Laboratory Diagnosis of Bacterial Gastroenteritis: Romney M. Humphries, Andrea J. Linscott

PRACTICAL GUIDANCE FOR CLINICAL MICROBIOLOGY (FORMERLY CUMITECHS)
Laboratory Diagnosis of Bacterial Gastroenteritis

Romney M. Humphries,a Andrea J. Linscottb
Pathology and Laboratory Medicine, University of California, Los Angeles, California, USAa; Department of Pathology, Ochsner Health System, New Orleans, Louisiana, USAb
SUMMARY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3
INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3
BACTERIAL PATHOGENS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4
Aeromonas Species. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4
Bacillus cereus. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5
Campylobacter Species. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5
Clostridium difficile. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .6
Clostridium perfringens. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7
Escherichia coli. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7
Listeria monocytogenes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7
Plesiomonas shigelloides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8
Salmonella Species . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8
Shigella Species . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9
Staphylococcus aureus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9
Vibrio and Vibrio-Like Species . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10
Yersinia enterocolitica and Yersinia pseudotuberculosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10
Emerging Enteropathogens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11
Bacteroides fragilis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11
Edwardsiella tarda . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .12
Escherichia albertii . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .12
Klebsiella oxytoca . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .12
Providencia alcalifaciens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .12
GENERAL LABORATORY TESTING CONSIDERATIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .12
Specimen Collection. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13
Transport Media and Storage Conditions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13
Specimen Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13
Stool Culture Workup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
Traditional algorithms for the identification of enteric pathogens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
MALDI-TOF MS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .18
Susceptibility Testing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .18
Nonculture Detection Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .20
Molecular Testing by Syndromic Panels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21
Reporting Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .22
CONCLUDING REMARKS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .22
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .22
AUTHOR BIOS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .31
SUMMARY INTRODUCTION
Bacterial gastroenteritis is a disease that is pervasive in both the
developing and developed worlds. While for the most part bacte-
rial gastroenteritis is self-limiting, identification of an etiological
O ver 1.7 billion global cases of diarrheal disease are reported
annually (http://www.who.int/mediacentre/factsheets/fs330
/en/index.html) and are associated with an estimated 2.2 million
agent by bacterial stool culture is required for the management of
deaths. The burden of diarrheal disease is most critical in devel-
patients with severe or prolonged diarrhea, symptoms consistent
oping countries, facilitated by unsafe water supplies, poor sanita-
with invasive disease, or a history that may predict a complicated
tion, and nutritional deficiencies. Diarrheal disease in children
course of disease. Importantly, characterization of bacterial en-
teropathogens from stool cultures in clinical laboratories is one of aged 5 years in these countries is devastating, where repeated
the primary means by which public health officials identify and diarrheal episodes contribute to malnutrition, which in turn puts
track outbreaks of bacterial gastroenteritis. This article provides these children at heightened risk of acquiring infectious diarrhea
guidance for clinical microbiology laboratories that perform stool
cultures. The general characteristics, epidemiology, and clinical
manifestations of key bacterial enteropathogens are summarized. Citation Humphries RM, Linscott AJ. 2015. Laboratory diagnosis of bacterial
Information regarding optimal specimen collection, transport, gastroenteritis. Clin Microbiol Rev 28:331. doi:10.1128/CMR.00073-14.
and processing and current diagnostic tests and testing algorithms Address correspondence to Andrea J. Linscott, [email protected].
is provided. This article is an update of Cumitech 12A (P. H. Gil- Copyright 2015, American Society for Microbiology. All Rights Reserved.
ligan, J. M. Janda, M. A. Karmali, and J. M. Miller, Cumitech 12A, doi:10.1128/CMR.00073-14
Laboratory diagnosis of bacterial diarrhea, 1992).
January 2015 Volume 28 Number 1 Clinical Microbiology Reviews cmr.asm.org 3

Humphries and Linscott
TABLE 1 Types of bacterial gastroenteritisa

Parameter Secretory gastroenteritis Inflammatory gastroenteritis Invasive gastroenteritis
Location Proximal small intestine Colon Distal small intestine
Type of illness Watery diarrhea Dysentery Enteric fever
Stool examination No fecal leukocytes Fecal polymorphonuclear leukocytes Fecal mononuclear leukocytes (if patient
has diarrhea)
Mechanism Enterotoxin or bacterial adherence/invasion Bacterial invasion or cytotoxins cause Bacteria penetrate the mucosa and
causes a shift in water and electrolyte mucosal damage that leads to invade the reticuloendothelial system
excretion/adsorption inflammation
Classic pathogens Vibrio cholerae, ETEC, Clostridium Shigella, STEC, Salmonella (not Salmonella Salmonella Typhi/Paratyphi, Yersinia
perfringens, Bacillus cereus, Staphylococcus Typhi/Paratyphi), Vibrio enterocolitica
aureus parahaemolyticus, Clostridium difficile,
Campylobacter
a
Adapted from reference 321 with permission of the publisher.
and is associated with stunting and impaired cognitive develop- patient management (7). Rather, the primary goal for the patient
ment (1, 2). While less common in high-income countries, diar- with acute diarrhea is symptomatic relief, rehydration (or preven-
rheal diseases remain a significant health concern. There are an tion of dehydration), and potentially preventing transmission of
estimated 211 to 375 million episodes of diarrheal illnesses each the infection. In contrast, a bacterial stool culture is indicated for
year in the United States, with 1.8 million hospitalizations and patients with severe or prolonged diarrhea, those with symptoms
3,100 deaths (3). Many of these cases are foodborne. The Food- consistent with invasive disease, or those with a medical history
borne Diseases Active Surveillance Network (FoodNet) at the predictive of complications associated with their gastrointestinal
Centers for Disease Control and Prevention (CDC) reported disease (3, 6, 810). For example, the American College of Gastro-
1,000 foodborne outbreaks that resulted in 48 million illnesses, enterology recommends a routine stool culture for a patient who
128,000 hospitalizations, and 3,000 deaths from 10 sites in the presents with any of the following symptoms: severe or persistent
United States over a 15-year period (4). It is important to note that diarrhea, temperature of 38.5C, bloody diarrhea, or the pres-
many cases of foodborne diarrheal illness are not part of a recog- ence of stool leukocytes, lactoferrin, or occult blood (6). The IDSA
nized outbreak and thus are not captured by the FoodNet data (5). similarly recommends that stool cultures be performed for a pa-
Diarrhea is defined by the Infectious Diseases Society of Amer- tient with diarrhea for 1 day, fever, dehydration, systemic ill-
ica (IDSA) and the American College of Gastroenterology (ACG) ness, bloody stools, or a clinical history that would include bacte-
as the passage of three or more loose or liquid stools per day. It can
rial pathogens in the differential diagnosis (3).
be further be classified by the duration of symptoms (3, 6). Pa-
In addition to the value for patient care, a bacterial stool cul-
tients with acute diarrhea have symptoms lasting less than 14 days.
ture is an important tool for public health. Isolates recovered from
Those with diarrhea for 14 days, but 1 month are said to have
stool cultures performed by clinical laboratories are used to iden-
persistent diarrhea. Those experiencing diarrhea for longer than
30 days are said to have chronic diarrhea. Diarrhea may be infec- tify and track outbreaks at the local, national, and international
tious, i.e., caused by bacteria, viruses, or parasites, but with in- levels. The dilemma with some of the newer test methods, includ-
creasing frequency in high-income nations, the etiology of diar- ing molecular assays, is the lack of organism recovery, which is
rhea is noninfectious. In these cases, diarrhea is caused by food currently needed for public health investigations.
intolerances, reactions to medication, intestinal disorders such as The objectives for this practical guideline are to discuss the
irritable bowel syndrome, or intestinal diseases, including Crohns more common bacterial organisms associated with diarrheal dis-
disease, ulcerative colitis, and celiac disease. In these instances, ease, briefly describe emerging bacterial pathogens associated with
laboratory tests for infectious etiologies, including a bacterial stool diarrheal disease, describe stool specimen collection, transport,
culture, are useful for diagnosis by either ruling out or ruling in a and processing, and discuss test methods used to identify these
common infectious process (3). bacterial agents and antimicrobial susceptibility testing.
The primary mechanisms for bacterial gastroenteritis are (i)
excessive secretion of fluids in the proximal small intestine in- BACTERIAL PATHOGENS
duced by the action of luminal toxins expressed by enteropatho-
Aeromonas Species
gens or by minimally invasive bacteria, (ii) inflammatory or cyto-
toxic damage of the ileal or colonic mucosa which may produce Over 26 different species of Aeromonas have been described to
blood and pus, or (iii) penetration of the bacterium through the date, but the vast majority of these are of limited clinical or public
mucosa to the reticuloendothelial system, as is the case with ty- health significance. Aeromonas spp. are ubiquitous in aquatic hab-
phoid fever. Classic examples of bacteria that cause these various itats, and concentrations peak when water temperatures rise sub-
syndromes are presented in Table 1. Regardless of mechanism, stantially during the summer months. Consumable products such
most cases of bacterial gastroenteritis are self-limiting, and, with a as poultry, lamb, veal, pork, and ground beef can harbor Aeromo-
few exceptions, neither empirical antimicrobial therapy nor bac- nas spp. Consumption of contaminated foods or potable water or
terial stool culture is indicated (3). For most patients who present accidental ingestion of untreated water during recreation are the
with acute diarrhea, symptoms have resolved by the time bacterial most common sources of infection. In humans, Aeromonas spp.
culture results are available, and these generally do not change are not considered to be normal gastrointestinal flora, and the
4 cmr.asm.org Clinical Microbiology Reviews January 2015 Volume 28 Number 1

estimated human intestinal carrier/colonization rate is extremely reports have documented fulminant hepatic failure and death as-
low in healthy persons. sociated with emetic B. cereus (3134). The emetic toxin is most
Most authoritative documents list Aeromonas spp. as accepted often found in starchy foods, such as fried rice, pastry, and noodles
enteropathogens, although there still are no bona fide outbreaks of (35).
gastroenteritis attributable to this genus (11, 12). The incidence of The diarrheal syndrome is characterized by abdominal cramps,
Aeromonas-associated gastroenteritis on a global basis varies dra- pain, and watery diarrhea within 8 to 16 h of ingestion of food that
matically in association with geographic and socioeconomic fac- contains viable vegetative cells or spores of B. cereus. The symp-
tors. In developing countries where sanitary conditions are sub- toms of this diarrheal illness are similar to those seen with Clos-
standard, the reported incidence of Aeromonas diarrhea can be tridium perfringens food poisoning (35). Symptoms typically re-
high, ranging from approximately 4% to 22% (1316). In indus- solve with 12 to 24 h (35). Although rare, fatalities have occurred
trialized countries, regardless of patient population and sample with B. cereus diarrheal disease (29). In the diarrhea syndrome, 3
size, Aeromonas-associated gastroenteritis has been reported at pore-forming enterotoxins are expressed by the vegetative cells in
frequencies of 0% to 10% (17, 18). the small intestine, which damage the ileal epithelial cell mem-
Aeromonas diarrhea presents as either an acute watery diarrhea branes. The 3 enterotoxins are hemolysin BL (HBL), nonhemo-
(enteritis) or as a more invasive bloody form resembling dysentery lytic enterotoxin (NHE), and cytotoxin K (25, 35).
or enterocolitis (17). The secretory form is much more common Individuals at increased risk of B. cereus diarrheal disease in-
than the dysenteric variety. A third, extremely rare variation of clude those with lowered stomach acidity, such as is seen in pa-
Aeromonas gastroenteritis presents as a cholera-like illness with tients with achlorydria or the elderly (36). B. cereus has been iso-
profound watery diarrhea. Most intestinal infections associated lated from the stools of 0 to 43% healthy children and adults, at
with Aeromonas spp. are self-limiting, although chronic diarrhea various concentrations. However, these cases represent transient
exceeding for 1 year has been described (19, 20). colonization, most likely obtained from low-level exposure from
Several potential serious complications can result secondary to the environment (24, 37, 38).
Aeromonas gastroenteritis, including ulcerative colitis, pan colitis,
segmental colitis, or inflammatory bowel disease (17). In a few Campylobacter Species
instances, cases of hemolytic-uremic syndrome (HUS) associated Campylobacter is one of the leading causes of bacterial diarrhea
with Aeromonas hydrophila or Aeromonas veronii biovar sobria worldwide (39). FoodNet estimates that 1.3 million persons in the
have been reported in infants and adults (21). Some Aeromonas United States are affected each year by Campylobacter infections
spp. have been shown to carry the Shiga toxin (Stx) genes 1 and 2 (40). The true incidence may be up to 35 times higher due to
(22), and development of HUS in patients infected with Aeromo- undiagnosed or unreported cases (41). Geographic variation in
nas spp. may be attributable to this virulence factor. The most rates of campylobacteriosis has been consistently observed in the
serious complication of Aeromonas gastroenteritis is translocation United States between 1996 and 2006, with the mean annual rate
from the gut into the circulatory system, producing frank septice- of culture-confirmed campylobacteriosis being 5-fold higher in
mia (23). This situation typically exists in persons with underlying California (34 cases per 100,000 population) than in other states
conditions, including hepatic cirrhosis or malignancies of the cir- (42). The reason for this difference is unclear, but does not appear
culatory systems. Attributable fatality rates due to Aeromonas sep- to be associated with increased physician visits, laboratory test
sis range from 32% to 45% (17). ordering, or exposure to risk factors among patients in California
compared to other states.
Bacillus cereus Campylobacter inhabits the intestinal tracts of food animals,
B. cereus is ubiquitous in the environment, being found in decay- such as poultry, cattle, swine, and sheep, and domestic pets, in-
ing organic matter, soil, freshwater and salt water, vegetables, and cluding cats and dogs. The organism rarely causes disease in ani-
the intestinal tracts of invertebrates (24). The spores are resistant mals but is shed in the feces. Meat typically becomes contaminated
to heat, freezing, and drying and can survive gamma radiation and with animal feces harboring Campylobacter spp. during slaughter-
pasteurization processes (25). Hydrophobic in nature, the spores ing. Transmission of the organism is typically foodborne, by in-
can adhere to cooking and food surfaces (26, 27). B. cereus spores gestion of undercooked contaminated meat and meat products or
can germinate in foods that are not promptly cooled and refriger- contaminated dairy products. In addition, waterborne infections
ated after meals or in food heated for prolonged periods at tem- occur, via consumption of contaminated water and ice. Contact
peratures below 60C. Outbreak surveillance data from 2009 and with infected animals, particularly cats and puppies, has also been
2010 documented 427 illnesses associated with 25 outbreaks in the shown to be a route of transmission. The typical incubation period
United States due to B. cereus (28). for Campylobacter is 2 to 5 days, but it may be up to 10 days (43).
There are two distinct syndromes associated with Bacillus cereus Most cases of Campylobacter enteritis are sporadic, but the inci-
food poisoning: an emetic syndrome and a diarrheal syndrome. dence increases starting in March and throughout the summer
The emetic syndrome is due to intoxication by a preformed toxin months. Outbreaks associated with Campylobacter have been due
ingested in food. The emetic toxin, called cereulide, is a plasmid- to consumption of raw milk or well water contaminated with ef-
encoded peptide that is resistant to heat, proteolysis, and acid. As fluent from livestock operations (4446). Higher rates of Campy-
such, the toxin is not destroyed by gastric acids or proteolytic lobacter enteritis are seen in those 4 years of age and 15 to 44
enzymes in the intestinal tract or by food reheating (29). Cereulide years of age (47). Travelers to developing countries are also at
is responsible for symptoms of nausea and vomiting (25, 29, 30), increased risk of Campylobacter enteritis.
which appear within 1/2 to 6 h after ingestion (30). These symp- Campylobacter jejuni subsp. jejuni and Campylobacter coli are
toms are similar to those seen with Staphylococcus aureus entero- the most common Campylobacter species associated with diar-
toxins. Symptoms usually resolve within 6 to 24 h, but rare case rheal illness. C. jejuni is responsible for 90% of cases (43, 48).

