Iman M. FawzyClinical Pathology MD.
PhDMansoura, Egypt
SamplingSamplinginin
MicrobiologyMicrobiology
Iman M. FawzyClinical Pathology MD.
PhDMansoura, Egypt
The best use of microbiologic lab.
involves sending only relevant
specimens.
For obtaining good quality sample for
microbiologic examination, certain
precautions should be considered.
Rapid transporting of the specimens to the lab.
Collection of specimens before antibiotic therapy.
Sample collection as early as possible in the disease.
Containers used for collection should be sterile, tightly capped, and clearly labeled.
Cleaning the site of infection
General precautionsGeneral precautionsGeneral precautionsGeneral precautions
Any specimen should be accompanied by request containing:
Patient's name, age, gender, in or outpatient, ward number, home area .
Type & source of specimen, date & time of collection.
Investigation(s) required.
Clinical note summarizing the patient's illness, suspected diagnosis, antimicrobial therapy.
Name of clinical officer .
Request formRequest formRequest formRequest form
Proper Sampling in Clinical Microbiology Laboratory
Collection of good quality specimens Depends on:
1. The optimal time of specimen collection .2. The correct type of specimen 3. Well collected specimens with minimum
contamination from normal flora of the patient or the person collecting the specimen.
4. Adequate amounts of each specimens and appropriate no. of specimens
5. Clearly labeled safe specimens
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1 -Optimal time of collection of specimens: 1 -Optimal time of collection of specimens:
Specimens for the culture of bacteria must be collected before the start of antibiotics
Blood films for malarial parasites are usually best collected just as the patient's temperature starts to rise
When infective endocarditis is suspected, three blood culture sets can be collected within a 24 h period irrespective of the temperature of the patient .
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1 -Optimal time of collection of specimens: 1 -Optimal time of collection of specimens:
Serology is usually most satisfactory when a fourfold or greater rising antibody titre to a pathogen can be demonstrated in paired sera.
Specimens for electron microscopy or isolation of viruses are most likely to give positive results when collected during the most acute stages of the disease
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2 -Correct types of specimens 2 -Correct types of specimens
Patients with possible bacterial meningitis should have blood cultures as well as cerebrospinal fluid collected.
Cervical, urethral and preferably rectal swabs should be collected rather than high vaginal swabs from female patients with suspected gonorrhoea.
Pernasal swabs should always be collected from children who may have pertussis rather than a throat or ordinary nose swab.
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3- Well- collected specimens with minimal contamination from normal flora
3- Well- collected specimens with minimal contamination from normal flora
All staff should become aware of the importance of minimizing the contamination of specimens.
Poor-quality specimens include saliva instead of sputum or a salivary-mucoid sputum sample instead of a mucopurulent specimen from a patient with pneumonia .
Mid-stream specimens of urine to avoid excessive contamination.
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3- Well- collected specimens with minimal contamination from normal flora
3- Well- collected specimens with minimal contamination from normal flora
Throat swab collected should not touch the buccal mucosa or tongue .
A high vaginal swab should be collected using a vaginal speculum which should not be wet with antiseptic solution with care not to touch the lower region or perineum.
Blood or cerebrospinal fluid (CSF) cultures can be contaminated by the skin flora of the patient or from the doctor .
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4 -Adequate quantity of the specimens 4 -Adequate quantity of the specimens
The collection of adequate quantities of early morning sputum.
At least two samples of faeces on different days are desirable from patients with diarrhoea.
When carriage of Salmonella typhi is investigated in a food handler, 6 samples of faces should be cultured.
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4 -Adequate quantity of the specimens 4 -Adequate quantity of the specimens
Patients with diarrhea at least 2 specimens of faces is collected for culture of Salmonellae or Shigella.
Serological investigations usually require paired sera.
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5 -Clearly labeled and safe containers 5 -Clearly labeled and safe containers
Microbiological investigations should be placed in leak-proof containers.
Each container should be enclosed in a plastic bag.
Examples of microbiological hazards to staff handling leaking containers include TB, and viruses such as HBV and HIV.
Urine SamplesUrine Samples
Morning sample.
Washing the site with soap & water 3 times,and in female from front to backward.
Mid stream sample for routine culture & 24h (3 times) for T.B.
In children:Suprapubic aspiration Adhesive bag
Urine SamplesUrine Samples
If the patients is already catheterized, catheter sample can be used.
Sterile, dry, wide-necked, leak proof container is used.
Collection of 10 – 20 ml urine.
To preserve the sample, (0.Ig /10ml urine) boric acid is used.
Urine SamplesUrine Samples
When gonorrhea is suspected
immediate culture (bed side) or
using transport medium
Blood SamplesBlood Samples
During peak of fever.
