Investigation of faecal specimens for enteric pathogens

Microbiology

Diarrhoea may be defined as unusual frequency of bowel action (usually at least three times in a 24 hour period), passing loose, watery, unformed faeces. The consistency of the stools is more important than the frequency: frequently passed formed stools are not considered to be diarrhoea. It may be associated with symptoms such as abdominal cramps, nausea and malaise, and with vomiting, fever and consequent dehydration. Patients with visible blood and mucus in the faeces suggesting inflammation of the bowel, accompanied by symptoms such as abdominal cramps and constitutional disturbance, may be said to be suffering from dysentery.

A wide range of bacterial pathogens, viruses and parasites are capable of causing diarrhoea by a number of mechanisms. Routine screening of faecal samples includes screening for Salmonella species, Shigella species, E.coli 0157 and Campylobacter species.

Additional Screening;

Vibrio cholera can be requested if there is suspicion that the patient has ingested contaminated water or seafood or travelled to endemic areas.

Yersinia enterocolitica which causes Yersiniosis is a zoonotic infection. Y. enterocolitica can be isolated from wild and domestic animals, environmental samples and food samples.

Sample Type:

Stool. 1-2g is sufficient for routine culture. In an appropriate sterile leak proof container.

Temperature: 2-8°C

Turnaround Time:

48h for a negative result.

72h for a positive result.

*Excludes Sundays and Bank Holidays

Sample Stability:

2 days @ 2-8°C

Instrument / Procedure:

Manual Culture

Units:
Reference Range:
Precautions:

PLEASE NOTE: Samples and accompanying relevant patient/ isolate data maybe referred for confirmatory or further laboratory testing to Reference laboratories. Relevant Public Health departments may also be notified IF a notifiable disease is identified under the Infectious Diseases (Amendment) Regulations 2020 (S.I. No. 53/2020).

Preparation of patient: Collect specimens soon as possible after onset of symptoms and before antimicrobial therapy where possible.

Precautions: Specimens of faeces should be transported to the laboratory and processed as soon as possible. Important pathogens such as Shigella species may not survive the pH changes that occur in faeces specimens which are not promptly delivered to the laboratory, even if refrigerated. If processing is delayed, refrigeration is preferable to storage at ambient temperature. Delays of over 48hrs are undesirable.

Specimen may be passed into a clean, dry, disposable bedpan or similar container and transferred into an appropriate sterile leak proof containers and place in sealed plastic bags. The specimen is unsatisfactory if any residual soap, detergent or disinfectant remains in the pan.

Faecal samples should be liquid or semi formed i.e. take the shape of the container.

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SAMPLE REQUIREMENTS FOR COAGULATION TESTS

PROCEDURE

Sample Requirements and Collection

  • Patients should be relaxed pre-venepuncture. Excessive stress and exercise will increase FVIII, vWF antigen and fibrinolysis. Venous occlusion should be avoided.  
  • Difficult venepuncture with trauma may lead to platelet activation with release of PF4 from alpha granules.
  • Venous blood should be collected into coagulation tubes containing Sodium Citrate 3.2%, 0.105M.
  • Specimens must be mixed immediately post venepuncture to avoid clot activation, by GENTLY inverting the tubes 5 to 10 times.
  • The ratio of whole blood to anticoagulant is crucial to clotting times. A target blood to anticoagulant ratio of 9:1 is optimal.  Under- or over- filled specimens will not be processed this can adversely affect results.  
  • Any warfarin treatment should be mentioned on the request form.
  • Sample rejection Criteria: Clotted sample, grossly hemolyzed sample, underfilled/overfilled specimen, unlabeled sample, mismatched patient ID, aged samples, wrong sample tube (citrate tube only).

