Beaumont. Laboratory. Quick Reference Guide: Microbiology

Transcription

1 Beaumont Laboratory Quick Reference Guide: Microbiology

2 Beaumont s Clinical Microbiology and Molecular Pathology Laboratories provide a full spectrum of tests ranging from traditional culture to state-of-theart molecular methods for the detection of medically important bacteria, fungi, parasites and viruses. In addition, the Laboratories provide information about the susceptibility of bacteria and select viruses to antimicrobial agents. The Laboratories consistently strive to deliver innovative technologies to help physicians, hospitals, and long-term care facilities obtain the right answer at the right time. Not only does Beaumont Laboratory provide testing for simple to complex cases, it also trains Michigan s future clinical laboratory scientists. Our top trainees often continue their careers at Beaumont Laboratory, thus we retain the most talented clinical laboratory scientists. These new graduates work alongside our highly skilled clinical laboratory scientists who have been with the organization for numerous years. This means that when your patient s specimens arrive in our laboratory, you can be assured that the most accurate test results will be obtained in a timely manner. You can count on our staff the way your patients count on you. Our experts are led by: Bobby Boyanton, Jr., M.D. Medical Director, Clinical Microbiology Laboratory Associate Medical Director, Molecular Pathology Associate Director of Residency Training Associate Professor, Department of Pathology and Laboratory Anatomic and Clinical Pathology, American Board of Pathology Subspecialty Molecular Genetic Pathology, American Board of Pathology Special interests Molecular applications for infectious disease testing, C. difficile disease, translational research Barbara Robinson-Dunn, Ph.D. Technical Director, Clinical Microbiology Laboratory Professor, Department of Pathology and Laboratory American Board of Medical Microbiology Special interests Laboratory Detection of Emerging Infectious Diseases, Antimicrobial Susceptibility Testing, Fungal and Mycobacterial Diseases Elizabeth Wey, M.D. Attending Pathologist and Hematopathologist Assistant Professor, Department of Pathology and Laboratory Anatomic and Clinical Pathology, American Board of Pathology Subspecialty Hematology, American Board of Pathology Domnita Crisan, M.D., Ph.D. Medical Director, Molecular Pathology Laboratory Professor, Department of Pathology and Laboratory Clinical Pathology, American Board of Pathology High Complexity Laboratory Director-Molecular Pathology, American Board of Bioanalysis Special interests Molecular Pathology, Hematopathology Vaishali Pansare, M.D. Chief, Pathology and Laboratory Medicine, Grosse Pointe Medical Director, Beaumont Laboratory Outreach Associate Professor, Department of Pathology and Laboratory Anatomic and Clinical Pathology, American Board of Pathology Subspecialty Cytopathology, American Board of Pathology Special interests Gynecologic Cytology, Prostate Pathology

