Some studies reported up to 80% of patients with irritable bowel syndrome (IBS) have SIBO (using the hydrogen breath test). Subsequent studies demonstrated statistically significant reduction in IBS symptoms following therapy for SIBO.

There is a lack of consensus however, regarding the suggested link between IBS and SIBO. Other authors concluded that the abnormal breath results so common in IBS patients do not suggest SIBO, and state that "abnormal fermentation timing and dynamics of the breath test findings support a role for abnormal intestinal bacterial distribution in IBS." There is general consensus that breath tests are abnormal in IBS; however, the disagreement lies in whether this is representative of SIBO. More research is needed to clarifiy this possible link.

Certain people are more predisposed to the development of bacterial overgrowth because of certain risk factors. These factors can be grouped into three categories: (1) disordered motility or movement of the small bowel or anatomical changes that lead to stasis, (2) disorders in the immune system and (3) conditions that cause more bacteria from the colon to enter the small bowel.

Problems with motility may either be diffuse, or localized to particular areas. Diseases like scleroderma and possibly celiac disease cause diffuse slowing of the bowel, leading to increased bacterial concentrations. More commonly, the small bowel may have anatomical problems, such as out-pouchings known as diverticula that can cause bacteria to accumulate. After surgery involving the stomach and duodenum (most commonly with Billroth II antrectomy), a "blind loop" may be formed, leading to stasis of flow of intestinal contents. This can cause overgrowth, and is termed "blind loop syndrome".

Disorders of the immune system can cause bacterial overgrowth. Chronic pancreatitis, or inflammation of the pancreas can cause bacterial overgrowth through mechanisms linked to this. The use of immunosuppressant medications to treat other conditions can cause this, as evidenced from animal models. Other causes include inherited immunodeficiency conditions, such as common variable immunodeficiency, IgA deficiency, and hypogammaglobulinemia.

Finally, abnormal connections between the bacteria-rich colon and the small bowel can increase the bacterial load in the small bowel. Patients with Crohn's disease or other diseases of the ileum may require surgery that removes the ileocecal valve connecting the small and large bowel; this leads to an increased reflux of bacteria into the small bowel. After bariatric surgery for obesity, connections between the stomach and the ileum can be formed, which may increase bacterial load in the small bowel.

Proton pump inhibitors, a class of medication that are used to reduce stomach acid, is associated with an increased risk of developing SIBO.

In recent years, several proposed links between SIBO and other disorders have been made. However, the usual methodology of these studies involves the use of breath testing as an indirect investigation for SIBO. Breath testing has been criticized by some authors for being an imperfect test for SIBO, with multiple known false positives.

Hospitals are primary transmission sites for CRE-based infections. Up to 75% of hospital admissions attributed to CRE were from long-term care facilities or transferred from another hospital. Suboptimal maintenance practices are the largest cause of CRE transmission. This includes the failure to adequately clean and disinfect medication cabinets, other surfaces in patient rooms, and portable medical equipment, such as X-ray and ultrasound machines that are used for both CRE and non-CRE patients.

Thus far, CRE have primarily been nosocomial infectious agents. Almost all CRE infections occur in people receiving significant medical care in hospitals, long-term acute care facilities, or nursing homes. Independent risk factors for CRE infection include use of beta-lactam antibiotics and the use of mechanical ventilation. Patients with diabetes have also been shown to be at an elevated risk for acquiring CRE infections. When compared to other hospitalized patients, those admitted from long-term acute care (LTAC) facilities have significantly higher incidence of colonization and infection rates. Another 2012 multicenter study found that over 30% of patients with recent exposure to LTAC were colonized or infected with CRE. A person susceptible to CRE transmission is more likely to be female, have a greater number of parenteral nutrition-days (meaning days by which the person received nutrition via the bloodstream), and to have had a significant number of days breathing through a ventilator.

Infections with carbapenem-resistant "Klebsiella pneumoniae" were associated with organ/stem cell transplantation, mechanical ventilation, exposure to antimicrobials, and overall longer length of stay in hospitals.

