial meningitis: Streptococcus pneumoniae, Neisseria meningitidis, Haemophilus influenzae, Listeria monocytogenes (in elderly and immunocompromised) 3
  • Brain abscess: Streptococci, staphylococci, anaerobes, gram-negative bacilli 6
  • CNS shunt infections: Coagulase-negative staphylococci, Staphylococcus aureus, gram-negative bacilli 6

Intra-abdominal Infections

  • Peritonitis/Intra-abdominal abscess: Escherichia coli, Klebsiella pneumoniae, Bacteroides fragilis, Clostridium species, Peptostreptococcus species 6, 3
  • Biliary infections: Gram-negative aerobic and facultative organisms (Escherichia coli, Klebsiella), enterococci 6
  • Liver abscess: Escherichia coli, Klebsiella pneumoniae, anaerobes 6

Bloodstream Infections (Septicemia)

  • Community-acquired: Escherichia coli, Streptococcus pneumoniae, Staphylococcus aureus (account for ~60% of cases) 8
  • Hospital-acquired: Escherichia coli, Staphylococcus aureus, coagulase-negative staphylococci, other Enterobacteriaceae, Pseudomonas aeruginosa 8
  • Catheter-related: Coagulase-negative staphylococci, Staphylococcus aureus, Candida species 4, 8

Ocular Infections

  • Keratitis:
    • Contact lens-associated: Pseudomonas aeruginosa, Fusarium, Acanthamoeba 6
    • Post-surgical: Coagulase-negative staphylococci, Propionibacterium acnes 6
    • Post-traumatic: Environmental gram-negative rods, Nocardia, fungi, environmental mycobacteria 6
  • Endophthalmitis:
    • Post-operative: Gram-positive organisms (coagulase-negative staphylococci predominating) 6
    • Endogenous: Candida albicans, Aspergillus, Staphylococcus aureus, Streptococcus pneumoniae, Klebsiella pneumoniae, Pseudomonas aeruginosa 6

Cardiovascular Infections

  • Infective endocarditis:
    • Native valve: Streptococcus species (50%), Staphylococcus species (36%), HACEK organisms (Haemophilus, Actinobacillus, Cardiobacterium, Eikenella, Kingella) 6, 9
    • Prosthetic valve: Coagulase-negative staphylococci, Staphylococcus aureus, enterococci, gram-negative bacilli, fungi 6

Special Considerations in Immunocompromised Hosts

Neutropenic Patients

  • Early infections: Coagulase-negative staphylococci, Staphylococcus aureus, viridans group streptococci, enterococci, Escherichia coli, Klebsiella, Enterobacter, Pseudomonas aeruginosa 6
  • Later infections: Candida species, Aspergillus species, resistant gram-negative bacilli 6

HIV/AIDS Patients

  • Common opportunistic pathogens: Pneumocystis jirovecii, Candida albicans, Cryptococcus neoformans, Cryptosporidium, Toxoplasma gondii, mycobacteria 10

Clinical Pearls and Pitfalls

  • Polymicrobial infections are common in diabetic foot infections, intra-abdominal infections, and necrotizing soft tissue infections 6
  • Antibiotic resistance is increasing in many common pathogens, particularly MRSA, penicillin-resistant pneumococci, and ESBL-producing gram-negative bacilli 7, 4
  • Structural abnormalities (e.g., urinary stones, obstructions) can lead to persistent infections with organisms like Proteus that produce urease 7
  • Empiric therapy should be guided by the most likely pathogens for a specific body site while considering local resistance patterns 3, 2
  • In neutropenic patients, the signs and symptoms of infection may be muted despite serious infection, with fever often being the only early sign 6

Understanding these patterns helps guide appropriate empiric antimicrobial therapy while awaiting culture results, potentially reducing morbidity and mortality from infectious diseases.

References

1
Research

Microbiology of bacterial respiratory infections.

The Pediatric infectious disease journal, 1998

6
Guideline

Guideline Directed Topic Overview

Dr.Oracle Medical Advisory Board & Editors, 2025

7
Guideline

Chronic Cystitis

Praxis Medical Insights: Practical Summaries of Clinical Guidelines, 2025

8
Research

The causative organisms of septicaemia and their epidemiology.

The Journal of antimicrobial chemotherapy, 1990

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Professional Medical Disclaimer

This information is intended for healthcare professionals. Any medical decision-making should rely on clinical judgment and independently verified information. The content provided herein does not replace professional discretion and should be considered supplementary to established clinical guidelines. Healthcare providers should verify all information against primary literature and current practice standards before application in patient care. Dr.Oracle assumes no liability for clinical decisions based on this content.

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