Citrobacter farmeri – Introduction, Morphology, Pathogenicity, Lab Diagnosis, Treatment, Prevention, and Keynotes

Citrobacter farmeri - Introduction, Morphology, Pathogenicity, Lab Diagnosis, Treatment, Prevention, and Keynotes


Citrobacter farmeri is a Gram-negative, facultatively anaerobic bacterium that belongs to the Enterobacteriaceae family. Here’s a brief introduction:

General Characteristics

  1. Morphology and Staining: Rod-shaped bacterium that is Gram-negative.
  2. Oxygen Requirements: Facultatively anaerobic, meaning it can grow in both oxygen-rich and oxygen-deprived environments.
  3. Culture Characteristics: They usually grow on standard bacteriological media and can produce colonies that may resemble those of other Enterobacteriaceae on agar plates.

Ecology and Pathogenicity

  1. Natural Habitat: Found in various environmental niches including water, soil, and the intestines of humans and animals.
  2. Clinical Importance: Some strains can be opportunistic pathogens, causing infections such as urinary tract infections, respiratory tract infections, septicemia, and meningitis, particularly in compromised hosts. It’s worth noting that while Citrobacter species can be pathogenic, C. farmeri is less frequently associated with human disease than other species like C. freundii.
  3. Antimicrobial Resistance: Resistance to various antibiotics has been observed in some Citrobacter species, making treatment of infections a challenge in some cases.

Biochemical Identification

Many Citrobacter species, including C. farmeri, can be differentiated from other Enterobacteriaceae based on their ability to utilize citrate as a sole carbon source (hence the name “Citro-“).

Genetic and Genomic Insights

Research into the genomes of Citrobacter species has provided insights into their pathogenicity, resistance mechanisms, and evolution. The genetic adaptability of Citrobacter spp. can contribute to their survival in different environments and their ability to cause disease in humans.


Citrobacter farmeri is a member of the Enterobacteriaceae family, which consists of several genera of Gram-negative bacteria. Here’s a description of the morphology of Citrobacter farmeri:

  1. Cell Shape: Citrobacter farmeri is a rod-shaped bacterium, also known as bacillus.
  2. Gram Staining: It is Gram-negative, meaning it does not retain the violet crystal violet stain but is counterstained with safranin, giving it a pink/red appearance under the microscope.
  3. Size: Typically, it is about 1-5 µm in length, though the exact size can vary.
  4. Motility: Many strains of Citrobacter, including C. farmeri, possess flagella and are motile. The flagella are peritrichous, meaning they are spread all over the surface of the cell.
  5. Arrangement: These bacteria are usually solitary but can sometimes be found in pairs (diplobacilli) or short chains.
  6. Capsule: Some strains can produce a polysaccharide capsule which can be visualized using special staining techniques like negative staining.
  7. Spore Formation: Citrobacter species, including C. farmeri, do not form endospores.


Citrobacter farmeri is one of several species within the genus Citrobacter. While Citrobacter species are known to be opportunistic pathogens, especially in compromised hosts, it’s important to note that not all strains or species are equally pathogenic, and C. farmeri is less frequently implicated in human diseases compared to some other species like C. freundii.

However, when Citrobacter species do cause infections, they can be responsible for a variety of clinical manifestations:

Urinary Tract Infections (UTIs)

Some Citrobacter species can cause UTIs, especially in patients with long-term catheters or other predisposing conditions.

Neonatal Meningitis

This is a serious infection that Citrobacter species, particularly C. koseri, are known to cause. Infants infected may suffer severe complications such as brain abscesses.

Respiratory Infections

In patients who are immunocompromised or have underlying lung conditions, Citrobacter species can cause pneumonia or other respiratory tract infections.


This is a bloodstream infection which can be caused by Citrobacter species, especially in patients with compromised immune systems or other underlying health conditions.

Wound Infections

Post-surgical or trauma-related wounds can sometimes become infected by Citrobacter species, particularly in hospital settings.

Other Infections

Depending on the host’s condition and the site of entry, Citrobacter can cause other infections like intra-abdominal infections, osteomyelitis, and skin infections.

The pathogenicity of Citrobacter species, including C. farmeri, is attributed to a combination of factors:


Like other Gram-negative bacteria, the lipopolysaccharide (LPS) present in their outer membrane can act as an endotoxin, triggering inflammatory responses


Some strains produce a polysaccharide capsule, which can protect the bacterium from phagocytosis and enhance its virulence.

