- Blood Culture
- Gastrointestinal tract
- Respiratory tract
- Eye, Ear, Nose and Sinuses
- Urine tract
- Genital tract
- Wounds and Abscesses
- Semen and Breast culture
- Stool samples for culture, Ova and Parasites
- Mycology Testing for the presence of Mold or Yeast and Identification
For best recovery of microorganisms, it is best to collect blood during fever or chills. Multiple blood collections may be indicated in some cases for better recovery. The patient should not be on antibiotics for at least 1 week and if the patient is taking antibiotics, that should be indicated on the sample submission form. If yeast is suspected, that should be indicated on the sample submission form so that we use special procedures for isolating and identifying yeast.
Turnaround time: 10-12 days
Cost: $225 (if antibiotics sensitivity is performed on any isolated organisms, there is an additional cost of $125)
- Stool should be collected in a sterile, wide mouth container
- specimen should not be contaminated with water or urin
- The container should be placed in plastic zip lock bag (biohazard bag)
- Specimen container must be identified with : Name of patient, age, date and time of collection
- The request form must accompany the specimen, preferably with presumptive diagnosis, or the symptoms at the time of collection as this would guide us if special media should be used in order to isolate fastidious organisms
- The sample submission form must list the phone/fax number of the physician or clinic.
- Three specimens are recommended for recovery of parasite because the probability of detecting clinically relevant parasite in a single stool specimen may be low.
- Fresh specimens are requried for the recovery of motile live protozoa
- For ova and parasite examination, and if delays are anticipated, please use stool transport containers with preservatives ( FORMALIN, SODIUM…POLYVINIL ALCOHOL)
- If the presence of Clostridium difficile toxin is suspected, liquid or soft stool should be collected directly into a clean, dry container
- Rectal Swabs is not indicated for toxin testing. It is reserved for detecting Shigella, Campylobacter and anal carriage of bacteria (multiresistant bacteria and group B Streptococci).
- Rotavirus infection: Causes dehydration in infants and children under 2 years of age.
- Rotaviruses are able to survive on the environmental surface at ambient temperature and are resistant to physical inactivation.
- Clinical significance: Cause severe gastroenteritis in infants, can cause biliary atresia and central nervous system disease.
Collection,transport and storage of specimen
Stool are the major source of specimen, vomit can be used.
- specimen should be collected within 48 hours of illness
- stools samples can be stored at 4°c for weeks if not tested immediately after collection.
- Freshly expectorated mucus and inflammatory cells (pus cells), sputum.
- Sputum expectorated: patient rinse or gargle with water to remove excess oral flora
- Instruct patient to cough deeply to produce a lower respiratory specimen. Inhalation of vapors from boiling water with salt can stimulate expectoration
- Collect in a sterile container
- Upper tract (Oropharynx , Nasopharynx and Middle Ear secretions).
- Lower tract (Larynx, Trachea, Bronchi and Lungs) secretions, washes or biopsy materiel collected during endoscopy.
- Saliva, oro-pharyngeal secretions are inappropriate
- Nasopharyngeal swab, Sinus washing, swab of tonsils , Lung aspirates or Biopsy
- Drainage of external ear, Sputum specimens, broncho-alveolar lavage…..
Identification: Biochemical identification, Bacitracin disk for ß hemolytic Streptococci Sensitivity test: Kirby Bauer Method
- Suppurative material from the conjunctiva of an infected eye should be collected from the cul de sac or from the inner canthus .
- Sample both eyes with separate swabs
- Medium may be inoculated at time of collection (call lab. to request inoculation medium)
- Smear may be prepared at time of collection.
- Possibility of keratitis caused by Amoeba (Acanthamoeba) is possible in patients using soft contact lenses
- If Trachoma is suspected, conjunctival scraping should be smeared to detect Chlamydial antigen (this procedure should be performed by an Ophthalomologist (Testing for Chlamydia is by PCR)
- Corneal scraping: collected by ophthalmologist
- Use sterile spatula, scrape ulcers or lesion and inoculate directly onto medium (or into a sterile tube for PCR testing if Chlamydia is suspected)
- Prepare 2 smears
- Carefully clean gingival margin and supragingival tooth surface to remove saliva, debris and plaque.
