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Table 27.

Laboratory Diagnosis of Gastroenteritis, Infectious, and Toxin-Induced Diarrhea

Abbreviations: CMV, cytomegalovirus; DFA, direct fluorescent immunoassay; EDTA, ethylenediaminetetraacetic acid; EHEC, enterohemorrhagic ; EIA, enzyme immunoassay; GDH, glutamate dehydrogenase; NAAT, nucleic acid amplification test; PVA, polyvinyl alcohol; RT, room temperature; SAF, sodium acetate formalin transport.

A routine stool culture in most laboratories is designed to detect spp, spp, spp, and O157 or Shiga toxin–producing .

If the specimen cannot be transported to the laboratory within 2 hours, then it should be placed in vial containing Cary-Blair transport medium and transported to the laboratory within 24 hours.

It is recommended that laboratories routinely process stool specimens for the presence of Shiga toxin–producing strains of including O157:H7. However, in some settings, this testing may be done only on specific request.

Available as part of some multiplex panels.

Specialized cultures are required to detect these organisms in stool specimens. In many cases, such cultures are performed only in public health laboratories and only in the setting of an outbreak. The laboratory should be notified whenever there is a suspicion of infection due to one of these pathogens.

, , and cause diarrheal syndromes that are toxin mediated. An etiologic diagnosis is made by demonstration of toxin in stool. Toxin assays are either performed in public health laboratories or referred to laboratories specializing in such assays.

Testing for toxin is either performed in public health laboratories or referred to laboratories specializing in such testing. The toxin is lethal and special precautions are required for handling. Note that it is considered a bioterrorism agent and rapid sentinel laboratory reporting schemes must be followed. Immediate notification of a suspected case to the state health department is mandated. For this purpose, 24-hour hotlines are available.

Implicated food materials may also be examined for toxin, but most hospital laboratories are not equipped for food analysis.

The role of as a pathogen remains controversial. In the absence of other pathogens, it may be important where symptoms persist. Reporting semi-quantitative results (rare, few, many) can help determine significance and is a College of American Pathologists accreditation requirement for participating laboratories.

Detection of in immunocompromised patients may require the use of Baermann technique or agar plate culture.

and testing is often offered and performed together as the primary parasitology examination. Further studies should follow if a travel history or clinical symptoms suggest parasitic disease.

These stains may not be routinely available.

Also available as part of some multiplex panels.

Asymptomatic shedding is common.

Norovirus antigen assays have limited sensitivity and specificity and are not recommended for clinical use.

Enteric adenoviruses may not be recovered in routine viral culture.

A negative viral load test does not necessarily rule out CMV disease. Gastrointestinal disease due to CMV may be present in patients with negative viral load.

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Table 27.

Laboratory Diagnosis of Gastroenteritis, Infectious, and Toxin-Induced Diarrhea

Abbreviations: CMV, cytomegalovirus; DFA, direct fluorescent immunoassay; EDTA, ethylenediaminetetraacetic acid; EHEC, enterohemorrhagic ; EIA, enzyme immunoassay; GDH, glutamate dehydrogenase; NAAT, nucleic acid amplification test; PVA, polyvinyl alcohol; RT, room temperature; SAF, sodium acetate formalin transport.

A routine stool culture in most laboratories is designed to detect spp, spp, spp, and O157 or Shiga toxin–producing .

If the specimen cannot be transported to the laboratory within 2 hours, then it should be placed in vial containing Cary-Blair transport medium and transported to the laboratory within 24 hours.

It is recommended that laboratories routinely process stool specimens for the presence of Shiga toxin–producing strains of including O157:H7. However, in some settings, this testing may be done only on specific request.

Available as part of some multiplex panels.

Specialized cultures are required to detect these organisms in stool specimens. In many cases, such cultures are performed only in public health laboratories and only in the setting of an outbreak. The laboratory should be notified whenever there is a suspicion of infection due to one of these pathogens.

, , and cause diarrheal syndromes that are toxin mediated. An etiologic diagnosis is made by demonstration of toxin in stool. Toxin assays are either performed in public health laboratories or referred to laboratories specializing in such assays.

