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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.

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Testing

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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.

Find a test

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

 

Microbiology Requisition

 

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

Phone:

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

 

Download Microbiology Requisition

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

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

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

Testing

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.

Find a test


close Testing
Submit a Sample

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

 

Microbiology Requisition

 

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

Phone:

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

 

Download Microbiology Requisition

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
Our Faculty

Niaz Banaei, MD

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

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.

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