Laboratory Investigation of

Infectious Diarrhoea
Key Messages

• Laboratory investigations are not routinely required for

most patients with acute diarrhoea

• A single stool specimen for faecal culture is usually

appropriate

• Giardia and cryptosporidium should only be requested if

there are risk factors

• “Ova and parasites” is rarely indicated

• Notifiy the MOH in outbreaks

Introduction

• Infectious diarrhoea is the most common cause of

diarrhoea

• Leading cause of childhood death in undeveloped

countries

• In New Zealand, the elderly are most vulnerable

• On average 1.2 – 1.9 diarrhoea illness/person/year

• NZFSA estimates 6.5 million cases/year and 5 million lost

working days
Defining diarrhoea

Diarrhoea is a change in bowel habit for the individual that

results in substantially more frequent and looser stools.
Diarrhoea may be defined as:

• Acute if the duration of symptoms is <14 days

• Persistent if it has lasted > 14 days

• Chronic when symptoms have been present for more

than four weeks
Differential diagnosis
Consider:
• Gastrointestinal infection
• An associated symptom of an acute systemic
infection/illness
• Drugs/diet
• Gastrointestinal conditions - acute abdomen e.g.
appendicitis, inflammatory bowel disease, malabsorption,
tumour
• Others as clinical picture dictate e.g. thyrotoxicosis
Causes of acute infectious
diarrhoea in New Zealand

Bacterial Virus
Campylobacter Norovirus
Salmonella Rotavirus
Clostridium difficile Enteric adenoviruses
Yersinia
Protozoa
Shigella
Giardia
E coli 0157*
Cryptosporidium
Vibrio

*E coli 0157 = verotoxin producing E coli (VTEC)

Clinical details

For people with acute diarrhoea, it is important to:

• determine the severity of their condition

• identify if a pathogen may be causative

• to check the physical status of the person

History: assessing severity

• Frequency and duration

• Presence of blood or mucus, abdominal pain, or fever

• Signs of dehyration

• General medical history/social support

• Pregnant women who may infect newborn

History: identifying pathogen

• Alternative water sources, consumption of raw or

undercooked meat, raw seafood (Vibrio),
unpasteurised milk (E coli, Salmonella, campylobacter)

• Travel to undeveloped area (wide range pathogens)

• Unwell patient contacts (Shigella, E coli, Salmonella,

Campylobacter, Giardia)
History: identifying pathogen
…contd

• Recent hospitalisation or antibiotics (C. difficle)

• Swimming in fresh water lake, swimming pools (E coli,

Salmonella, Campylobacter, Cryptosporidium)

• Recent visit to farm, or contact with pets with diarrhoea (E

coli, Salmonella, Campylobacter, Cryptosporidum)
Physical examination

• Vital signs/abdominal examination/other examination as

indicated

• Determine the hydration status of patient

• Exclude other causes

Indications to send specimens to
the laboratory

Specific investigations are not required for most patients.

A laboratory diagnosis is useful for people who:

• may have an infection that could benefit from specific

therapy,

• are at risk of severe complications,

• at risk of spreading infection, or

• are involved in an outbreak.

What samples are required?

No risk factors No laboratory tests

Culture Single fresh stool sample

Giardia and Single fresh stool sample

crytpsporidium

Ova, cysts, parasites 1-3 stool samples

Which tests to request?
Culture Giardia Ova, C.diff
crypto cysts

No risk factors No tests

Food handler +
< 5 years +
Childcare attendance + +
Rural + +
Raw seafood +
Blood in diarrhoea +
Antibiotics/chemo +
Recent hospitalisation +
>70 years + +
Immunocompromised + + +
Travel/immigrant + + +
Persistant diarrhoea + + +
Faecal culture first: send only one
sample

• Approximately 150 000 faecal cultures are requested

each year New Zealand

• Most of these are part of a series of faecal culture tests i.e.

two or more specimens sent over several days.

• When testing is required, a single faecal culture is the

appropriate first line test
Giardia and Cryptosporidium:
direct antigen test on single faecal specimen

• Testing is indicated when a person has diarrhoea:

– For longer than seven days
– Following recent overseas travel, tramping trip or
drinking from rivers/springs
– Following attendance at a child care centre
– Is immunocompromised
– Cryptosporidium is also associated with lambs
and calves, and there are occasionally
outbreaks in swimming pools.
Ova and cysts are rarely indicated

• In New Zealand the most likely causes of parasite

diarrhoea are Giardia and Cryptosporidium.