Campylobacter upsaliensis, which was first isolated from dogs with ulations, such as hospitalized patients and long-term-care facility
diarrhea, has also been shown to cause human disease. The inci- residents. Previous antimicrobial use and previous C. difficile in-
dence of C. upsaliensis among patients with diarrhea may be un- fection (CDI) are predictors of colonization in these populations
derappreciated, as the organism cannot grow on the selective me- (6870). C. difficile is acquired through the ingestion of spores via
dia typically used to recover Campylobacter in clinical laboratories the fecal-oral route or through exposure to spores in the environ-
(4951). Other Campylobacter spp. associated with gastroenteritis ment. A recent study demonstrated that only a third of CDI cases
include Campylobacter fetus subsp. fetus, Campylobacter lari, could be linked by whole-genome sequencing of isolates to a
Campylobacter concisus, Campylobacter jejuni subsp. doylei, and symptomatic patient, whereas the remainder of cases were attrib-
Campylobacter hyointestinalis (48, 52). uted to exposure from the environment or asymptomatic carriers
C. jejuni and C. coli cause indistinguishable infections (48). Be- (71).
fore the onset of diarrhea, a febrile period with malaise, abdominal C. difficile is the primary pathogen associated with antibiotic-
pain, and myalgia occurs in about 50% of symptomatic patients associated colitis (72, 73). In the United States, the rate of CDI
(43). Diarrhea is characterized by loose watery stools, with or increased 4-fold between 1993 and 2009 but leveled off at 110 per
without blood. Blood and fecal white cells may be present. Ab- 100,000 hospital stays in 2009 (74). By far the highest rate of CDI
dominal cramping can mimic pain associated with acute appen- is among patients aged 65 and older, with over 1,000 cases per
dicitis. In most cases, the diarrhea is self-limited, resolving within 100,000 hospitalizations in 2009 reported for this age group (74).
a week without antimicrobial therapy. However, relapse occurs in In 2005, the NAP1/027/B1 strain emerged in Canada, Europe,
5 to 10% of untreated patients (43). Extraintestinal Campylobacter and the United States, concomitant with a significant rise in mor-
infections such as bacteremia, urinary tract infections, cholecysti- bidity and mortality associated with CDI over those in previous
tis, hepatitis, pancreatitis, nephritis, meningitis, abortion, and years (75, 76). At the time, this change in severity of CDI was
neonatal sepsis have also been reported (53). Campylobacter bac- attributed to the hypervirulent nature of the NAP1/027/B1
teremia is typically uncommon, but it occurs more frequently in strain. NAP1/027/B1 has since become the predominant strain in
patients with HIV infection, malignancy, and liver disease (54). many locations, and it continues to be associated with high mor-
Bacteremia and extraintestinal infections are also more common tality and relapse rates (77). Early studies pointed to heightened
in neonates and the elderly (55). toxin expression (78), more efficient sporulation (79, 80), expres-
Autoimmune complications, such as reactive arthritis and Guil- sion of the binary toxin, and fluoroquinolone resistance (75) as
lain-Barr syndrome (GBS), can occur post-Campylobacter infec- reasons for the epidemiological success of this strain. However,
tion (56). Reactive arthritis affects 2 to 4% of patients postcampy- some studies questioned the relevance of the NAP1/027/B1 strain
lobacteriosis and is characterized by pain and joint swelling that type in disease severity (81, 82), and it has since been confirmed
lasts for several weeks to a year (48). In 5% of cases, arthritis is that not all NAP1/027/B1 strains express larger quantities of toxin
chronic or relapsing (57). Symptoms typically begin 3 to 40 days than historical strains (83).
postdiarrhea and most commonly affect the knees (58). GBS is an The range of symptoms associated with infection with toxigenic
acute paralytic disease of the peripheral nervous system and is seen C. difficile includes asymptomatic carriage, mild to moderate di-
in approximately 0.1% of Campylobacter cases. Lipooligosaccha- arrhea, and pseudomembranous colitis (PMC). Patients may
rides of C. jejuni, which mimic human ganglioside, elicit autoan- present with a brief, self-limiting diarrhea or with profuse watery
tibodies that then react with peripheral nerve targets (56). The diarrhea similar to that in cholera (84). Fever, abdominal cramp-
onset of GBS usually occurs within 2 to 21 days of the diarrheal ing, and leukocytosis can be seen in individuals with more severe
illness (59). diarrhea. Persons with PMC present with abdominal pain, fever,
marked leukocytosis, and severe diarrhea that may be bloody.
Clostridium difcile Poor prognostic indicators include a rapid increase in the periph-
Clostridium difficile is an obligately anaerobic, spore-forming eral white blood count with an increase in band forms and a sud-
Gram-positive rod. The spores of C. difficile are resistant to stom- den absence of diarrhea (85).
ach acid, heat, and many commercial disinfectants used in hospi- The most common conditions associated with CDI are dehy-
tals (60). Following ingestion, exposure of the spores to bile salts dration and electrolyte disorders, which may affect up to 92% of
in the small intestine triggers germination (61). Pathogenic strains patients. Less frequent conditions associated with CDI include
of C. difficile harbor a pathogenicity locus (PaLoc) that encodes septicemia, hypoalbuminemia, renal failure, septic shock, ascites,
the organisms two main virulence factors: toxin A, an enterotoxin and peritonitis. The more severe complications of CDI include
(encoded by tcdA), and toxin B, a highly potent cytotoxin (en- intestinal perforation and toxic megacolon. While these severe
coded by tcdB) (62). The individual role of these two toxins in complications are only observed in 0.1% to 3% of all CDI cases
disease are controversial. Clinical isolates of C. difficile that do not (74, 86, 87), the mortality associated with toxic megacolon is high,
express toxin A have been isolated from symptomatic patients (63, ranging from 38% to 80% (86, 88).
64), albeit rarely, whereas toxin B-deficient strains have not. Both Recurrence of CDI is seen in 10% to 20% of cases after initial
toxin A- and toxin B-deficient mutants remain capable of causing symptom resolution (89). Recurrent infections are attributable to
disease in hamsters, although both are attenuated compared to the both relapse (i.e., spores that are not killed by antimicrobial ther-
wild-type strain (65). apy, which can then germinate once therapy is completed) and
C. difficile can readily be found in soil and the intestinal tracts of reinfection with a new strain (9093). However, it is important to
animals and humans. C. difficile colonization rates are as high as note that patients who are asymptomatically colonized with C.
50% in healthy infants and children 1 year of age (66, 67), difficile are at decreased risk for CDI, although the reason for this
whereas 3% to 5% of healthy adults are colonized (67). Much remains unclear (94).
higher rates of colonization, 10 to 50%, are seen in high-risk pop- Exposure to antimicrobial agents and exposure to health care

facilities are hallmark risk factors for CDI. While almost all anti- Ruminants, such as cattle, are the major reservoir for STEC.
microbial agents have been associated with CDI, the most com- Poor sanitation, fecal runoff into rivers and streams, and inade-
mon are penicillins, second- and third-generation cephalospo- quate control measures in the meat and food processing industries
rins, clindamycin, and fluoroquinolones (84, 95). As stated have all led to the recovery of STEC from virtually any consumable
previously, advanced aged (65 years) is also an important risk product. Infection with STEC occurs following consumption of
factor for CDI; this age group has over 10-fold the number of CDI these contaminated products. Infections occur predominantly in
hospitalizations than the general population in the United States the summer months but can be observed year round (102).
(74). Other, less well-defined risk factors for CDI include use of The incidence of STEC infections in the United States is moni-
gastric acid suppressors, stool softeners, laxatives, and/or enemas, tored by FoodNet. In 2012, the incidence of O157 STEC was 1.12
chemotherapy, and gastrointestinal surgery (96). per 100,000 population, and the incidence of non-O157 STEC was
1.16 per 100,000 (103). Among the non-O157 STEC strains, O26,
Clostridium perfringens O103, O111, O121, O45, and O145 are the most common sero-
Clostridium perfringens is ubiquitous in the environment and can types isolated in the United States (104). The incidence of STEC in
be found in the feces of humans and animals. Food poisoning with other developed countries varies; it is as low as 0.4 per 100,000 in
C. perfringens requires ingestion of a high burden of vegetative Australia (105) and as high as 5.33 per 100,000 in Ireland (106).
cells, usually 108. The typical mechanism for this is food contam- The incidence of STEC is much higher in developing countries
inated with C. perfringens that is improperly cooked, stored, and such as Argentina and India, but formal surveillance data are not
reheated. Spores that survived the initial heating processes germi- available for these countries.
nate and proliferate during a slow cooling of food or when the STEC disease presents as enteritis that may quickly progress to
food is insufficiently reheated. Following ingestion, the organism hemorrhagic colitis (107). The chief symptoms included bloody
sporulates upon entry into the small intestine, which is concomi- diarrhea, abdominal pain, nausea, and vomiting (108). Impor-
tant with expression of an enterotoxin that is responsible for pa- tantly, not all STEC infections are associated with bloody diarrhea
tient symptoms. C. perfringens serotype A is the most common (109, 110), and so laboratory algorithms that only test bloody
serotype associated with food poisoning and diarrhea (97, 98). specimens for STEC are no longer considered standard of care.
From 2009 to 2010, there were 60 confirmed C. perfringens The most common and serious complication of STEC infection is
foodborne outbreaks and 3,225 reported illnesses, making C. per- the development of HUS, which typically presents 5 to 13 days
fringens the second most common cause of bacterial foodborne after the onset of diarrhea (11). HUS is life-threatening and con-
disease in the United States in this time period (28). Symptoms sists of the triad of renal failure, microangiopathic hemolytic ane-
most often associated with C. perfringens food poisoning are wa- mia, and thrombocytopenia. The mortality rate connected with
tery diarrhea, severe abdominal cramping and pain, and vomiting. HUS is 3% to 5% (111). It has been estimated that 61% of all HUS
The onset of symptoms ranges from 8 to 24 h after the ingestion of cases are related to STEC infection (111). HUS has been observed
contaminated food. The illness is self-limiting, and symptoms re- more frequently in O157 (11% of cases) versus non-O157 (1% of
solve within 24 h. cases) STEC infections (104). Approximately 15% of children
A rare type of food poisoning called enteritis necroticans or 10 years of age develop HUS following STEC infection. How-
pig-bel is associated with the ingestion of food, usually pork, ever, in the recent outbreak of O104 STEC in Germany, 22% of
heavily contaminated with C. perfringens serotype C. This organ- children developed HUS (112114). It should be noted that this
ism produces a beta toxin that causes intestinal wall necrosis. Pig- outbreak was caused by an atypical STEC strain that harbored
bel has a mortality rate of 40% and primarily affects malnourished enteroaggregative E. coli virulence factors in addition to the Shiga
persons, especially children (99). C. perfringens has also been toxins. HUS occurs much less frequently among adults and is
linked to antibiotic-associated diarrhea that does not cause pseu- associated predominantly with advanced age (75 years) (115).
domembranous colitis (73, 100). Increased rates of HUS have been more frequently associated with
Stx2-expressing STEC strains. Exposure to antibiotics also in-
Escherichia coli creases the risk of HUS in children (114). However, recent data
Escherichia coli was initially considered to only be a commensal demonstrated that treatment with ciprofloxacin reduced the risk
residing in the gastrointestinal tract. However, several pathogenic of HUS in patients infected with the 2011 German O104 STEC
variants (pathotypes) are now recognized and associated with di- strain (116). These data are supported by a recent meta-analysis of
arrheal diseases. Although E. coli is easy to identify to species level, studies between 1980 and 2011 (117). Despite this, the decision to
it is extremely difficult to recognize strains belonging to different treat a patient with STEC infection with antimicrobials remains
pathotypes of diarrheagenic E. coli, as these are defined by the controversial. In addition, use of antimotility agents has been as-
expression of one or more group-specific virulence factors. The sociated with longer duration of bloody diarrhea, as well as pro-
six major diarrheagenic pathotypes described to date are entero- gression to HUS (118).
pathogenic E. coli, Shiga toxin-producing E. coli (STEC), entero-
invasive E. coli (EIEC), enterotoxigenic E. coli, enteroaggregative Listeria monocytogenes
E. coli, and adherent invasive E. coli (101). Of these, only STEC is The genus Listeria is composed of six species, of which Listeria
routinely identified by most clinical and public health laborato- monocytogenes is the common human pathogen, causing intesti-
ries, and it will be the focus of the discussion here. STEC is defined nal as well as extraintestinal infections. L. monocytogenes is a com-
by the presence of a Shiga toxin 1 (Stx1) and/or Shiga toxin 2 mon environmental inhabitant of soil, vegetation, and animals
(Stx2) gene. Historically, these isolates were called enterohemor- (119). Because Listeria spp. can survive under acidic and salt-en-
rhagic E. coli (EHEC) or verocytotoxin-producing E. coli (VTEC). hanced conditions in foods and can grow at refrigeration temper-
STEC includes both O157 and non-O157 serotypes of E. coli. atures (4C), they have the capacity to survive and multiply in

