Anaerobic infections: Etiology, Characteristics, Diagnosis

By Acharya Tankeshwar •  Updated: 04/22/22 •  4 min read

Anaerobic infections range from local abscesses to life-threatening infections. In most of the cases, our own normal flora (i.e. endogenous origin) are involved but in some exogenous sources play a role.

Anaerobic infections are normally polymicrobial; these may include obligate aerobes, facultative anaerobes or microaerophiles as concomitant microorganisms. In polymicrobial infections, these different types of bacteria can coexist: for example, facultative anaerobes can deplete the amount of oxygen present, making the environment conducive for strict anaerobe for growth.

The site of the infection may be non-sterile body parts or the sterile site, when the normal skin or mucous flora reach there via local trauma, surgery or viscus perforation (for example appendicitis if not diagnosed and treated timely, may lead to perforation of appendix thus giving enteric anaerobes access to the peritoneal cavity). Tissue necrosis and impaired clearance of a sterile site (chronic sinusitis, pneumonia) also predispose to anaerobic infections.  

Common locations of infections involving anaerobic bacteria (Image source: Koneman, Ref-1)

Common anaerobic infections are:

  1. Brain abscess
  2. Dental infections (dental abscesses, gingivitis, and periodontitis)
  3. Head and neck infections ( suppurative infections of retropharyngeal abscess, peritonsillar abscess, cervical lymphadenitis, deep neck abscesses, and parotitis)
  4. Abdominal abscesses,
  5. Aspiration pneumonia,
  6. Bite infections (animal/human),
  7. Brain abscesses,
  8. Lung abscesses, and
  9. Necrotizing infections of soft tissue.

Etiological agents of anaerobic infections

Name of the Organism Gram characteristics Anaerobic infection
Clostridium difficile Gram-Positive, spore-forming bacilli C. difficile  hospital-acquired (nosocomial) diarrhea
Clostridium perfringens Gram-Positive, spore-forming bacilli Gas gangrene (myonecrosis) or soft tissue infections
Clostridium botulinum Gram-Positive, spore-forming bacilli Infant botulism, food-borne botulism, and wound botulism.
Actinomyces israelii  Gram-positive, non-spore-forming bacilli Actinomycosis 
Propionibacterium acne Gram-positive, non-spore-forming bacilli Acne vulgaris
Bifidobacterium Gram-positive, non-spore-forming bacilli Usually non-pathogenic but it may cause chronic otitis media, abdominal abscesses, and peritonitis in children.
Lactobacillus Gram-positive, non-spore-forming bacilli Organism with low pathogenic potential but its involvement has been seen in abdominal abscesses, aspiration pneumonia, and bacteremia, particularly in neonates.
Peptococcus and Peptostreptococcus Gram-positive, cocci Chronic otitis media, chronic sinusitis, aspiration pneumonia, and pelvic inflammatory disease
Bacteroides fragilis Gram-negative, non-spore-forming bacilli Intra-abdominal abscesses, aspiration pneumonia, brain abscesses etc.
Fusobacterium spp Gram-negative, non-spore-forming bacilli Peritonsillar abscesses 
Campylobacter spp Gram-negative, non-spore-forming bacilli Acute gastroenteritis
Prevotella spp Gram-negative, non-spore-forming bacilli Peritonsillar abscesses, retropharyngeal abscesses as well as perineal or perianal infections such as a pilonidal abscess; mostly in children.
Veillonella spp Gram-negative, diplococci Abdominal abscesses and aspiration pneumonia in children

Common clues to anaerobic infections are:

Laboratory diagnosis

Culture and isolation of anaerobic organisms are not easy due to their fastidious nature. Proper collection and transport of the sample are of utmost importance to increase their recovery.

Commonly used methods for anaerobic bacterial cultures are:  

  1. McIntosh-Fildes jar
  2. GasPak
  3. Modified candle-jar system
  4. Anaerobic glove box
  5. Coy anaerobic chambers
  6. Pre-reduced anaerobically sterilized medium
  7. Sodium azide selective medium and
  8. Anoxomat

Presumptive identification of anaerobic bacteria can be done using macroscopic examination, examination of Gram-stained smears, cultural characteristics in differential agar media and results of spot tests.

Earlier, microbiologist used to rely on the phenotypic characteristics of the anaerobes for their identification but nowadays various commercial microsystems (RapID ANA II (Remel), the RapID CB-Plus (Remel), the BBL Crystal ANR ID (BD Microbiology Systems) and the RapID 32A (bioMérieux, Inc.) are available for the identification of anaerobes. Other methods of identification are; determination of metabolic products by Gas-Liquid Chromatography, use of molecular and mass spectrometric methods (e.g., MALDI-TOF) etc.


Treatment of anaerobic infections usually requires a combination of surgical (debridement of necrotic tissue or amputation of a limb) and medical measures.

Antibiotic therapy for anaerobic infections is different from that used for many infections involving aerobes or facultative anaerobes. Frequently used drugs for anaerobic infections are penicillin G, chloramphenicol, clindamycin, metronidazole, ampicillin/sulbactam, piperacillin/tazobactam, ticarcillin/clavulanate, meropenem, doripenem and vancomycin. Choice of antimicrobial agents varies with the bacterial species involved.

References and further reading

  1. Koneman’s Color Atlas And Textbook Of Diagnostic Microbiology (check the latest edition)
  2. Noor A, Khetarpal S. Anaerobic Infections.

Acharya Tankeshwar

Hello, thank you for visiting my blog. I am Tankeshwar Acharya. Blogging is my passion. As an asst. professor, I am teaching microbiology and immunology to medical and nursing students at PAHS, Nepal. I have been working as a microbiologist at Patan hospital for more than 10 years.

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4 responses to “Importance of Gram Stain in Anaerobic Bacteriology”

  1. Ivana says:

    Can you explain what did you mean when you said “positive gram stain and negative culture”? Thank you in advance.

    • Tankeshwar Acharya says:

      If any sample contains “anaerobic bacteria”, in Gram stainining you will be able to see them but those organisms wont grow in routine culture media (as they needs anerobic condition for growth), so the culture will be negative.

  2. Raj says:

    Why is the modification in Gram staining used for the anaerobes?

  3. devahi says:

    good explanation , i wish to know if we can do pour plate method for oral infections for isolating microorganisms form dental plaque materials can you explain the way of organisms to be gor from pour plate method to demonstrate to a UG

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