• Testing for ova and cysts is only indicated for people

who have:

– Recently travelled to countries with poor food or

water sources

– Recently immigrated

– Eosinophilia with diarrhoea lasting longer than 15

days

– Immunocompromised status
Viral Causes

• Viral infection is probably the most common cause

of infectious diarrhoea
• Rotavirus is a common cause of diarrhoea in infants
and young children
– Management should focus on hydration status.
– Faecal testing is not routinely indicated.
• Norovirus is frequently implicated in outbreak
situations.
– Laboratory testing in outbreaks is managed by
the Medical Officer of Health.
Clostridium difficile toxin

• C. difficile is the major identifiable cause of

antibiotic-associated diarrhoea.

• The prevalence of asymptomatic colonisation of the

bowel ranges from <5% in the community to over
20% in hospitalised patients. It is more prevalnt in the
elderly.

• C. difficile toxin testing is indicated for patients who

develop diarrhoea while in hospital, on antibiotics or
receiving chemotherapy.
Listeria monocytogenes

• Infection with Listeria monocytogenes can cause

febrile gastroenteritis accompanied by
bacteraemia and sometimes meningitis.

• Infection during pregnancy may be complicated by

amnionitis and foetal infection.

• Diagnosis requires blood cultures.

Clinical information is important
for the laboratory

• Blood and mucus in the stool, hemolytic-uremic

syndrome (HUS) will generate culture on a special
agar for E. coli 0157 (VTEC).

• Ingestion of raw seafood will generate culture

specific for Vibrio species.

• Recent hospitalisation or antibiotic will generate

testing for Clostridium difficile toxin.
Specimen collection

• Most laboratories have patient information sheets

available explaining specimen collection.
• Rectal swabs may be used for babies or children when
collection of a faecal specimen is impractical.
• The causative agent in cases of infectious gastroenteritis is
most likely to be found in faeces specimens obtained
when the patients are actually experiencing diarrhoea.
• The yield from faeces collected in convalescence is
reduced.
• Patients should collect enough faeces to approximately
half fill the specimen container.
• Specimens should be kept cool (preferably at 4°C) and
taken to the laboratory as soon as possible and within 24
hours.
 Specimen containers
Test Specimen container

Culture Fresh stool with no additive

Giardia and Crypto Fresh stool with no additive

Rotavirus Fresh stool with no additive

Ova, cysts, parasites Check with your local

laboratory. Some will provide
a special container with
fixative, others will accept
fresh samples and add
fixative themselves.
Notifiable diseases

• Notification of diseases and conditions is a legal

requirement under the Health Act 1956.

• Disease surveillance can be used to help prevent

and control the spread of diseases.

• Both GPs and laboratories are required to notify the

Medical Officer of Health of the possibility of a
notifiable disease.

• The local public health unit will manage the testing

of faecal specimens in an outbreak situation.
Conditions that are notifiable to a Medical Officer of
Health
Acute gastroenteritis * Yersiniosis

Campylobacteriosis Cholera

Giardiasis Taeniasis

Cryptosporidiosis Typhoid and paratyphoid

fever
Shigellosis Listeriosis

Salmonellosis

*Not every case of acute gastroenteritis is necessarily notifiable – only those

where there is a suspected common source or from a person in a high risk
category (eg, food handler, early childhood service worker, etc) or single
cases of chemical, bacterial, or toxic food poisoning such as botulism, toxic
shellfish poisoning (any type) and disease caused by verocytotoxic E. coli.
Cases and rates per 100 000 population of
notifiable diseases in New Zealand for 2005
and 2006.

Disease 2005 2006

Cases Rates Cases Rates

Campylobacteriosis 13836 337.6 15873 383.5

Cryptosporidiosis 889 21.7 736 17.8
Gastroenteritisa 557 13.6 931 22.5
Giardiasis 1231 30.0 1214 29.3
Salmonellosis 1382 33.7 1335 32.3
Shigellosis 183 4.5 102 2.5
VTEC/STEC infection 92 2.2 87 2.1
Yersiniosis 407 9.9 487 11.8
Causative agent: Campylobacter

• Sources of infection: Contaminated food or water, in

particular undercooked chicken or other meats .
• Incubation period: 1 to 10 days (usually 2 to 5 days )
• Symptoms: Watery or bloody diarrhoea, abdominal
pain and nausea preceded by muscle pain,
headache and fever. Symptoms may last 1 day to 1
week or longer (usually 5 days).
• Organism Survival: Organism survives better in food
under refrigeration than at room temperature.
Rapidly deactivated by heating to 55oC
• Treatment: Usually none, but fluids may be given.
Some cases warrant treatment with antibiotics.
Causative agent: Salmonella

• Sources of infection: Undercooked food e.g.

chicken, eggs and meat; food or water
contaminated with faeces from an infected person
or animal
• Incubation period: 6-48 hours (usually 12-36 hours).
• Symptoms: Diarrhoea, abdominal pain, vomiting,
nausea and fever lasting 1-7 days.
• Organism Survival: Salmonella can survive up to 28
days under refrigeration, even on the surface of
vegetables which have become contaminated.
Deactivated by heating to 70oC
• Treatment: The infection is usually self-limiting
although fluid replacement may be required.
Causative agent: E coli 0157:H7