Transportation and Storage

  • PT/INR specimens should be transported to the laboratory at room temperature.
  • Coagulation specimens should ideally be analysed within 4 hours of collection. Where this is not possible, centrifuge specimens at room temperature (RT) @ 1500RCF for at least 15 minutes, and then carefully remove the plasma from the cells, transfer to a fresh plastic plain tube and freeze at -20oC.  
  • Non-frozen coagulation specimens should be transported at RT ASAP to avoid deterioration of labile factors V and VIII.
  • Collection of blood through intravenous lines that have been previously flushed with heparin should be avoided. In the event blood is drawn from an indwelling catheter, the line should be flushed with 5ml of saline, and the first 5ml of blood or 6 times the line volume be drawn off and discarded before coagulation tube is filled.
  • Effect of freezing on Coagulation Specimens.
  • A 14days in-house study on the effect of freezing, on coagulation specimens at -20oC, showed that there was negligible and clinically non-significant effect of freezing on coagulation specimen results. Therefore frozen citrated coagulation samples are stable for 14 days at -20oC, post centrifugation. This study is available in-house for reference.
ESR Ref Ranges
Units of Measurement
MALE
FEMALE
>50 Years
mm/hr
0 - ≤12
0 - ≤15
<50 Years
mm/hr
0 - ≤8
0 - ≤10
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Analyte
Units of Measurement
MALE
FEMALE
WBC
10^9/L
4.0–10.0
4.0 - 10.0
RBC
10^12/L
5.0 ± 0.5
4.3 ± 0.5
HB
g/dL
15.0 ± 2.0
13.5 ± 1.5
HCT
L/L
0.45 ± 0.05
0.41 ± 0.05
MCV
fL
92 ± 9
92 ± 9
MCH
pg
29.5 ± 2.5
29.5 ± 2.5
MCHC
g/dL
33.0 ± 1.5
33.0 ± 1.5
PLT
10^9/L
280 ± 130
280 ± 130
MPV
fL
N/A
N/A
RDW
%
11.6 - 14.0
11.6 - 14.0
#Neut
10^9/L
2.0 – 7.0
(40 - 80%)
#Lymph
10^9/L
1.0 – 3.0
(20 - 40%)
#Mono
10^9/L
0.2 – 1.0
(2 - 10%)
#Eos
10^9/L
0.02 – 0.5
(1 - 6%)
#Baso
10^9/L
0.02 – 0.1
(<1 - 2%)
Analyte
Units of Measurement
MALE & FEMALE
WBC
10^9/L
Birth: 18 ± 8
Day 3: 15 ± 8
Day 7: 14 ± 8
Day 14: 14 ± 8
1 Month: 12 ± 7
2 Months: 10 ± 5
3–6 Months: 12 ± 6
1 Year: 11 ± 5
2–6 Years: 10 ± 5
6–12 Years: 9 ± 4
RBC
10^12/L
Birth: 6.0 ± 1.0
Day 3: 5.3 ± 1.3
Day 7: 5.1 ± 1.2
Day 14: 4.9 ± 1.3
1 Month: 4.2 ± 1.2
2 Months: 3.7 ± 0.6
3–6 Months: 4.7 ± 0.6
1 Year: 4.5 ± 0.6
2–6 Years: 4.6 ± 0.6
6–12 Years: 4.6 ± 0.6
HB
g/dL
Birth: 18.0 ± 4.0
Day 3: 18.0 ± 3.0
Day 7: 17.5 ± 4.0
Day 14: 16.5 ± 4.0
1 Month: 14.0 ± 2.5
2 Months: 11.2± 1.8
3–6 Months: 12.6 ± 1.5
1 Year: 12.6 ± 1.5