large numbers in a variety of refrigerated foods (119, 120). A high organism (130132). Coinfection with P. shigelloides and other
percentage (32%) of foods recalled by the FDA involve L. mono- enteropathogens has been reported (132, 133), and some evidence
cytogenes (121). The major risk factor associated with L. monocy- suggests that P. shigelloides causes diarrhea only as a coinfecting
togenes gastroenteritis is the consumption of foods heavily con- pathogen, rather than on its own (133). Both secretory and dys-
taminated (107 to 109 CFU/g or ml) with L. monocytogenes (122). entery-type diarrhea have been reported with P. shigelloides infec-
The incidence of L. monocytogenes gastroenteritis is unknown. tions (130, 134). Most infections are characterized by self-limiting
Surveillance data from the CDC and other sources, including diarrhea with blood or mucus, abdominal cramps, vomiting, and
FoodNet, have focused on invasive listeriosis (bacteremia and fever (130). While most diarrheal episodes are described as acute,
central nervous system infection) as a consequence of foodborne there have been reported chronic cases lasting over 2 weeks (135).
infection. In 2011, the incidence of invasive listeriosis was 0.31 per
100,000 population. Many patients with invasive listeriosis have a Salmonella Species
history of gastrointestinal symptoms that consist of diarrhea, nau- Salmonella, a member of the family Enterobacteriaceae, is a facul-
sea, vomiting, and fever. This, coupled with reports of L. monocy- tatively anaerobic Gram-negative rod. Salmonella taxonomy is a
togenes outbreaks of gastroenteritis (122, 123), suggests that L. complicated matter, with two species in the genus: Salmonella
monocytogenes may be an infrequent cause of gastroenteritis in enterica and Salmonella bongori. Salmonella enterica has six sub-
patients with negative bacterial stool cultures. One 2005 Canadian species (S. enterica subsp. enterica, S. enterica subsp. salamae, S.
study found the maximum incidence of L. monocytogenes-associ- enterica subsp. arizonae, S. enterica subsp. diarizonae, S. enterica
ated diarrhea to vary from 0.2% to 0.5%, depending upon the subsp. indica, and S. enterica subsp. houtenae) that can be further
population studied (123). On rare occasions, Listeria ivanovii has serotyped using the Kauffmann-White-Le Minor scheme, based
been reported to cause diarrhea in severely immunosuppressed on the properties of their somatic (O), flagellar (H), and capsular
individuals (124). polysaccharide (Vi) antigens (136, 137). There are over 2,500 se-
The typical incubation period for gastrointestinal infection is 24 rotypes of S. enterica (136, 137). Because of the diversity of the
h; however, it can range from 6 h to as long as 10 days (120). Once genus, several isolates may be difficult to identify due to atypical
symptoms begin, diarrhea lasts for 1 to 3 days (122). In a study of biochemical reactions.
cases of gastroenteritis linked to outbreaks, attack rates ranged Salmonella colonizes the intestinal tracts of vertebrates. Some
from 50% to 90% and the median number of stools/day was 12 serotypes, including Salmonella enterica subsp. enterica serotype
(range, 3 to 50) (122). The syndrome is typically characterized by Typhi (Salmonella Typhi), are only found in human hosts. The
a febrile illness with diarrhea, headache, and arthralgia/myalgia. majority of Salmonella cases occur as the result of ingesting con-
Other, less frequently encountered complications include abdom- taminated food or water. Salmonella can also be acquired by con-
inal pain, nausea, vomiting, dizziness, lymphadenopathy, and tact with domestic animals and their food products, farm animals
presence of a rash (12, 122). Fever, which occurs in 60% to 100% or animals in petting zoo, and exotic pets like turtles, hedgehogs,
of infected persons, is a cardinal feature associated with L. mono- and iguanas (138142). Salmonella can also be transmitted from
cytogenes diarrhea. person to person via the oral-fecal route.
The most serious complication of listeriosis is invasive disease, The incidence of Salmonella infections in the United States in
including septicemia and meningitis. L. monocytogenes has tro- 2011 was 1,645 per 100,000 population (143), with higher rates in
pism for the brain and as a result can cause encephalitis, rhomb- late summer and early fall. Worldwide, there are an estimated 94
encephalitis (brain stem encephalitis), and brain abscess. The case million cases of nontyphoidal Salmonella gastroenteritis and
fatality rate for most cases of listeriosis with comorbidities has about 155,000 deaths (144). In developing countries, and the In-
been reported to be between 20% and 40% (125). dian subcontinent in particular, typhoidal isolates cause the ma-
Reputed risk factors associated with acquiring L. monocytogenes jority of disease and are associated with an estimated 21.6 million
gastroenteritis include gastric acidity, use of antacids, use of H2 annual cases and 216,500 deaths (145). In sub-Saharan Africa,
receptor antagonists, and use of laxatives (119, 122, 126). In addi- nontyphoidal Salmonella, predominantly the Salmonella Typhi-
tion, those with inflammatory bowel disease (IBD) and Crohns murium ST313 strain, are a significant cause of bloodstream in-
disease may have a more frequent incidence of Listeria diarrhea (as fections in both children and adults (146, 147). In the United
opposed to Campylobacter or Salmonella) (123, 126). States, the most common serotypes reported are Salmonella En-
teritidis, Salmonella Typhimurium, and Salmonella Newport
Plesiomonas shigelloides (143).
Plesiomonas shigelloides is the sole oxidase-positive member of the Nontyphoidal salmonellosis consists of diarrhea, nausea, head-
Enterobacteriaceae family. While P. shigelloides has been associated ache, and abdominal cramps, which last for 4 to 7 days. Fever may
with diarrheal disease in numerous reports, a definitive causal be present and usually resolves in 24 to 48 h. The disease is typi-
relationship with P. shigelloides has yet to be established through cally limited to the lamina propria of the small intestine, and an-
volunteer or animal studies (127). timicrobial therapy is not indicated. Extraintestinal manifesta-
P. shigelloides is found in aquatic environments and has been tions, such as bacteremia, septic arthritis, urinary tract infections,
isolated from both cold-blooded and warm-blooded animals. In and osteomyelitis, are seen in 5% of cases (148153). Some indi-
humans, there has been a reported prevalence rate of 0.01% to viduals may become asymptomatic carriers of the organism, and
5.5% in asymptomatic individuals (128, 129). Transmission oc- shedding occurs for several weeks to a few months.
curs primarily through the consumption of seafood, such as oys- Typhoid fever is caused by Salmonella Typhi, and a similar syn-
ters and shellfish, or water that has been contaminated with sew- drome is caused by Salmonella Paratyphi A, Salmonella Paratyphi
age. Most cases of P. shigelloides diarrheal illness are sporadic; C, and tartrate-negative variants of Salmonella Paratyphi B. In
however, there have been reported outbreaks associated with the typhoid, the organism disseminates from the lamina propria to

the reticuloendothelial system in infected phagocytes via lym- (161). S. dysenteriae type 1 is responsible for classic dysentery,
phatic and hematogenous routes. Fever, malaise, anorexia, head- which is manifested by fever, abdominal cramping, and bloody
aches, and vomiting are common symptoms of typhoid and typi- stool. Sepsis occurs primarily in malnourished pediatric patients
cally start 1 to 3 weeks after infection. Patients may have diarrhea in developing countries and is most commonly caused by S. flex-
following ingestion of the organism, but many do not. Rose spots, neri (163). Long-term carriage (1 year) occurs but is rare (164).
which are blanching maculopapular lesions 2 to 4 mm in diame- Meningitis, pneumonia, and urinary tract infections (UTIs) are
ter, are seen in 5 to 30% of cases. A complication of untreated rare complications of shigellosis and are most commonly seen
typhoid fever is the erosion of the blood vessels in the Peyers with S. flexneri and S. sonnei (165167). Notably, 40% of UTIs are
patches, which can lead to intestinal hemorrhage (145). The or- asymptomatic and 35% are culture negative (167). Reactive ar-
ganism persists in the mesenteric lymph nodes, gallbladder, and thritis has been reported in 1 to 3% of cases from outbreak data
bone marrow for years. Five to 10 percent of patients will have a (161). The onset of reactive arthritis occurs within 3 weeks of
relapse of infection, typically 2 to 3 weeks following resolution of gastrointestinal symptoms, with the duration of symptoms rang-
symptoms (154). Up to 10% of asymptomatic patients will being from a few days to a few months; only S. flexneri has been
come carriers, and 1 to 4% of these will shed for more than 1 year associated with reactive arthritis.
(154). HUS is the most serious complication of shigellosis. HUS oc-
The severity of Salmonella disease depends on the inoculating curs in 13% of cases of S. dysenteriae type 1 shigellosis and is
dose (155), infecting serotype (151), and predisposing host fac- attributable to the expression of Stx1 by this organism (168).
tors. Children under 1 year of age have the highest incidence of However, in rare cases, non-S. dysenteriae species of Shigella have
Salmonella in the United States (143). Because Salmonella must been isolated from children with HUS (168, 169). S. dysenteriae
survive the gastric acid barrier in order to gain access to the small type 1 HUS is seen mainly in children 5 years old in Asia and
intestine where it causes disease, patients with decreased gastric Africa.
acid production, from advanced age, gastrectomy, or H2 receptor
antagonists, are at increased risk of infection. Individuals with Staphylococcus aureus
impaired cellular immunity (e.g., AIDS) or altered phagocyte S. aureus food poisoning is an intoxication caused by the ingestion
function (e.g., sickle cell anemia) are at increased risk for both of preformed, heat-stable enterotoxin. There are 21 known staph-
invasive nontyphoid Salmonella infections and typhoid (156, ylococcal enterotoxins, but phage-encoded staphylococcal en-
157). However, these individuals do not appear to have more se- terotoxin A is the most frequently reported cause of S. aureus food
vere typhoid infections should they become infected (158, 159). In poisoning worldwide (170172). Coagulase-negative staphylo-
the United States, nearly all cases of typhoid and paratyphoid fever cocci (CoNS) can also acquire enterotoxins, but the reported cases
are in returning travelers and immigrants (160). or outbreaks of CoNS food poisoning have been limited (173,
174).
Shigella Species S. aureus is ubiquitous in the environment and colonizes the
Shigella species are host adapted to humans but have been docu- skin and mucous membranes of many mammals and birds (175).
mented in rare instances from dogs and primates (161). They can In humans, the anterior nares is the most commonly colonized
be acquired from ingestion of a variety of foods or water contam- site, and the organism is shed on to healthy skin (176). The rate of
inated with human feces, sexually during oral-anal sex, or by persistent carriage of S. aureus is reported to be 10 to 35%, and the
laboratory workers. The four species of Shigella are Shigella dysen- rate of intermittent colonization ranges from 20 to 75% (176,
teriae, Shigella flexneri, Shigella boydii, and Shigella sonnei. Trans- 177). For those individuals harboring S. aureus, the organism can
mission by person-to-person contact is common for Shigella spp. be transferred from their hands while preparing food. S. aureus is
because of a low infectious dose of 10 to 100 organisms (161). most commonly found in foods such as cream-filled pastries,
Between 2009 and 2010, Shigella accounted for 508/8,523 (2%) of cream pies, and sandwich fillings. However, food products in-
reported illnesses associated with foodborne outbreaks (28). The volved in S. aureus food poisoning differ widely from one country
incidence of Shigella infections reported by FoodNet in the United to another (175). The CDC estimates that there are approximately
States in 2011 was 3.24 per 100,000 and ranged from 0.99 to 6.78 241,000 cases of foodborne illnesses in the United States caused by
per 100,000, depending on the region (143). S. aureus annually.
Shigellosis and dysentery are diseases associated primarily with A rapid onset of symptoms is characteristic of S. aureus food
poor hygiene and lack of access to medical care. Approximately poisoning. General malaise, nausea, vomiting, stomach cramps,
150 million cases are reported annually in developing countries, in and diarrhea can occur within 30 min of ingestion of the contam-
contrast to 1.5 million cases in industrialized nations. Of impor- inated food. The typical incubation period is 2 to 7 h, with symp-
tance, one multicenter study found that half of patients with cul- toms resolving in about 12 h (11). Patients with staphylococcal
ture-negative, bloody stools were positive by PCR for Shigella, food poisoning are not febrile. In most cases, medical treatment is
suggesting that the actual incidence of Shigella is grossly underes- not required. However, hospitalization for the severity of symp-
timated (162). Shigellosis symptoms range from watery diarrhea toms may be seen in 10% of those with S. aureus food poisoning
to mucoid and/or bloody stools, which can be accompanied by (178). Severe dehydration may be seen in young children and
fever, malaise, and abdominal pain. In one study of 1,114 culture- elderly patients (178).
confirmed patients followed for 14 days or longer, 29% (241) re- S. aureus food poisoning requires consumption of food or bev-
ported diarrhea persisting for 14 days (162). Factors associated erages harboring the staphylococcal enterotoxins. Unsafe food
with persistence were age, fever, mucoid diarrhea, vomiting, and handling practices, including neglecting to wash hands prior to
abdominal pain. Headache and nuchal rigidity are common, with handling food and to promptly refrigerate prepared foods, are the
95% and 39% of patients reporting these symptoms, respectively primary reason for intoxication.