People most likely to acquire carbapenem-resistant bacteria are those already receiving medical attention. In a study carried out at Sheba medical center, there was a trend toward worse Charleson Comorbidity scores in patients who acquired CRKP during ICU stay. Those at highest risk are patients receiving an organ or stem cell implantation, use of mechanical ventilation, or have to have an extended stay in the hospital along with exposure to antimicrobials. In a study performed in Singapore, the acquisition of ertapenem-resistant Enterobacteriaceae to the acquisition of CRE. Exposure to antibiotics, especially fluoroquinolones, and previous hospitalization dramatically increased the risk of acquisition carbapenem-resistant bacteria. This study found that carbapenem-resistant acquisition has a significantly higher mortality rate and poorer clinical response compared to that of the ertapenem-resistance acquisition.

Bacteruria (also known as urinary tract infection) caused by CRKp and CSKp have similar risk factors. These include prior antibiotic use, admittance to an ICU, use of a permanent urinary catheter, and previous invasive procedures or operations. A retrospective study of patients with CRKp and CSKp infection asserted that the use of cephalosporins (a class of β-lactam antibiotics) used before invasive procedures was higher in patients with CRKp infection, suggesting that it is a risk factor.

In a three-year study, the prevalence of CRE was shown to be proportional to the lengths of stays of the patients in those hospitals. Policies regarding contact precaution for patients infected or colonized by Gram-negative pathogens were also observed in hospitals reporting decreases in CRE prevalence.

One case study showed that patients with a compromised immune response are especially susceptible to both CRE exposure and infection. In one study, an elderly patient with acute lymphoblastic leukemia being treated in a long-term care facility contracted a CRE infection. Her age and condition, combined with her environment and regulation by a catheter and mechanical ventilation, all contributed to a higher susceptibility. This highlights the importance of finding the source of the bacteria, as members of this class of patients are at continued risk for infection. Infection control and prevention of CRE should be the main focus in managing patients at high risk.

Another major risk factor is being in a country with unregulated antibiotic distribution. In countries where antibiotics are over-the counter and obtainable without a prescription, the incidence and prevalence of CRE infections were higher. One study from Japan found that 6.4% of healthy adults carried ESBL (mostly cefotaximase)-producing strains compared to 58.4% in Thailand, where antibiotics are available over the counter and without prescription. An Egyptian research group found that 63.3% of healthy adults were colonized.

In February 2015, the FDA reported about a transmission risk when people undergo a gastroenterology procedure called endoscopic retrograde cholangiopancreatography, where an endoscope enters the mouth, passes the stomach, and ends in the duodenum; if incompletely disinfected, the device can transmit CRE from one patient to another. The FDA's safety communication came a day after the UCLA Health System, Los Angeles, notified more than 100 patients that they may have been infected with CRE during endoscopies between October 2014 and January 2015. The FDA had issued its first notice about the devices in 2009.

There are several risk factors that increase the likelihood of developing bacteremia from any type of bacteria. These include:

- HIV infection

- Diabetes Mellitus

- Chronic hemodialysis

- Solid organ transplant

- Stem cell transplant

- Treatment with glucocorticoids

- Liver failure

Gram negative bacterial species are responsible for approximately 24% of all cases of healthcare-associated bacteremia and 45% of all cases of community-acquired bacteremia. In general, gram negative bacteria enter the bloodstream from infections in the respiratory tract, genitourinary tract, gastrointestinal tract, or hepatobiliary system. Gram-negative bacteremia occurs more frequently in elderly populations (65 years or older) and is associated with higher morbidity and mortality in this population.

"E.coli" is the most common cause of community-acquired bacteremia accounting for approximately 75% of cases. E.coli bacteremia is usually the result of a urinary tract infection. Other organisms that can cause community-acquired bacteremia include "pseudomonas aeruginosa", "klebsiella pneumoniae", and "proteus mirabilis". "Salmonella" infection, despite mainly only resulting in gastroenteritis in the developed world, is a common cause of bacteremia in Africa. It principally affects children who lack antibodies to Salmonella and HIV+ patients of all ages.

Among healthcare-associated cases of bacteremia, gram negative organisms are an important cause of bacteremia in the ICU. Catheters in the veins, arteries, or urinary tract can all create a way for gram negative bacteria to enter the bloodstream. Surgical procedures of the genitourinary tract, intestinal tract, or hepatobiliary tract can also lead to gram negative bacteremia. "Pseudomonas" and "enterobacter" species are the most important causes of gram negative bacteremia in the ICU.

CRE resistance depends upon a number of factors such as the health of the patient, whether the patient has recently undergone a transplant, risk of co-infection, and use of multiple antibiotics.

