Enterobacter Infections Workup

Updated: Jun 02, 2022
  • Author: Susan L Fraser, MD; Chief Editor: Michael Stuart Bronze, MD  more...
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Laboratory Studies

Microbiological studies

The most important test to document Enterobacter infections is culture.

Direct Gram staining of the specimen is also very useful because it allows rapid diagnosis of an infection caused by gram-negative bacilli and helps in the selection of antibiotics with known activity against most of these bacteria. The specimen submitted to the microbiology laboratory should represent the infectious process in evolution.

When the patient presents with signs of systemic inflammation (eg, fever, tachycardia, tachypnea) with or without shock (eg, hypotension, decreased urinary output), blood cultures are mandatory. Older and debilitated patients or patients receiving nonsteroidal anti-inflammatory drugs, steroids, or immunosuppressive therapy may be bacteremic in the absence of any sign of inflammation. In addition, hypothermia is a characteristic of particularly severe sepsis.

In the laboratory, growth of Enterobacter isolates is expected to be detectable in 24 hours or less. Enterobacter species grow rapidly on selective (ie, MacConkey) and nonselective (ie, sheep blood) agars. After growth in blood or on agar plates has been confirmed, the bacterial colonies are identified through various, usually automated, methods. When identification of a particular isolate is difficult, newer molecular (rRNA or PCR) methods can be used in certain laboratories. Mass spectrometry (MALDI-TOF) is also used in some laboratoties for organism identification, the detection of resistance genes and in outbreak investigations.  [29, 30]

Blood culture details

Two sets (with one aerobic and one anaerobic bottle in each set) should be obtained 20-30 minutes apart, from 2 different sites (if possible). If the patient has a central venous catheter, one set should be drawn through it. In the adult patient, 8-10 mL of blood should be collected in each bottle. Enterobacteriaceae ferment glucose and should thus grow in both bottles.

Growth in the presence and absence of oxygen is very important early information permitting a presumptive diagnosis of Enterobacteriaceae bacteremia because nonfermentative gram-negative bacilli (eg, Pseudomonas, Acinetobacter, Stenotrophomonas) cannot usually grow in the absence of oxygen.

Lower respiratory tract specimens

Routine Gram staining of sputum is mandatory for every specimen to evaluate the degree of contamination.

A good specimen should show few epithelial cells and many white cells unless the patient is severely neutropenic. In the case of pneumonia, the pathogen (ie, in this article, gram-negative bacilli) should be easily visualized with a high-power lens under oil immersion.

A poor-quality specimen should not be cultured because the identification of organisms that colonize the oropharynx is not helpful for the management of the infection and can cause confusion regarding the cause of the pneumonia. With a lower respiratory tract infection, a significant number of organisms (gram-negative bacilli) should be visible after direct staining. The threshold of optical detection of these bacteria is approximately 105 bacteria/mL. A positive culture result with a negative Gram stain result likely represents colonization rather than infection, at least in untreated patients.

Endotracheal secretions obtained from intubated patients via fluid from bronchoalveolar lavage or bronchoscopy are often contaminated with upper respiratory secretions, and the same caution should be applied in the interpretation of culture results as in the interpretation of sputum specimens. However, bronchoscopy specimens obtained through a protective shield are not contaminated or are only slightly contaminated. Specimens obtained by bypassing the oropharynx (eg, transthoracic biopsy, open lung biopsy) are sterile, and any bacterial growth should be considered significant.

All other specimens

Pus and joint, pleural, pericardial, peritoneal, and cerebrospinal fluids; bile; urine; and biopsy specimens of the skin and subcutaneous tissues, muscles, bone, and any other specimen should be promptly transported to the laboratory for rapid Gram staining and culture (or kept refrigerated for the shortest possible period).

Ophthalmologic specimens, such as those obtained from patients with endophthalmitis, are so small that the frequent recommendation is that they be injected into a blood culture bottle. This practice is also favored for potentially infected ascites fluid, as some evidence in the literature suggests that this method is more sensitive than direct plating on agar.

Intravenous and intra-arterial catheters should also be cultured if catheter sepsis is suggested. The catheter tip is rolled over the agar. Any growth of more than 15 colonies likely represents, according to studies by Maki et al, catheter infection rather than contamination. [31]

Drugs to include for antimicrobial susceptibility testing

For nonfastidious gram-negative bacilli, potential antimicrobial activity should be tested in vitro. The choice of specific antibiotics to be tested should reflect the availability of each drug in the pharmacy of each institution.

Penicillins should include ampicillin and at least one of the extended-spectrum penicillins (eg, carboxy, ureido, or acylaminopenicillin) such as ticarcillin, mezlocillin, or piperacillin. The addition of ticarcillin-clavulanic acid or piperacillin-tazobactam is optional.

Cephalosporins include a first-generation drug of this class of antibiotics, such as cefazolin, and a third-generation drug with and without Pseudomonas activity, such as ceftriaxone or ceftazidime, as well as the fourth-generation cephalosporin cefepime.