Vibrio and Vibrio-Like Species accompanied by multiple bowel movements over a short period of
The genus Vibrio is currently comprised of over 60 species. A time. Incubation periods for cholera typically span from 18 h to 5
number of other species traditionally associated with this genus days (190). Asymptomatic colonization is relatively common in
have been recently reclassified into phylogenetically related neigh- areas of endemicity due to constant exposure to the infecting
boring clades, including Grimontia hollisae (Vibrio hollisae). Of agent under unsanitary conditions. For symptomatic persons,
the more than 60 Vibrio or Vibrio-like species that have been de- clinical presentations of cholera range from a mild to moderate
scribed, only a few these taxa have been consistently associated diarrhea to a more fulminant form termed cholera gravis (190).
with bacterial gastroenteritis, with the two major species being Cholera gravis is characterized by the release of large volumes of
Vibrio cholerae and Vibrio parahaemolyticus. Less frequent, but water (500 to 1,000 ml/h), which rapidly leads to severe dehydra-
still of concern, are Vibrio mimicus, Vibrio fluvialis, Vibrio vulnifi- tion, shock, and death over a short period of time if left untreated.
cus, and G. hollisae. The more severe forms of cholera are associated with pandemic
Vibrio and vibrio-related bacteria are widely distributed in salt- strains bearing the O1 serogroup that carry a series of virulence
water environments with salt concentrations of 17 to 37 ppt. genes, the two most important of which are those for cholera toxin
Freshwater habitats with low salt concentrations (0.5 ppt) can and toxin-coregulated pilus (191). Cholera toxin is typically only
harbor nonhalophilic Vibrio spp. such as V. cholerae and V. mim- found in O1 El Tor or the epidemic O139 Bengal strains, although
icus. Because of their intimate association with the marine envi- other serogroups (O75 and O141) occasionally harbor these ele-
ronment, Vibrio spp. can be found in many inhabitants of this ments as well and produce cholera-like disease.
macroecosystem, including shellfish such as oysters, clams, Gastroenteritis caused by non-O1, non-O139 serogroups of V.
shrimp, and scallops. cholerae is typically milder and self-limiting, since they normally
The preeminent pathogen of this group is V. cholerae, which can lack the cholera toxin gene. These non-O1, non-O139 isolates
cause sporadic, epidemic, and pandemic cholera. The WHO esti- nevertheless cause the vast majority of V. cholerae gastrointestinal
infections in the United States. While disease caused by these iso-
mates that over 1.4 billion persons worldwide are at risk of devel-
lates is typically mild, fatal cases of non-O1, non-O139 V. cholerae
oping cholera each year, with an estimated 2.8 million cases oc-
can occur (192).
curring annually and with over 130,000 deaths (179, 180). Today,
V. parahaemolyticus is the most common cause of Vibrio-asso-
the highest incidence of cholera is found in Africa and the south-
ciated diarrhea in the United States. The most frequent symptoms
ern regions of Asia. Two serogroups of V. cholerae, O1 (El Tor
linked to V. parahaemolyticus enteritis include diarrhea with ab-
biotype) and O139, are responsible for the ongoing pandemic of
dominal cramps, with approximately half of all infected individ-
cholera disease.
uals having a febrile illness (193). Two prominent symptoms, nau-
Cholera is not common in the United States, but the incidence
sea (76%) and vomiting (55%), help to distinguish diarrhea
of vibriosis (V. parahaemolyticus, V. vulnificus, and V. alginolyti-
caused by this species from other vibriosis or other enteritides
cus) is increasing. There are an estimated 80,000 illnesses with 500
associated with bacteria.
hospitalizations and 100 deaths each year due to Vibrio illnesses in
Unlike with many other enteric pathogens, secondary compli-
the United States, based upon data submitted through the Cholera cations due to Vibrio gastroenteritis are rare. The principle com-
and Other Vibrio Illness Surveillance (COVIS) system and Food- plication that can arise from enteric infection is secondary spread
Net (181, 182). These cases include not only patients with diarrhea to the bloodstream, producing septicemia. In the case of V. chol-
but also those with primary septicemia, wound infections, and erae, virtually all such bacteremias are caused by non-O1, non-
otitis externa caused by Vibrio spp. The annual incidence of vibri- O139 isolates (194). Other, infrequently encountered Vibrio spe-
osis in the United States has increased from 0.09 to 0.15 per cies that have been demonstrated to cause septicemia subsequent
100,000 population in 1996 to 0.28 to 0.42 per 100,000 in 2010, to primary gastrointestinal infections include V. fluvialis and G.
with the highest incidence in coastal areas (181). hollisae (195, 196).
V. parahaemolyticus is responsible for many outbreaks of food- In the case of cholera, most infections arise in areas of endemic-
associated gastroenteritis worldwide. In Japan, it has been one of ity through contaminated water and nonhygienic conditions
the most important causes of foodborne diarrhea since the 1960s which perpetuate persistence of O1. However, persons can also
(183). This species has also been responsible for the global spread develop cholera through ingestion of contaminated shellfish or
of a pandemic clone, O3:K6, causing gastroenteritis in such di- seafood products containing high concentrations of V. cholerae.
verse locales as North, Central, and South America, the Indian For other Vibrio and Vibrio-like infections, the two major risk
subcontinent, parts of Africa and Europe, and Indonesia from factors for acquiring disease are consumption of contaminated
1996 through 2004 (184). Other clonal strains, such as O4:K12, seafood and foreign travel. Vibrio spp. have naturally been recov-
have caused more restricted outbreaks of disease, such as on the ered from many different types of seafood, including oysters, mus-
west coast of the United States (185). V. mimicus has been re- sels, clams, shrimp, and tilapia (197). A large number of seafood
ported to cause at least two outbreaks of diarrheal disease (186, vehicles have been implicated in vibriosis outbreaks associated
187). The number of studies and case reports worldwide describ- with non-V. cholerae vibrios (186, 193).
ing gastrointestinal infections cause by V. fluvialis seems to be
increasing as well (188, 189). In the United States, V. fluvialis is Yersinia enterocolitica and Yersinia pseudotuberculosis
typically the third most common Vibrio species associated with There are currently 18 species within the genus Yersinia, nine of
gastroenteritis, following V. parahaemolyticus and non-O1, non- which are isolated from humans. Yersinia enterocolitica, the most
O139 V. cholerae. well-established enteropathogen of the genera, has two subspecies
The chief clinical features of cholera are an afebrile, painless, described, Y. enterocolitica subsp. enterocolitica and Y. enteroco-
watery diarrhea associated with V. cholerae O1 El Tor infection, litica subsp. paleartica, which can be distinguished by sequencing

of the 16S rRNA gene (198). Y. enterocolitica subsp. paleartica difficulty swallowing and breathing, may occur and require im-
O:3/4 is the dominant serotype worldwide (199). Yersinia pseudo- mediate medical attention (161). In these cases, Y. enterocolitica
tuberculosis is also enteropathogenic but is more commonly asso- can be isolated from throat cultures.
ciated with sepsis. Y. frederiksenii, Y. kristensenii, Y. intermedia, Y. The two most common sequelae of Y. enterocolitica infection
mollarettii, Y. bercovieri, and Y. rohdei can be isolated from hu- are reactive arthritis and erythema nodosum, an immunologically
mans (including patients with diarrhea), but they are not believed mediated disease resulting in inflammation of subcutaneous adi-
to be pathogenic except in rare cases in individuals with underly- pose tissue with eruption of painful nodular lesions (205). In one
ing disorders (161, 200). Pathogenic strains of Y. enterocolitica are large study of 571 patients, 7% and 3% of 571 patients reported
determined by the biotype and serotype. reactive arthritis or erythema nodosum, respectively (205). The
Y. enterocolitica and Y. pseudotuberculosis can be isolated from a onset of reactive arthritis generally occurs 3 weeks after enteritis,
host of animals, birds, foods, and environmental sources (201). and the longer the duration of gastrointestinal symptoms, the
Animal sources of human infections include hares, rodents, cats greater the likelihood that reactive arthritis will develop (161).
(Y. pseudotuberculosis), and dogs (Y. enterocolitica). Environmen- Joint inflammation generally subsides spontaneously after 1 to 12
tal sources include soil, water, and sewage (161). Pigs are a major months, but 10% of patients will develop chronic arthritis (206).
reservoir for both Y. enterocolitica and Y. pseudotuberculosis infec- Approximately 80% of patients developing reactive arthritis carry
tions worldwide (201203). the HLA-B27 allele (206). Septic arthritis is less commonly en-
Between 1996 and 1999, FoodNet determined an annual inci- countered and is not associated with HLA-B27 (161).
dence of Y. enterocolitica in the United States of 1.0/100,000 per- Because some Y. enterocolitica serotypes are unable to synthe-
sons, with the greatest rates of infection in blacks and Asians (203). size siderophores (compounds that sequester iron from the host),
Between 1996 and 2009, FoodNet active surveillance noted a de- patients with iron overload disease are more susceptible to infec-
cline in the overall annual incidence (0.5/100,000 persons) of Y. tion (161, 201). Y. enterocolitica can be acquired from blood trans-
enterocolitica, with rates in blacks also declining from 3.9 to 0.4 per fusions, as the organism readily grows at lower temperatures used
100,000 by 2009 (203). The overall rate of Y. enterocolitica re- to store blood products. The development and severity of disease
ported by FoodNet in 2011 was 0.34 per 100,000 (143). The high are dependent on the species of Yersinia (other than Y. enteroco-
infection rate in blacks has been associated with homemade chit- litica) and the Y. enterocolitica bioserotype acquired (200, 204).
terlings (pork intestines), and educational efforts have been cited
as a possible explanation for the decrease in infections in this eth-
Emerging Enteropathogens
nic group. Infection rates are highest in children (201). In the
United States, 32% of cases occurred in children 1 year old and This guideline provides technical information on enteropatho-
47% in children 5 years old (203). Similar epidemiology is seen gens most commonly encountered in clinical practice; however,
outside the United States; in China, 44% of cases are reported in there are many additional bacteria that have been associated with
children 3 years of age (202). Y. enterocolitica infections are clas- gastroenteritis. Limited information is available for the majority
sically documented to occur in the autumn and winter; however, a of these, and they are reviewed elsewhere (207). Several of these
study of yersiniosis in Europe conducted over a 3-year period agents have enough clinical importance and high enough fre-
found no clear seasonal pattern (201, 202), and winter trends in quency to mention here. It should be stressed, however, that test-
yersiniosis in high-risk populations have also diminished in the ing for these organisms is not part of routine bacterial stool cul-
United States (203). tures in the clinical microbiology laboratory at this point, due to
Y. pseudotuberculosis most commonly causes mesenteric adeni- the difficulty in differentiating these organisms from resident flora
tis, which manifests as an appendicitis-like syndrome with fever in stool.
and right lower quadrant abdominal pain. Y. pseudotuberculosis Bacteroides fragilis. Strains of B. fragilis carrying an 6-kb
can also cause severe septicemia (161). Symptoms associated with pathogenicity island produce a zinc metalloprotease enterotoxin
sepsis include fever, diarrhea, abdominal pain or tenderness, an- that has been known by several different names, including B. fra-
orexia, nausea, vomiting, and malaise. Mortality rates range from gilis toxin and fragilysin (208, 209). These enterotoxigenic B. fra-
28% to 100% in treated and untreated cases, respectively (161). gilis strains (ETBF) not only have been implicated as a cause of
Y. enterocolitica gastrointestinal disease ranges from self-limit- diarrheal disease in children under 5 years of age but more recently
ing enteritis with diarrhea, low-grade fever, and abdominal pain have been associated with inflammatory diarrhea in children and
to severe disease such as terminal ileitis and mesenteric lymphad- adults (210). A meta-analysis of 17 studies that evaluated the as-
enitis which also mimics appendicitis (203205). Onset is gener- sociation of ETBF with diarrheal disease found that 12 (71%) of
ally 24 to 48 h following ingestion, with illness lasting between 7 the studies demonstrated a higher frequency of ETBF in patients
and 14 days, but symptoms may persist for up to 2 to 12 months with diarrhea than in controls (211). In contrast, a recent Indian
(201, 205). Bloody stools occur in 20 to 46% of cases, and host study found no difference in the rate of isolation of ETBF as a sole
susceptibility, number of ingested organisms, and serotype are pathogen from children with and without diarrhea (212). This
determining factors for severity of disease (201). Severe cases may suggests that other, mitigating factors may play a role in the infec-
require hospitalization due to dehydration; in one study, 27% of tive process for ETBF.
571 patients were hospitalized (205). Currently, there is no easy method to detect ETBF. Potential B.
Sepsis is uncommon and is often associated with cardiovascu- fragilis isolates can be recovered from stool on Bacteroides bile
lar, dermal, or pulmonary conditions and abscesses. Pharyngitis, esculin agar (Becton Dickinson, Sparks, MD) and then tested for
with sore throat and fever as the predominant symptoms, is not enterotoxigenicity in vitro using PCR for the Bacteroides fragilis
unusual in yersiniosis; in one multistate outbreak, 14 of 172 (8%) toxin gene (bft) (212). Alternatively, the cytopathic effect (CPE)
patients reported pharyngitis. Fulminant symptoms, including produced by fragilysin on HT29/C1 (human colon) cell lines can

