Citrobacter freundii: Introduction, Morphology, Pathogenicity, Lab Diagnosis, Treatment, Prevention, and Keynotes

Citrobacter freundii: Introduction, Morphology, Pathogenicity, Lab Diagnosis, Treatment, Prevention, and Keynotes


Citrobacter freundii is a species of Gram-negative bacteria that belongs to the Enterobacteriaceae family. It is a facultative anaerobe, meaning it can survive in both aerobic (oxygen-rich) and anaerobic (oxygen-deprived) conditions. It is commonly found in the environment, including soil, water, and sewage, as well as in the human gastrointestinal tract as part of the normal flora.

While Citrobacter freundii is generally considered to be a harmless commensal bacterium, meaning it can coexist with humans without causing harm, it can also act as an opportunistic pathogen. In certain situations, it can cause infections, particularly in individuals with weakened immune systems or underlying health conditions.

Some common infections caused by C.  freundii include urinary tract infections (UTIs), respiratory tract infections, wound infections, and bloodstream infections. It can also cause infections in other parts of the body, such as the lungs, central nervous system, and abdominal cavity. The symptoms of these infections can vary depending on the site of infection but may include fever, pain, inflammation, and general signs of infection.

Citrobacter freundii, like other Enterobacteriaceae members, can develop antibiotic resistance. This can limit the effectiveness of treatment options and increase the difficulty of managing infections caused by this bacterium. It is important to perform antibiotic susceptibility testing to guide appropriate treatment decisions.


Citrobacter freundii has a characteristic morphology that helps distinguish it from other bacteria. Here are some key features of its morphology:

  1. Shape: It is a rod-shaped bacterium, also known as a bacillus. It appears as a straight or slightly curved rod under a microscope.
  2. Size: The average size of this bacterium cells ranges from 1 to 3 micrometers in length and about 0.5 to 1 micrometer in width.
  3. Gram Staining: It is classified as a Gram-negative bacterium. This means that it does not retain the crystal violet stain during the Gram staining process and instead takes up the counterstain (safranin) that makes it appear pink or red under a microscope.
  4. Motility: It is motile, possessing multiple peritrichous flagella. These flagella are evenly distributed around the cell and allow the bacterium to move actively in liquid environments. The motility of C. freundii can be observed using microscopy or specific motility tests.
  5. Colony Appearance: When grown on agar plates, Citrobacter freundii colonies typically appear as round, smooth, and slightly mucoid (viscous) colonies. The color can range from creamy white to light yellow or pinkish.


Citrobacter freundii can be both a commensal bacterium, residing harmlessly in the gastrointestinal tract, and an opportunistic pathogen capable of causing infections, particularly in individuals with compromised immune systems or underlying health conditions. The pathogenicity of Citrobacter freundii is attributed to various factors and mechanisms it possesses. Here are some key aspects of its pathogenicity:

  1. Adhesion and Colonization: It has surface structures, such as pili and fimbriae, that aid in adhesion to host tissues, allowing it to establish colonization and initiate infection. Adherence to host cells is a crucial step for pathogenic bacteria to resist host defenses and multiply.
  2. Biofilm Formation: It is capable of forming biofilms, which are complex communities of bacteria attached to surfaces. Biofilms provide protection against antibiotics and host immune responses, making infections more difficult to treat.
  3. Production of Toxins: It can produce various toxins and enzymes that contribute to its pathogenicity. For example, it can produce hemolysins, which can cause the destruction of red blood cells. It also produces cytotoxic factors that can damage host cells and contribute to tissue damage.
  4. Antibiotic Resistance: Citrobacter freundii, like many other bacteria, can develop antibiotic resistance. This resistance can limit the effectiveness of treatment options and complicate the management of infections caused by this bacterium.
  5. Opportunistic Infections: It  primarily causes opportunistic infections, meaning it takes advantage of weakened host defenses or compromised host tissues. It commonly infects immunocompromised individuals, such as those with underlying diseases, the elderly, or patients in healthcare settings.

Citrobacter freundii infections can manifest in various clinical presentations, including urinary tract infections (UTIs), respiratory tract infections, wound infections, bloodstream infections (bacteremia), and intra-abdominal infections. The severity of the infections can range from mild to severe, depending on the host’s immune status and the site of infection.