Iron-acquisition systems

These systems allow the bacterium to sequester iron from the host, an essential nutrient for bacterial growth.

Antibiotic resistance

Over time, many Citrobacter strains have acquired resistance to commonly used antibiotics, complicating treatment and increasing their potential to cause prolonged infections.

Lab Diagnosis

Lab diagnosis of Citrobacter farmeri, as with many other bacterial species, involves a combination of culture techniques, morphological examination, and biochemical testing. Here are the general steps and methods used for the lab diagnosis of C. farmeri:

Sample Collection


  • The specimen is cultured on standard bacteriological media.
  • Blood Agar and MacConkey Agar are commonly used. On MacConkey agar, Citrobacter species typically produce lactose-fermenting colonies which appear pink or red.

Morphological Examination

  • Observe colony characteristics such as color, size, and shape.
  • Perform a Gram stain to identify its Gram-negative, rod-shaped morphology.

Biochemical Testing

  • A series of tests can be done to differentiate Citrobacter from other Enterobacteriaceae and to identify the specific species.
  • Triple Sugar Iron (TSI) Agar: Citrobacter species typically produce acid/acid (yellow/yellow) reactions, indicating glucose and lactose/sucrose fermentation.
  • Simmons’ Citrate Agar: As their name suggests, Citrobacter species utilize citrate as their sole carbon source and will turn the medium from green to blue.
  • Indole Production: C. farmeri is typically indole negative.
  • Urease Test: Some Citrobacter species can produce urease, but the results may vary for C. farmeri.
  • Methyl Red and Voges-Proskauer tests: Can also help in differentiation.

Antimicrobial Susceptibility Testing

  • Given the potential for antibiotic resistance, this test is crucial. It helps determine which antibiotics the bacteria are sensitive or resistant to, guiding appropriate treatment.

Molecular Methods

  • Techniques such as PCR (Polymerase Chain Reaction), ribotyping, and DNA sequencing can be used for precise identification and differentiation of Citrobacter species, especially in research or reference labs.
  • These methods are particularly useful when traditional biochemical tests are inconclusive or when rapid identification is needed.

Automated Systems

  • Many modern clinical microbiology labs use automated systems like the VITEK 2 (bioMérieux), MicroScan (Beckman Coulter), or BACTEC (BD) which can quickly identify bacteria and determine antibiotic susceptibility. These systems use a combination of biochemical and other tests and provide results often within hours.


Treatment for infections caused by Citrobacter farmeri typically involves antimicrobial agents. However, the choice of the specific agent is based on the type and site of the infection, as well as the results of antimicrobial susceptibility testing. Some Citrobacter species have shown resistance to various antibiotics, making it crucial to choose the appropriate agent based on laboratory findings. Here are general guidelines for the treatment:

Empirical Therapy

  • Before the results of susceptibility testing are available, a broad-spectrum antibiotic may be started, especially if the infection is severe.
  • Third-generation cephalosporins (like ceftriaxone or cefotaxime), fluoroquinolones (like ciprofloxacin), or aminoglycosides (like gentamicin) might be used empirically.

Targeted Therapy

  • Once the results of the susceptibility tests are available, the treatment can be adjusted accordingly.
  • If the strain is found to be resistant to the initially chosen antibiotic, the therapy needs to be switched to a more appropriate agent.

Extended-spectrum β-lactamase (ESBL) Producing Strains

  • Some Citrobacter strains produce ESBL, which renders them resistant to many commonly used antibiotics.
  • For infections caused by ESBL-producing strains, carbapenems (like imipenem, meropenem, or ertapenem) might be chosen.

Combination Therapy

In severe cases or when facing resistant strains, a combination of antibiotics might be used to ensure adequate coverage and synergistic bacterial killing.

Duration of Therapy

The length of treatment varies based on the type of infection. For instance, uncomplicated urinary tract infections might require a shorter duration than osteomyelitis or endocarditis.

Supportive Care

Patients might require supportive measures such as intravenous fluids, pain management, or respiratory support, depending on the severity and type of infection.


In some cases, such as abscess formation or severe wound infections, surgical intervention might be necessary alongside antibiotic therapy.


