Microbiology Laboratory Clinical Services 


The busiest area of the laboratory, the Bacteriology section cultures specimens such as blood, urine, throat, cerebrospinal fluid, biopsies of tissue, and various wounds to determine what kind of bacteria are involved in the disease. Identifying the bacteria and their susceptibility to antibiotics allows for targeted therapy and early cure of infection. 

Our laboratory is staffed with a team of dedicated, licensed professionals who process these specimens, grow them on various agar media, identify the bacteria that grow, and perform antibiotic susceptibility testing. There are hundreds of species of bacteria 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. 

Antibiotic susceptibility tests are performed against pathogenic and potentially pathogenic bacteria to help the clinician choose the most appropriate antibiotic to treat a particular infection. The methodology used at Mount Sinai incorporates technology that was actually developed by the aerospace industry to test bacteria in space and utilizes sophisticated computer programs to more accurately predict the antibiotic profile of the bacteria isolated from the specimen. This computer program has been augmented by the Microbiology Laboratory Director to take into account the types of antibiotic resistance we see here in New York City. 


This section of the laboratory deals with the culture and isolation of yeasts and molds from specimens. Yeasts like Candida albicans are found causing infections like oral thrush (infection in the mouth), vaginitis, and candidemia (where yeast are found circulating in the blood). Patients who have certain underlying diseases are more likely to have candidemia. Another species of yeast, Cryptococcus neoformans, is found in pigeon droppings and causes meningitis (infection in the brain and spinal column) in the elderly, and in individuals whose immune system is depressed. 

When you think of molds you may think of athlete’s foot or ringworm (a fungus infection) but there are many other molds that can cause very serious infections. Aspergillus is a type of fungus that is found widely in the environment but can cause very serious infections in the lung and other areas of the body. The Microbiology Laboratory cultures specimens for fungal culture using media specific to the types of specimens submitted for culture. Yeasts can be identified using tests similar to those used to identify bacteria, but molds are identified by their growth characteristics and their microscopic appearance. A technologist must train for several years to be an expert in fungal identification. Treatment of fungal infections requires the use of drugs that are specific for yeasts and molds and are different from normal antibiotics. 


The incidence of tuberculosis has declined significantly since the early 1990s in the United States and in NYC. 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 country. 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 and other methods. 


Parasites cause a wide variety of diseases in humans ranging from diarrhea to fatal infections of the brain. There are also parasites that are transmitted to humans through an insect bite such as from a mosquito or a tick. Babesia are parasites that resemble malarial parasites but are endemic to our area of the United States. We see these quite often in the warmer months from people who walk in the woods or through high grass and pick up an infected tick that attaches to the person and transmits the parasite to the individual. Malaria is transmitted through the bite of an infected mosquito. Although malaria is not native to the United States people acquire the infection when they travel to an area where malaria is present. That is why it is important to take anti-malarial medication when traveling to these areas. The laboratory diagnoses these diseases by looking at smears made from the patient’s blood and identifying which of the four different kinds of malarial parasite it is. Intestinal parasites can be identified by examining stool specimens for the presence of parasite eggs, larval or adult forms. The laboratory has staff members that are proficient in identifying these parasites. 


Viruses are the most common cause of infections in humans. They range from common cold viruses to the potentially more serious influenza virus to deadly viruses like rabies, Ebola, yellow fever, and smallpox. We have come a long way in preventing viral illnesses with the development of vaccines, however we do not have vaccines for all viruses. Our lab still cultures for viruses but because culturing takes time, we also use techniques that allow us to identify the virus in only 48 hours using monoclonal antibodies directed against the virus of interest. 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. It is important to remember that antibiotics are not effective against viral infections; such antibiotic use may even cause some bacteria to become resistant to that antibiotic, making it ineffective if needed in the future. 

Molecular Microbiology 

The laboratory utilizes several types of instruments to perform molecular analysis on patient samples. One of the newest acquisitions is an instrument that can test stool sample for the presence of the C. difficile (C. diff) Toxin B gene using a technique called Real-Time PCR. We can tell in less than one hour if a patient is infected with C. diff.. Prior to surgery, we also use this instrument to determine if a patient is colonized with a bacterial strain called Staphylococcus aureus. Using appropriate antibiotics in such patients lessens the likelihood that the patient will get infected by his own bacteria during surgery. The lab also has the ability to use molecular methods to aid in treatment decisions. This 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.

Learn more about the types of tests offered.