be evaluated (211). Both methods are employed only for research patients requires detection of the species-specific K. oxytoca cyto-
purposes at this time. toxin by detection of CPE on HEp-2, CHO, or HeLa cells (232
Edwardsiella tarda. E. tarda is one of four species currently 234). In a recent study of 5,581 stool specimens submitted for C.
residing in the genus Edwardsiella of the family Enterobacteriaceae difficile testing at an acute-care health system in China, 2.1% of
and is the only species considered pathogenic for humans. A com- specimens harbored K. oxytoca, but only 29.1% of these strains
mon inhabitant of fish, reptiles, marine animals, and aquatic birds were cytotoxin producing (235).
(213, 214), E. tarda can also be recovered from water. Approxi- A second highly suggested, but unproven, syndrome attributed
mately 80% of reported human illnesses attributed to E. tarda to K. oxytoca is diarrhea. Although one study found no correlation
involve infections of the gastrointestinal tract (213). Data from a between the presence of K. oxytoca and diarrhea (236), a later
number of studies suggest that E. tarda is associated with 0.3% to study found a high percentage of cytotoxin-positive K. oxytoca
1.0% cases of gastroenteritis (161, 213). Asymptomatic carriage of isolated from patients with health care-associated diarrhea that
E. tarda has been reported (12). did not develop into AAHC (235). In the latter study, a specific
E. tarda-associated diarrhea can present in one of several selective medium termed SCITB (Simmons citrate-inositol-tryp-
forms, the most common of which is watery diarrhea. Other diar- tophan-bile salts) was developed to recover K. oxytoca from stools.
rheal syndromes linked to E. tarda include dysentery, chronic di- This medium has been shown to improve the recovery of K. oxy-
arrhea, and enteric fever (213, 215). Risk factors for acquiring E. toca over that with MacConkey (MAC) agar by 30% (235). This
tarda diarrhea include consumption of contaminated fish or sea- medium could greatly aid in determining the significance of K.
food, accidental ingestion of contaminated water, exposure to wa- oxytoca from mild to moderate cases of diarrhea.
ter from ornamental aquariums, and handling pet turtles (216 Providencia alcalifaciens. A British survey of travelers to Med-
221). Person-to-person transmission has also been postulated but iterranean countries between 1987 and 1988 found a significant
currently remains unsubstantiated (222). Two populations association between the recovery of P. alcalifaciens and diarrheal
thought to be particularly susceptible to E. tarda infection are disease (237). These initial findings have been subsequently sup-
persons 50 years of age and young children 5 years of age (213, ported by other studies describing individual cases of P. alcalifa-
223). ciens-associated diarrhea and at least three outbreaks of gastroin-
Escherichia albertii. E. albertii was described as a new species in testinal disease, including one large outbreak involving 270
the genus Escherichia in 2003 (224). Most of the initial strains were children in Japan (238240). P. alcalifaciens strains implicated in
misidentified as Hafnia alvei prior to the establishment of E. alber- diarrheal disease are invasive in HEp-2 cell monolayers, although
tii as a species and were isolated from fecal samples from Bangla- the type of diarrhea that they produce is secretory (239, 241); some
deshi children experiencing diarrheal illnesses. Subsequent evi- strains additionally produce a cytolethal distending toxin (242).
dence suggests that E. albertii is isolated fairly frequently from Persons most at risk of developing P. alcalifaciens diarrhea are
patients with diarrheal disease (225, 226). The organism harbors those who are involved in foreign travel or have consumed con-
known enteropathogenic virulence factors (227, 228) and has taminated foods containing the organisms (237, 243).
been associated with a major outbreak of gastroenteritis involving Most isolates of P. alcalifaciens recovered from diarrheal stools
48 persons (229). have been isolated in pure culture, as predominant flora, or with-
E. albertii grows well on routine enteric agars, is frequently out any other recognizable enteropathogens being detected (237,
misidentified biochemically as Hafnia, Salmonella, Citrobacter, or 240, 243). A selective medium, termed PAM (Providencia alcalifa-
inactive E. coli strains (230), and may not be included in the data- ciens medium), has been described for the recovery of this species
bases of commercial identification systems. The important phe- from feces (244). This medium has subsequently been modified as
notypic features distinguishing E. albertii from E. coli include a PMXMP (polymyxin-mannitol-xylitol medium for Providencia)
negative indole reaction and inability to ferment lactose, D-sorbi- and used with success (242, 243).
tol, and D-xylose (224). Phylogenetic studies indicate that Shigella
boydii type 13, already known not to belong to the true shigellae, is, GENERAL LABORATORY TESTING CONSIDERATIONS
in fact, a member of the species E. albertii (227). In the 10th edition At this time, diagnosis of bacterial gastroenteritis is by the routine
of the Manual of Clinical Microbiology, the species is broken down stool culture. Two key exceptions to this are the use of antigen
into two biogroups. Biogroup 1 represents the original E. albertii and/or nucleic acid amplification tests for the detection of (i) C.
strains and biogroup 2 represents isolates formerly referred to as S. difficile and, to a lesser extent, (ii) STEC and (iii) Campylobacter.
boydii 13. E. albertii can be identified by 16S rRNA gene sequenc- In addition, food poisoning caused by B. cereus, C. perfringens, and
ing and by matrix-assisted laser desorption ionizationtime of S. aureus is infrequently diagnosed by clinical laboratory testing,
flight mass spectrometry (MALDI-TOF MS). as few patients seek medical intervention for their symptoms,
Klebsiella oxytoca. Since the late 1970s and early 1980s, K. oxy- which are short-lived. In cases of outbreak investigations for these
toca has been sporadically linked to cases of antibiotic-associated organisms, feces, food, and/or vomitus is collected by, or sent to,
hemorrhagic colitis in Japan and other locations around the world local or state public health officials, and testing is performed at
(231). In 2006, in an elegant series of clinical observations and public health laboratories. Laboratory diagnosis of listeriosis as-
histopathological studies on six patients with antibiotic-associ- sociated with human diarrhea is also extremely difficult to make at
ated hemorrhagic colitis (AAHC) convincingly established K. oxy- this time. Diagnosis can be made either via epidemiological link-
toca as the etiological agent in persons negative for Clostridium age to other cases of diarrhea in which L. monocytogenes has been
difficile (232). C. difficile-negative patients who are at higher risk of isolated or by isolation and identification of L. monocytogenes
developing K. oxytoca colitis include those previously receiving from stool in persons with gastrointestinal symptoms (120). Cur-
penicillins or on nonsteroidal anti-inflammatory drugs (232). At rently there is no standard protocol for detection of listeriae from
present, confirmation of K. oxytoca colitis in C. difficile-negative human stools, and it is unclear what methods or procedures are

likely to yield maximum recovery rates. Because of these limita- value for repeat testing, regardless of method, for CDI (258260).
tions, recovery of L. monocytogenes from stool should not be at- In addition, many laboratories have developed rejection criteria
tempted routinely in clinical microbiology laboratories. This test- for specimens submitted within a defined interval of time follow-
ing is better suited to reference and/or public health laboratories. ing a positive result, as many patients will remain colonized with
C. difficile following successful treatment (70). Finally, C. difficile
Specimen Collection testing should not be performed on infants (i.e., patients 1 year
Feces collected in the acute phase of a diarrheal disease is the of age) due to their high colonization rate.
specimen of choice when bacterial gastroenteritis is suspected. If
liquid or soft, approximately 5 ml should be collected (245), and if Transport Media and Storage Conditions
formed, 0.5 to 2 g is adequate for culture (245, 246). Clear instruc- Transport media used for fecal specimens include Stuarts, Aimes,
tions should be given for proper specimen collection. Feces should or Cary-Blair (261, 262) medium. Fresh stool specimens should be
be collected in a clean, dry container with a tight lid and should transported to the laboratory and processed within 2 h of collec-
not be contaminated with urine, barium, or toilet paper (which tion (263); this is in particular critical to the survival of Shigella
may contain barium salts). Specimen containers or collection de- and Campylobacter (264). If the specimen cannot be processed
vices should be labeled with the patients full name and two addi- within 2 h, it should be placed in Cary-Blair transport medium;
tional patient identifiers, such as medical record number and date refrigeration of the specimen in Cary-Blair medium at 4C prior to
of birth. processing will best conserve bacterial enteropathogens, with the
Rectal swabs are generally considered less sensitive than stool exception of Shigella (265, 266).
for culture, but there are certain patient populations for which a
properly collected rectal swab may be acceptable. For instance, a Specimen Processing
rectal swab is a useful specimen to collect from infants and young Fecal specimens, if submitted fresh and not in preservative, should
children, or when trying to recover Shigella (247249). Rectal be macroscopically observed for areas that contain blood and/or
swabs must be inserted deep enough into the rectum, approxi- mucus, as these will contain the highest number of enteric patho-
mately 1 in. beyond the anal sphincter, and carefully rotated, so gens and should be used for culture. Gram staining is not typically
that feces can be collected and visible on the swab. The swab useful when performed on stool, with the key exception of cam-
should then be placed in all-purpose transport medium and sent pylobacteriosis. In these cases, again with fresh, unpreserved stool
to the laboratory. In addition to feces, blood, bone marrow, specimens, the characteristic seagull-shaped campylobacters can
and/or urine samples may be collected for patients presenting be visualized in stool when carbol-fuchsin is used as a counter-
with symptoms consistent with typhoid fever. Duodenal contents stain, with a sensitivity ranging from 66 to 94% in patients with
may also be acceptable for these cases. acute enteritis (48). However, Gram staining on stool specimens is
In cases of suspected extraintestinal Salmonella infections, not routinely performed as part of stool culture testing and should
blood and urine specimens should be collected in addition to be performed only on special request.
stool. In suspected cases of typhoid fever, blood and/or bone mar- The battery of primary plating media used for routine bacterial
row specimens should be collected in the first week of fever and fecal cultures will vary from laboratory to laboratory, depending
stool and urine in subsequent weeks. The yield of Salmonella Ty- on the patient population and organisms routinely isolated. Me-
phi is best from bone marrow, in particular after antimicrobials dium selection is also driven by test requisition. At a minimum,
have been started (250). routine fecal culture setup should be designed to optimize the
While in up to 94% of cases, the etiological agent is recovered recovery of Salmonella, Shigella, Campylobacter, and STEC. Thus,
from the first specimen submitted, collection of a second fecal fecal specimens received for culture should be planted to 4 media:
specimens may be needed to rule out a bacterial cause of infection, (i) MacConkey (MAC) agar, (ii) a selective/differential medium
especially in instances where patient symptoms persist (246). designed for the recovery of Salmonella and Shigella, (iii) a me-
Many have documented that the yield of fecal culture for patients dium designed for the recovery of Campylobacter, and (iv) a me-
hospitalized for more than 3 days is poor, excluding C. difficile (8, dium designed for the recovery of STEC O157 and/or enrichment
251257). For this reason, laboratories should restrict testing to broth for testing for the presence of Shiga toxins. Many laborato-
outpatients and those hospitalized for less than 3 days. Exceptions ries also include a blood agar plate (BAP), in order to aid with the
to this rule may include patients with HIV infection, severe neu- recovery of Aeromonas spp., Plesiomonas spp., and Vibrio spp.,
tropenia, suspected nondiarrheal manifestations of enteric infec- whereas other add this on request only. Table 2 presents an over-
tions (such as erythema nodosum, polyarthritis, etc.), a suspected view of some of the more common media used for fecal cultures,
nosocomial outbreak, or in some instances pediatric patients, their intended use, and growth characteristics of some of the
from whom collection of a specimen may be difficult in the first 3 more common enteropathogenic bacteria when isolated on
days of hospitalization. these media.
Similarly, laboratories should develop and enforce strict speci- Selective media appropriate for fecal cultures include xylose-
men rejection criteria for C. difficile testing. Testing should not be lysine-deoxycholate (XLD), salmonella-shigella (SS), Hektoen
performed on asymptomatic patients (i.e., those with formed enteric (HE), brilliant green (BG), or bismuth sulfite (BS) me-
stools), given the high rates of colonization among some patient dium or a chromogenic medium designed for the recovery and
populations. The exception to this policy is in cases where ileus is detection of specific enteropathogens. The value of chromogenic
suspected (89), although this occurrence is rare and should in- media has been demonstrated in a number of studies that reported
volve physician consultation with the laboratory prior to testing. improved sensitivity and specificity over traditional selective/dif-
Repeat testing of negative specimens should also be discouraged ferential media for the recovery of Salmonella, Shigella, STEC,
or altogether prohibited. Several studies have shown the lack of Vibrio, and Yersinia (267271). However, these media are more