Carbapenem minimal inhibitory concentrations (MICs) results may be more predictive of clinical patient outcomes than the current categorical classification of the MICs being listed as susceptible, intermediate, or resistant. The study aimed to define an all-cause hospital mortality breakpoint for carbapenem MICs that were adjusted for risk factors. Another objective was to determine if a similar breakpoint existed for indirect outcomes, such as the time to death and length of stay after infection for survivors. Seventy-one patients were included, of which 52 patients survived and 19 patients died. Classification and regression tree analysis determined a split of organism MIC between 2 and 4 mg/liter and predicted differences in mortality (16.1% for 2 mg/liter versus 76.9% for 4 mg/liter). In logistic regression controlling for confounders, each imipenem MIC doubling dilution doubled the probability of death. This classification scheme correctly predicted 82.6% of cases. Patients were accordingly stratified to MICs of ≤2 mg/liter (58 patients) and ≥4 mg/liter (13 patients). Patients in the group with a MIC of ≥4 mg/liter tended to be more ill. Secondary outcomes were also similar between groups. Patients with organisms that had an MIC of ≥4 mg/liter had worse outcomes than those with isolates of an MIC of ≤2 mg/liter.

At New York Presbyterian Hospital, part of Columbia University Medical Center in New York, NY, a study was conducted on the significant rise in carbapenem resistance in "K. pneumoniae" from 1999 to 2007. Following a positive blood culture from a patient, overall mortality was 23% in 7 days, 42% in 30 days, and 60% by the end of hospitalization. The overall in-hospital mortality rate was 48%.

At Soroka Medical Center, an Israeli university teaching hospital, a study was done between October 2005 and October 2008 to determine the direct mortality rate associated with carbapenem-resistant "K. pneumoniae" bloodstream infections. The crude mortality rate for those with the resistant bacteremia was 71.9%, and the attributable mortality rate was determined to be 50% with a 95% confidence interval. The crude mortality rate for control subjects was 21.9%. As a result of the study, Soroka Medical Center started an intensive program designed to prevent the spread of carbapenem-resistant "K. pneumoniae."

A 2013 retrospective study at the Shaare Zedek Medical Center of patients with urinary tract infections (bacteriuria) caused by carbapenem-resistant "Klebsiella pneumoniae" (CRKp) showed no statistically significant difference in mortality rates from patients with bacteriuria caused by carbapenem-susceptible "K. pneumoniae" (CSKp). A 29% mortality rate was seen in patients with CRKp infection compared to a 25% mortality rate in patients with CSKp infections that produced extended-spectrum beta-lactamase (ESBL). Both mortality rates were considerably higher than that of patients with drug-susceptible urosepsis. Most patients in the study suffered from other illnesses, including dementia, immune compromise, renal failure, or diabetes mellitus. The main risk factor for death found by the study was being bedridden, which significantly increased the chance of death. This suggests that the deaths were due to reasons other than bacteriuria. Total length of hospitalization was somewhat longer in patients with CRKp infections (28 ± 33 days compared to 22 ± 28 days for patients with CSKp infection).

In a case-control study of 99 patients compared with 99 controls at Mount Sinai Hospital (Manhattan), a 1,171 bed tertiary care teaching hospital, 38% of patients in long-term care that were afflicted with CRE died from "K. pneumoniae" infection. Patients had risk factors including diabetes, HIV infection, heart disease, liver disease, renal insufficiency, one was a transplant recipient. 72% of patients who were released from the hospital with CRE were readmitted within 90 days.

A 2008 study at Mount Sinai identified outcomes associated with Carbapenem-resistant "Klebsiella pneumoniae" infections, in which patients in need of organ or stem cell transplants, mechanical ventilation, prolonged hospitalization, or prior treatment with carbapenems, had an increased probability of infection with Carbapenem-resistant "K. pneumoniae". A combination of antibiotics worked to treat infection and survival rates of infected patients increased when the focus of infection was removed.

CRE infections can set in about 12 days after liver transplantation, and 18% of those patients died a year after transplantation in a 2012 study.

Enteroinvasive "Escherichia coli" (EIEC) is a type of pathogenic bacteria whose infection causes a syndrome that is identical to shigellosis, with profuse diarrhea and high fever. EIEC are highly invasive, and they use adhesin proteins to bind to and enter intestinal cells. They produce no toxins, but severely damage the intestinal wall through mechanical cell destruction.

It is closely related to "Shigella".