• Sources of infection: In New Zealand, most from

food or water contaminated by the faeces of a
ruminant animal; or direct spread from an infected
person
• Incubation period: 3 to 9 days (mean 4 days)
• Symptoms: Symptoms range from no symptoms to
kidney disease and death. In more serious cases
there is a period of bloody diarrhoea followed by
HUS*. The elderly may suffer from TTP#.
• Organism Survival: Survives well in chilled and frozen
foods Rapidly deactivated by heating to 71oC.
• Treatment: Usually none, but fluids may be given.
Special management for HUS and TTP

* HUS = haemolytic uraemic syndrome

# TTP = thrombotic thrombocytopaenic purpura
Causative agent: Giardia /
cryptosporidium

• Sources of infection: Food or water contaminated with

faeces from an infected person or animal.
• Incubation period: Giardia: One to 3 weeks after infection.
(mean about 7 – 10 days) Crypto: 1 – 12 days (mean
about 7 days)
• Symptoms: May be asymptomatic or cause GI upset.
Serious disease may occur in the immunocompromised.
Symptoms may last from 4 to 6 weeks, and consist of
diarrhoea followed by flatulence, foul-smelling stools and
cramps.
• Organism Survival: In general the cysts are stable and can
last for long periods (months) in the environment. Heating
cysts to 60-70oC for 10 min inactivates them. Treatment:
Most cases are self-limiting, but antibiotics may be
indicated.
Causative agent: Shigella

• Sources of infection: Food or water contaminated with

faeces from an infected person or animal;
• Incubation period: 12 hours to 4 days. In outbreaks
incubation times of up to 36 hours are observed.
• Symptoms: Abdominal pain, diarrhoea, fatigue, malaise
and fever. Mucus and occasionally blood appear in the
faeces. The illness may progress to the “colonic phase”
within 1-3 days where the symptoms are intense cramps
as well as frequent and painful bowel movements. Lasts
for 3 to 14 days.
• Organism Survival: In general they survive best at low
temperatures (subzero and refrigeration). Can survive
storage in butter for more than 100 days at – 20oC and
4oC. Rapidly inactivated at temperatures above 65oC.
• Treatment: Antibiotic treatment is not required in milder
cases. Resistance is common.
Causative agent: Yersinia

• Sources of infection: Food or water contaminated with

faeces from an infected person or animal: farm animals
(especially pigs), infected pets (puppies and kittens)
• Incubation period: Approximately 7 days, range 1-11 days
• Symptoms: Abdominal pain, headache, fever, diarrhoea,
nausea and vomiting. Often produces a watery/mucoid
diarrhoea in children. Approximately 2/3 of cases report
being ill for >1 week.
• Organism Survival: Can grow in the presence or absence
of oxygen. Able to grow in refrigerator temperatures.
Rapidly inactivated at 60oC.
• Treatment: Usually self limiting, antibiotics do not reduce
the severity or duration of the illness. May used in more
serious manifestations of the disease.
Instructions for the collection of
faeces

• Label the specimen jar carefully, with your name,

age/date of birth and date of collection.
• Place a large clean container (e.g. disposable container)
in the toilet bowl. Pass faeces directly into the container.
• Do not contaminate faeces with urine.
• Using a wooden spatula or similar, scoop enough of the
faeces to at least half fill the specimen jar. If a specimen
jar is not available, place a sample at least as large as a
golf-ball into a clean jar.
• Dispose of excess faecal matter from container into the
toilet, then place inside 2 plastic bags and dispose of in
domestic waste.
• Screw the lid on the specimen jar firmly. Place in a zip-lock
plastic bag.
• Keep specimen cool but DO NOT FREEZE.
 Natural Toxins in Food
Food Precautions
Apple and Eat no more than 1-2 apricot kernels per day. Young children
pear seeds should avoid swallowing seeds
Apricot and
peach kernels
Parsnip Avoid parsnip that are damaged or mouldy. Levels of toxin drop
with cooking. Discard cooking water
Potatoes Do not eat sprouts or green potatoes, they remain toxic even
when cooked. Store potatoes in the dark, to minimise production
of glycoalkaloids (green potatoes)
Kidney beans Kidney beans must be soaked (for 5 hours) prior to cooking. As few
as 4 – 5 raw beans can produce symptoms.
Rhubarb Large quantities of rhubarb would need to be consumed to cause
death.
Zucchini Very occasionally occurs in home grown zucchini, rarely found in
commercially grown zucchini. Discard zucchini with unpleasant
smell or bitter taste.
Cassava Grinding cassava to a fine powder effectively removes the toxin.

Bamboo shoots Can be fatal. Degrades easily with prolonged boiling to safe levels