Division of Infectious Diseases

microBio (Part 4): Dr. Mark Rupp on the Future of ID

This post is the final part of a multi-part installment exploring the career and life of Dr. Mark Rupp, outgoing Chief of Infectious Disease at UNMC. If you missed our first post introducing Dr. Rupp and this series, part 2 exploring Dr. Rupp’s career, or part 3 exploring his life outside of medicine, see the linked posts to catch up. Otherwise, read on to learn more about Dr. Rupp’s outlook on the future of ID and advice for the next generation of ID professionals.


How do you avoid burnout?

I think a little introspection and self-reflection really helps.  In our line of work, it is not hard to find very worthy people who, through no fault of their own, are dealing with truly daunting challenges.  Many of us have so much for which to be grateful. Many people in the world would jump at the chance to switch places with us. Keeping these things in mind goes a long way to avoiding a doom and gloom/burnout cycle. Also, I think that the 24-hour news feed, social media, and the pace of communication – constantly texting, checking posts, and emails, lends itself to a frantic, chaotic mindset.  Setting aside the phone for a while, turning off the TV and radio, and getting outside in nature is a great way to recalibrate.

What advice do you have for those considering ID?

Infectious Diseases is a wonderful field. In many instances, ID docs are able to cure their patients fully and restore them to health.  There is rarely a dull moment – a new bug, outbreak, or resistance trait is always just around the corner.  Also, the people who chose ID as their field of specialization are some of the smartest, most interesting, and most pleasant folks in the world – you’ll have great colleagues and coworkers!

Where do you see the field of ID going in the next 10 years?

I only see the need for ID specialists growing in the coming years.  We’ll continue to see a quick pace in the development of better ways to diagnose infections and AI/ML assisting us in the clinics. The interface between public health, funding, politics, and social media will continue to be challenging.  ID specialists who have additional skills in IT, data analysis, population health, patient safety/quality improvement, and mass media/communication will be in high demand.  The way in which our country funds health insurance and healthcare will continue to be problematic, as will healthcare access issues – these issues are global but will impact the practice of infectious diseases in the coming years.  Antimicrobial resistance will only increase and ID specialists will be needed to steer how to best treat these complex patients.  The big wild card is when we will see the next pandemic.

What keeps you excited about ID to this day?

As I mentioned earlier “you‘ve got to love them bugs”  – new pathogens, new virulence determinants, new resistance traits. In addition, interacting with students and trainees keeps you on your toes.

-Dr. Mark E. Rupp

Where to Find Us: IDWeek 2024- Talks, Panels, and More

Next week begins IDWeek 2024, and UNMC will have a very strong showing at the conference! Below, we have gathered info on all oral presentations, panel participation, and other involvement from UNMC ID personnel, so read on to see where you can find us in Los Angeles this week!


microBio (Part 3): Dr. Mark Rupp, the Life

This post is part of a multi-part installment exploring the career and life of Dr. Mark Rupp, outgoing Chief of Infectious Disease at UNMC. If you missed our first post introducing Dr. Rupp and this series or part 2 exploring Dr. Rupp’s career, see the linked posts to catch up. Otherwise, read on to learn more about Dr. Rupp’s life, interests, and hobbies.


A recent hiking trip to Escalante in Utah (the little pink person in the corner is Elizabeth – Dr. Rupp’s wife)  

What are your favorite pastimes/hobbies?

Up until fairly recently (pandemic casualty) I played indoor soccer with an “old timers” club.  With the arrival of grandchildren, I enjoy spending time with them and watching them grow up so very quickly.  Gardening is a favorite pastime, as is spending evenings on the backyard deck with friends and neighbors. The high point of my year is an annual backpacking trip with my adult children in a remote wilderness area – truly off the grid.

What are your favorite genres of book/movie/music?

I’ve always thought that life is a bit better when you are reading a good book and I usually have a book or two that I am engaged with. I favor American history, but also enjoy science, current events, economics, politics, etc. Once in a while, my wife will steer me to great fiction. For example, I just finished Eric Larson‘s “The Demon of Unrest’ about the days just before the Lincoln inauguration and the initiation of the Civil War (some interesting parallels to the modern day) and I’ve started Hampton Sides’ “The Wide Wide Sea” about Captain James Cook’s 3rd and final voyage. I definitely recommend Abraham Verghese and the Covenant of Water. A few other recent worthy reads include Wasteland – by Oliver Franklin Wallis, Caste – by Isabel Wilkerson, and The Deadly Rise of Anti-Science – by Peter Hotez.  

