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Escherichia Coli Infections Workup

  • Author: Tarun Madappa, MD, MPH; Chief Editor: Michael Stuart Bronze, MD  more...
Updated: Jan 11, 2016

Laboratory Studies

All patients with suspected E coli infection should undergo routine CBC count with differential to evaluate for leukocytosis or a left shift.

Gram stain results determine if the organism is gram-negative, but findings do not distinguish among the other aerobic gram-negative bacilli that cause similar infectious diseases.

E coli is a gram-negative bacillus that grows well on commonly used media. It is lactose-fermenting and beta-hemolytic on blood agar. Most E coli strains are nonpigmented. The image below shows Escherichia coli on Gram staining.

Escherichia coli on Gram stain. Gram-negative bac Escherichia coli on Gram stain. Gram-negative bacilli.

In the image below Escherichia coli can be seen growing on MacConkey agar.

Escherichia coli culture on MacConkey agar. Escherichia coli culture on MacConkey agar.

Definitive diagnosis is based on the isolation of the organism in the microbiology laboratory from clinical specimens. Specimens may be blood, urine, sputum, or other fluids such as cerebrospinal, biliary, abscess, and peritoneal.

Recovery of the organism in contaminated sites, such as sputum and wounds, must be analyzed in the context of the patient's clinical state to determine if it represents colonization or infection. Recovery from sterile sites, such as the CSF, should be considered diagnostic of infection.

Lumbar puncture and a CSF culture positive for E coli establish the diagnosis of acute E coli meningitis; however, lumbar puncture is not justified in all babies presenting with sepsis. Indications for lumbar puncture include positive blood culture results, abnormal neurological signs, and detection of bacterial antigens in the urine.

Patients with pneumonia should undergo blood cultures and sputum Gram stain and culture. The results of a Gram stain of the sputum help to differentiate a good specimen (many PMN leukocytes, few squamous epithelial cells) from a bad specimen (few PMN leukocytes, many squamous epithelial cells). In addition, obtain the sputum culture before antibiotic therapy is initiated.

In enteric infections, the causative organism is suggested based on the clinical presentation and the characteristic of the patient's stool. Enterotoxigenic E coli (ETEC), enteropathogenic E coli (EPEC), enteroaggregative E coli (EAggEC), and enteroadherent E coli (EAEC) infections produce watery stools without inflammatory cells. Enteroinvasive E coli (EIEC) infection produces dysentery-type stools, and enterohemorrhagic E coli (EHEC) infection produces hemorrhagic-type stools.

In urinary tract infections, a urine dipstick test may be performed to rapidly determine if the patient has pyuria or bacteriuria based on the detection of leukocyte esterase and nitrites, respectively. Definitive diagnosis is based on urine culture results. Collect the specimen from a midstream clean void or from the catheter in patients with an indwelling Foley catheter. Colonization must be differentiated from infection based on urinalysis results. In cases of infection, pyuria is usually present.


Imaging Studies

In pneumonia, chest radiography or CT scanning is indicated.

In cholecystitis/cholangitis, ultrasonography or CT scanning of the RUQ is indicated.

In intra-abdominal abscess, abdominal and pelvic CT scanning is indicated; abscesses may be missed on sonograms.

In UTI, ultrasonography or CT scanning may be performed to help evaluate the kidneys and to look for any other source of abscess, stones, or obstruction.


Other Tests

E coli strains that cause diarrhea can be differentiated based on results from tests that are not widely used, such as DNA probes and polymerase chain reaction.

EPEC can be identified based on findings from serotyping, assays of adherence, and DNA probes. These tests are difficult to perform and not available widely. Also, results are difficult to interpret.

EIEC can be identified based on results from animal pathogenicity tests such as the Sereny test.

EHEC can be identified by looking for the major serotype involved, 0157:H7.

EHEC strains are cultured in a sorbitol MacConkey agar. Strains that are sorbitol-negative are then serotyped with 0157:H7 antisera.

EAEC and EAggEC are identified based on their adherence pattern on tissue culture cells. Serotyping is not useful.



The following procedures may be indicated:

  • Meningitis - Lumbar puncture with CSF Gram stain/culture
  • Pneumonia - Bronchoscopy, blood and urine cultures
  • Cholecystitis/cholangitis - Decompression of biliary system through endoscopic drainage, sphincterotomy for stone extraction, or endoscopic cholangiography
  • Intra-abdominal abscess - Aspiration and drainage
  • UTI - In cases of ureteral obstruction, placement of stent or stone extraction
  • Prostatic hypertrophy - Transurethral prostatectomy or transurethral resection of the prostate (TURP)
  • Prostatic abscess - Drainage
Contributor Information and Disclosures

Tarun Madappa, MD, MPH Attending Physician, Department of Pulmonary and Critical Care Medicine, Christus Spohn-Shoreline Hospital

Tarun Madappa, MD, MPH is a member of the following medical societies: American College of Chest Physicians, American Thoracic Society

Disclosure: Nothing to disclose.