Laboratory Diagnosis

The laboratory diagnosis of Citrobacter freundii involves a combination of techniques to identify and confirm the presence of the bacterium in clinical samples. Here are some common methods used for laboratory diagnosis:

  1. Sample Collection: The first step is to collect appropriate clinical specimens, depending on the suspected site of infection. This can include urine for urinary tract infections, blood for bloodstream infections, wound swabs for wound infections, sputum or respiratory secretions for respiratory tract infections, etc.
  2. Microscopic Examination: A microscopic examination of Gram-stained smears from the clinical sample can provide initial information about the presence of Gram-negative bacilli and their morphology. Citrobacter freundii will appear as Gram-negative rods under the microscope.
  3. Culture: The next step is to isolate Citrobacter freundii from the clinical sample. The sample is streaked onto appropriate culture media, such as blood agar or MacConkey agar, and incubated at the optimal temperature (usually around 37°C) for 18 to 24 hours. It typically forms smooth, round colonies with a characteristic appearance (described earlier) on agar plates.
  4. Biochemical Tests: Several biochemical tests are performed to identify Citrobacter freundii and differentiate it from other bacteria. These tests include indole production, citrate utilization, urease production, hydrogen sulfide production, and various sugar fermentation tests. Citrobacter freundii exhibits specific patterns of positive and negative results in these tests, aiding in its identification.
  5. Antibiotic Susceptibility Testing: It is important to determine the antibiotic susceptibility profile of Citrobacter freundii to guide appropriate treatment. This is typically done using methods like the disc diffusion method or automated systems, where the bacterium is exposed to a panel of antibiotics, and the growth inhibition or resistance is measured.
  6. Molecular Techniques: In some cases, molecular techniques like polymerase chain reaction (PCR) may be used to confirm the presence of Citrobacter freundii and detect specific genes associated with its pathogenicity or antibiotic resistance.

It is important to perform these laboratory diagnostic procedures in a clinical laboratory setting following standard protocols and guidelines to ensure accurate and reliable results. The identified Citrobacter freundii strain should be correlated with the clinical presentation and patient’s symptoms for an appropriate diagnosis and treatment plan.


The treatment of Citrobacter freundii infections typically involves antimicrobial therapy. However, the choice of antibiotics depends on the site and severity of infection, as well as the antibiotic susceptibility profile of the specific C. freundii strain. It is important to perform antibiotic susceptibility testing to guide appropriate treatment decisions. Here are some commonly used antibiotics for Citrobacter freundii infections:

  1. Carbapenems: Carbapenems, such as meropenem or imipenem, are often considered the drugs of choice for severe Citrobacter freundii infections. They have broad-spectrum activity and are effective against many Gram-negative bacteria, including Citrobacter species.
  2. Third-Generation Cephalosporins: Ceftriaxone and ceftazidime are examples of third-generation cephalosporins that can be effective against Citrobacter freundii. However, resistance to these antibiotics has been reported, so susceptibility testing is important.
  3. Fluoroquinolones: Some fluoroquinolones, such as ciprofloxacin, may be effective against Citrobacter freundii infections. However, resistance to this class of antibiotics has also been observed, so susceptibility testing is crucial.
  4. Aminoglycosides: Aminoglycosides, like gentamicin, can have activity against Citrobacter freundii. They are often used in combination with other antibiotics for synergistic effects. Again, susceptibility testing should guide the use of aminoglycosides.
  5. Other Antibiotics: Depending on the susceptibility profile, other antibiotics, such as trimethoprim-sulfamethoxazole, piperacillin-tazobactam, or tigecycline, may be considered as treatment options.

It’s important to note that the choice of antibiotics should be based on local susceptibility patterns, individual patient factors, and the specific Citrobacter freundii strain’s resistance profile. In some cases, multiple antibiotic agents may be required, especially for severe or complicated infections. Additionally, appropriate management of the underlying condition and supportive care are essential components of treatment.


