Stool diagnostics

The range of pathogens that has to be considered in cases of gastro-intestinal tract infections is very extensive (Table 1) It is not justified, neither from a medical nor an economic perspective, to include all pathogens during testing. For this reason, the procedure in the microbiological laboratory is based in principle on the step-by-step diagnosis of KIST et al. (2013): Qualitätsstandards in der mikrobiologisch-infektologischen Diagnostik, issue 9: Infektionen des Darms.

Table 1
Gastric pathogens

Bacteria   Viruses
Salmonella enteritis Rotaviruses
Samonella typhi Adenoviruses (certain serotypes)
Shigella species Coronaviruses
Enteropathogenic E. coli (EPEC) Caliciviruses
Enterohaemorrhagic E. coli (EHEC) Astroviruses
Enteroinvasive E. coli (EIEC) Noroviruses
Enterotoxic E. coli (ETEC) Enteroviruses
Enteroaggregative E. coli (EAEC)  
Yersinia enterocolitica  
Yersinia pseudotubeculosis Protozoa
Vibrio cholerae Giardia lamblia
Vibrio species Entamoeba histolytica
Aeromonas species Blasticytis hominis
Plesiomonas shigelloides Cryptosporidium species
Campylobacter species Isospora belli
Clostridium difficile Sarcocystis species
Food poisoning pathogens: Cyclospora cayetanensis
Clostridium perfringens  
Clostridium botulinum  
Bacillus cereus  
Staphylococcus aureus  
   
„Facultative intestinal pathogenic bacteria”  
„Atypical” mycobacteria  
   
Fungi Worms
Microsporidia Trematoda (flukes)
  Cestoda (tape worms)
  Nematodes (threadworms)

The basic principles (guidelines) for step-by-step diagnostics are:

1. Macroscopic assessment of the stool sample
Macroscopic assessment of the stool is carried out by the laboratory. Classification is according to:

  • Well-formed, solid stool samples
  • Mushy/loose to watery stool samples
  • Very watery/bloody/slimy stool samples

2. Anticipated incidence of pathogens in Germany (Central Europe)

3. Patient age

4. Assignment as an „out-patient” or „in-patient”

With in-patients, it is important to know whether the patient was hospitalised because of enteritis or whether enteritis was diagnosed during the in-patient stay. Assignment to specific departments, such as oncology, transplantation, intensive care, etc., is important.
5. Clinical symptoms and medical history
Information on clinical symptoms and other medical history data can give considerable clues for the aetiology of cases of diarrhoea. Symptoms such as fever, vomiting, tenesmus, recurrent abdominal discomfort, suspected appendicitis, arthritis, etc. along with medical history information such as any stays abroad, antibiotic therapy, a recent surgical intervention, immunosuppression or food history should be noted on the referral form.

In light of these guidelines and the specific requests of the sender, the following step-by-step diagnostic procedures are performed in the microbiological laboratory:

Stage I

Criteria
No information on the clinical picture of a case of diarrhoea.
Stool consistency: unremarkable (solid, well-formed)

Requests: Stool tested for typhoid, paratyphoid, enteritis, dysentery

Tests for the following pathogens:

1. Basic diagnostics

  • Salmonella
  • Shigella
  • Yersinia

2. Special cases in addition to the basic diagnostics

Travel history

  • Parasites
Stage II

Criteria:
Stool consistency: mushy, mushy/loose, watery and/or information about symptoms of enteral infection

Request: Test stool for intestinal pathogens

Tests for the following pathogens:

1. Basic diagnostics

  • Salmonella
  • Shigella
  • Yersinia
  • Campylobacter

2. Special cases in addition to the basic diagnostics

Small children < 3 years

  • ECP (enteropathogenic E. coli)
  • Viruses

Travel history

  • Parasites
  • Aeromonas
  • Vibrio

Antibiotic therapy and/or surgical intervention

  • Clostridium difficile (GDH toxin)
  • Fungi (semi-quantitative)
Stage III

Criteria
Stool consistency: very watery, watery/bloody/slimy and/or serious symptoms

Request: Test stool for intestinal pathogens (extended stool diagnostics)

Tests for the following pathogens:

1. Basic diagnostics

  • Salmonella
  • Shigella
  • Yersinia
  • Campylobacter
  • ECP (enteropathogenic E. coli)
  • Clostridium difficile (GDH toxin)
  • Aeromonas
  • Vibrio
  • Viruses

2. Special cases in addition to the basic diagnostics

Small children < 3 years

  • Parasites

Travel history

  • Parasites

Immunosuppression

  • Atypical mycobacteria
  • Fungi (semi-quantitative), microsporidia
  • FDPB (faculative intestinal pathogenic bacteria)
  • Parasites

For special clinical issues, the following tests are indicated Kidney failure, HUS (haemorrhagic uraemic syndrome), TPP (thrombotic thrombocytopenic purpura) and a history of diarrhoea (regardless of the stool consistency):

  • Enterohaemorrhagic E. coli (EHEC)
  • Salmonella
  • Shigella
  • Campylobacter
  • Yersinia

Signs of appendicitis, arthritis, erythema nodosum or similar skin symptoms

  • Salmonella
  • Shigella
  • Campylobacter
  • Yersinia enterocolitica, including testing for antibodies

Persistent or recurrent diarrhoea for longer than 3 weeks

  • Salmonella
  • Shigella
  • Campylobacter
  • Clostridium difficile (culture, toxin)
  • Enteropathogenic E. coli (EPEC)
  • Enterohaemorrhagic E. coli (EHEC)
  • Enteroaggregative E. coli (EAEC)
  • Yersinia enterocolitica, including testing for antibodies
  • Parasites

Children up to 6 years hospitalised because of diarrhoea

  • Salmonella
  • Shigella
  • Campylobacter
  • Enteropathogenic E. coli (EPEC)
  • Enterohaemorrhagic E. coli (EHEC)
  • Rotaviruses, adenoviruses and astroviruses

Suspected food poisoning

  • Salmonella
  • Campylobacter spec.
  • Clostridium difficile (semiquantative culture, toxin)
  • Staphylococcus aureus (toxin)
  • Bacillus cereus

Concluding remarks
To ensure efficient, professional and economic processing of stool samples, the doctor submitting them should observe the following points:

  • Important information from the medical history and details of the patient’s symptoms should be noted on the referral note.
  • The test order should be formulated in such a way that the processor in the laboratory has no doubts about the corresponding diagnostics range that it is to be assigned to.

The following order descriptions are feasible and advisable:

  • Stool tested for typhoid, paratyphoid, enteritis, dysentery (corresponds to stage I)
  • Stool tested for intestinal pathogens (corresponds to stage II or stage III, depending on the consistency of the stool)
  • Specific test orders based on special suspected diagnoses
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