Microbiology

TEST ORDERING INSTRUCTIONS: If being transported, CSF must be stored at room temperature at room temperature and delivered immediately to the laboratory. This test does not include cell counts (order separately if required). SAMPLE TYPE: At least 0.5-1ML CSF in sterile leak proof container. If multiple tests are required, minimum is 5ml divided between 3-4 sequentially labelled tubes. When this is done, tube 2 is used for microbiological tests. Further details on this can be found at: Youtube Video

SAMPLE TYPES: Variable therefore anatomic sites MUST be specified. Examples: A. Swabs (non-throat, non-HVS) Wound swabs (superficial/deep) Ear, nasal, eye, skin, ulcer, abscess swabs Environmental/OT sterility swabs B. Fluids (excluding CSF): Ascitic (peritoneal), pleural, synovial (joint), pericardial fluid, cyst, surgical irrigation or drain fluid C. Tissues & devices Tissue biopsy (soft tissue) Bone tissue Periprosthetic tissue Prostheses/implants (e.g., joint hardware) SAMPLE COLLECTION INSTRUCTIONS General principles: 1. Collect before initiation of antibiotics where clinically feasible. 2. Use aseptic technique for sterile site specimens. 3. Clearly indicate anatomical site and clinical diagnosis. 4. Avoid contamination with normal flora. Swabs 1. Use sterile synthetic swab with transport medium (Amies/Stuart ± charcoal). 2. Sample from deep infected area, not surface debris. 3. For abscesses: aspirate preferred over swab. Fluids 1. Collect via sterile aspiration into: sterile leak-proof container OR inoculated blood culture bottles (may improve yield). 2. Minimum volume: 1–5 mL (more improves yield). Tissue / bone 1. Submit sterile tissue pieces, not swabs. 2. Place in sterile container with small amount of sterile saline (do not immerse). 3. Do NOT place in formalin. Prostheses / implants 1. Place entire device in sterile container. 2. If large, send representative portions aseptically. SAMPLE HANDLING INSTRUCTIONS General principles: transport to the lab ASAP, ideally within 2–4 hrs of collection. If delay expected, most specimens may be refrigerated for up to 24 hours (swabs in transport medium may remain stable up to 48 hours). Ambient transport (20–25°C) is acceptable for short durations—preferably ≤8–12 hours for swabs and ≤4 hours for sterile fluids and tissues. Use appropriate transport media (e.g., Amies/Stuart for swabs) and sterile, leak-proof containers for fluids and tissues.

Sample types which can be submitted for this test are variable e.g. blood, body fluid, bone marrow, CSF, ear sample, eye sample, tissue biopsy, urine etc. The sample type / anatomic site MUST BE SPECIFIED. For most specimens, ship in ambient temperature. Never freeze. Collect before antifungals whenever possible. Collect in a sterile container This test does NOT include fungal AST.

Vaginal swab in sterile transport media. Preferably 2 swabs. HVS collection can be done on site but attracts additional charges.

Sample type: Gastric biopsy specimens (antral and/or corpus mucosal biopsies) collected via upper GI endoscopy. Patient preparation: Patient should ideally be off PPIs for 2 weeks and off antibiotics for 4 weeks prior to collection to maximize yield. Sample (biopsy) handling: Place immediately into appropriate transport medium (e.g., sterile saline, brain-heart infusion broth, or a commercially prepared H. pylori transport medium such as Port-A-Cul or equivalent anaerobic transport). DO NOT PLACE IN FORMALIN (this is for histology only — formalin is incompatible with culture). Deliver promptly to the lab. Transport refrigerated.

Instructions depend on reason for the test i.e. 1) For INFERTILITY assessment - abstinence for minimum of 48 hours and maximum 7 days required. Patient should be issued with (& explained to) the written test instructions 2) For POST-VASECTOMY assessment, test should be done at least 2-3 months post vasectomy. Patient must have been sexually active (>20 ejaculations) since the procedure was done. Abstinence is not a requirement for post-vasectomy clients. Test components: Macroscopic (color, viscosity), microscopic (sperm concentration, sperm count, motility, morphology) and chemical examination (pH +/- fructose).

Synovial fluid in leak proof container. Fluid type must be specified on the request form

2ml of CSF in Sterile leak proof tube

3ml of variable, i.e., pleural fluid, peritoneal/ ascitic fluid, synovial/ joint fluid, etc.

10g stool in leak proof container. Refrigerated Clinical history required