After the "E. coli" strain penetrates through the epithelial wall, the endocytosis vacuole gets lysed, the strain multiplies using the host cell machinery, and extends to the adjacent epithelial cell. In addition, the plasmid of the strain carries genes for a type III secretion system that is used as the virulent factor. Although it is an invasive disease, the invasion usually does not pass the submucosal layer. The similar pathology to shigellosis may be because both strains of bacteria share some virulent factors. The invasion of the cells can trigger a mild form of diarrhea or dysentery, often mistaken for dysentery caused by "Shigella" species. The illness is characterized by the appearance of blood and mucus in the stools of infected individuals or a condition called colitis.

Dysentery caused by EIEC usually occurs within 12 to 72 hours following the ingestion of contaminated food. The illness is characterized by abdominal cramps, diarrhea, vomiting, fever, chills, and a generalized malaise. Dysentery caused by this organism is generally self-limiting with no known complications.

Enterovirulent classes of "E. coli" are referred to as the EEC group (enterovirulent "E. coli"):

1. Enteroinvasive "E. coli" (EIEC) invades (passes into) the intestinal wall to produce severe diarrhea.

2. Enterohemorrhagic "E. coli" (EHEC): A type of EHEC, "E. coli" 0157:H7, can cause bloody diarrhea and hemolytic uremic syndrome (anemia and kidney failure).

3. Enterotoxigenic "E. coli" (ETEC) produces a toxin that acts on the intestinal lining, and is the most common cause of traveler's diarrhea.

4. Enteropathogenic "E. coli" (EPEC) can cause diarrhea outbreaks in newborn nurseries.

5. Enteroaggregative "E. coli" (EAggEC) can cause acute and chronic (long-lasting) diarrhea in children.

It is currently unknown what foods may harbor EIEC, but any food contaminated with human feces from an ill individual, either directly or via contaminated water, could cause disease in others. Outbreaks have been associated with hamburger meat and unpasteurized milk.

Immunodeficiency or immunosuppression can be caused by:

- Malnutrition

- Fatigue

- Recurrent infections

- Immunosuppressing agents for organ transplant recipients

- Advanced HIV infection

- Chemotherapy for cancer

- Genetic predisposition

- Skin damage

- Antibiotic treatment leading to disruption of the physiological microbiome, thus allowing some microorganisms to outcompete others and become pathogenic (e.g. disruption of intestinal flora may lead to "Clostridium difficile" infection

- Medical procedures

- Pregnancy

- Ageing

- Leukopenia (i.e. neutropenia and lymphocytopenia)

The lack of or the disruption of normal vaginal flora allows the proliferation of opportunistic microorganisms and will cause the opportunistic infection - bacterial vaginosis.

Opportunistic infections caused by Feline Leukemia Virus and Feline immunodeficiency virus retroviral infections can be treated with Lymphocyte T-Cell Immune Modulator.

The common routes of transmission for the disease-causing bacteria are fecal-oral, person-to-person sexual contact, ingestion of contaminated food (generally unpasteurized (raw) milk and undercooked or poorly handled poultry), and waterborne (i.e., through contaminated drinking water). Contact with contaminated poultry, livestock, or household pets, especially puppies, can also cause disease.

Animals farmed for meat are the main source of campylobacteriosis. A study published in PLoS Genetics (September 26, 2008) by researchers from Lancashire, England, and Chicago, Illinois, found that 97 percent of campylobacteriosis cases sampled in Lancashire were caused by bacteria typically found in chicken and livestock. In 57 percent of cases, the bacteria could be traced to chicken, and in 35 percent to cattle. Wild animal and environmental sources were accountable for just three percent of disease.

The infectious dose is 1000–10,000 bacteria (although ten to five hundred bacteria can be enough to infect humans). "Campylobacter" species are sensitive to hydrochloric acid in the stomach, and acid reduction treatment can reduce the amount of needed to cause disease.

Exposure to bacteria is often more common during travelling, and therefore campylobacteriosis is a common form of travelers' diarrhea.

The World Health Organization recommends the following:

- Food should be properly cooked and hot when served.

- Consume only pasteurized or boiled milk and milk products, never raw milk products.

- Make sure that ice is from safe water.

- If you are not sure of the safety of drinking water, boil it, or disinfect it with chemical disinfectant.

- Wash hands thoroughly and frequently with soap, especially after using the toilet and after contact with pets and farm animals.

