Microbiology
A Subspecialty Of Clinical Pathology
About Microbiology
Stanford Health Care’s Microbiology Laboratory tests for microorganisms such as bacteria, fungi, and parasites to diagnose and guide antimicrobial therapy in patients with infectious diseases. The laboratory also assists Infection Control and Prevention to contain and prevent further spread of infectious diseases.
Testing
Submit a Sample
Our Faculty
Stanford’s Microbiology offers a full range testing for bacteria, fungi and parasites. Our services include:
Bacteriology
We offer routine bacteriology with isolation, identification, and antibiotic susceptibility testing utilizing a combination of phenotypic and nucleic acid amplification tests (NAATs). Matrix-Assisted Laser Desorption/Ionization-Time of Flight (MALDI-TOF) mass spectrometry is used to identify bacteria. Semiautomated antibiotic susceptibility testing is performed for same-day antibiotic susceptibility testing of blood isolates.
Colonizing organisms can easily overwhelm less robust microbes of huge clinical importance unless media specific for cystic fibrosis samples are employed. Stanford’s Microbiology team has years of experience handling samples from cystic fibrosis patients and we use phenotypic assay and NAATs to improve speed and accuracy of results.
Mycology
Microbiology offers a range of fungal cultures with yeast and mold identification using phenotypic methods, MALDI-TOF and NAATs. We also offer yeast and mold MIC susceptibility testing using a broth microdilution method.
Mycobacteriology
We offer direct PCR for detection of M. tuberculosis complex in sputum and other specimen types for rapid diagnosis of tuberculosis. Mycobacterial isolation on culture and antibiotic susceptibility testing are offered for various specimen types. Mycobacterial identification is performed using multiplexed, real-time PCR, MALDI-TOF, and ribosomal RNA gene sequencing. Interferon gamma release assay (Quantiferon test) is available for diagnosis of latent tuberculosis infection.
Parasitology
We offer a gastroenteritis PCR panel that detects enteric protozoan parasites along with bacteria and viruses. We also offer worm and tick identification.
Molecular Microbiology
When a rapid diagnosis is needed or when conventional microbiology fails to diagnose an infection, our lab utilizes molecular tools such as PCR and sequencing to make a diagnosis. NAATs offered include:
- Fungal cell-free DNA PCR panel
- Fungal PCR panel
- Bacterial 16S PCR amplicon sequencing
- Fungal ribosomal (ITS2 and 28S) PCR amplicon sequencing
- Protozoa ribosomal PCR amplicon sequencing
- Gastroenteritis PCR panel
- Meningitis/Encephalitis PCR panel
- Bordetella pertussis NAAT
- Strep Group A and C/G PCR
- Strep Group B PCR
- M. tuberculosis complex PCR
- Clostridioides difficile PCR
- Plasmodium screening NAAT
- Plasmodium species PCR
- Antibiotic resistance: mecA, vanA, erm41, rpoB, carbapenemase PCR
Immunoserologic Testing
Acute infections caused by bacterial or fungal pathogens are characterized or diagnosed via detection of the antigen or antibody. Tests offered includes: Helicobacter pylori, Cryptococcal antigen test, and Aspergillus galactomannan. Latent tuberculosis infection is diagnosed with interferon gamma release assay (Quantiferon test).
Test Directory
Find tests related to Microbiology Services.
Sample Submission
All specimens must be accompanied by a Stanford requisition and all samples must be labeled with the patient’s name, and at least one other unique identifier.
Proper specimen collection is vital to ensuring an accurate test result. For detailed collection instructions by individual test, please explore our test directory.
Shipping
Samples should be shipped or delivered via courier to:
Stanford Clinical Laboratories
Attn: Specimen Processing
3375 Hillview Avenue
Palo Alto, CA 94304
Customer Service Phone: 1-877-717-3733
New Client Inquiries
To arrange to be set up as a new client, please contact:
ClinOpsContracts@stanfordhealthcare.org.