2–6 Years: 12.5 ± 1.5
6–12 Years: 13.5 ± 2.0
HCT
L/L
Birth: 0.60 ± 0.15
Day 3: 0.56 ± 0.11
Day 7: 0.54 ± 0.12
Day 14: 0.51 ± 0.12
1 Month: 0.43 ± 0.10
2 Months: 0.35 ± 0.07
3–6 Months: 0.35 ± 0.08
1 Year: 0.34 ± 0.04
2–6 Years: 0.37 ± 0.03
6–12 Years: 0.40 ± 0.05
MCV
fL
Birth: 110 ± 10
Day 3: 105 ± 13
Day 7: 107 ± 19
Day 14: 105 ± 19
1 Month: 104 ± 12
2 Months: 95 ± 8
3–6 Months: 76 ± 8
1 Year: 78 ± 6
2–6 Years: 81 ± 6
6–12 Years: 86 ± 9
MCH
pg
Birth: 34 ± 3
Day 3: 34 ± 3
Day 7: 34 ± 3
Day 14: 34 ± 3
1 Month: 33 ± 3
2 Months: 30 ± 3
3–6 Months: 27 ± 3
1 Year: 27 ± 2
2–6 Years: 27 ± 3
6–12 Years: 29 ± 4
MCHC
g/dL
Birth: 33.0 ± 3.0
Day 3: 33.0 ± 4.0
Day 7: 33.0 ± 5.0
Day 14: 33.0 ± 5.0
1 Month: 33.0 ± 4.0
2 Months: 32.0 ± 3.5
3–6 Months: 33.0 ± 3.0
1 Year: 34.0 ± 2.0
2–6 Years: 34.0 ± 3.0
6–12 Years: 34.0 ± 3.0
PLT
10^9/L
Birth: 100 – 450
Day 3: 210 – 500
Day 7: 160 – 500
Day 14: 170 – 500
1 Month: 200 – 500
2 Months: 210 – 650
3–6 Months: 200 – 550
1 Year: 200 – 550
2–6 Years: 200 – 490
6–12 Years: 170 – 450
Reticulocytes
10^9/L
Birth: 120 – 400
Day 3: 50 – 350
Day 7: 50 – 100
Day 14: 50 - 100
1 Month: 20 – 60
2 Months: 30 – 50
3–6 Months: 40 – 100
1 Year: 30 – 100
2–6 Years: 30 – 100
6–12 Years: 30 – 100
#Neut
10^9/L
Birth: 4 – 14
Day 3: 3 – 5
Day 7: 3 – 6
Day 14: 3 – 7
1 Month: 3 – 9
2 Months: 1.0 – 5
3–6 Months: 1 – 6
1 Year: 1 – 7
2–6 Years: 1.5 – 8
6–12 Years: 2 – 8
#Lymph
10^9/L
Birth: 3 – 8
Day 3: 2 – 8
Day 7: 3 – 9
Day 14: 3 – 9
1 Month: 3 – 16
2 Months: 4 – 10
3–6 Months: 4 – 12
1 Year: 3.5 – 11
2–6 Years: 6 - 9
6–12 Years: 1 - 5
#Mono
10^9/L
Birth: 0.5 – 2.0
Day 3: 0.5 – 1.0
Day 7: 0.1 – 1.7
Day 14: 0.1 – 1.7
1 Month: 0.3 – 1.0
2 Months: 0.4 – 1.2
3–6 Months: 0.2 – 1.2
1 Year: 0.2 – 1.0
2–6 Years: 0.2 – 1.0
6–12 Years: 0.2 – 1.0
#Eos
10^9/L
Birth: 0.1 – 1.0
Day 3: 0.1 – 2.0
Day 7: 0.1 – 0.8
Day 14: 0.1 – 0.9
1 Month: 0.2 – 1.0
2 Months: 0.1 – 1.0
3–6 Months: 0.1 – 1.0
1 Year: 0.1 – 1.0
2–6 Years: 0.1 – 1.0
6–12 Years: 0.1 – 1.0
Reference Ranges:
Age
Absolute Reference Range
Age
% Reference Range
0 - 1 day
324 - 617 x109/L
0 - 1 day
1.72 - 8.62%
1 - 5 days
85 - 400 x109/L
1 - 5 days
1.9 - 9.1%
5 days - 1 mth
34.2 - 724 x109/L
5 days - 1 mth
0.1 - 6.9%
1 - 3 mths
21.3 - 205 x109/L
1 - 3 mths
0.1 - 6.27%
3 - 12 mths
8.0 - 171 x109/L
3 - 12 mths
0.1 - 4.7%
1 - 3 yrs
55.6 - 120 x109/L
1 - 3 yrs
0.35 - 2.95%
3 - 7yrs
16.4 - 120.7 x109/L
3 - 7yrs
0.25 - 2.57%
Adult
35.2 - 122.8 x109/L
Adult
0.75 - 2.7%
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