3 AGBAC/LAB5462 Antigen, Bacterial CSF ANTIGEN TESTS Antigens tested for and reported (if sufficient sample is received) include: H. influenzae type B, Group B Streptococcus, Neisseria meningitidis (serotypes A,C,Y,W135), Strep. pneumoniae Sterile Screw Capped Tube AGCRC/LAB6765 Antigen, Cryptococcal CSF If positive, titer is performed CSF: Sterile Screw Capped Tube AGCRS/LAB6766 Antigen, Cryptococcal Serum If positive, titer is performed Serum: Plain Red Top AGCRP/LAB3409 Antigen, Cryptosporidium Stool, Stool Aspirate If positive, DFA confirmation is performed SAF or Cary Blair AGGRD/LAB5465 Antigen, Giardia Stool, Stool Aspirate SAF or Cary Blair AGHPY/LAB5466 Antigen, H. pylori Stool, Stool Aspirate AGFLU Antigen, Influenza A/B No longer available. Order Rapid Influenza and RSV (NAAT) AGLUR/LAB2234 Antigen, Legionella UR Urine (all types) Only reports presence or absence of Legionella pneumophila serogroup 1 or Gray Top Urine Tube AGROT/LAB5469 Antigen, Rotavirus Stool, Stool Aspirate, Rectal Swab Must have visible fecal matter on rectal swabs AGRSV Antigen, RSV No longer available. Order Rapid Influenza and RSV (NAAT) AGSP/LAB5471 Antigen, Strep. pneumoniae CSF, Urine (all types) AGTRI Antigen, Trichomonas Vaginal Swab FFLA/LAB5513 Fecal Lactoferrin Assay Stool AGSSA/LAB5472 Strep Screen, Group A Pharynx, Throat SOFT TEST CODE/ CXACA/LAB5474 CXAFB/LAB5475 CXABL CXANA/LAB5476 CXBLD/LAB3006 Must be received in the Microbiology Department within 30 minutes of collection. Can not be performed if patient is consuming breast-milk: order Fecal Leukocyte Test For swabs submitted as tonsils : select Source: throat and Site: tonsils CULTURE TESTS CSF: Sterile Screw Capped Tube Urine: or Gray Top Urine Tube Culture, Acanthamoeba Culture, AFB Culture, AFB Blood Culture, Anaerobic Culture, Blood Corneal Scrapings, Contact Lens, Contact Lens Case and Solution Venipuncture, Intravenous Line, Autopsy CXBM/LAB5478 Culture, Bone Marrow Bone Marrow CXCTR/LAB5481 Culture, C. trachomatis CXCT/LAB5479 Culture, Cath Tip Cath Tip CXCSF/LAB3402 Culture, CSF CSF Multiple sources available on CXEAR/LAB5484 Culture, Ear External Ear Canal The healthcare provider usually inoculates the specimen onto Nutrient Agar Plates provided by the Microbiology Department AFB stain included, except if source is blood or bone marrow IUD specimens should be submitted to the laboratory within 3 hours. Standard: two sets of bottles (aerobic and anaerobic), each w/ 8-10 cc per bottle Pediatric: (aerobic) bottle available for children, 1-3 cc recommended Isolator tube (preferred), refer to Lab Test Directory for other collection containers Several cath tip types are available on a SITE (Foley cath tips are not appropriate for culture) Susceptibility test performed if appropriate Includes Gram stain, susceptibility performed if appropriate Gram stain included, susceptibility performed if appropriate SITE available for descriptors Blood: 10ml Isolator Tube or Other sources: Sterile Screw IUD: Other Sources: Blood Culture Bottles Pediatric Isolator Tube Viral Transport Medium (M4-RT, UVT, UTM, M5) Sterile Screw Capped Tube 1

4 CXEYE/LAB5485 CXFLD/LAB3405 CXFBL/LAB5488 CXFDM/LAB5489 CXFUN/LAB5487 CXGC/LAB5490 CXGEN/LAB5491 CXGRA/LAB5492 CXGAS/LAB5492 CXLEG CXMDR/LAB5496 CXMRS/LAB5497 CXPER/LAB5498 CXQUA/LAB5499 CXRES/LAB5500 Culture, Eye Culture, Fluid CULTURE TESTS continued Culture, Fungus Blood Culture, Fungus Hair, Skin, Nail Culture, Fungus Routine Culture, GC Culture, Genital Culture, Group A Strep Culture, Group A Strep with Susecptibility Culture, Legionella Culture, MDR-XDR* Culture, MRSA Culture, Pertussis Culture, Quantitative Bacterial Culture, Respiratory Eye, Conjunctiva, Corneal Scrapings, Corneal Swab Amniotic, Aqueous, Ascitic, Autopsy, Bile, Gastric, Pancreatic, Pericardial, Peritoneal, Peritoneal Dialysate, Pleural, Prostatic, Semen, Synovial, Vitreous Blood Venipuncture, Blood Line, Autopsy Hair, Skin, Nails Cervix, Endocervix, Eye, Anorectal, Genital Lesion, Labia, Penis, Pharynx, Rectal Swab, Synovial Fluid, Throat, Urethra, Vagina, Vaginal/Cervix Cervix, Endocervix, Genital Lesion, Labia, Penis, Urethra, Vagina, Vaginal/Cervix Throat, Pharynx, Perianal, Perirectal Throat, Pharynx, Perianal, Perirectal Broncheoalveolar Lavage (BAL), Bronchial Wash, Broncheal Brush, Endotracheal Aspirate, Lung, Sputum, Tracheal Aspirate, Transtracheal Aspirate Nares: Screening only. : clearing a patient from MRSA precautions. Gram stain included, susceptibility performed if appropriate SITE available for descriptors Gram stain test included, susceptibility performed if appropriate Use generic source Fluid if no options on source list fit SITE is available for descriptors OR add Order Comment with details DO NOT SUBMIT SPECIMEN ON A SWAB: submit fluid specimen for optimal recovery of agents Isolator Tube (preferred): 10cc adults, up to 1.5cc children Fungus stain included (unless submitted on culture medium) SITE is available for descriptors or add Order Comment with details Fungus stain included for select sources DO NOT REFRIGERATE Gram stain included only on male urethral and sterile sites Gram stain included for male urethral specimens only SITE is available for descriptors or add Order Comment with details Source (tonsils): select THROAT source, free text tonsils in SITE field Source (tonsils): select THROAT source, free text tonsils in SITE field. Only to be used for patients with a penicillin allergy Specimens obtained from bronchial sources are preferred for optimal recovery of this organism Test rules in/out MDR (multiply drug resistant) and XDR (extremely drug resistant) organisms *Should only be ordered by Infection Control staff Please list suspected organism request in the Order Comment field Screening test only. Susceptibility not performed. Has been replaced by B. pertussis by nucleic acid amplification (IBPNA) Gram stain included. 0.5g of tissue needed to perform test Gram stain included on select sources Swab: Scrapings: Sterile Screw Isolator Tube or Petri Dish Urethra: E swab (Green Top) Urethra: E swab (Green Top) Throat, Pharynx: Nasopharynx: E swab (Green Top) Other (i.e. sputum): Sterile Screw 2

