Infectious Disease Compendium



(2017 IDSA Guidelines)(2014 Review)

There are a lot of quantitative scientific definitions of diarrhea. For me, like Justice Potter (PubMed), I know it when I see it. Suffice it to say, if you have frequent soft or watery or bloody diarrhea and get A LOT of reading done, you have diarrhea.

Stool cultures and now multiplex PCR are the way to diagnose. Although the PCR technology will find more pathogens than the culture, it it very costly: "Pathogen recovery from CIDT-positive specimens varied based on pathogen type: Salmonella (72%), Shigella (64%), STEC (57%), and Campylobacter (26%) (PubMed)."

Stool for WBC, despite the official recommendations, rarely adds to the workup of the case as it is neither specific nor sensitive and it usually doesn't change whether or not you send all the other studies.

Also, stool for O&P is a waste of time on any patient who develops diarrhea greater then 48 hours after admission. Unless, of course, you have a specific history that suggests a parasite. Or a really bad cafeteria.

Stool cultures have almost no yield if the patient has been in the hospital for more than 3 days (unless you have a hospital acquired outbreak) (PubMed).

Interestingly, IBS is a common sequela of most bacterial enteritis (PubMed), (PubMed).

Epidemiologic Risks

You eat the pathogen in one form or another, see the microbiology below. It is rarely the last meal eaten as it takes time for the organisms to multiple and cause disease. But everyone credits the last meal as the source.

The food at the store comes from all over the world, and with food comes the stool and pathogens of the humans and animals from the farm of origin. Please member that food often has animal poo on it. There was an outbreak of E. coli O157/HUS on strawberries linked to deer poop and Campylobacter on peas linked to wild birds. Fried food: mans greatest invention to prevent infectious gastroenteritis. The even have deep fried beer.

From the CDC, these are the top ten foods most likely to make you sick:

Leafy greens were involved in 363 outbreaks and about 13,600 illnesses, mostly caused by norovirus, E. coli, and salmonella.

Eggs, involved in 352 outbreaks and 11,163 reported cases of illness. Tuna, involved in 268 outbreaks and 2,341 reported cases of illness. Oysters, involved in 132 outbreaks and 3,409 reported cases of illness. Potatoes, involved in 108 outbreaks and 3,659 reported cases of illness. Cheese, involved in 83 outbreaks and 2,761 reported cases of illness. Ice cream, involved in 74 outbreaks and 2,594 reported cases of illness. Tomatoes, involved in 31 outbreaks and 3,292 reported cases of illness. Sprouts, involved in 31 outbreaks and 2,022 reported cases of illness. Berries, involved in 25 outbreaks and 3,397 reported cases of illness.

I am bummed to see ice cream on the list, but gratified that beer was not. Win a few, lose a few.

And more from the CDC (PubMed): "Increased risk for enteric infection among workers in agriculture, health care, food, and personal care occupations might be related to workplace exposures to pathogens. Campylobacteriosis or salmonellosis should be considered when workers have symptoms compatible with these diseases." What? I should think of those organisms in patients with compatible symptoms? What a concept.

And if Yelp suggests GI symptoms after a visit to a restaurant, take it seriously. The NY Health Department used Yelp to identify outbreaks that would have otherwise been missed (PubMed).

Don't think bottled water is protective; in Spain it was the source of norovirus (PubMed).

Diarrhea is common in the ICU, it is usually neither infectious or C. difficile. ICU diarrhoea (worse than diarrhea) is usually NOT infectious (at 9%), specifically NOT C. difficile, but is associated with a worser outcome (PubMed). Not that C. difficile isn't an infection (PubMed).

Of course, it comes down to whether or not you are a mutant. As the title says, and it says it all, "Single Nucleotide Polymorphisms in the Promoter of the Gene Encoding the Lipopolysaccharide Receptor CD14 Are Associated With Bacterial Diarrhea in US and Canadian Travelers to Mexico."

Warm weather is bacillary diarrhea weather "a 1°C rise in mean temperature, mean maximum temperature, and mean minimum temperature might lead to 14.8%, 12.9%, and 15.5% increases in the incidence of bacillary dysentery disease, respectively." (PubMed). Many of the bacillary diarrheas are increasing as the world warms: Campylobacter, Vibrio and E. coli (Pubmed).

Kudoa septempunctata causes watery diarrhea from eating sushi from Paralichthys olivaceus (olive flounder ) with > 1300 people involved in Japan. I just know that will be on the ID Boards (PubMed).

Prevention with probiotics? Short answer: they decrease antibiotic associated diarrhea by about 42%, but the studies are, well, crappy (PubMed). Yes I can stoop that low.

