Specimens include, but are not limited to, swabs from wounds, tissue, nasal/throat swabs, urine, stool, sputum, and various body fluids. A variety of bacteria, fungi, mycobacteria, parasites, and viruses may be detected in these patient samples. 

Specimens are accepted at all hours and result turn-around time varies depending on the test.  Routine testing performed in Microbiology includes but is not limited to:

Identification and Susceptibility

Bacteria, mycobacteria, and fungi from patient specimens are grown and isolated on a variety of types of agar  and broth media.  Identification of the isolated organisms are based on macroscopic and microscopic appearance of the organism, biochemical, enzymatic, and molecular testing.

Antimicrobial susceptibility testing is also performed to determine which antibiotic should be used for treatment of the infection.  Preliminary results for bacterial cultures are generally available within 24 hours, and results for fungal and mycobacterial cultures are generally available within 1 week. 


The OSF HealthCare Saint Francis Medical Center Laboratory is one of a few laboratories in Illinois that can perform the innovative mass spectometry technology known as Matrix Assisted Laser Desorption Ionization Time-of-Flight, or MALDI-TOF.  MALDI-TOF works by preparing a target slide with an organism and a matrix solution.  Through a cutting-edge process, a spectrum is created that represents the protein makeup of the sample.  This spectrum is then compared to other known spectra of bacteria and fungi located in a large database, allowing for identification of the sample down to the family, genus and species level.  Identification can be accomplished in 10-15 minutes once the organism has been cultured and isolated, which is several hours shorter than prior methodologies.

Molecular Methods

Polymerase Chain Reaction (PCR) is the most commonly used molecular technique to detect and study microbes. As compared to other methods, sequencing and analysis is definitive, reliable, accurate and fast. Results from molecular methods can be obtained in as little as 2 to 48 hours, depending on the type of test requested.


Used for detection of Clostridium difficile in stool specimens, Staphylococcus aureus and MRSA in nasal swabs and blood cultures, Influenza A & B in nasopharyngeal specimens, Enterovirus from CSF and also performs Prothrombin Gene G20210A Analysis (Factor II) and Factor V Leiden genotyping

FilmArray PCR

Able to detect 21 different respiratory targets, both viral and bacterial, in nasopharyngeal specimens. Also used for rapid identification of organisms present in some positive blood cultures, enabling earlier treatment for sepsis

SmartCycler PCR

Aids performance of lab developed assays for detection of Bordetella pertussis and Bordetella parapertussis in nasopharyngeal specimens as well as Herpes Simplex Viruses 1 and 2 in specimens from sites other than mucous membranes (primarily CSF)


Test for rapid identification of Herpes Simplex Viruses 1&2 in specimens collected from mucous membranes (genital, oral, rectal, etc.)

Our molecular menu also includes testing for HIV viral load, HCV viral load, Chlamydia trachomatisNeisseria gonorrheaGardnerella vaginalisCandida albicans, and Trichomonas vaginalis.