Overview

The UAB Clinical Microbiology Laboratory offers comprehensive testing for detection, isolation, characterization and susceptibility testing of infectious agents. We are a 24/7 receiving core laboratory for processing and analyzing all microbiology samples for the core UAB Medicine system, including:

  • UAB Hospital, including UAB Emergency Department
  • UAB Women’s and Infants’ Center
  • UAB Callahan Eye Hospital, including UAB Callahan Emergency Department
  • UAB Highlands Hospital, including UAB Highlands Emergency Department
  • UAB Gardendale Emergency Department
  • Kirklin Clinic and Whitaker Clinic
  • 10 additional UAB Medicine satellite offices and outpatient clinics throughout the Birmingham metro area

We utilize rapid direction detection methods where feasible for optimal patient care, including immunologic, mass spectrographic, and nucleic acid based assays. Our facilities include a BL2 main laboratory and a BL3 satellite laboratory for mycobacteriology and analysis of other airborne or high-risk agents.

We also coordinate our analytical capabilities with multiple reference laboratories within and adjacent to the UAB Hospital complex:


  • The UAB Fungal Reference Lab, which also incorporates selected virology, antimicrobial susceptibility, and bacteriology capabilities, is closely coordinated by its director, Dr. Sixto Leal.
  • The Virology Laboratory housed at Children’s Hospital of Alabama is a routine provider of specialized virology services to our laboratory and takes part in GME activities with UAB residents.
  • The UAB Mycoplasma Reference Laboratory is a nationally recognized center of excellence for culturing and susceptibility testing for clinical samples of rare and highly fastidious Mycoplasma species and related organisms.

Our Faculty

Sixto M. Leal, MD, PhD
Assistant Professor, Laboratory Medicine
Section Head, Microbiology
Director, Fungal Reference Lab
Director, COVID-19 Testing Unit
Specialties: Mycology, Bacteriology

William H. Benjamin, PhD
Professor, Laboratory Medicine
Head, BSL-3 Laboratory
Specialties: Molecular Microbiology, Mycobacteriology, Parasitology

Allen W. Bryan, Jr., MD, PhD
Assistant Professor, Laboratory Medicine
Assistant Section Head, Microbiology
Microbiology Consultant, VA Medical Center-Birmingham
Specialties: Bacteriology, ID/Susceptibility, Blood Cultures, Quality

Residency/Fellowship Training

Residents in the UAB Medicine AP/CP Program are required to complete a 3-month intensive primary rotation in the Microbiology Laboratory, simultaneous with their rotation in Immunology. After completing this rotation, residents have the option to pursue additional 1-month elective rotations to further hone their knowledge and skills.

Residents on Microbiology will attend weekly microbiology laboratory section meetings, where the attendings, lab supervisor, lead technologists, and key support personnel gather to make management decisions and report on progress with projects. In addition, daily rounds and weekly plate-round presentations are scheduled for day-to-day management of cases and demonstrations of the lab for infectious disease fellows and other house staff. Mycology rounds are held twice weekly and heavily involve residents observing and determining the species of positive mold cultures. Residents will assist the day attending on call with any pages that arise during working hours.

Didactic sessions, including lectures and case series discussions, are conducted throughout the rotation. Both residents and infectious disease fellows attend the didactics, which cover the key aspects of each subfield of clinical microbiology. In addition, residents are expected to attend the weekly infectious disease case conference, as well as observe the microbiology contribution to monthly system-wide interdisciplinary committees (Infection Prevention, Antimicrobial Stewardship, etc.) Residents will complete bench shifts in conjunction with our highly skilled technologists, including experiences at the main bacteriology workspace, the mycobacteriology lab, the molecular laboratory, and the partner virology laboratory at Children’s Hospital.

A 2-hour oral examination at the end of the primary rotation provides an assessment to the resident of their state of knowledge in the field. As clinical microbiology is a discipline of many details, the typical resident will wish to return to the subject in preparation for examinations and clinical practice; the oral exam provides a roadmap for future individualized study.