Preventing infections caused by Citrobacter farmeri, as with many other opportunistic pathogens, primarily involves measures to reduce transmission and bolster host defenses. Here are some general preventive measures:

Hand Hygiene

  • Proper hand hygiene is the cornerstone of preventing bacterial transmission. Wash hands regularly with soap and water for at least 20 seconds, especially after using the restroom, before eating, and after handling any materials that might be contaminated.
  • In healthcare settings, the use of alcohol-based hand sanitizers is also effective, especially when soap and water aren’t immediately available.

Environmental Cleaning

  • Regularly clean and disinfect surfaces, especially in hospital environments where Citrobacter species can be found. This is crucial for areas like intensive care units, neonatal units, and other high-risk zones.
  • Ensure that instruments, devices (like catheters), and other equipment are appropriately sterilized before use.

Safe Food and Water Practices

  • Ensure that water sources are clean and treated, especially in areas where waterborne infections are prevalent.
  • Cook food thoroughly, practice safe food handling, and store food appropriately.

Isolation Precautions in Healthcare Settings

  • Patients known to be infected with or colonized by Citrobacter (or other multi-drug resistant organisms) should be isolated to prevent the spread to other patients.
  • Healthcare workers should use personal protective equipment, such as gloves and gowns, when dealing with such patients.

Proper Use of Antibiotics

  • Overuse and misuse of antibiotics can lead to increased antibiotic resistance. Only use antibiotics when prescribed by a healthcare professional and always complete the full course, even if symptoms improve.
  • Healthcare professionals should ensure they’re prescribing antibiotics judiciously and based on susceptibility testing when possible.

Catheter Care

Since urinary tract infections are one potential manifestation of Citrobacter infections, ensure that catheters are appropriately placed, maintained, and removed as soon as they are no longer necessary.


While there isn’t a vaccine specifically for Citrobacter infections, ensuring that individuals are up-to-date with their vaccines can prevent co-infections and bolster overall health.


  • Healthcare workers should be trained about the risks of Citrobacter and other opportunistic pathogens, ensuring they’re equipped with the knowledge to manage and prevent infections.
  • Patients, particularly those in high-risk groups, should be educated about potential sources of infection and ways to protect themselves.


Here’s a concise list of keynotes on Citrobacter farmer-


Citrobacter farmeri is a Gram-negative, rod-shaped bacterium belonging to the Enterobacteriaceae family.


It’s found in various environments, including water, soil, and the intestines of humans and animals.


C. farmeri is an opportunistic pathogen, causing infections more frequently in compromised hosts. It can lead to conditions like urinary tract infections, septicemia, respiratory infections, and, in rare cases, neonatal meningitis.

Lab Diagnosis


  • Empirical therapy may involve broad-spectrum antibiotics, but final treatment should be based on antimicrobial susceptibility testing.
  • Carbapenems may be used for ESBL-producing strains.

Antibiotic Resistance

Some strains have shown resistance to multiple antibiotics, emphasizing the importance of susceptibility testing before treatment.


  • Emphasize hand hygiene and environmental cleaning.
  • In healthcare settings, implement isolation precautions and ensure proper catheter care.
  • Practice safe food and water consumption.


While it can be pathogenic, the majority of infections occur in individuals with predisposing factors. Proper identification and treatment are vital, given its potential for antibiotic resistance.

Further Readings

Textbooks on Medical Microbiology

  • “Medical Microbiology” by Patrick R. Murray, Ken S. Rosenthal, and Michael A. Pfaller.
  • “Clinical Microbiology Made Ridiculously Simple” by Mark Gladwin and Bill Trattler.

Journal Articles

  • PubMed is a great resource for searching scientific articles. You can find studies related to the pathogenesis, antibiotic resistance, clinical manifestations, and other aspects of Citrobacter farmeri.

Centers for Disease Control and Prevention (CDC)

  • The CDC often has resources related to specific pathogens, including guidelines for identification, treatment, and prevention.

World Health Organization (WHO)

  • WHO also has reports and guidelines on many pathogens, especially if they have caused outbreaks or are of particular concern globally.

Clinical and Laboratory Standards Institute (CLSI)

  • This organization provides guidelines on the laboratory identification and antibiotic susceptibility testing of pathogens, including Citrobacter spp.

Online Microbiology Resources

  • Websites like MicrobeOnline and The Microbiology Society provide valuable information about various pathogens, including their characteristics and significance.

Review Articles

  • Look for review articles in scientific journals related to Citrobacter spp. These provide comprehensive overviews on the current state of research and can be especially valuable if you’re interested in a specific aspect like antibiotic resistance or virulence mechanisms.
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