Department of Medicine

Department of Medicine

   Division of Infectious Diseases


Programs and Laboratories


Antibiotic Management Program

The Antibiotic Management Program (AMP) is a joint initiative of the Department of Medicine (Division of Infectious Diseases) and the Department of Pharmacy and Therapeutics. The program is staffed by faculty in both departments, and includes 6 infectious diseases attending physicians and 4 pharmacists. AMP is directed by Drs. M. Hong Nguyen (MD) and Brian Potoski (PharmD).  The program's mission is to improve clinical outcomes of patients by providing timely and appropriate antimicrobial therapy, while minimizing unnecessary antimicrobial use.  This mission contributes to the prevention of superinfections due to pathogenic organisms (such as Clostridium difficile) and antimicrobial resistance.  The AMP goals are achieved by requiring prior approval for select antimicrobials via a dedicated stewardship phone and pager, as well as providing prospective follow-up of existing antimicrobial orders. This ensures appropriate selection and dose at initiation of therapy, as well as the opportunity to review ongoing therapy for opportunities to streamline and ensure optimal durations. Stewardship efforts are enhanced through the use of TheraDoc®, an integrated decision support software system, which allows for real-time identification of opportunities for intervention, thereby enhancing time to intervention and maximizing stewardship efficiency. Lastly, the AMP is committed to the education of the healthcare team by publishing in both electronic and hardcopy format, an Antibiotic Guide to facilitate proper antibiotic selection within the Institution's formulary and a protocolized approach to therapy. AMP also regularly participates in the educational lecture series for ID fellows and medical residents, and presents at the Infectious Diseases and Medicine Grand Rounds. The global expansion of antimicrobial resistance has become a public health crisis. Accordingly, the AMP has partnered with the XDR Pathogen Laboratory and Center of Innovative Antimicrobial Therapy (CIAT) to define the role of new antimicrobial agents and identify the best possible therapies for patients infected by extensively- or pan-drug resistant pathogens. Moreover, the AMP continues in a long tradition of working in collaboration with the clinical microbiology laboratory, most recently engaged with the lab to establish a Diagnostic Management Team (DMT). The DMT will identify and evaluate novel molecular-based assays to provide rapid and accurate detection of infecting pathogens, and develop criteria for their use. The resulting information will be interpreted and communicated to clinicians at the bedside through the AMP who will further assist in selection and optimization of appropriate antimicrobial therapy. For further information on the AMP, please contact Dr. M. Hong Nguyen (


UPMC Extensive Drug Resistant Pathogen Laboratory

Infections due to Gram-negative bacteria that are resistant to most or all classes of antibiotics have increased dramatically throughout the world, particularly since the development of new antibiotics has slowed. These "suberbug" infections, which have garnered widespread attention in the popular media and medical literature, are a particular problem at UPMC and comparable centers that care for large populations of immunosuppressed hosts, and other patients at risk for complicated infections.  The mission of the UPMC XDR (extensive drug resistant) Pathogen Lab is to identify optimal antimicrobial regimens against XDR pathogens recovered from UPMC patients, and to collaborate with the Antimicrobial Management Program (AMP) and clinical services in managing and improving outcomes of patients infected with these pathogens. The XDR Lab pursues this mission in a systematic, stepwise fashion:  1) Identification of most active antimicrobial agents and combinations against particular XDR isolates, as determined by time-kill assays in vitro; 2) Identification of genetic mechanisms of resistance for isolates, using molecular approaches such as targeted DNA sequencing, whole genome sequencing; 3) Correlating antimicrobial activity during time-kills with genetic resistance mechanisms of isolates, thereby identifying molecular markers that predict likelihoods of treatment responses in patients; 4) Devising treatment regimens against specific pathogens that are most likely to be active based on laboratory and genetic data; and 5) Working with AMP and clinical services to assure that optimal drugs and dosing regimens are used in patients.  Most recently, the XDR Lab has expanded its efforts to prospectively test new antimicrobial agents that are currently being evaluated in Phase 2 and 3 clinical trials, so that they can be most effectively incorporated into the care of UPMC patients once approved by the Food and Drug Administration. Since its inception, the XDR Pathogen Lab has been an international leader in the treatment of highly-resistant Gram negative infections. Particularly successful initiatives include the following: 1) identifying a carbapenem-colistin combination as the most active regimen against XDR- Acinetobacter baumannii (Ab) isolates at UPMC, and instituting treatment strategies that reduced mortality among transplant recipients with XDSR-Ab infections from >90% to <20%; 2) developing an institution-specific treatment algorithm for carbapenem-resistant Klebsiella pneumoniae (CRKP) infections with antimicrobial regimens based on isolate genetics and susceptibility patterns, which has significantly reduced mortality rates among patients with bacteremia, shortened lengths of hospital stay, and resulted in substantial cost savings; and 3) most recently, being the first group in the world to detect  the real-time emergence of CRKP resistance to the newly-approved antibiotic ceftazidime-avibactam, identify genetic resistance mechanisms, and demonstrate that these mechanisms restored susceptibility to carbapenems.  Based on the last data, we have revised the UPMC algorithm for treating CRKP.  Moving forward, we will measure the impact of our implementation of the revised algorithm on outcomes, lengths of stay, and costs.   For further information on the XDR Pathogen Laboratory, please contact Dr. M. Hong Nguyen (


Microbial Genomic Epidemiology Laboratory

The mission of the Microbial Genomic Epidemiology Laboratory (MiGEL), a component of the Infectious Diseases Epidemiology Research Unit, is to improve and conduct microbial genomic epidemiologic investigations of hospital and community-acquired bacterial infections. The laboratory is focused on using genomic, phylogenetic and bioinformatic approaches to identify genetic relationships among bacterial pathogens that present serious threat to public health. In this regard, MiGEL supports UPMC Infection Prevention by identifying hospital outbreaks. Ongoing MiGEL projects include: 1) development, validation, and implementation of bacterial whole genome sequencing (WGS) for detection of bacterial outbreaks for infection prevention, 2) development and implementation of bioinformatic methods for rapid interpretation of WGS data, 3) integration of bacterial WGS data and mining of the electronic medical record to detect hospital associated bacterial transmission in real-time, 4) investigation of the microbiome composition obtained from peri-rectal surveillance swabs as a method to predict infection in hospitalized patients and for surveillance of important hospital associated bacteria. In addition, MiGEL performs comparative WGS analysis and phylogenetic investigations of important global populations of Neisseria meningitidis. These studies have contributed to an improved understanding of N. meningitidis population structure, clonal emergence, and global spread. In addition, MiGEL provides training in molecular epidemiology to masters and doctoral students, infectious diseases fellows, and visiting international scientists. For further information on MiGEL, please contact Dr. Lee Harrison (