- Using a periodontal scaler, carefully remove sub gingival lesion material and transport it to an anaerobic transport system (call lab. for collection kit)
- Specimens: midstream collection technique, catheter collection and supra pubic aspiration
- Specimens must be transported to the laboratory within 30 minutes of collection or stored under refrigeration for no longer than 36 hours.
- A colony count of 10⁵ cfu/ml or higher is a indicative of urinary tract infection ( UTI).
- When colony count is between 10⁴-10⁵ cfu/ml or when 2 or more species are recovered, the decision to identify the organisms and perform sensitivity test depend of many factors ( symptoms, growth and urinanalysis…..).
- Culture of catheterization or supra pubic urine specimen are identified even with low colonies count.
- Collection of genital specimen from males: Urethral discharge, when urethral discharge is scant, collect the first early morning specimen before urination.
- Clean urethral meatus with soap and water
- Insert a small swab into the anterior urethra ( 2 to 4 cm), rotate the swab and immediately transfer into the transport medium
- Do not store genital specimens in a refrigerator (room temperature is recommended)
- Use swab transport medium provided by laboratory or doctor’s office
Collection of genital specimen from females
- Cervical secretions, aspiration of secretion, endometrial specimen and intra uterine device (anaerobic bacteria and Nocardia).
- Vaginal secretions: wipe away old secretions , obtain secretions from the mucosal membrane of the vaginal wall with a sterile swab or pipette.
- Bartholin gland secretions: disinfect skin with iodine preparation and aspirate fluid from ducts.
- Use swab transport medium provided by the laboratory or doctor’s office
WOUNDS AND ABSCESSES
- Collection of specimen: surface wounds are often colonized with environmental bacteria and swabs samples often do not reflect the true cause of the infection process. The wound area should be cleaned prior to sample collection to remove skin contaminants
- Aspiration of pus or any fluid from the deep wounds and abscess with a sterile needle and syringe is the most desirable method for collection.
- When using a swab, it is recommended to wear sterile gloves and avoid the adjacent skin margins
- Remove surface exudate by wiping with sterile saline
Blood for culture, CSF, Tissue, peripheral catheters, Indwelling central venous catheter, Implantable device. Please call lab. to request blood culture bottles prior to blood collection
SPECIMEN REJECTION CRITERIA
Improper collection or transport
Poor labeling: Specimen without label or request form, prolonged transport, leaking container, (Anaerobic culture for a specimen transported aerobically), container not sterile, dry specimen, specimen received in formalin.
The following antibiotics are used for specific isolates
Gram positive Cocci
Staphylococci: Penicillin, Oxacillin or Methicillin, Vancomycin, Clindamycin, Azithromycin or Erythromycin or Clarithromycin, Trimethoprim-Sulfamethoxazole, Gentamicin, Tetracycline, Rifampicin.
Enterococcus spp: Penicillin or Ampicillin, Vancomycine, Gentamicin ( high level resistance screen only), Streptomycin (high level resistance screen only), Ciprofloxacine, Norfloxacin, Nitofurantoin and Tetracycline.
Streptococcus pneumoniae:Penicillin, Amoxicillin or Amoxicillin-Acid clavulanic, Erythromycin, Trimethoprim-Sulfamethoxazole, Ceftriaxone or cefotaxim, cefuroxim, Vancomycin, Tetracycline, Imipenem.
Other Streptococci spp: Penicillin or Ampicillin, Erythromycin, Vancomycin, Clindamycin, Cefotaxime or Ceftriaxone, Azithromycin or Clarithromycin, Ofloxacin.