5 CXSA/LAB5501 CXSTR CXSTL/LAB5503 CXTIS/LAB5504 CXTRI/LAB5505 CXUU/LAB5506 CULTURE TESTS continued Culture, Staph. aureus Culture, Sterility Culture, Stool Culture, Tissue Culture, Trichomonas Culture, Ureaplasma Select sources available on options list Duodenal Aspirate, Stool, Stool Aspirate, Rectal Swab Urines (all types), Cervix, Endocervix, Genital Lesion, Labia, Semen, Vagina*, Vaginal/ Cervix*, Urethra Urines (all types), Cervix, Endocervix, Genital Lesion, Labia, Semen, Vagina, Vaginal/ Cervix, Urethra CXUR/LAB5507 Culture, Urine Urines (all types) CXVIR/LAB5508 CXVBL CXVRE/LAB0912 CXWND/LAB5510 CXWNS/LAB5511 Culture, Virus Culture, Virus Blood Culture, VRE Culture, Wound Deep Culture, Wound Superficial Stool, Stool Aspirate, Rectal Swab, Urine Nose, Nasal, enter Nares for source at Order Entry This test is reserved for Cardiovascular, Orthopaedic and Neurosurgical Services. Only orderable in SOFT: please submit sample with paper requisition and client-specific information Includes culture for Salmonella, Shigella, Campylobacter, and E. coli O157 Includes E. coli Shiga Toxins 1 & 2 testing (except rectal swabs and stool/duodenal aspirates) Special Note if other organisms are requested, enter them in in the Order Comment Field (e.g. Yersinia, Vibrio, Plesiomonas, Aeromonas) Gram stain included, susceptibility performed if appropriate Use generic source Tissue if no options on source list SITE is available for descriptors and free text or add Order Comment with details Includes direct examination and culture (if direct exam is negative) If submitted in Diamonds media, no direct exam performed *vag or vag/cervix specimens should be tested with the AFFIRM and/or Trichomonas Antigen Test for optimal results Urine specimens must be delivered to the Microbiology laboratory within 30 minutes from collection Must be submitted in viral transport media (M4-RT, Indwelling Cath Urines = Foley, long term in-dwelling cath urines Straight Cath Urines = in and out cath urines VZV and/or Adenovirus DFA tests included on select sources Susceptibility not performed Gram stain included, susceptibility performed if appropriate Use generic source Wound if no options on source list fit SITE is available for descriptors and free text or add Order Comment with details Gram stain included, susceptibility performed if appropriate Use generic source Wound if no options on source list fit SITE is available for descriptors and free text or add Order Comment with details Cary Blair > 1 g of tissue: Sterile Screw Capped Container with 1mL of sterile, non-bacteriostatic saline < 1 g of tissue: Eswab (White Top) Diamond s Medium Fluid: (amniotic, semen, prostatic secretions, urine) - Swabs: urethra, vagina, cervix - Dacron or polyester swabs with aluminum or plastic shafts in UTM Gray Top Urine Tube (4-5ml of urine) Tissue: Viral Transport Medium (M4-RT, BAL /CSF/Body Fluid/Urine/Stool: Blood: 8-10 ml in EDTA tube Stool: Cary Blair Urine: Gray Top Urine Transport Tube (4-5ml of urine) Rectal Swab: Swabs: Aspirates: Sterile Screw Swabs: Aspirates: Sterile Screw Capped Container 3