Probiotics are also beneficial in preventing C. difficile, in one meta analysis by 66% (Reference). I tend to suggest yogurt over the pills.

One good randomized trial demonstrated no benefit from probiotics (PubMed), so who do you believe? The meta or the good trial? At what point to you let the preponderance of data overrule an individual study (PubMed)? Got me. For Salmonella probiotics did not do sh....... anything (PubMed).

The most recent review confuses me (PubMed): it says that probiotics prevent C. difficile associated diarrhea but not C. difficile infection and I will be damned if I can find a definition of either in the text. Are they not the same?

For travelers diarrhea, use of an alcohol hand sanitizer can help prevent illness and save a vacation (PubMed). PO alcohol has not been systematically evaluated, at least as a diarrhea preventative.

PPI's increase the risk not only for gastroenteritis but hospitalization as well (PubMed). Acid is good man. Just not the brown acid (Reference).


Aeromonas, Bacillus, Bacteroides fragilis (it can cause a "marked abdominal pain and nonfebrile inflammatory diarrhea" due to an enterotoxin (PubMed)), E. coli, E. albertii, Entamoeba histolytica, Campylobacter, Clostridia difficile, CMV, Cyclosporidia, Cryptosporidia (MSM a risk), Giardia, Isospora, Klebsiella oxytoca (associated with antibiotic associated hemorrhagic colitis with Augmentin the most common culprit (PubMed, PubMed), Kudoa septempunctata, Listeria monocytogenes (your lab will not be looking for it), Laribacter, Norovirus (10% of hospitalized diarrhea will be due to Noro; major cause, especially in outbreaks and 15% of travelers, especially to Mexico (Pubmed)), Plesiomonas, Salmonella, Sapovirus, Shigella (MSM a risk), Vibrio (Cholera is found in the US SW (PubMed)), Yersinia. And more. Diarrhea is popular in the microbial world as a way to reproduce.

Bradyrhizobium enterica in patients with umbilical-cord hematopoietic stem-cell transplantation.

Empiric Therapy

Depends on which of the above organisms you are concerned about. Most will get better on their own and do not need treatment. For bacillary diarrhea, usually a quinolone or rifaximin except for Campylobacter jejuni which is resistant to quinolones.

Travelers diarrhea can be prevented with a quinolone or rifaximin (PubMed); it is about 50% effective and the number needed to treat is 6. So is it worth it? For the individual who has spent significant time and money to travel, probably. As another drop in the bucket of world wide antibiotic use promoting resistance, I am not so sure

If you treat Clostridia difficile empirically it may result in false-negative PCR: "For PCR, 14%, 35%, and 45% of positive CDI tests converted to negative after 1, 2, and 3 days of treatment, respectively (PubMed)."

If you suspect E. coli O157:H7 and its brethren, avoid quinolones as it markedly up regulates toxin in comparison to other antibiotics (PubMed), although that test tube pearl is not supported clinically (PubMed).

Some E. albertii can be enterohemorrhagic or enteropathogenic and misidentified by the lab as E. coli (PubMed), can cause outbreaks (PubMed), and is almost certainly missed by your lab.

For TREATMENT of travelers diarrhea, a quinolone may be better than rifaximin (PubMed). Or not. A single-dose azithromycin, levofloxacin, or rifaximin with loperamide were equal for the treatment of acute watery travlers diarrhea (PubMed).

Curiously, prevention of travelers diarrhea prevents irritable bowel syndrome.

Irritable Bowel Syndrome: rifaximin 400 mg tid po for 10 days decreases symptoms of IBS by 40% for 10 weeks (PubMed).


If you suspect Hemolytic-Uremic Syndrome (HUS) and/or E. coli O157:H7 or O111, may not want to treat as you are more likely to progress to HUS. There is increasing data to suggest that irritable bowel syndrome is common after bacillary diarrhea (PubMed).

Loperamide is of benefit in travelers diarrhea (PubMed).

Be wary of where you eat: 4% of food handlers at luxurious tourist hotels in Nairobi, Kenya had pathogenic E. coli.

Norovirus can cause chronic diarrhea in transplant and hematologic malignancy patients.


Stool for WBC, despite the official recommendations, rarely adds to the workup of the case as it is neither specific nor sensitive and it usually doesn't change whether or not you send all the other studies.

Also, stool for O&P is a waste of time on any patient who develops diarrhea greater then 48 hours after admission. Unless, of course, you have a specific history that suggests a parasite. Or a really bad cafeteria.

Curious Cases

Relevant links to my Medscape blog

With three letters I predict the future.

Gimme that old time diarrhea

Don't ask, but you will receive anyway

235 days later

A Sigh. Then a Diagnosis or Two.

The Flux

Last Update: 06/21/18.