Our Testing

Our services include:

Aerobic and Anaerobic Bacteriology

The Bacteriology Section isolates and identifies clinically significant microorganisms from a wide variety of submitted clinical specimens, and provides antimicrobial susceptibility testing services for UAB clinical practitioners.

Our blood cultures and select body fluid cultures are continuously incubated and monitored by our BacT/Alert™ systems, including the next-generation Virtuo™ instruments. We maintain ongoing quality improvement projects in conjunction with the nursing staff of the UAB Medicine system to achieve optimum collection of blood cultures and minimize contamination of specimens.

Depending on availability and appropriateness, rapid analyses may be applied to blood specimens via T2Candida™ and/or positive blood cultures via ePlex™ nucleic acid assay instruments for accelerated diagnosis in time-critical situations.

Skilled technologists conduct isolation and characterization of routine bacteriology cultures daily. MALDI-TOF technology is utilized for identification in all routine bacteriology workups, with adjunctive biochemical and immunologic methods for backup and/or confirmation. Rapid susceptibility results for bacteria are provided by our automated Microscan™ instruments, with disk diffusion and E-test™ used as additional methods for in-house testing of antimicrobial activity. Further identification and susceptibilities are available through reference laboratories, including the co-located Fungal Reference Laboratory.

Yeast specimens isolated in the course of bacteriology analysis are transferred to the Mycology Section or Fungal Reference Laboratory as appropriate.

Mycology

The Mycology Section performs identifications of pathogenic molds, dimorphic fungi, and yeasts isolated or recovered from clinical samples. Identification by gross and microscopic examination is supplemented by serologic procedures for general verification and for auxiliary detection of Histoplasma, Blastomyces, and other appropriate species.

Molecular Virology

UAB Molecular Virology utilizes COBAS platforms for quantitative RT-PCR for HIV, CMV, HCV, HBV and qualitative HPV. In addition, various platforms are used for laboratory developed tests (LDTs) for BK virus, EBV, and Parvovirus B19.

As part of our SARS-CoV-2 / COVID-19 testing program, we are utilizing all our modalities as well as a newly installed Cepheid GeneXpert platform to conduct one of the highest throughput sites for academic testing in the nation. The GuideSafeTM testing collection and analysis system implemented by Dr. Sixto Leal has permitted processing of over 10,000 specimens per day with 48-hour turnaround time, supporting multiple university sites and complementing coordinated symptom monitoring and trace-and-test programs.

Mycobacteriology

The BSL3 laboratory is used for processing specimens for mycobacterial isolation and identification. Over 7000 specimens are processed per year, with a 4% overall positivity rate and approximately 15 new M. tuberculosis cases annually. We collaborate closely with our colleagues in the Division of Infectious Disease and Jefferson County Health Department to maintain follow up on tuberculosis patients.

Our detection methods include a 1280-sample capacity, continuous-monitoring liquid incubation platform (BD MGIT) as well as culturing on traditional Middlecrook 7H11 media. Acid-fast (AFB) smears are reported within 24 hours, with weekly confirmation of positives via HOLOGIC AccuProbe. UAB Medicine has a highly active non-tuberculosis mycobacterial (NTM) clinic, and our patient population also includes cystic fibrosis patients with Mycobacterium abscessus.

Parasitology

We use MERIFLUORR Cryptosporidium/Giardia immunofluorescence for detecting Giardia and Cryptosporidium as a screen for parasite-caused diarrhea. Complete ova and parasite (O&P) consisting of formalin ethyl acetate sedimentation and trichrome staining examinations are performed on patients with risk factors.

Contact Us

Sixto M. Leal Jr., M.D., Ph.D.
Assistant Professor, Laboratory Medicine
Director, Clinical Microbiology, Fungal Reference Laboratory
The University of Alabama at Birmingham
619 19th Street South, W287B
Birmingham, AL 35249-7331
smleal@uabmc.edu