6 CULTURE TESTS continued HPYLU/LAB5515 H. pylori Urease Antral Biopsy, Gastric Biopsy CXOID Org ID w/susceptibility Culture Isolate CXORG Organism Identification Culture Isolate SOFT TEST CODE/ Allow agar medium to warm to room temperature. The endoscopist MUST inoculate specimen onto agar medium Inoculated media with microbial growth submitted from healtcare provider Susceptability testing if apppropriate Inoculated media with microbial growth submitted from healthcare provider MOLECULAR TESTS (Nucleic Acid Amplification Tests NAAT) Inoculated agar medium container Culture Plates with bacterial growth Culture Plates with bacterial growth IUBKG, ISBKG BK Virus Quantitation Urine (IUBKG), Serum (ISBKG) IBPNA Bordetella pertussis Nasopharyngeal Swab E swab (Green Top) CTOX/LAB5531 C. difficile Toxin Stool, Stool Aspirate Liquid Stool Only ICNG Chlamydia trachomatis/ Neisseria gonorrhoeae IQCMG CMV quantitation Plasma Female: Cervix, Endocervix, Vagina, Urine Male: Urethra, Urine IEVNA Enterovirus CSF and NP swab SSB/LAB5182 Group B Strep Screen IHBVG/LAB6397 HBV quantitation Serum, Plasma IHCVG/LAB6530 HCV genotype Serum, Plasma IHQLG HCV qualitative Serum, Plasma IQHCG/LAB6403 HCV quantitation Serum, Plasma XHIVG HIV-1 genotype Plasma IHIVG/LAB6399 HIV-1 quantitation Plasma PAPT/LAB6278 Combined PAP and HPV DNA Test Vagina, Vaginal/Cervix, Vaginal/ Anorectal, Vaginal/Rectal Cervix or Endocervix HPVO/LAB6674 HPV DNA Test Cervix or Endocervix IHSVG HSV 1/2 CSF, Skin lesions, Ocular Fluid, Amniotic Fluid C. trachomatis (ICTG) and N. gonorrhoeae (INGG) may be separately ordered, but is not recommended. Specimens must be spun down within 6 hours of collection, plasma removed and stored When PCR test is positive, culture and antimicrobial susceptibility testing will be performed at no additional charge Specimens must be spun down within 6 hours of collection, plasma or serum removed and stored Specimens must be spun down within 6 hours of collection, plasma or serum removed and stored No longer available. Order HCV quantitation (IQHCG). Specimens must be spun down within 6 hours of collection, plasma or serum removed and stored Specimens must be spun down within 6 hours of collection, plasma removed and stored Specimens must be spun down within 6 hours of collection, plasma removed and stored Please answer required ask-at-order-entry questions to determine when High Risk HPV DNA testing is to be performed: a) Any Interpretation (HPV testing is always performed with the PAP), or b) If ASCUS (HPV testing only performed if PAP result is ASCUS). This is a stand alone High Risk HPV DNA test (i.e. does NOT include PAP test) Swabs: Viral Transport Medium (M4-RT, Urine: 5 ml preferred CSF: NP Swab: Viral Transport Media (M4-RT, Serum (SST, Red-Top) or Serum (SST, Red-Top) or Serum (SST, Red-Top) or ThinPrep ThinPrep Fluids: Swabs: Viral Transport Media (M4-RT, IMTBG Mycobacterium tuberculosis BAL, Bronch Wash, Sputum, CSF 4

