The Division of Clinical Microbiology is comprised of a team of clinical microbiologists, pathologists, and medical technologists. We provide services in bacteriology, mycology, mycobacteriology, parasitology, serology, virology, and molecular microbiology. We offer 24/7 specimen processing and testing in the following areas: blood cultures, malaria, stat gram stain reading, stat fungal stains, stat serologies, rapid tests, molecular respiratory virus testing and Clostridium difficile testing. Routine bacterial and viral cultures, antimicrobial susceptibility tests, chlamydia/gonorrhoeae/trichomonas nucleic acid testing and viral loads are run seven days per week during dayshift hours 8 am to 4 pm. We run specialized testing including mycobacteriology, routine serology, routine mycology, ova and parasite exams, and quantiferon gold testing on Monday through Friday 8 am to 4 pm. In addition, we forward testing to a variety of specialized public health labs including the New York City Department of Health and Mental Hygeine, the Wadsworth Center, National Jewish Respiratory Institute, and the Centers for Disease Control and Prevention.

For detailed information on our tests and specimen collection guidelines, refer to the Mount Sinai Test Directory (must be connected to the Mount Sinai intranet). 

Testing resources include:

Critical Value Notification List

Specimen Rejection Critera

NPL test requisition forms

CDC requisition form

Zika Virus Testing Instructions

We provide a wide range of services in bacteriology, mycology, mycobacteriology, parasitology, serology, virology, and molecular microbiology.

Learn more about our Clinical Services

The Microbiology Laboratory conducts a number of types of tests, including the following: 

Routine Testing

  • Cultures for bacteria, fungi, mycobacteria, and viruses on appropriately sent specimens
  • Blood cultures for bacteria and yeast on specimens sent in BACTEC blood culture bottles.
  • Routine identifications using Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS)
  • Automated, semi-automated and manual biochemical methods.
  • Antibiotic susceptibility tests on potentially pathogenic bacteria, according to the Clinical and Laboratory Standards Institute guidelines if there are methods and interpretative criteria available for the relevant bacterial species.
  • Susceptibility tests on isolates form sterile sites.
  • Parasite testing of stool and blood  on appropriate specimens.
  • Giardia and cryptosporidium antigen tests on all stool specimens sent for a parasite exam. 
  • Viral serology tests and syphilis testing.

Tests Upon Request

We do not conduct susceptibility testing on anaerobic organisms (those that can grow in the absence of oxygen) routinely, though we will do it on isolates from sterile body sites upon request.

Rapid Tests 

Stat gram stains are performed on cerebrospinal fluid and surgical specimens. The lab performs testing for Clostridium difficile on liquid stools 24 hours a day Monday through Fridays and 9 am to midnight weekends and holidays with a two-hour turn-around-time for specimens sent directly to Microbiology (Tube Station 74). We also perform 24/7 rapid molecular testing for Influenza and Respiratory Syncitial virus from nasopharyngeal swabs and aspirates placed into viral transport media and transported to the lab.

Molecular Tests 

In addition to C. difficile PCR, the laboratory will perform pre-surgical screening for S. aureus and Methicillin-resistant Staph. Aureus (MRSA) from nasal specimens and measure HIV-1, hepatitis C virus , hepatitis B virus, and cytomegalovirus levels (viral loads). We offer nucleic acid tests (Hologic APTIMA) for Chlamydia trachomatis, Neisseria gonorrhoeae, and Trichomonas on a variety of specimen types. We also offer a 20-target respiratory PCR panel that includes all major respiratory viruses and 3 bacterial targets: Bordatella pertussis, Mycoplasma pneumoniae, and Chlamydophila pneumoniae. First time positive sputum smears are all analyzed via tuberculosis (TB) PCR. We also perform Quantiferon Gold testing for TB screening. We are in the process of validating more molecular tests with the aim of significantly expanding the molecular microbiology menu. 

This laboratory focuses its translational research on the following:

  • Implementing novel molecular tests and whole genome sequencing in routine microbiological analyses as well as in outbreak investigations
  • Investigating use of susceptibility tests to accurately predict resistance, especially with highlyresistant carbapenemase producing strains of bacteria
  • Researching the use of chromogenic media and molecular based assays to detect bacteria harboring resistance genes
  • Expanding the range of MALDI-TOF MS analyses offered by our laboratory and investigating ways to use MALDI-TOF MS for susceptibility testing and antimicrobial stewardship

Dr. Hamula is a founding member of the Mount Sinai Pathogen Surveillance Group, which has developed a pipeline for whole genome sequencing of outbreak associated isolates in real-time. She is currently working on expanding whole genome sequencing analysis for clinical use.

The laboratory recently acquired a MALDI-TOF MS for routine bacterial identification and a set of BioFire FilmArray instruments, on which we currently run the respiratory pathogen panel. We are in the process of validating the BioFire Stool GI pathogen panel for diarrheagenic stools with planned implementation in the fall 2016. We also have a GeneXpert Infinity to perform Real-Time PCR testing for a variety of targets. Both the GeneXprt and FilmArray have rapid turnaround times (within two to four hours of receipt in lab). These systems use self-contained cartridges where sample extraction, PCR amplification, and detection occurs. This hands-free, self-contained operation allows this instrument to be used for stat testing as no batching of specimens is required. 

The microbiology team includes the following:

Angela Rendo, MS, MT (ASCP)
Chief Supervisor, Clinical Microbiology
Supervisor, Virology and Molecular Microbiology

Flora Samaroo, BA
Supervisor, Bacteriology

Edezar Aragon, BS
Supervisor, Mycobacteriology, Mycology, Parasitology

Karen Rodney-Ebey, BS
Supervisor, Evening Shift

Zaineb Bello, BA
Supervisor, Night Shift

Debbie Barackman, BS
Quality Assurance Manager, Clinical Microbiology