Chi Hiong U Go, MD Assistant Professor, Department of Internal Medicine, Texas Tech University Health Science Center at Odessa

Chi Hiong U Go, MD is a member of the following medical societies: American College of Physicians-American Society of Internal Medicine

Disclosure: Nothing to disclose.

Specialty Editor Board

Francisco Talavera, PharmD, PhD Adjunct Assistant Professor, University of Nebraska Medical Center College of Pharmacy; Editor-in-Chief, Medscape Drug Reference

Disclosure: Received salary from Medscape for employment. for: Medscape.

Charles V Sanders, MD Edgar Hull Professor and Chairman, Department of Internal Medicine, Professor of Microbiology, Immunology and Parasitology, Louisiana State University School of Medicine at New Orleans; Medical Director, Medicine Hospital Center, Charity Hospital and Medical Center of Louisiana at New Orleans; Consulting Staff, Ochsner Medical Center

Charles V Sanders, MD is a member of the following medical societies: American College of Physicians, Alliance for the Prudent Use of Antibiotics, The Foundation for AIDS Research, Southern Society for Clinical Investigation, Southwestern Association of Clinical Microbiology, Association of Professors of Medicine, Association for Professionals in Infection Control and Epidemiology, American Clinical and Climatological Association, Infectious Disease Society for Obstetrics and Gynecology, Orleans Parish Medical Society, Southeastern Clinical Club, American Association for the Advancement of Science, Alpha Omega Alpha, American Association of University Professors, American Association for Physician Leadership, American Federation for Medical Research, American Geriatrics Society, American Lung Association, American Medical Association, American Society for Microbiology, American Thoracic Society, American Venereal Disease Association, Association of American Medical Colleges, Association of American Physicians, Infectious Diseases Society of America, Louisiana State Medical Society, Royal Society of Medicine, Sigma Xi, Society of General Internal Medicine, Southern Medical Association

Disclosure: Received royalty from Baxter International for other.

Chief Editor

Michael Stuart Bronze, MD David Ross Boyd Professor and Chairman, Department of Medicine, Stewart G Wolf Endowed Chair in Internal Medicine, Department of Medicine, University of Oklahoma Health Science Center; Master of the American College of Physicians; Fellow, Infectious Diseases Society of America

Michael Stuart Bronze, MD is a member of the following medical societies: Alpha Omega Alpha, American Medical Association, Oklahoma State Medical Association, Southern Society for Clinical Investigation, Association of Professors of Medicine, American College of Physicians, Infectious Diseases Society of America

Disclosure: Nothing to disclose.

Additional Contributors

Larry I Lutwick, MD Professor of Medicine, State University of New York Downstate Medical School; Director, Infectious Diseases, Veterans Affairs New York Harbor Health Care System, Brooklyn Campus

Larry I Lutwick, MD is a member of the following medical societies: American College of Physicians, Infectious Diseases Society of America

Disclosure: Nothing to disclose.


The authors and editors of Medscape Reference gratefully acknowledge the contributions of previous author Eleftherios Mylonakis, MD, to the development and writing of this article.

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Escherichia coli liver abscess.
Escherichia coli right pyelonephritis.
Escherichia coli on Gram stain. Gram-negative bacilli.
Escherichia coli culture on MacConkey agar.
Table. Differential Diagnoses of E coli Infection
Organism Ind* Urease Motility Glu Ferm† Lact Ferm‡ Sucr Ferm§ Malt Ferm|| Esc Hyd¶ Hyd Sulf TSI# Oxidase Orn Dec** Lys Dec††
E coli + - + + + +/- + - - - +/- +
Klebsiella pneumoniae - +/- - + + + + + - - - +
P mirabilis - + + + - - - - + - + -
Proteus vulgaris + + + + - + + +/- + - - -
Pseudomonas aeruginosa - +/- + +


- - - - - + - -
Enterobacter aerogenes - - + + + + + + - - + +
Enterobacter cloacae - - + + + + + - - - + -
Salmonella typhi - - + + - - + - + - - +
Citrobacter freundii +/- - + + + + + - +/- - - -
Serratia marcescens - +/- + + - + + + - - + +

†Glucose fermentation

‡Lactose fermentation

§Sucrose fermentation

||Maltose fermentation

¶Esculin hydrolysis

#Hydrogen sulfite on TSI

**Ornithine decarboxylase

††Lysine decarboxylase


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