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Test ID: EPFRP    
Bacterial Enteric Pathogens, Molecular Detection, PCR, Feces

Useful For Suggests clinical disorders or settings where the test may be helpful

Rapid, sensitive, and specific identification of the common bacterial causes of diarrhea; Campylobacter jejuni/coli, Salmonella species, Shigella species, enteroinvasive Escherichia coli, shiga toxin-producing Escherichia coli, and Yersinia species

Clinical Information Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test

Despite advances in water treatment, food safety, and sanitary conditions, acute diarrheal disease remains a leading cause of morbidity and mortality worldwide. Most bacterial enteric infections in the United States originate within the food supply chain. According to the CDC, 43% of laboratory-confirmed bacterial enteric infections in the United States are caused by Salmonella species, followed by Campylobacter species (33%), Shigella species (17%), shiga toxin-producing Escherichia coli (4.1%), and Yersinia species (0.9%).(1)


Although Salmonella, Campylobacter, Shigella, Yersinia species, and Escherichia coli O157:H7 are easily cultivated on standard selective and differential bacteriologic media, isolation and final identification are time consuming, delaying diagnosis for several days and putting patients at risk for untreated infection and spread of infection to others. For example, the time to final identification from stool culture for Salmonella, Shigella, and Yersinia species ranges from 3 to 5 days, and for Campylobacter species it ranges from 2 to 4 days. Furthermore, non-O157:H7 shiga toxin-producing Escherichia coli are not readily isolated in the clinical laboratory.


PCR detection of the most common agents of bacterial enteric infections directly from stool specimens is sensitive, specific, and provides same-day results, eliminating the need for culture in most cases. In addition, PCR provides physicians with a new tool in their care of patients and public health personnel in their investigation and control of the spread of these diseases.

Reference Values Describes reference intervals and additional information for interpretation of test results. May include intervals based on age and sex when appropriate. Intervals are Mayo-derived, unless otherwise designated. If an interpretive report is provided, the reference value field will state this.

Not applicable

Interpretation Provides information to assist in interpretation of the test results

A positive PCR result for any 1 of the specific assays (Campylobacter jejuni/coli, Salmonella species, Shigella species/enteroinvasive Escherichia coli, shiga toxin-producing Escherichia coli, or Yersinia species) indicates the presence of the respective organism in the specimen.


A negative result indicates the absence of detectable Salmonella species, Shigella species/enteroinvasive Escherichia coli, pathogenic Yersinia species, Campylobacter jejuni/coli and Shiga toxin DNA in the specimen, but does not rule out infection with these or other enteric pathogens. False-negative results may occur due to inhibition of PCR (known inhibition rate of <1%), sequence variability underlying the primers and/or probes or the presence of enteric pathogens in quantities less than the limit of detection of the assay or not targeted by the assays (eg, Vibrio cholerae).

Cautions Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances

Interfering substances in stool may affect the accuracy of this assay; results should always be interpreted in conjunction with clinical and epidemiological findings.


This test does not detect Aeromonas species, Vibrio species, Plesiomonas shigelloides, enterotoxigenic Escherichia coli, or other pathogens not specifically listed.

Supportive Data

Performance of the Campylobacter jejuni/coli, Salmonella species, Shigella species/enteroinvasive Escherichia coli, and Yersinia species PCR assays was evaluated with 392 stool specimens submitted for routine enteric pathogen culture. In total, 104 stool specimens were culture-positive for Campylobacter jejuni/coli (n=51), Salmonella species (n=42), Shigella species (n=6), and Yersinia species (n=5). Compared to culture, the overall sensitivity and specificity of PCR detection of these organisms were 92% and 98% (96/104 and 283/288), respectively from fresh or Cary-Blair stool (p,0.41); 87% and 98% (41/47 and 242/246), respectively from fresh stool (p,0.53); and 96% and 98% (55/57 and 41/42) respectively from Cary-Blair stool (p,0.56). For individual genera, PCR was as sensitive as culture, with the exception of Salmonella culture using selenite enrichment for which PCR was less sensitive than culture from fresh, but not Cary-Blair (p,0.03 and 1.00, respectively) stools.


The shiga toxin-producing Escherichia coli PCR assay was evaluated using 204 prospectively collected stool specimens, which were also tested for shiga toxin by EIA (ProSpecT STEC; Remel, Lenexa, KS) and by culturing on chromogenic agar (Chromagar O157; BD BBL, Sparks, MD). In addition, 85 archived stool specimens previously tested for Shiga toxin (by EIA) and/or Escherichia coli O157:H7 (by culture) were tested by PCR for stx1 and stx2, encoding shiga toxin 1 and shiga toxin 2. The PCR assay had 100% sensitivity and specificity compared to EIA and culture for specimens collected prospectively (4 of 204 specimens were positive) and compared to culture and/or EIA for archival specimens (42 of 85 specimens were positive).

Clinical Reference Provides recommendations for further in-depth reading of a clinical nature

1. Centers for Disease Control and Prevention. Preliminary FoodNet Data on the incidence of infection with pathogens transmitted commonly through food--10 States, 2008. MMWR Morb Mortal Wkly Rep 2009;58(13):333-337

2. Cunningham SA, Sloan LM, Nyre LM, et al: Three-hour molecular detection of Campylobacter, Salmonella, Yersinia, and Shigella species in feces with accuracy as high as that of culture. J Clin Microbiol 2010;48:2929-2933

3. Grys TE, Sloan LM, Rosenblatt JE, Patel R: Rapid and sensitive detection of Shiga toxin-producing Escherichia coli from nonenriched stool specimens by real-time PCR in comparison to enzyme immunoassay and culture. J Clin Microbiol 2009;47(7):2008-2012