Include at least one carbapenem, usually imipenem or meropenem, in accordance with available pharmaceutical agents in the institution.

Include aminoglycosides, usually gentamicin and tobramycin. Amikacin may be tested primarily or when bacteria show resistance to gentamicin and/or tobramycin.

Include a quinolone, such as ciprofloxacin or levofloxacin.

Include TMP-SMZ.

Some laboratories routinely add aztreonam.

A cephamycin, such as cefoxitin, is a useful addition to screen for some specific beta-lactamases, such as those of class C (see Medical Care).

Other antibiotics that may be considered for testing include tigecycline, eravacycline, polymyxin B, colistin, cefidericol, plazomicin, meropenem-vaborbactam, imipenem-cilastatin-relebactam, and ceftazidime-avibactam, especially when particularly resistant organisms are identified.

Methods and results of antimicrobial susceptibility testing

Different methods of testing are available.

One of the most popular is the Kirby-Bauer disk method, which is simple, reliable, and inexpensive but does not quantify the results in terms of minimal inhibitory concentration (MIC).

MIC methods include antimicrobial agar dilution, usually regarded as the criterion standard, or broth (micro) dilution. Manual methods are more time-consuming than disk methods for measuring MIC. Automation for broth microdilution methods is available from different manufacturers.

The results of sensitivity testing are expressed in millimeters of growth inhibition with disk testing or in mcg/mL in MIC testing.

These results are compared to breakpoints issued by the Clinical and Laboratory Standards Institute (CLSI) in order to determine if an organism is susceptible, intermediately susceptible, or resistant to the tested antimicrobial agent. The CLSI may not have breakpoints for some Enterobacter species or for some antibiotics.

Unfortunately, these elegant methods are not flawless, and reports of falsely susceptible (less frequently, falsely resistant) bacteria are by no means rare in daily clinical practice.

Many resistance mechanisms are not detectable with these routine tests, and this is particularly true for the production of some beta-lactamases (see Medical Care).

A good knowledge of the major resistance mechanisms is important for the interpretation of the crude sensitivity results. Consultation with a senior microbiologist and/or an infectious disease specialist should be considered when the organism is resistant to several antibiotics or when additional testing to newer antibiotics is being considered.

Other laboratory studies

Complete blood cell count, creatinine level, and electrolyte evaluation are part of the minimal investigation required for the management of Enterobacter infections.

Fluid analysis (eg, cells and differential, proteins, glucose, and in some cases pH, lactate dehydrogenase, and amylase) is required for pleural, articular, pericardial, peritoneal, and cerebrospinal fluids.

Urine analysis is always indicated for UTIs.

Tests for liver enzymes, creatine kinase, sedimentation rate, C-reactive protein, bone marrow examination, and microscopic examination of stained biopsy specimens are indicated according to the type of infection involved.


Imaging Studies

Imaging studies are an important part of the investigation and management of Enterobacter infections. Specific studies are chosen based on the organ or systems involved in the infectious process.

For chest infections, serial chest radiography, chest ultrasonography, and CT scanning are useful when pulmonary abscesses, pleural or pericardial effusions, empyema, and/or mediastinitis is a concern.

Intra-abdominal infections may require CT scanning and ultrasonography.

Endocarditis and intravascular infections may require echocardiography, preferably transesophageal. In some situations, nuclear indium scanning may be helpful.

UTIs may require renal ultrasonography. Occasionally, CT scanning and pyelography (ie, intravenous or retrograde) are useful.

Central nervous system and ophthalmic infections may require CT scanning and/or MRI.

Bone and joint infections may require plain radiography. CT scanning and/or MRI studies are helpful in selected cases of soft-tissue infections, osteomyelitis, and septic arthritis. Nuclear medicine studies, bone and gallium scans in particular, are frequently a useful complement to plain radiography. Findings from indium scans or other types of marked white blood cell scans are somewhat more specific for the diagnosis of deep infections than gallium scan, although they may be less sensitive. See the image below.

Radiograph of an open right tibial fracture in a 2 Radiograph of an open right tibial fracture in a 21-year-old male marine who was wounded when an improvised explosive device detonated while he was on patrol in Iraq.

New technologies such as positron emission tomography (PET) scans may be indicated in very selective cases, particularly for differentiation of neoplasia and infection.



Procedures indicated for various Enterobacter infections may include the following:

  • Removal of central venous catheters within 72 hours of gram-negative bacilli infections (This has been shown to lower the risk of relapse.)

  • Surgical or percutaneous drainage of infected collections

  • Endoscopic retrograde cholangiopancreatography or magnetic resonance cholangiopancreatography (MRCP) for biliary obstruction

  • Lumbar puncture for evaluation of CNS infections

  • Softtissue or bone needle biopsy

  • Aspiration of joint fluid 


Histologic Findings

Along with signs of infection (leukocytic infiltration), histology should reveal the presence of bacterial rods.