7 IMYCG/LAB6840 MOLECULAR TESTS (Nucleic Acid Amplification Tests NAAT) continued Mycoplasma pneumoniae Swabs (preferred): throat, nasopharyngeal Fluids (acceptable): BAL, bronchial washing, pleural, sputum Swabs: Viral Transport Media (M4-RT, Fluids: FLRSV/LAB6760 Rapid Influenza & RSV Nasopharyngeal Swab Results for Influenza A, Influenza B, and RSV reported Viral Transport Medium ( IRVPG Respiratory Virus Panel NP Swab, BAL, bronchial washing, sputum AFFRM/LAB5532 Vaginosis Screen Vagina, Vagina/Cervix IVZVG SOFT TEST CODE/ VZV CSF, skin lesions, Ocular Fluid, Amniotic Fluid Reports presence or absence of: Trich. vaginalis, G. vaginalis, and Candida spp. Skin lesions should be submitted in viral transport media (M4-RT, NON-CULTURE TESTS NP Swab: Viral Transport Media (M4-RT, UTM, UVT) BAL, bronchial washing, sputum: Affirm VPIII Ambient Temperature Transport System (ATTS) Viral Transport Medium ( FFQL/LAB5512 Fecal Fat, Qualitative Stool, Stool Aspirate, Rectal Swab FWBC/LAB5514 Fecal Leukocytes Stool, Stool Aspirate, Rectal Swab Order ONLY if patient is consuming breast milk. SAF IDPAR/LAB5516 LGDFA OP/LAB5519 Insect/Larvae Ident Legionella DFA Ova and Parasites Insect, Arthropod, Larvae, Skin Scraping, Worm Broncheoalveolar Lavage (BAL), Bronchial Wash, Bronchial Brush, Lung Stool, Stool Aspirate, Duodenal Aspirate, Urine, Sputum PINWM/LAB5520 Pinworm Exam Pinworm Paddle, Scotch Tape Prep SMBP/LAB5522 Smear, Blood Parasites Blood Line, Blood Venipuncture Test no longer available. Order Culture, Legionella. Pinworm paddle (preferred). Tape must be transparent. Specimens should be submitted STAT to the Microbiology Lab and received within 2 hours of collection. All smears are reviewed by a Pathologist or certified Laboratory Director, with an interpretation added to the final report STCSP/LAB5524 Stain, Cyclospora Stool, Stool Aspirate, Rectal Swab SAF STFUN/LAB5525 STGRM/LAB5526 Stain, Fungus* Stain, Gram *Included with Fungal Culture orders, does not need to be ordered individually. Not performed on blood, bone marrow, vaginal, cervix, endocervix, throat, pharynx, or if specimen has already been inoculated onto culture medium *Included on most aerobic culture tests automatically. NOT performed on the following sources: throat, pharynx, blood, cath tips and medical devices, stools, bone marrow, or if specimen has already been inoculated onto culture medium STISO/LAB5527 Stain, Isospora Stool, Stool Aspirate, Rectal Swab SAF STMIC/LAB5528 Stain, Microsporidium Stool, Stool Aspirate, Rectal Swab SAF Clean Airtight Container SAF Pinworm Paddle or Cellophane tape (placed on a glass slide in sterile, screwcapped container) or capillary blood (fingerstick) or Sterile Screw STNOR/LAB5529 Stain, Nocardia or Sterile Screw STPCP/LAB5530 Stain, Pneumocystis Broncheoalveolar Lavage (BAL), Bronchial Brush, Lung, Endotracheal Aspirate, Transtracheal Aspirate, Tracheal Aspirate, Sputum WP/LAB5523 Wet Prep Exam Vagina, Vagina/Cervix Specimens obtained from bronchial sources are preferred for optimal detection of this organism Includes direct exam and Trichomonas Antigen Test 5

8 Beaumont Laboratory Lab results are too important to go anywhere else. P11297g1_13086_121814