Contact Us
To submit a sample to Microbiology, please complete a requisition and send with sample to:
Stanford Clinical Laboratories
Attn: Specimen Processing
3375 Hillview Avenue
Palo Alto, CA 94304
Customer Service Phone:
1-877-717-3733
Medical Director:
Niaz Banaei, MD
To arrange to be set up as a new client, please contact:
ClinOpsContracts@
stanfordhealthcare.org
SAMPLE SUBMISSION LOGISTICS
For more information on submitting cases, see the links below:
All Requisitions
Download Stanford Requisitions for specimen submission.
Account Set-up
Information on personalized requisitions, supplies, shipping and courier pick-up.
Pricing Inquiries
Pricing inquiries and contract information.
Billing
Billing policies, information and questions.
Results Web Portal
Request access or log-in to our client results portal.
Specimen Collection and Handling
Specifications for Specimen Collection and Handling.
Consult Service FAQ's
Get answers to Frequently Asked Questions.
Niaz Banaei, MD
APPOINTMENTS
- Professor of Pathology and Medicine (Infectious Diseases)
- Director, Clinical Microbiology Laboratory
- Associate Director, Clinical Virology Laboratory
PRACTICE AREAS
- Clinical Laboratory Techniques
- Clinical Microbiology
- Clinical Pathology
- Molecular Microbiolgy
- Mycobacteriology
CONTACT
Email: nbanaei@stanford.edu
Phone: (650) 736-8052
More information about Niaz Banaei:
https://med.stanford.edu/profiles/niaz-banaei
https://profiles.stanford.edu/niaz-banaei
Benjamin Pinsky, MD, PhD
APPOINTMENTS
- Professor of Pathology and Medicine (Infectious Diseases)
- Director, Clinical Virology Laboratory
- Professor of Pediatrics (Infectious Diseases), by courtesy
PRACTICE AREAS
- Clinical Laboratory Techniques
- Clinical Pathology
- Infectious Diseases
- Molecular Pathology
- Point-of-Care Systems
- Virology
CONTACT
Email: bpinsky@stanford.edu
Phone: (650) 498-5575
More information about Benjamin Pinsky:
https://med.stanford.edu/profiles/benjamin-pinsky
https://profiles.stanford.edu/benjamin-pinsky
Stanford’s Microbiology offers a full range testing for bacteria, fungi and parasites. Our services include:
Bacteriology
We offer routine bacteriology with isolation, identification, and antibiotic susceptibility testing utilizing a combination of phenotypic and nucleic acid amplification tests (NAATs). Matrix-Assisted Laser Desorption/Ionization-Time of Flight (MALDI-TOF) mass spectrometry is used to identify bacteria. Semiautomated antibiotic susceptibility testing is performed for same-day antibiotic susceptibility testing of blood isolates.
Colonizing organisms can easily overwhelm less robust microbes of huge clinical importance unless media specific for cystic fibrosis samples are employed. Stanford’s Microbiology team has years of experience handling samples from cystic fibrosis patients and we use phenotypic assay and NAATs to improve speed and accuracy of results.
Mycology
Microbiology offers a range of fungal cultures with yeast and mold identification using phenotypic methods, MALDI-TOF and NAATs. We also offer yeast and mold MIC susceptibility testing using a broth microdilution method.
Mycobacteriology
We offer direct PCR for detection of M. tuberculosis complex in sputum and other specimen types for rapid diagnosis of tuberculosis. Mycobacterial isolation on culture and antibiotic susceptibility testing are offered for various specimen types. Mycobacterial identification is performed using multiplexed, real-time PCR, MALDI-TOF, and ribosomal RNA gene sequencing. Interferon gamma release assay (Quantiferon test) is available for diagnosis of latent tuberculosis infection.
Parasitology
We offer a gastroenteritis PCR panel that detects enteric protozoan parasites along with bacteria and viruses. We also offer worm and tick identification.