Testing for toxin is either performed in public health laboratories or referred to laboratories specializing in such testing. The toxin is lethal and special precautions are required for handling. Note that it is considered a bioterrorism agent and rapid sentinel laboratory reporting schemes must be followed. Immediate notification of a suspected case to the state health department is mandated. For this purpose, 24-hour hotlines are available.

Implicated food materials may also be examined for toxin, but most hospital laboratories are not equipped for food analysis.

The role of as a pathogen remains controversial. In the absence of other pathogens, it may be important where symptoms persist. Reporting semi-quantitative results (rare, few, many) can help determine significance and is a College of American Pathologists accreditation requirement for participating laboratories.

Detection of in immunocompromised patients may require the use of Baermann technique or agar plate culture.

and testing is often offered and performed together as the primary parasitology examination. Further studies should follow if a travel history or clinical symptoms suggest parasitic disease.

These stains may not be routinely available.

Also available as part of some multiplex panels.

Asymptomatic shedding is common.

Norovirus antigen assays have limited sensitivity and specificity and are not recommended for clinical use.

Enteric adenoviruses may not be recovered in routine viral culture.

A negative viral load test does not necessarily rule out CMV disease. Gastrointestinal disease due to CMV may be present in patients with negative viral load.

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Stool culture is indicated for detection of invasive bacterial enteric pathogens. When culture methods are employed, most laboratories routinely detect Salmonella , Shigella , and Campylobacter and, more recently, Shiga toxin–producing E. coli in all stools submitted for culture. Salmonella spp can take 24–72 hours to recover and identify to genus alone with the specific serotyping usually performed at the public health laboratory level. It is recommended that tests for the detection of Shiga toxin, or tests to specifically detect Shiga toxin–producing E. coli O157:H7 or other Shiga toxin–producing serotypes, be included as part of the routine test. However, in some settings, these tests may require a specific request. Tests that detect only E. coli O157:H7 will not detect the increasing number of non-O157 isolates being reported and may not detect all E. coli O157:H7 [ 143 ]. Screening algorithms that limit testing to bloody stools may also miss both O157 and non-O157 isolates. Screening of stool for toxin-producing E. coli is recommended for all pediatric patients.

Note that this attribute merely informs the compiler that a function always returns a sufficiently aligned pointer. It does not cause the compiler to emit code to enforce that alignment. The behavior is undefined if the returned poitner is not sufficiently aligned.

The alloc_size attribute can be placed on functions that return pointers in order to hint to the compiler how many bytes of memory will be available at the returned pointer. alloc_size takes one or two arguments.

Argument numbers are 1-based.

An example of how to use alloc_size

Note

This attribute works differently in clang than it does in GCC. Specifically, clang will only trace pointers (as above); we give up on pointers that are not marked as . In the vast majority of cases, this is unimportant, because LLVM has support for the attribute. However, this may cause mildly unintuitive behavior when used with other attributes, such as .

artificial (gnu::artificial)

The attribute can be applied to an inline function. If such a function is inlined, the attribute indicates that debuggers should associate the resulting instructions with the call site, rather than with the corresponding line within the inlined callee.

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Marks a function that dynamically tests whether a capability is held, and halts the program if it is not held.

Use __attribute__((assume_aligned(<alignment>[,<offset>])) on a function declaration to specify that the return value of the function (which must be a pointer type) has the specified offset, in bytes, from an address with the specified alignment. The offset is taken to be zero if omitted.

Note that this attribute provides information to the compiler regarding a condition that the code already ensures is true. It does not cause the compiler to enforce the provided alignment assumption.

The availability attribute can be placed on declarations to describe the lifecycle of that declaration relative to operating system versions. Consider the function declaration for a hypothetical function f :

The availability attribute states that f was introduced in macOS 10.4, deprecated in macOS 10.6, and obsoleted in macOS 10.7. This information is used by Clang to determine when it is safe to use f : for example, if Clang is instructed to compile code for macOS 10.5, a call to f() succeeds. If Clang is instructed to compile code for macOS 10.6, the call succeeds but Clang emits a warning specifying that the function is deprecated. Finally, if Clang is instructed to compile code for macOS 10.7, the call fails because f() is no longer available.

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