Microbiology Laboratory Clinical Services

Mount Sinai’s Microbiology Laboratory provides a wide range of services in Bacteriology, Mycology, Mycobacteriology, Parasitology, Serology, Virology, and Molecular Microbiology. A complete list of test codes and specimen collection guidelines can be found in the Mount Sinai Test Directory.

Bacteriology and Mycology

The busiest areas of the laboratory, the Bacteriology and Mycology sections culture specimens such as blood, urine, stool, throat, cerebrospinal fluid, biopsies of tissue, and various wounds.

Our laboratory is staffed with a team of dedicated, licensed professionals who process these specimens, grow them on various agar media, identify the organisms that grow, and perform antibiotic and antifungal susceptibility testing. We use mass spectrometry (MALDI-TOF MS) and biochemical tests to routinely identify bacteria and yeasts, and microscopic morphology to identify filamentous molds. There are hundreds of species of bacteria and fungi that can be isolated from clinical samples: Some are almost always pathogenic, some are pathogenic only to patients with suppressed immune systems, others colonize various areas of the body and do not cause disease, and yet others are considered normal inhabitants of a particular body region.

Antimicrobial susceptibility tests are performed against pathogenic and potentially pathogenic bacteria to help the clinician choose the most appropriate antibiotic or antifungal to treat a particular infection. Our methodology incorporates technology developed by the aerospace industry to test bacteria in space and utilizes sophisticated computer programs to more accurately predict the susceptibility profile of the pathogen isolated from the specimen. This computer program has been augmented by the Microbiology Laboratory Director to take into account the types of antimicrobial resistance seen in New York.


The incidence of tuberculosis has declined significantly since the early 1990s in the United States and in New York. This is due in large part to the advances in diagnostic testing and to the initiation of Directly Observed Therapy (DOT), first in New York and then in the rest of the United States. Tuberculosis remains a major health concern in other parts of the world. In addition to tuberculosis there are related species of mycobacteria that cause clinical disease in susceptible populations, and some are common environmental contaminants. Our laboratory uses a mycobacterial culture system that senses changes in gas pressure as a result of mycobacterial growth to detect cultures that contain these organisms. They are then identified using molecular probe technologies, PCR, and other methods.


The laboratory diagnoses parasitic infections by looking at smears made from the patient’s blood, specialized stains from the patient’s stool, and by direct examination of the parasites themselves. Intestinal parasites can be identified by examining stool specimens for the presence of parasite eggs, larval, or adult forms.

Virology and Molecular Microbiology

Our lab cultures for viruses but because culturing takes time, we also use rapid molecular techniques and techniques that allow us to identify the virus in only 48 hours using monoclonal antibodies. We also use molecular techniques to diagnose certain viral diseases as well as to monitor response to therapy for several viral infections such as HIV and Hepatitis C viruses.

Molecular microbiology is a constantly expanding field and many more tests will soon be available to help diagnose and treat infections using this and other molecular based technologies.