TABLE 2 Commonly used media for recovery of pathogenic bacteria from stool samples
Medium Intended use and notes
All-purpose broths
Gram-negative (GN) broth Selective enrichment for Gram-negative rods, specifically Salmonella and Shigella (subculture after 6 8 h
of incubation, not part of routine setup unless for STEC EIA), can be used for STEC EIA
Selenite F broth Selective enrichment for Gram-negative rods, specifically Salmonella and Shigella (subculture after 18 24 h
of incubation, may inhibit growth of some Shigella species) (not part of routine setup)
Organism-specific broths
Alkaline peptone water Selective enrichment broth for Vibrio, when requested (subculture to TCBS after 24 h of incubation)
MAC broth Can be used for STEC EIA, enrichment for Y. enterocolitica if incubated at 25C (not part of routine setup)
All-purpose agars
Hektoen enteric (HE) Selective medium for Gram-negative rods, differentiates lactose fermenters (yellow-orange) from
nonfermenters (blue or green), H2S production can be detected (black precipitate)
MacConkey (MAC) Selective medium for Gram-negative rods, differentiates lactose fermenters (pink) from nonfermenters
(colorless)
Salmonella-shigella (SS) Selective medium for Gram-negative rods, differentiates lactose fermenters (pink/red) from nonfermenters
(colorless), H2S production can be detected (black precipitate)
Xylose-lysine-deoxycholate (XLD) Selective medium for Gram-negative rods, differentiates lactose fermenters (yellow) from nonfermenters
(red), H2S production can be detected (black precipitate)
Highly selective/differential agars

Bismuth sulfite Isolation of Salmonella, including Salmonella Typhi (black on this medium)
Brilliant green Isolation of Salmonella (red, pink, or white with red halo on this medium), inhibits Salmonella Typhi and
Salmonella Paratyphi
Blood agar with ampicillin Isolation of Aeromonas (not part of routine setup unless specifically requested)
Campy Blood Isolation of Campylobacter
Campy CVA Isolation of Campylobacter
Campylosel Isolation of Campylobacter
Cefsulodin-Irgasan-novobiocin (CIN) Isolation of Yersinia enterocolitica or Aeromonas (deep red center and transparent margin [bulls eye
appearance] on this medium) (not part of routine setup)
Charcoal selective Isolation of Campylobacter
Charcoal-cefoperazone-deoxycholate agar Isolation of Campylobacter
(CCDA)
CHROMagar Salmonella Isolation of Salmonella (mauve-rose on this medium)
CHROMagar O157 Isolation of O157 STEC (mauve on this medium)
CHROMagar STEC Isolation of 6 most common STEC serogroups (mauve on this medium)
Cycloserine-cefoxitin-egg Isolation of Clostridium difficile (not part of routine setup unless requested)
yolk/cycloserine-cefositin-fructose
HardyChrom SS Isolation of Salmonella (black on this medium) and Shigella (teal on this medium)
Inositol-brilliant green-bile salt Isolation of P. shigelloides (white to pink on this medium) (not part of routine setup unless requested)
MacConkey agar with sorbitol (SMAC) or Isolation of E. coli O157 (colorless on this medium)
cefixime-tellurite SMAC (CT-SMAC)
Thiosulfate-citrate-bile salts-sucrose (TCBS) Isolation of Vibrio (not part of routine setup unless requested), V. cholerae is yellow on this medium,
V. parahaemolyticus is green on this medium, some vibrios are inhibited
expensive than traditional media and are not available for in vitro The isolation and identification of STEC by culture methods is
diagnostic use for Vibrio and Yersinia in the United States at this problematic, with the exception of O157 strains, most of which
time. express a delayed or negative D-sorbitol reaction. Media to detect
Campylobacter selective media include the blood-free charcoal- sorbitol-negative E. coli O157 strains include sorbitol-MacConkey
cefoperazone-deoxycholate agar (CCDA) and charcoal-based se- (SMAC) agar and a modification on SMAC agar which contains
lective agar and the blood-based Campy-CVA (cefoperazone, cefixime and tellurite (CT-SMAC agar). Sorbitol-negative E. coli
vancomycin, and amphotericin) and Skirrow medium. While appears as colorless colonies on both of these media, but CT-
Campy-CVA is most widely used in the United States, the use of a SMAC agar has the advantage of eliminating many enteric flora that
combination of media, including one that is charcoal based, in- grow on SMAC agar, including commensal E. coli. CHROMagar
creases the yield of Campylobacter by 10 to 15% (49). Campylo- O157 detects O157 serogroups, and CHROMagar STEC detects
bacter cultures must be incubated in a microaerobic atmosphere, both O157 and the six most common STEC serogroups other than
typically 5% O2, 10% CO2, and 85% N2, and at 42C (48) to op- O157 isolated in the United States (O26, O45, O103, O111, O121,
timize recovery and prevent overgrowth of enteric organisms. and O145). This product is labeled for research use only in the
Campylobacter media should be incubated for a minimum of 48 h United States, but a recent study demonstrated that CHROMagar
and examined at 24 and 48 h. STEC had a sensitivity of 89.1% and specificity of 86.7% (272). In

contrast, a second study found the specificity of CHROMagar difficult for even specialized reference laboratories. Matrix-as-
STEC to be 98.9% (273). If a laboratory attempts to detect STEC, sisted laser desorption ionizationtime of flight mass spectrome-
an enrichment broth, typically GN broth, should also be inocu- try (MALDI-TOF MS) is a newer proteomic technology that has
lated and incubated at 37C overnight for detection of Stx1 and the potential to revolutionize the traditional algorithms used for
Stx2 by immunoassay. the identification of enteric pathogens (276), and it can be a more
Several enteric pathogens require highly selective media and cost-effective alternative to colony screening and biochemical
will not be optimally recovered by the selection of the 4 or 5 media testing.
described above for routine fecal cultures. These include aero- Traditional algorithms for the identification of enteric patho-
monads, vibrios, yersiniae, and a number of the emerging entero- gens. The traditional approach to fecal stool culture workup (ex-
pathogens. The cost-effectiveness of routinely culturing for these cluding Campylobacter and STEC, which are described further
organisms will depend on the patient population served by an below) is shown in Fig. 1A. The basis for this process is to mini-
individual laboratory and potentially on the peak time of the year mize the cost associated with differentiating the plethora of non-
that these pathogens are active. For example, laboratories in the pathogenic Enterobacteriaceae in a fecal specimen from the rare
Gulf States may consider routine use of media to optimize the Salmonella and Shigella, which are isolated in only 3 to 5% of fecal
recovery of vibrios in addition to the battery of primary stool specimens submitted for culture. Typically this is accomplished by
culture media. A variety of specialized media have been designed selecting lactose nonfermenters and/or H2S producers, isolated on
and are commercially available for the recovery of these patho- the primary plates, and submitting these to a secondary screening
gens, but clearly not all can be stocked by routine clinical labora- test. This second screen may not be required if laboratories are
tories. Two that might be considered for areas these pathogens are using a chromogenic medium as part of the primary setup (Fig.
more endemic include cefsulodin-Irgasan-novobiocin (CIN) agar 1C) or if the volume of fecal cultures is low enough that going
and thiosulfate-citrate-bile salts-sucrose (TCBS) agar. CIN agar is directly to an identification kit is cost-effective. Regardless, the
used to recover both Aeromonas and Yersinia enterocolitica, second screening method used by most laboratories consists of
whereas TCBS is used for the recovery of Vibrio (http://www.cdc subculturing suspicious colonies to one or more tubed/slanted
.gov/cholera/pdf/laboratory-methods-for-the-diagnosis-of-vibrio media. The classic three-tube system consists of a triple sugar
-cholerae-chapter-4.pdf). Of note, TCBS agar has a short shelf life iron (TSI) agar, a lysine iron agar (LIA), and a Christensen urea
and should be made only as needed (it requires no autoclaving). agar. Alternative tubed media for secondary screening include
While it is excellent for the recovery of V. cholerae and V. parah- motility-indole-ornithine (MIO), motility-indole-lysine (MIL),
aemolyticus, not all pathogenic vibrio species will grow on this and motility-indole-lysine-sulfide (MILS) (277280). The most
medium. For instance, Grimontia hollisae grows poorly if at all on common biochemical reactions for enteric pathogens on TSI agar,
TCBS agar. These species may be detected on blood agar, which LIA, and urea agar (negative unless otherwise noted) are listed in
can be screened for oxidase-positive or hemolytic colonies for Table 3.
further evaluation. If not specifically requested, identification of aeromonads,
An enrichment broth was traditionally inoculated as part of vibrios, and P. shigelloides may be overlooked by the above ap-
routine fecal cultures; this practice was originally designed to aid proach. In particular, some strains of Aeromonas and Vibrio are
in the recovery of low levels of Salmonella, Shigella, and Campylo- lactose positive on MAC or sucrose-positive on HE and XLD me-
bacter. However, many laboratories have discontinued this prac- dia. If necessary, these organisms can be identified by screening
tice, as the yield does not justify the cost (274). Historic data from the BAP for oxidase-positive or beta-hemolytic colonies. Caution
individual laboratories should be used to help determine if sub- must be exercised, however, as not all aeromonads are hemolytic,
cultures from enrichment broth should be used or discontinued. in particular some isolates of Aeromonas caviae. Oxidase-positive
A key exception to this is the use of alkaline peptone water, pH 8.5 isolates are then further screened by evaluating the reactions on
to 8.6, enrichment for a minimum of 6 to 8 h at 35C to 37C for TSI agar and LIA and through the use of O/129 disks and salt
the recovery of V. cholerae if necessary. Failure to use enrichment tolerance for vibrios.
culture in addition to direct plating will result in a significant If Yersinia culture is requested, it may be difficult to isolate
percentage of V. cholerae-containing stools being reported out as from feces using routine stool culture protocols, as at 35C the
negative (275). organism grows more slowly than other flora. It is occasionally
recovered as pinpoint colonies on MAC or SS agar at 24 h. These
Stool Culture Workup colonies should be reincubated at 25C if possible, and if the col-
Bacterial fecal culture workup consists of examining culture me- onies have grown after 24 h (to 1 mm), they should be examined
dia for colonies that display phenotypic properties consistent with for Yersinia; colonies that remain pinpoint are most likely fecal
those of enteric pathogens (e.g., lactose negative, H2S producers, streptococci. If CIN agar is used, yersiniae are identified as bulls-
etc.). These colonies are then traditionally further screened using eye colonies with pink centers on this medium, due to fermenta-
select biochemical tests and, if yielding reactions consistent with tion of D-mannitol. Aeromonas and some Citrobacter, Serratia,
an enteropathogen, identified by further biochemical and/or Proteus, and Morganella strains may mimic Y. enterocolitica colony
antigenic testing by a variety of algorithms. Ultimately, these morphology on this medium, and so these isolates require final
traditional methods yield a precise identification, but they are identification. One strategy is to perform Voges-Proskauer and
time-consuming and labor-intensive. Further, the biochemical motility tests at 25C and 35C; Y. enterocolitica and Y. pseudotu-
properties of certain bacterial isolates may differ from the com- berculosis should be positive only for these at 25C.
mon phenotype of the species, hampering unambiguous identifi- Isolates that yield reactions consistent with enteropathogens
cation. The classic example of this is an inert E. coli strain mason these secondary screening media are further identified using
querading as Shigella. Resolving these anomalous bacteria can be either a manual identification system such as API 20E or an auto-

FIG 1 Strategies for the detection of Salmonella and Shigella on routine stool cultures. Where Hektoen enteric (HE) agar is specified, any agar listed in the text
is appropriate. (A) Traditional approach to fecal stool culture workup for Salmonella and Shigella. See Table 3 for reactions of enteric pathogens. (B) Approach
to identification of Salmonella and Shigella when using MALDI-TOF MS. See Table 4 for reactions of enteric pathogens. (C) Approach to identification of
Salmonella and Shigella if chromogenic medium is used as part of the primary setup. (D) Approach to use of a multiplex molecular assay for the detection of
Salmonella and Shigella.
mated identification system such as MicroScan, Vitek2, Phoenix, Antigenic testing, for example, by latex agglutination for so-
MALDI-TOF MS, etc. These systems perform well at identifying matic antigen, can be used to identify Shigella to the species level,
some enteropathogens but fall short for others. For instance, com- as many commercial systems may misidentify these strains as E.
mercial systems are notoriously poor at the correct identification coli. Antigen testing for the somatic, flagellar, and capsular anti-
of Vibrio species to both the genus and species levels (281, 282). gens of Salmonella may also be used to supplement commercial
This is due in part to the salt requirement of halophilic species test system identifications. Caution must be employed, as some
such as V. parahaemolyticus and V. fluvialis and to the fact that Citrobacter and E. coli strains may posses the Salmonella Typhi Vi
some species are phenotypically similar. A prime example of this capsular antigen.
situation is the phenotypic similarity between V. fluvialis and cer- Campylobacter species can be identified based on characteristic
tain Aeromonas spp. For such situations, only a limited number of Gram stain morphology, growth on selective media at 42C, and
tests are available to separate these species, such as growth in 0% positive catalase and oxidase reactions alone. Campylobacter ap-
and 6% salt, O/129 susceptibility, and gas production from D-glu- pears as gray, flat colonies on plated media and often spreads along
cose, tests normally not available on commercial panels or in most the streak lines. Campylobacter latex agglutination kits are avail-
diagnostic laboratories. Similarly, most systems are unable to able for culture confirmation to genus level, but sensitivity and
identify Aeromonas, Salmonella, Shigella, or Yersinia beyond the specificity vary depending on the manufacturer (283). For the
genus level; however, in most instances, this level of identification most part, routine reporting of species-level identification of
is sufficient. Similarly, identification of Salmonella to the genus Campylobacter when isolated from stool is unnecessary. Campy-
level when isolated from stool is generally sufficient, and clinical lobacter jejuni can be readily differentiated from other thermotol-
laboratories should forward isolates to regional or state public erant Campylobacter spp. by the hydrolysis of sodium hippurate,
health laboratories for further characterization. However, labora- but as some C. jejuni strains fail to hydrolyze hippurate, hip-
tories may make a concerted effort to rule out typhoidal Salmo- puricase-negative isolates should be reported as Campylobacter
nella serotypes, if possible, given the clinical significance of these spp.
organisms or if there will be a delay getting the isolate to the public Sorbitol-nonfermenting E. coli isolated on SMAC or CT-
health laboratory. Salmonella Typhi can be differentiated from SMAC agar should be tested in O157-specific antiserum or latex
other serotypes by the characteristic weak H2S reaction on a TSI reagents in order to confirm O157 STEC. Caution must be used
slant and a negative ornithine decarboxylase reaction. Salmonella with these reagents, as other species of bacteria may cross-react
Paratyphi A can be differentiated from other salmonellae by neg- with O157 antiserum, requiring biochemical confirmation of E.
ative H2S, lysine, and citrate reactions. coli prior to reporting.