- Wash fruits and vegetables thoroughly, especially if they are to be eaten raw. Peel fruits and vegetables whenever possible.

- Food handlers, professionals and at home, should observe hygienic rules during food preparation.

- Professional food handlers should immediately report to their employer any fever, diarrhea, vomiting or visible infected skin lesions.

Travelers often get diarrhea from eating and drinking foods and beverages that have no adverse effects on local residents. This is due to immunity that develops with constant, repeated exposure to pathogenic organisms. The extent and duration of exposure necessary to acquire immunity has not been determined; it may vary with each individual organism. A study among expatriates in Nepal suggests that immunity may take up to seven years to develop—presumably in adults who avoid deliberate pathogen exposure.

Conversely, immunity acquired by American students while living in Mexico disappeared, in one study, as quickly as eight weeks after cessation of exposure.

The primary source of infection is ingestion of fecally contaminated food or water. Attack rates are similar for men and women.

The most important determinant of risk is the traveler's destination. High-risk destinations include developing countries in Latin America, Africa, the Middle East, and Asia. Among backpackers, additional risk factors include drinking untreated surface water and failure to maintain personal hygiene practices and clean cookware. Campsites often have very primitive (if any) sanitation facilities, making them potentially as dangerous as any developing country.

Although traveler's diarrhea usually resolves within three to five days (mean duration: 3.6 days), in about 20% of cases, the illness is severe enough to require bedrest, and in 10%, the illness duration exceeds one week. For those prone to serious infections, such as bacillary dysentery, amoebic dysentery, and cholera, TD can occasionally be life-threatening. Others at higher-than-average risk include young adults, immunosuppressed persons, persons with inflammatory bowel disease or diabetes, and those taking H2 blockers or antacids.

Micro-organisms are known to survive on inanimate ‘touch’ surfaces for extended periods of time. This can be especially troublesome in hospital environments where patients with immunodeficiencies are at enhanced risk for contracting nosocomial infections.

Touch surfaces commonly found in hospital rooms, such as bed rails, call buttons, touch plates, chairs, door handles, light switches, grab rails, intravenous poles, dispensers (alcohol gel, paper towel, soap), dressing trolleys, and counter and table tops are known to be contaminated with "Staphylococcus", MRSA (one of the most virulent strains of antibiotic-resistant bacteria) and vancomycin-resistant "Enterococcus" (VRE). Objects in closest proximity to patients have the highest levels of MRSA and VRE. This is why touch surfaces in hospital rooms can serve as sources, or reservoirs, for the spread of bacteria from the hands of healthcare workers and visitors to patients.

A number of compounds can decrease the risk of bacteria growing on surfaces including: copper, silver, and germicides.

In Belgium the prevalence of nosocomial infections is about 6.2%. Annually about 125,500 patients become infected by a nosocomial infection, resulting in almost 3000 deaths. The extra costs for the health insurance are estimated to be approximately €400 million/year.

Common multidrug-resistant organisms are usually bacteria:

- Vancomycin-Resistant Enterococci (VRE)

- Methicillin-Resistant "Staphylococcus" "aureus" (MRSA)

- Extended-spectrum β-lactamase (ESBLs) producing Gram-negative bacteria

- "Klebsiella" "pneumoniae" carbapenemase (KPC) producing Gram-negatives

- Multidrug-Resistant gram negative rods (MDR GNR) MDRGN bacteria such as "Enterobacter species", "E.coli", "Klebsiella pneumoniae", "Acinetobacter baumannii", "Pseudomonas aeruginosa"

A group of gram-positive and gram-negative bacteria of particular recent importance have been dubbed as the ESKAPE group ("Enterococcus faecium", "Staphylococcus aureus", "Klebsiella pneumoniae", "Acinetobacter baumannii", "Pseudomonas aeruginosa" and Enterobacter species).

- Multi-drug-resistant tuberculosis

HCAP is a condition in patients who can come from the community, but have frequent contact with the healthcare environment. Historically, the etiology and prognosis of nursing home pneumonia appeared to differ from other types of community acquired pneumonia, with studies reporting a worse prognosis and higher incidence of multi drug resistant organisms as etiology agents. The definition criteria which has been used is the same as the one which has been previously used to identify bloodstream healthcare associated infections.

HCAP is no longer recognized as a clinically independent entity. This is due to increasing evidence from a growing number of studies that many patients defined as having HCAP are not at high risk for MDR pathogens. As a result, 2016 IDSA guidelines removed consideration of HCAP as a separate clinical entity.