Molecular Microbiology
When a rapid diagnosis is needed or when conventional microbiology fails to diagnose an infection, our lab utilizes molecular tools such as PCR and sequencing to make a diagnosis. NAATs offered include:
- Fungal cell-free DNA PCR panel
- Fungal PCR panel
- Bacterial 16S PCR amplicon sequencing
- Fungal ribosomal (ITS2 and 28S) PCR amplicon sequencing
- Protozoa ribosomal PCR amplicon sequencing
- Gastroenteritis PCR panel
- Meningitis/Encephalitis PCR panel
- Bordetella pertussis NAAT
- Strep Group A and C/G PCR
- Strep Group B PCR
- M. tuberculosis complex PCR
- Clostridioides difficile PCR
- Plasmodium screening NAAT
- Plasmodium species PCR
- Antibiotic resistance: mecA, vanA, erm41, rpoB, carbapenemase PCR
Immunoserologic Testing
Acute infections caused by bacterial or fungal pathogens are characterized or diagnosed via detection of the antigen or antibody. Tests offered includes: Helicobacter pylori, Cryptococcal antigen test, and Aspergillus galactomannan. Latent tuberculosis infection is diagnosed with interferon gamma release assay (Quantiferon test).
Test Directory
Find tests related to Microbiology Services.
close Testing
Sample Submission
All specimens must be accompanied by a Stanford requisition and all samples must be labeled with the patient’s name, and at least one other unique identifier.
Proper specimen collection is vital to ensuring an accurate test result. For detailed collection instructions by individual test, please explore our test directory.
Shipping
Samples should be shipped or delivered via courier to:
Stanford Clinical Laboratories
Attn: Specimen Processing
3375 Hillview Avenue
Palo Alto, CA 94304
Customer Service Phone: 1-877-717-3733
New Client Inquiries
To arrange to be set up as a new client, please contact:
ClinOpsContracts@stanfordhealthcare.org.
Contact Us
To submit a sample to Microbiology, please complete a requisition and send with sample to:
Stanford Clinical Laboratories
Attn: Specimen Processing
3375 Hillview Avenue
Palo Alto, CA 94304
Customer Service Phone:
1-877-717-3733
Medical Director:
Niaz Banaei, MD
To arrange to be set up as a new client, please contact:
ClinOpsContracts@
stanfordhealthcare.org
SAMPLE SUBMISSION LOGISTICS
For more information on submitting cases, see the links below:
All Requisitions
Download Stanford Requisitions for specimen submission.
Account Set-up
Information on personalized requisitions, supplies, shipping and courier pick-up.
Pricing Inquiries
Pricing inquiries and contract information.
Billing
Billing policies, information and questions.
Results Web Portal
Request access or log-in to our client results portal.
Specimen Collection and Handling
Specifications for Specimen Collection and Handling.
Consult Service FAQ's
Get answers to Frequently Asked Questions.
close Submit a Sample
Niaz Banaei, MD
APPOINTMENTS
- Professor of Pathology and Medicine (Infectious Diseases)
- Director, Clinical Microbiology Laboratory
- Associate Director, Clinical Virology Laboratory
PRACTICE AREAS
- Clinical Laboratory Techniques
- Clinical Microbiology
- Clinical Pathology
- Molecular Microbiolgy
- Mycobacteriology
CONTACT
Email: nbanaei@stanford.edu
Phone: (650) 736-8052
More information about Niaz Banaei:
https://med.stanford.edu/profiles/niaz-banaei
https://profiles.stanford.edu/niaz-banaei
Benjamin Pinsky, MD, PhD
APPOINTMENTS
- Professor of Pathology and Medicine (Infectious Diseases)
- Director, Clinical Virology Laboratory
- Professor of Pediatrics (Infectious Diseases), by courtesy
PRACTICE AREAS
- Clinical Laboratory Techniques
- Clinical Pathology
- Infectious Diseases
- Molecular Pathology
- Point-of-Care Systems
- Virology
CONTACT
Email: bpinsky@stanford.edu
Phone: (650) 498-5575
More information about Benjamin Pinsky:
https://med.stanford.edu/profiles/benjamin-pinsky
https://profiles.stanford.edu/benjamin-pinsky
close Our Faculty
Residencies and Fellowships
Clinical Pathology Residency Programs
Stanford Pathology offers Clinical Pathology residencies as well as a combination Anatomic Pathology/Clinical Pathology Residency.
Clinical Fellowships
Stanford offers an ACGME-accredited Fellowship in Medical Microbiology.