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TABLE 3 Summary of identification characteristics and diagnostic test methods available in the United Statesa
Clinical laboratory diagnostic test methods
Chromogenic Antigen Clinical symptoms Public health laboratory
Organism(s) Growth characteristics Key biochemical reactions Culture agar detection NAAT used for diagnosis referral
Aeromonas spp.b BA, beta-hemolytic Oxidase positive; TSI, K/A, gas;
LIA, K/A or A/A
Bacillus cereusb BA, beta-hemolytic Food and stool cultured for
outbreak investigations
Campylobacter spp. Campylobacter medium, gray-white colonies Oxidase positive, catalase positive,
sodium hippurate positive for
C. jejuni
Clostridium difficileb NA NA
Clostridium perfringensb NA NA Food and stool cultured for
Clinical Microbiology Reviews

Edwardsiella tardab Lactose nonfermenter with H2S production TSI, K/A, H2S, gas; LIA, K/K or
on HE, MAC, XLD, SS K/NC, H2S
Escherichia coli O157 SMAC, sorbitol nonfermenter TSI, K/A or A/A, gas; LIA, K/A or
A/A
Escherichia coli, STEC SMAC, sorbitol fermenter (unless O157) TSI, K/A or A/A, gas; LIA, K/A or
A/A
Listeria monocytogenesb BA, beta-hemolytic Food and stool cultured for
Salmonella spp. Lactose nonfermenter with H2S production TSI, K/A, H2S, gas; LIA, K/K or
on HE, MAC, XLD, SS A/A or K/NC (rare), H2S
Shigella spp. Lactose nonfermenter on HE, MAC, XLD, SS TSI, K/A; LIA, K/A or A/A
Staphylococcus aureusb NA NA Food and stool cultured for
Yersinia enterocoliticab CIN, pink bulls eye; lactose nonfermenter on TSI, A/A or K/A; LIA, K/A or A/A;
MAC; ferments sucrose on HE urea positive
Vibrio spp.b TCBS, sucrose fermentation seen with Oxidase positive; TSI, A/A or K/A;
V. cholerae; no sucrose fermentation for LIA, K/A or A/A
V. parahaemolyticus; V. vulnificus is
January 2015 Volume 28 Number 1

sucrose fermentation variable
a
Abbreviations: BA, blood agar; HE Hektoen enteric agar; MAC, MacConkey agar; XLD, xylose-lysine-deoxycholate agar; SS, salmonella-shigella agar; CIN, cefsulodin-Irgasan-novobiocin agar; TCBS, thiosulfate-citrate-bile salts-
sucrose agar; SMAC, MAC with sorbitol; TSI, triple sugar iron agar; LIA, lysine iron agar; A, acid; K, alkaline; NC, no change; NA, not applicable.
b
The organism is not part of the routine stool culture, and culture should be performed only on request.
MALDI-TOF MS. Because of the low cost associated with per- Antimicrobial Resistance Monitoring System (NARMS). Primary
forming a MALDI-TOF identification, many laboratories have agents used to treat Campylobacter include ciprofloxacin and
begun to identify bacterial isolates phenotypically consistent with erythromycin. Fluoroquinolone resistance has been reported with
enteric pathogens directly off the primary plates (Fig. 1B), rather increasing frequency in the United States among both human and
than performing additional screening tests. MALDI-TOF MS can animal isolates of C. coli and C. jejuni. In 1990, NARMS noted no
be performed within the FDA-approved package insert on colo- resistance to ciprofloxacin, whereas in 2011, 24.2% of Campylo-
nies picked from the primary BAP and, in the case of the Vitek MS, bacter isolates tested were resistant to ciprofloxacin (295). This
from the MAC plate. Alternatively, testing can be run as a labora- trend of increasing resistance may be related to the historical use
tory-developed test on colonies picked from other selective media of veterinary fluoroquinolones in animal feed as growth promot-
routinely used for stool cultures (XLD, SS, HE, etc.) (284). Some ers (296). In contrast, resistance to erythromycin remains low, at
have shown that SS and HE agars yield only genus-level identifi- 1.8% as reported in 2011. Because of increasing resistance, testing
cations (284). For Campylobacter, colonies isolated on Campylo- of Campylobacter isolates from individuals with severe illness or
sel and Columbia blood agar are FDA cleared on the Vitek MS and prolonged symptoms may be warranted. Susceptibility testing is
perform well for species-level identification (285288). In con- performed by broth microdilution in cation-adjusted Muller-
trast, spectra are not generated when isolates are taken directly Hinton broth (CA-MHB) and incubation in a microaerobic at-
from modified CCDA; colonies isolated on this medium require mosphere at either 35C or 42C. Disk diffusion for ciprofloxacin
subculture on a less selective medium prior to MALDI-TOF anal- and erythromycin can be performed; no zone of inhibition indi-
ysis (286). cates resistance, but the appearance of any zone of inhibition re-
MALDI-TOF MS performs well for the identification of Sal- quires confirmation by an MIC method (293).
monella (to the genus level), and Campylobacter. However, the Resistance documented by NARMS for nontyphoidal Salmo-
current IVD and RUO systems and databases cannot differentiate nella isolates to the antimicrobial agents commonly used to treat
E. coli from Shigella or E. coli from STEC or other E. coli patho- severe Salmonella infections was 2.5% to ceftriaxone, 1.2% to tri-
types and cannot identify Salmonella to the serotype (276). The methoprim-sulfamethoxazole, and 1% to ciprofloxacin (295).
technology is rapidly approaching these targets, through special In contrast, fluoroquinolone resistance was much higher in ty-
extraction protocols and selection of stable, pathogen-specific phoidal isolates, with 7.3% of Salmonella Typhi and 2.1% of Sal-
biomarkers (289292), which can be internally verified by indi- monella Paratyphi A isolates documented as resistant to cipro-
vidual laboratories. In addition, one or both of the IVD MALDI- floxacin. An additional 64.2% and 95.1% of these isolates,
TOF systems can be used to identify the other enteric pathogens respectively, had ciprofloxacin MICs in the intermediate range
described in this article, with the exceptions of B. cereus, P. shigel- (0.12 to 0.5 g/ml). Azithromycin is an alternative agent recom-
loides, E. albertii, and P. alcalifaciens. The performance of MALDI- mended for the treatment of invasive salmonellosis by the World
TOF MS is detailed in Table 4. Health Organization and the American Academy for Pediatrics.
However, no CLSI breakpoints exist at present for Salmonella for
Susceptibility Testing azithromycin. An epidemiological cutoff (ECOFF) (i.e., MIC cut-
Antimicrobials are not routinely indicated for the treatment of off defining the upper end of the wild-type population) of 32
otherwise healthy patients with bacterial gastroenteritis, as infec- g/ml has been used to indicate resistance, and based on this
tions typically resolve spontaneously. In some cases, the use of ECOFF, 0.2% of nontyphoidal Salmonella isolates were consid-
antimicrobials can be detrimental to the host, such as the use of ered resistant to azithromycin by the CDC 2011 NARMS data
antimicrobials for STEC infection, which puts the patient at in- (295).
creased risk for HUS, or for Salmonella, which may increase the Among Shigella isolates tested by NARMS in 2011, 2.4% were
rate of clinical relapse and prolong carriage (3). Routine suscepti- resistant to ciprofloxacin and 3.1% to azithromycin, again using
bility testing is therefore also not indicated for bacteria isolated an ECOFF breakpoint of 32 g/ml. Notably, resistance to azi-
from stool cultures (293, 294). Exceptions to this generalization thromycin was species dependent, with 10% of Shigella flexneri
may be bacteria isolated from infants 6 months of age, the el- isolates (n 58) testing resistant. Trimethoprim-sulfamethoxa-
derly or immunocompromised, or patients with prolonged dis- zole resistance among Shigella isolates in 2011 was high (66.9%),
ease. In these cases, communication with the physician will aid in whereas only 1.7% resistance to ceftriaxone was documented. If
determining the need for susceptibility testing and the antimicro- laboratories perform susceptibility testing on Salmonella or Shi-
bial agents to be tested. If the laboratory identifies Salmonella Ty- gella, it is important to remember that first- and second-genera-
phi or Salmonella Paratyphi A from stool, consideration should be tion cephalosporins, cephamycins, and aminoglycosides may to
given to susceptibility testing. Additionally, the isolation of any of be appear active in vitro but are not effective clinically, and the
the organisms described here from an extraintestinal site warrants isolates should not be reported as susceptible (294).
susceptibility testing. In 2009, the CDC started annually tracking antimicrobial resis-
Current standards for susceptibility testing conditions and in- tance in Vibrio spp other than V. cholerae as part of NARMS. In
terpretive criteria for members of the Enterobacteriaceae (E. coli, E. 2011, 95.1% of V. alginolyticus isolates were resistant to ampicillin,
tarda, Salmonella, Shigella, and Yersinia spp.) are available from whereas 40.3% of V. parahaemolyticus and 4.8% of V. vulnificus
the Clinical and Laboratory Standards Institute (CLSI) M100 S24 isolates were resistant (295). No isolates in 2011 tested resistant to
standard (294). Recommendations for Aeromonas, Campylobac- the fluoroquinolones or tetracycline, and 0.3% were resistant to
ter, and Vibrio are provided by the CLSI in the M45 A2 document trimethoprim-sulfamethoxazole. Antimicrobial therapy is not re-
(293). In the United States, the CDC monitors antimicrobial required to manage cholera but may shorten the duration and re-
sistance among Campylobacter, Salmonella, Shigella, E. coli O157, duce severity of disease. Similarly, otherwise healthy individuals
and Vibrio species other than V. cholerae as part of the National with diarrhea caused by non-V. cholerae Vibrio spp. usually re-

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TABLE 4 MALDI-TOF for the identification of enteric pathogens
Organism Performance of MALDI-TOFa FDA-cleared organismsb Notes Reference(s)
Aeromonas Present in IVD and commercial RUO databases; Biotyper, genus only; Vitek MS, genus only Preliminary data promising 322
performance not well documented
Campylobacter Excellent for genus and species identification; many species Vitek MS, C. jejuni, C. coli FDA cleared for colonies grown on Campylosel 285288
in RUO databases and brucella blood agar; cannot perform
directly from mCCC
E. tarda Present in IVD and commercial RUO databases; Vitek MS only
performance not well documented
Clinical Microbiology Reviews

P. shigelloides Present in commercial RUO databases; performance not No
well documented
Salmonella Good identification to genus Biotyper, genus only; Vitek MS, genus only Performance better with MAC vs SS or HE agar; 291, 323
serotype-specific biomarkers have been
identified
Shigella Cannot distinguish from E. coli by use of IVD or No Shigella-specific biomarkers have been 292
commercial RUO databases identified
STEC Cannot distinguish STEC (or other pathotypes) from E. No E. coli pathotype-specific biomarkers have been 290
coli by use of IVD or commercial RUO databases identified
Vibrio Present in IVD and commercial RUO databases; Vitek MS, V. cholerae, V. parahaemolyticus,
performance not well documented V. vulnificus
Yersinia Present in IVD and commercial RUO databases; Biotyper, Y. enterocolitica, Y. pseudotuberculosis;
performance not well documented Vitek MS, Y. enterocolitica, Y.
pseudotuberculosis, Y. frederikenii,
Y. intermedia, Y. kristensenii
a
IVD, in vitro diagnostic device; RUO, research use only.
b
FDA clearance as of 7 March 2014. Check with manufacturer or FDA.org for most up-to-date information.
January 2015 Volume 28 Number 1

TABLE 5 C. difficile diagnostic algorithms

Algorithm, test(s)a Result Action
GDH with reflex, GDH antigen Negative Report as no C. difficile present
Positive Reflex to NAAT; reporting based on NAAT results
GDH/toxin lateral-flow assay, GDH antigen and toxin A/B Both negative Report as no C. difficile present
Both positive Report as C. difficile toxin present
Negative/positive or positive/negative Reflex to NAAT
Toxin NAAT, NAAT Negative Report as no C. difficile present