Multiple drug resistance (MDR), multidrug resistance or multiresistance is antimicrobial resistance shown by a species of microorganism to multiple antimicrobial drugs. The types most threatening to public health are MDR bacteria that resist multiple antibiotics; other types include MDR viruses, fungi, and parasites (resistant to multiple antifungal, antiviral, and antiparasitic drugs of a wide chemical variety). Recognizing different degrees of MDR, the terms extensively drug resistant (XDR) and pandrug-resistant (PDR) have been introduced. The definitions were published in 2011 in the journal "Clinical Microbiology and Infection" and are openly accessible.

In some studies, the bacteria found in patients with HCAP were more similar to HAP than to CAP; compared to CAP, they could have higher rates of "Staphylococcus aureus" ("S. aureus") and "Pseudomonas aeruginosa", and less "Streptococcus pneumoniae" and "Haemophilus influenzae". In European and Asian studies, the etiology of HCAP was similar to that of CAP, and rates of multi drug resistant pathogens such as "Staphylococcus aureus" and "Pseudomonas aeruginosa" were not as high as seen in North American studies. It is well known that nursing home residents have high rates of colonization with MRSA. However, not all studies have found high rates of S. aureus and gram-negative bacteria. One factor responsible for these differences is the reliance on sputum samples and the strictness of the criteria to discriminate

between colonising or disease-causing bacteria. Moreover, sputum samples might be less frequently obtained in the elderly.Aspiration (both of microscopic drops and macroscopic amounts of nose and throat secretions) is thought to be the most important cause of HCAP. Dental plaque might also be a reservoir for bacteria in HCAP.

Bacteria have been the most commonly isolated pathogens, although viral and fungal pathogens are potentially found in immunocompromised hosts (patients on chronic immunosuppressed medications, solid organ and bone marrow transplant recipients). In general, the distribution of microbial pathogens varies among institutions, partly because of differences in patient population and local patterns of anti microbial resistance in hospitals and critical care units' Common bacterial pathogens include aerobic GNB, such as "Pseudomonas aeruginosa", "Acinetobacter baumanii", "Klebsiella pneumoniae", "Escherichia coli" as well as gram-positive organisms such as "Staphylococcus aureus". In patients with an early onset pneumonia (within 5 days of hospitalization), they are usually due to anti microbial-sensitive bacteria such as "Enterobacter" spp, "E. coli", "Klebsiella" spp, "Proteus" spp, "Serratia mare scans", community pathogens such as "Streptococcus pneumoniae, Haemophilus influenzae", and methicillin-sensitive "S. aureus" should also be considered.

Pneumonia that starts in the hospital tends to be more serious than other lung infections because: people in the hospital are often very sick and cannot fight off germs. The types of germs present Ina hospital are often more dangerous and more resistant to treatment than those outside in the community. Pneumonia occurs more often in people who are using a respirator. This machine helps them breathe. Hospital-acquired pneumonia can also be spread by health care workers, who can pass germs from their hands or clothes from one person to another. This is why hand-washing, wearing grows, and using other safety measures is so important in the hospital.

One study suggests that on very long trips in the wilderness, taking multivitamins may reduce the incidence of diarrhea.

The risk of acquiring infectious diarrhea in the wilderness arises from inadvertent ingestion of pathogens. Various studies have sought to estimate diarrhea attack rates among wilderness travelers, and results have ranged widely. The variation of diarrhea rate between studies may depend on the time of year, the location of the study, the length of time the hikers were in the wilderness,

the prevention methods used, and the study methodology.

The National Outdoor Leadership School (NOLS), which emphasizes strict hand-washing techniques, water disinfection and washing of common cooking utensils in their programs, reports that gastrointestinal illnesses occurred at a rate of only 0.26 per 1000 program days. In contrast, a survey of long-distance Appalachian Trail hikers found more than half the respondents reported at least one episode of diarrhea that lasted an average of two days. (Infectious diarrhea may last longer than an average of two days; certain forms of non-infectious diarrhea, caused by diet change etc., can be of very brief duration). Analysis of this survey found occurrence of diarrhea was positively associated with the duration of exposure in the wilderness. During any given four-week period, as many as 7.2% of Americans may experience some form of infectious or non-infectious diarrhea. A number of behaviors each individually reduced the incidence of diarrhea: treating water; routinely washing hands with soap and water after defecation and urination; cleaning cooking utensils with soap and warm water; and taking multi-vitamins.