Sterilizing the site of venipuncture with alcohol 70% & iodine .
Samples for aerobic blood culture are collected in the green capped bottles, while those for anaerobic blood culture are collected in the red capped bottles.
Blood SamplesBlood Samples
For adults at least, 5mL of blood are collected
while for infants and children 2mL of blood only are collected.
For automated blood culture system special bottles are used.
Blood is introduced through the rubber cap.
Blood SamplesBlood Samples
•Serum can be used for culture on fluid medium.
•Blood for serological diagnosis is collected in screw capped tubes without anticoagulant.
Body Fluids SamplesBody Fluids Samples
Sterilizing the site with alcohol 70% and iodine.
Rapid transporting to the lab especially for CSF.
Using wide mouth, sterile containers to which 0.3ml of 20% Na citrate is added to prevent clot formation.
Sputum SamplesSputum Samples
Morning sample.
Washing the mouth with water and brushing the teeth.
Sputum rather than saliva .
In infants, gastric lavage can be used.
Sputum SamplesSputum Samples
An alternative method, the tongue is depressed and cough is induced by touching the larynx, material from the trachea expelled during the cough will adhere on the swab.
Samples for T.B. are 3 consecutive morning samples.
SwabsSwabs
It is a sample device
consist of sterile pledget of absorbent material, usually cotton-wool or synthetic fiber, mounted on a thin wire or stick.
Swabs for Bacterial (red) and Viral (green) Cultures
SwabsSwabs
The absorbent material may be inhibitory to the pathogens, some swabs may be treated to prevent inhibitory effect:
Boiling the swab in phosphate buffer Coating the swab with serum Or coating the swab with albumin or charcoal
SwabsSwabs
Uses of swabs:for taking specimens of exudates from nostrils
ear, skin, throat, wounds and other accessible lesions.
baby swabs: very fine swab.
SwabsSwabs
Uses of swabs:pernasal swab: used for diagnosis
of whooping cough. It is passed along the floor of nasal cavity to reach the nasopharyx . It is small with flexible wire .
post nasal swab: the terminal 20mm of long stiff metal wire is bent at an angle of 45 o to be introduced through the mouth to reach nasopharynx. Used for diagnosis of meningococcal carrier.
SwabsSwabs
Uses of swabs:Laryngeal swab : used for obtaining
sample from bronchial secretion for diagnosis of TB. About 50 mm of the wire is bent at an angle of 60 o .
High vaginal swab used fort diagnosis of genorrhea and puerperal fever . It is about 22cm long to reach endocervix.
Throat SwabsThroat Swabs
Washing the mouth with water.
Depression of the tongue with tongue depressor.
Sample from posterior pharynx or tonsils.
Swab should not touch the buccal mucosa.
WoundsWounds
Clean the wound with sterile gauze soaked in sterile saline.
Squeeze the wound.
Swab pus or squeezed exudates.
Eye SwabsEye Swabs
Washing of eyes by water and soap.
Apply swab from lower conjunctival fornix .
Ear SwabsEar Swabs
Clean the site with sterile saline.
Dry the area.
Apply swab to get specimen.
Stool SamplesStool Samples
Stool is collected in wide-mouth container.
Stool is collected in leak proof sterile container into which the excreta can be passed directly.
Alternatively, rectal swab may be taken.
Stool SamplesStool Samples
For preserving Salmonella, place several drops of luiquid faces or faecal emulsion on a sheet of filter paper and allow it to dry and preserve it in a cellophane envelop for transporting to the lab. In the lab a saline suspension of material from the filter paper is plated on a selective media.
For Cholera. The faeces is sent in bile peptone medium to prevent the death of Vibrio cholera .
Gynacologicol samplingGynacologicol sampling
Cervical swab is preferred rather than vaginal ones.
Dry, sterile speculum should be used or moistened with sterile warm water.
No bimanual examination performed.
Gynacologicol samplingGynacologicol sampling
Cleanse the cx. with swab moistened with sterile saline.
Sterile swab is used for sample collection by rotating it in the cervix.
When gonorrhea is suspected immediate culture (bed side) or using transport medium .
Sampling for Mycologic examSampling for Mycologic exam
Clean the site with alcohol 70%.
Sterile scalpel is used for scrapping.
Sterile scissor is used for trimming the nails.
Scales are transferred in clean dark paper.
For systemic mycosis, precautions are those for blood culture.
Sampling for Clinical VirologySampling for Clinical Virology
Collection of specimen during most active stage of the disease.
Samples as urine , stool , CSF , sputum are transported directly to the lab while swabs from throat , nose vesicles , cervix are transported in VTM.
If delay is in due, keep specimens at 4 0C.
Biohazard label should be used for containers of HBV, HCV and HIV.
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