Positive Report as C. difficile toxin present
a
GDH, glutamate dehydrogenase; NAAT, nucleic acid amplification test.
cover spontaneously. When indicated, vibrios can be tested for ing algorithms are outlined in Table 5: (i) performing a GDH EIA
susceptibility by a method similar to that used for the Enterobac- with follow-up confirmatory toxin NAAT on GDH-positive spec-
teriaceae. For testing halophilic species, preparation of the inocu- imens, (ii) performing a combination GDH and toxin A/B EIA
lum in 0.85% NaCl solution for both disk diffusion and broth and confirming specimens for which the two test results do not
microdilution testing is recommended by the CLSI (293). match by toxin NAAT, or (iii) performing NAAT alone on all
Susceptibility testing is not routinely indicated for C. difficile, as specimens.
most isolates are susceptible to both metronidazole and vancomy- In addition to C. difficile, STEC infections are increasingly being
cin, agents commonly used to treat CDI. Almost all cases are cur- diagnosed by culture-independent methods, as these methods al-
rently identified by nonculture methods. low for the detection of both O157 and non-O157 STEC infec-
tions (102). In 2009, the CDC published recommendations that
Nonculture Detection Methods
stool samples submitted from patients with acute community-
Recovery of C. difficile by anaerobic culture is possible but should acquired diarrhea and patients with possible HUS be simultane-
not be used as a primary diagnostic test for C. difficile infection ously cultured using selective and differential media for E. coli
because of long turnaround times. Rather, three test methods are O157 and assayed for the detection of Stx1 and Stx2 (102). The
commonly used detect the presence of toxigenic C. difficile in stool Joint Commission issued a change to the hospital laboratory Ele-
specimens. These methods are glutamate dehydrogenase (GDH) ment of Performance Standard for QSA.04.06.01 in 2013, which is
enzyme immunoassays (EIAs), toxin A/B enzyme immunoassays, consistent with the CDC recommendations. If laboratories are
and toxin A/B gene nucleic acid amplification tests (NAATs).
unable to perform a non-culture-based method for the detection
GDH is a cell wall enzyme that is abundant in C. difficile, and while
of non-O157 STEC, this testing should be sent to a reference lab-
EIAs for this antigen are a sensitive screen for the presence of C.
oratory. Laboratory testing options are shown in Table 6. Stx im-
difficile, they suffer from poor specificity, as they do not distin-
munoassays are performed on enrichment broths, typically GN
guish toxigenic from nontoxigenic strains (297). The presence of a
broth, that have been incubated at 37C overnight, and they detect
toxigenic strain must therefore be confirmed on all GDH-positive
(and in some cases differentiate) Stx1 and Stx2. Some assays are
specimens before a positive C. difficile result is reported. This can
also FDA cleared for use directly on stool, with no broth enrich-
be accomplished in a number of ways, including cell culture cyto-
toxicity neutralization assay (CCCN), but most laboratories per- ment, but performance varies among manufacturers. Several
form either a toxin A/B EIA or a toxin gene NAAT on GDH- studies have demonstrated improved sensitivity for the detection
positive specimens. Commercial toxin A/B EIAs suffer from poor of STEC over culture through the use of these immunoassays (307,
sensitivity compared to both cytotoxigenic culture and CCCN. 308), for both O157 and non-O157 STEC. Any broths that test
Sensitivity for the presence of toxigenic C. difficile is as low as 40 to positive for Stx should be forwarded to the local or state public
50% in some studies (297, 298). For this reason, detection of C. health laboratory for isolate recovery and further characterization.
difficile by toxin EIA alone is no longer considered adequate to rule The immunoassays can be performed off stool directly, but with
out CDI. Toxin gene NAATs offer the highest sensitivity and spec- much lower sensitivity (e.g., roughly 70%).
ificity among the different test options but are significantly more Finally, several antigen detection assays have been developed
expensive than the EIA-based methods. Furthermore, because for the detection of Campylobacter from stool specimens. These
toxin A and/or B is required for CDI, the clinical significance of enzyme immunoassays (EIAs) detect a surface antigen, called the
specimens that test negative for their presence by CCCN or EIA Campylobacter-specific antigen, by use of either a microplate or
but are positive by NAAT (or culture) has been brought into ques- lateral-flow immunochromatographic format. The antigen detec-
tion. Some have suggested that such cases represent colonization, tion assay does not differentiate between C. jejuni and C. coli.
rather than infection, by C. difficile (297, 299, 300). However, be- Several studies have reported that while these antigen tests are
cause of the poor sensitivity of the antigen tests for toxins A/B more rapid and convenient than culture, up to 50% of positive
compared to cytotoxicity assays, performing toxin A/B detection results cannot be confirmed by other methods (309313). Regard-
tests alone will miss clinically significant cases (298). less, due to the low positive predictive value of these tests, labora-
Many have proposed testing algorithms, using one or more of tories may elect to confirm antigen-positive specimens by culture
the three test methods, aimed at optimizing C. difficile diagnostic (310). Possible algorithms for the detection of Campylobacter are
performance and minimizing cost (301306). Three of these test- outlined in Table 7.

TABLE 6 Testing options for STEC

Option Procedurea Advantage(s) Disadvantage(s)
Culture for O157 (i) Plant specimen to chromogenic or selective Generates isolate for further Does not detect non-O157 STEC,
medium (SMAC, CT-SMAC), (ii) perform latex public health study does not detect sorbitol-
agglutination for O157 or MUG test to identify fermenting O157 STEC, misses
sorbitol-nonfermenting colonies of E. coli, non-O157 STEC
(iii) refer isolate to public health laboratory
Toxin testing (i) Inoculate specimen to GN broth and incubate Detects all STEC, may Requires additional work on part
overnight, (ii) perform antigen detection test for differentiate Stx1 and Stx2 of public health lab to find
Shiga toxins I and II; (iii) refer positive broths to STEC from GN broth, antigen
public health laboratory tests are expensive, may only
be 50% as sensitive as NAAT
Culture and toxin testing Perform both culture and toxin testing in parallel Covers all STEC, rapid recovery Cost and labor of additional
of most frequent serotype testing to laboratory
(O157)
Nucleic acid amplification test (i) Perform NAAT (laboratory developed or IVD) Most sensitive method, Not well validated to date, does
for stx1 and stx2 that detects the Shiga toxin genes directly from multiplex assays allow not yield isolate for public
stool, (ii) attempt to recover positive isolates, detection of many enteric health laboratory
inoculate to GN broth to forward to public pathogens
health laboratory, or forward positive
specimens to public health laboratory
a
SMAC, sorbitol MacConkey agar; CT-SMAC, cefixime-tellurite SMAC; MUG, 4-methylumbelliferyl--D-glucuronide.
Molecular Testing by Syndromic Panels GI Panel detects C. jejuni, C. coli, C. upsaliensis, C. difficile, P.
In recent years, syndromic panels for infectious diseases have shigelloides, Salmonella, Y. enterocolitica, V. parahaemolyticus, V.
gained popularity, in particular for screening patients who present vulnificus, V. cholerae, and the five diarrheagenic E. coli pathotypes
with influenza-like illness for respiratory viruses. As of the writing (enteroaggregative, enteropathogenic, enterotoxigenic, Shiga tox-
of this article, five multiplex nucleic acid tests were FDA approved in-producing, and enteroinvasive E. coli), along with Shigella. In
for the detection of organisms associated with gastroenteritis. The addition to the bacterial targets, the Biofire GI Panel detects Cryp-
Prodesse ProGastro SSCS assay (Hologic Gen-Probe, San Diego, tosporidium, Entamoeba histolytica, Cyclospora cayetanensis, Giar-
CA) detects Salmonella, Shigella, Campylobacter, and STEC. The dia lamblia, adenovirus 40/41, astrovirus, rotavirus A, sapovirus,
Luminex xTAG GPP detects the organisms listed above as well as and norovirus. While not FDA cleared, the Seeplex Diarrhea-V
C. difficile toxin A/B, adenovirus 40/41, rotavirus A, norovirus, ACE (Seegene, Seoul, South Korea) has received CE marking for
Giardia lamblia, Cryptosporidium, and Entamoeba histolytica. The use in Europe. Numerous laboratory-developed multiplexed mo-
BD MAX enteric bacterial panel (BD, Sparks, MD) detects C. je- lecular assays that target enteric bacterial pathogens directly from
juni and C. coli, Salmonella spp., Shigella spp./enteroinvasive E. fecal specimens have been described in the literature (314, 315).
coli (EIEC), and the stx1 and stx2 genes. The Nanosphere Verigene Use of these tests to replace conventional cultures remains con-
enteric pathogen test detects Campylobacter group, Salmonella troversial. While it is clear that molecular assays offer improved
spp., Vibrio group, Y. enterocolitica, and stx1 and stx2. The BioFire sensitivity over culture (314, 316), there are concerns regarding
TABLE 7 Testing options for Campylobacter

Option (time for
result) Procedurea Advantages Disadvantages
Culture (24 days) (i) Plant specimen to Campylobacter selective Yields an isolate (for public Requires special equipment (42C incubator,
medium and incubate at 42C under health or susceptibility ability to generate microaerobic
microaerobic conditions (report negative testing), most specific atmosphere), Campylobacter is fastidious
cultures after 48 72 h), (ii) Campylobacter method and many may not grow in culture unless
identified by Gram stain and positive conditions are ideal, takes 2 4 days for
catalase and oxidase reactions (or MALDI- result
TOF), (iii) Campylobacter latex or sodium
hippurate can be used to differentiate
C. jejuni
Antigen detection test Perform antigen detection test following Rapid, easily batched Concerns regarding specificity (may need to
(same day) manufacturers instructions confirm positive results by culture), does
not yield an isolate for further testing
NAAT Perform NAAT (LDT or IVD) that detects Most sensitive method, Not well validated to date, does not yield
Campylobacter directly from stool (may multiplex assays allow isolate for further testing
include extraction of nucleic acids) detection of many
enteric pathogens
a
NAAT, nucleic acid amplification test; LDT, laboratory-developed test; IVD, in vitro diagnostic device.

specificity issues for the highly multiplexed panels (317). These CONCLUDING REMARKS
molecular tests will detect organisms currently identified by rou- The potential number of bacteria associated with gastroenteritis is
tine stool cultures. However, it should be kept in mind that while now estimated to approach or exceed 40 individual species (207).
routine fecal cultures may detect less frequent enteropathogens, In contrast to this, both routine traditional and more contempo-
they are designed to optimize recovery of Salmonella, Shigella, rary molecular methods may screen for only 4 or 5 organisms (3,
Campylobacter, and STEC. Perhaps the most pressing concern re- 246, 319). The number and type of agents routinely sought by the
garding the uptake of this new technology is that testing does not microbiology laboratory should be driven by geographic locale
yield an isolate that could be used for surveillance for antimicro- and patient history (foreign travel, disease symptomatology and
bial resistance or for subtyping to support the identification and underlying preexisting medical conditions). The importance of
investigation of outbreaks. Thus, laboratories that opt to use mo- laboratory-clinician communication cannot be overemphasized
lecular assays should consult with their local or state public health for complicated cases, as patient-tailored testing is rarely feasible
laboratory to determine whether specimens positive for Salmo- with the limited patient information that accompanies specimens
nella, Shigella, Campylobacter, or STEC should be forwarded to the received by the laboratory. Similarly, laboratories should ensure
local or state public health laboratory for epidemiological studies that physicians understand what organisms are screened for by the
(Fig. 1D). routine bacterial stool culture, as this is infrequently apparent to
the general practitioner or even to many specialists. This being
said, all clinical laboratories that perform stool cultures can pro-
Reporting Results vide useful information for patients with Salmonella, Shigella,
The laboratory report should reflect results for each organism STEC, and Campylobacter. The future role of bacterial stool cul-
routinely included in screening. For example, a negative routine tures may be diminished by the emergence of nonculture diagnos-
fecal culture should be reported as no Salmonella, Shigella, Cam- tic test methods for enteric pathogens. However, several pressing
pylobacter, or STEC isolated. If the laboratory routinely adds a issues remain regarding these new technologies, including the per-
TCBS for the detection of Vibrio, a negative result would be indi- formance of these tests and the issue of not providing an isolate to
cated by no Salmonella, Shigella, Campylobacter, STEC, or Vibrio the public health laboratory as has been the practice in the past.
isolated. In contrast, recovery of any enteric pathogen, including These concerns are yet to be resolved (320). Nonetheless, these
those not specifically screened for, should be reported. The follow- technologies have the potential for routine detection of entero-
ing organisms, for which the clinical significance of a stool isolate pathogens that have eluded most clinical microbiology laborato-
is less clear, should be reported with an indication of the number ries to date.
of colonies recovered on the primary plates: Aeromonas, P. shigel-
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Romney M. Humphries, Ph.D., D(ABMM), is Andrea J. Linscott, Ph.D., D(ABMM), is the

an Assistant Professor in the Department of Pa- clinical microbiologist in the Department of Pa-
thology and Laboratory Medicine in the David thology at Ochsner Health System, New Or-
Geffen School of Medicine at the University of leans, LA. She received her Ph.D. at the Univer-
California, Los Angeles. She is also the Section sity of North Texas under the direction of the
Chief for Clinical Microbiology at the UCLA late Dr. Gerard A. ODonovan. Dr. Linscott
Health System and program codirector for completed an ASM Committee on Postgradu-
UCLAs Committee on Postgraduate Education ate Education Programs (CPEP) fellowship in
Programs (CPEP) fellowship program. Dr. medical and public health microbiology at the
Humphries received her undergraduate degree University of California, Los Angeles. She has
in biochemistry from the University of Leth- served as committee member for both CPEP
bridge, Canada. She completed her Ph.D. in bacterial pathogenesis in the and ABMM. Her main passion is making clinical microbiology approachable
laboratory of Dr. Glen Armstrong at the University of Calgary, Canada. for all levels of expertise through either written words or lecture.
There, she investigated novel anti-infective strategies for the prevention of
bacterial gastroenteritis caused by enteropathogenic Escherichia coli. She
subsequently completed a CPEP fellowship in medical and public health
microbiology at the University of California, Los Angeles, under the direc-
tion of Dr. Michael Lewinski. At UCLA, under the guidance of Ms. Janet
Hindler, Dr. Humphries developed a passion for antimicrobial susceptibility
testing in the clinical laboratory. Her research focuses include the detection
and characterization of pathogens that cause gastrointestinal diseases and
the development of novel methods for detection and characterization of
emerging antimicrobial resistance.

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PRACTICAL GUIDANCE FOR CLINICAL MICROBIOLOGY (FORMERLY CUMITECHS)

Laboratory Diagnosis of Bacterial Gastroenteritis

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TABLE 1 Types of bacterial gastroenteritisa

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Highly selective/differential agars

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Clinical Microbiology Reviews

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Clinical Microbiology Reviews

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TABLE 5 C. difficile diagnostic algorithms

Toxin NAAT, NAAT Negative Report as no C. difficile present

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TABLE 6 Testing options for STEC

TABLE 7 Testing options for Campylobacter

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