Gram Negative Bacilli
Enterobacteriaceae: Ampicillin, Cefazolin or Cephalotin, Amoxicillin/clavulanic acid, Cefoxitin, Cefotetan, Cefotaxime or Ceftriaxone, Gentamicin, Amikacin, Trimethoprime-Sulfamethoxazole, Tetracycline, Nitrofurantoine, ciprofloxacin, Norfloxacin, Ofloxacin.
Pseudomonas aeruginosa: Ticarcillin, Carbenicillin, Piperacillin, Ceftazidime, Ticarcillin/clavulanic acid, Aztreonam, Imipenem, Amikacin, Gentamicin, Tobramicin, Ciprofloxacin.
Penicillin, Ceftriaxone, Cefuroxime, Tetracycline, Spectinomycin, Ciprofloxacin or Ofloxacin.
Ampicillin, Trimethoprime-Sulfamethoxazole, Amoxicillin/clavulanic acid, Azithromycin or Clarithromycin, Cefuroxime, Ceftriaxone, Cefotaxime, Tetracycline, Ciprofloxacin or Ofloxacin, Rifampicin.
Penicillin G, Metronidazole, Clindamycin, Imipenem, Cefoxitin, Ceftriaxone, Cefotaxime, Amoxicillin/clavulanic acid, Chloramphenicol, Piperacillin.
- Intestinal parasites: Giardia lamblia and Entamoeba histolytica infections are 2 of the most common protozoal infections seen worldwide. They can cause significant morbidity and in some cases mortality if untreated
- Other less pathogenic commensal protozoa exist and can cause subclinical disease
- Collection of specimen: stool fresh and preserved.
- Fresh specimen are received for the detection of organisms motility, they must be examined on receipt
- Preserved specimen are not indicated for wet mount and detection of motility.
- Entamoeba histolytica: can be found worldwide but is more prevalent in tropical and subtropical regions.
- In the US, Amoebiasis is frequent in immigrants from South and Central America and South East Asia.
- Clinical significance: Colitis, Liver Abscess. The majority of infections with E.histolytica and E.dispar are asymptomatic.
- The laboratory diagnosis of amoebiasis can be made from stool examination, material obtained from sigmoidoscopy, tissue biopsy specimen and abscess aspirates.
Direct examination: Direct wet preparation and concentration procedures will be performed Flagellates:
Giardia, Dientamoeba, Chilomastix, Enteromonas and Rotatomonas.
Pathogenic flagellates are: Giardia lamblia, Dientamoeba fragilis and Trichomonas vaginalis.
Transmission is via ingestion of food or water
Specimen is fresh stool
Direct examination: Wet mount and permanent stained smear of fecal material are the predominant specimen used to diagnose infections with flagellates.
Giardia lamblia: The diagnosis of Giardia is established by the microscopic examination of stool for the presence of cysts and or trophozoites.
Nucleic Acid Detection Technique: We also offer Giardia lamblia detection by PCR.
The advantage of PCR is the increased sensitivity compared to direct examination
Deep Mycoses: Blastomycosis, Coccidiomycosis, Sporotrichsis
Opportunistic Mycoses: Aspergillosis, Candidosis, Geotrichosis
Subcutaneous Mycoses: Maduramycosis (Mycetoma), Sporotrichosis (Sporothrix schenkii).
Superficial Mycoses: Tinea versicolor, Dermatomycoses ( Dermtophytes), Tinea and Onychomycosis.
Common specimen collection sites for recovery of Clinically Significant Fungi:
Blood (Yeast), CSF (Cryptococcus neoformans), Sterile fluid, Bone marrow, KT IV, Ear external, Hair, Skin, Nails, Medical devices, Urine, Vaginal, Tissue, Prostatic fluid (Blastomycosis).
Swabs samples are not adequate for recovery of fungi.
Direct examination: It is highly recommended that a direct microscopic examination be made for fungal specimens. Hyphae, yeast formws small budding yeast will be reported
Skin scales, nail scraping and hair should be examined after potassium hydroxide (KOH 10 %) treatment.
Incubation: 30°c for 3 weeks.
Specimen collected for yeast (Vaginal and oropharyngeal) are incubated for1 week.