A variety of pathogens can cause infectious diarrhea, and most cases among backpackers appear to be caused by bacteria from feces. A study at Grand Teton National Park found 69% of diarrhea affected visitors had no identifiable cause, that 23% had diarrhea due to "Campylobacter" and 8% of patients with diarrhea had giardiasis. Campylobacter enteritis occurred most frequently in young adults who had hiked in wilderness areas and drunk untreated surface water in the week prior. Another study tested 35 individuals before and after a trip to the Desolation Wilderness of California. Giardia cysts were found in fecal samples from two people after the trip, but they were asymptomatic. A third person was empirically treated for symptoms of giardiasis.

Fecal-oral transmission may be the most common vector for wilderness acquired diarrhea. There are differing opinions regarding the importance of routine disinfection of water during relatively brief backcountry visits.

In Germany, 90% of cases of infectious enteritis are caused by four pathogens, Norovirus, Rotavirus, "Campylobacter" and "Salmonella". Other common causes of infectious enteritis include bacteria such as "Shigella" and "E. coli," as well as viruses such as adenovirus, astrovirus and calicivirus. Other less common pathogens include "Bacillus cereus, Clostridium perfringens, Clostridium difficile" and "Staphylococcus aureus".

"Campylobacter jejuni" is one of the most common sources of infectious enteritis, and the most common bacterial pathogen found in 2 year old and smaller children with diarrhoea. It has been linked to consumption of contaminated water and food, most commonly poultry and milk. The disease tends to be less severe in developing countries, due to the constant exposure which people have with the antigen in the environment, leading to early development of antibodies.

Rotavirus is responsible for infecting 140 million people and causing 1 million deaths each year, mostly in children younger than 5 years. This makes it the most common cause of severe childhood diarrhoea and diarrhea-related deaths in the world. It selectively targets mature enterocytes in the small intestine, causing malabsorption, as well as inducing secretion of water. It has also been observed to cause villus ischemia, and increase intestinal motility. The net result of these changes is induced diarrhoea.

Enteritis necroticans is an often fatal illness, caused by β-toxin of "Clostridium perfringens". This causes inflammation and segments of necrosis throughout the gastrointestinal tract. It is most common in developing countries, however has also been documented in post-World War II Germany. Risk factors for enteritis necroticans include decreased trypsin activity, which prevent intestinal degradation of the toxin, and reduced intestinal motility, which increases likelihood of toxin accumulation.

Fever and sickness behavior and other signs of infection are often taken to be due to them. However, they are evolved physiological and behavioral responses of the host to clear itself of the infection. Instead of incurring the costs of deploying these evolved responses to infections, the body opts to tolerate an infection as an alternative to seeking to control or remove the infecting pathogen.

Subclinical infections are important since they allow infections to spread from a reserve of carriers. They also can cause clinical problems unrelated to the direct issue of infection. For example, in the case of urinary tract infections in women, this infection may cause preterm delivery if the person becomes pregnant without proper treatment.

The CDC recommends hand-washing and avoiding potentially contaminated food and untreated water.

Boiling suspect water for one minute is the surest method to make water safe to drink and kill disease-causing microorganisms such as "Giardia lamblia" if in doubt about whether water is infected. Chemical disinfectants or filters may be used.

According to a review of the literature from 2000, there is little evidence linking the drinking of water in the North American wilderness and Giardia. CDC surveillance data (for 2005 and 2006) reports one outbreak (6 cases) of waterborne giardiasis contracted from drinking wilderness river water in Colorado. However, less than 1% of reported giardiasis cases are associated with outbreaks.

Person-to-person transmission accounts for the majority of "Giardia" infections and is usually associated with poor hygiene and sanitation. "Giardia" is found on the surface of the ground, in the soil, in undercooked foods, and in water, and on hands without proper cleaning after handling infected feces. Water-borne transmission is associated with the ingestion of contaminated water. In the U.S., outbreaks typically occur in small water systems using inadequately treated surface water. Venereal transmission happens through fecal-oral contamination. Additionally, diaper changing and inadequate hand washing are risk factors for transmission from infected children. Lastly, food-borne epidemics of "Giardia" have developed through the contamination of food by infected food-handlers.

Some intestinal parasitic infections may play a role in irritable bowel syndrome and other long-term sequelae.