Preventing Citrobacter freundii infections involves general measures to reduce the risk of acquiring and spreading the bacterium. Here are some preventive measures that can be followed:

  1. Hand Hygiene: Practicing good hand hygiene is essential in preventing the transmission of Citrobacter freundii and other infectious agents. Wash your hands thoroughly with soap and water for at least 20 seconds, especially after using the restroom, before handling food, and after coming into contact with potentially contaminated surfaces or objects.
  2. Infection Control in Healthcare Settings: In healthcare facilities, strict infection control measures should be implemented to prevent the spread of Citrobacter freundii infections. This includes proper hand hygiene, adherence to isolation precautions (e.g., contact precautions for infected or colonized patients), and appropriate disinfection and sterilization of equipment and surfaces.
  3. Proper Food Handling and Preparation: It  can be present in contaminated food, so it’s important to follow safe food handling and preparation practices. This includes washing fruits and vegetables thoroughly, cooking food to appropriate temperatures, avoiding cross-contamination between raw and cooked foods, and storing food properly.
  4. Water and Environmental Safety: Ensuring clean and safe water sources is important to prevent infections. Proper treatment and disinfection of water supplies can help reduce the risk of contamination. In healthcare settings, maintaining clean and disinfected surfaces, equipment, and instruments is crucial.
  5. Infection Prevention in Long-Term Care Facilities: In long-term care facilities, such as nursing homes or assisted living centers, infection prevention measures should be implemented. This includes surveillance for infections, appropriate hand hygiene, isolation precautions when necessary, and staff education on infection control practices.
  6. Antibiotic Stewardship: Responsible and judicious use of antibiotics is crucial in preventing the development and spread of antibiotic-resistant strains of Citrobacter freundii. Antibiotics should only be prescribed when necessary, and healthcare professionals should follow local guidelines and recommendations for appropriate antibiotic use.

It’s important to note that Citrobacter freundii is primarily an opportunistic pathogen and does not typically cause infections in healthy individuals with intact immune systems. However, following these preventive measures can help minimize the risk of infection, especially in vulnerable populations or healthcare settings.


Here are some key points to remember about Citrobacter freundii:

  1. Citrobacter freundii is a Gram-negative bacterium belonging to the Enterobacteriaceae family.
  2. It is commonly found in the environment, including soil, water, and sewage, as well as in the human gastrointestinal tract as part of the normal flora.
  3. While usually a harmless commensal bacterium, it can act as an opportunistic pathogen and cause infections, particularly in individuals with weakened immune systems or underlying health conditions.
  4. C. freundii can cause a variety of infections, including urinary tract infections (UTIs), respiratory tract infections, wound infections, bloodstream infections, and infections in other body sites.
  5. Its pathogenicity is attributed to factors such as adhesion and colonization abilities, biofilm formation, toxin production, and antibiotic resistance.
  6. Laboratory diagnosis involves sample collection, microscopic examination, culture, biochemical tests, antibiotic susceptibility testing, and sometimes molecular techniques.
  7. Treatment of Citrobacter freundii infections typically involves antimicrobial therapy, with antibiotics such as carbapenems, third-generation cephalosporins, fluoroquinolones, or aminoglycosides, depending on susceptibility testing.
  8. Prevention of Citrobacter freundii infections includes practicing good hand hygiene, infection control measures in healthcare settings, proper food handling, water and environmental safety, and responsible antibiotic use.

Remember, specific cases may vary, and it’s important to consult with a healthcare professional for individualized diagnosis and treatment.

Further Readings

  1. Tindall, B. J., et al. (2017). The Valid publication of the names Citrobacter freundii, Citrobacter youngae, Citrobacter braakii, Citrobacter werkmanii, Citrobacter sedlakii, and Citrobacter pasteurii. International Journal of Systematic and Evolutionary Microbiology, 67(7), 2557-2561.
  2. Fernández-Cruz, A., et al. (2018). Citrobacter freundii: An Overview of Clinical Pathology and Laboratory Diagnosis. Journal of Clinical Medicine, 7(7), 262.
  3. Iosifidis, E., et al. (2020). Citrobacter freundii bloodstream infection in children: A systematic review. International Journal of Infectious Diseases, 97, 369-376.
  4. Stumpf, A. N., et al. (2020). Citrobacter freundii urinary tract infections: Review of the literature. JMM Case Reports, 7(10), 1-7.
  5. Jamil, M. A., et al. (2021). Citrobacter freundii: An emerging uropathogen with multidrug resistance in a tertiary care hospital, Karachi, Pakistan. Pakistan Journal of Medical Sciences, 37(3), 650-654.
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