Where have you lived? Which was your favorite?

My father was a geologist who worked for an oil company, and we moved around the western US oil fields as I was growing up – born in Kansas, lived in Oklahoma, Colorado, and moved to Houston, Texas, in high school.  I went to UT Austin and Baylor College of Medicine and then went out to Virginia for 7 years of post-doctoral training.  UNMC was my first “real job” – my dad kidded me about finishing 27th grade as I joined faculty at UNMC.  I’ve lived in Nebraska longer than any other place.  I truly believe that “you should bloom where you are planted” and every place I’ve lived has been full of wonderful people, places, and opportunities.   

-Dr. Mark E. Rupp

microBio (Part 2): The Career of Dr. Mark Rupp

This post is part of a multi-part installment exploring the career and life of Dr. Mark Rupp, outgoing Chief of Infectious Disease at UNMC. If you missed our first post introducing Dr. Rupp and this series, catch up here. Otherwise, read on to learn more about Dr. Rupp’s career in medicine and his impact on UNMC.


Dr. Rupp and the Staphylococcal Research Lab
Dr. Rupp receiving the UNMC Distinguished Scientist Award (2013)
Dr. Rupp and the Clinical Trials Office (CTO) he directed for over a decade

It has been incredibly gratifying to help the UNMC ID Division grow from the 3 UNMC faculty in 1992 to the over 30 faculty, over one dozen specialized APPs, 6 Fellows, and dozens of support staff and clinical researchers that make up the Division today and to witness UNMC ID blossom into a nationally well-recognized Division with excellent training programs, state of the art clinical care, and vibrant clinical research. UNMC ID is known for expertise in immunocompromised host ID that has been developed over the years by Drs. Kalil, Florescu (who tragically died in 2023), Freifeld, and Zimmer; HIV care capably led by Dr. Swindells for many years and more recently by Drs. Fadul and Bares; Orthopedic ID led by Drs. Hewlett and Cortes-Penfield; and Community Practice led by Dr. Starlin.  Many other faculty are involved in our programs in infection prevention, antimicrobial stewardship, OPAT, biocontainment, telehealth, DEI/Advocacy, and other areas.  We are truly fortunate to have so many smart, talented, and hardworking people call UNMC ID their professional home. UNMC ID is a wonderful mix of persons of different ages, genders, ethnic backgrounds, and religious/cultural beliefs – it is a place where people are comfortable and can achieve their full potential.

-Dr. Mark E. Rupp

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Announcing ‘microBio’: a blog-ography featuring prominent voices in ID and beyond

We are thrilled to announce a new blog post series on the UNMC ID blog: microBio. microBio is a biographical exploration of the lives and careers of ID physicians and scientists at UNMC segmented into multiple periodic installations. In this series, we will gain a deeper understanding of the professionals and leaders who have worked tirelessly to make UNMC ID better.

Who better to be our inaugural featured physician than Dr. Mark Rupp, outgoing Chief of Infectious Disease here at UNMC. Dr. Rupp has been an incredibly impactful force for good during his tenure at UNMC ID. We recently recognized his continued service in educating the public on ID topics on Rural Health Matters, a television show that features experts discussing various health topics and their impact on farmers, ranchers, and rural Americans. In the same vein, he was also recently awarded the prestigious Bartee Advocacy of Science Award in recognition of his exceptional community engagement as a scientist. Dr. Rupp has also garnered national recognition as well, having previously served as president of the Society for Hospital Epidemiology of America (SHEA) and as a consultant for the FDA, CDC, NIH, and the VA. He has also published well over 100 peer-reviewed scientific articles. As you will see during the series of upcoming microBio posts, these achievements only scratch the surface of the positive changes he oversaw in the Division and University at large. Dr. Rupp plans to stay on as faculty for several more years, and we thank him for his leadership through pandemics, outbreaks, and impressive growth in the Division.

Please tune in to the upcoming 3 microBio posts exploring Dr. Rupp’s career, life, and advice/outlook for the next generation of ID professionals. For now, though, enjoy a sneak peek below, where Dr. Rupp offers how he got interested in medicine and how that interest matured into a passion for ID?


I have had a life-long interest in biology/life science.  My mother related that she thought I would be a doctor when I showed an interest during elementary school in microbiologists and “Microbe Hunters” a book published back in 1926 by the famous bacteriologist Paul De Kruifl (and no, despite common belief, I was not around to work with Dr. De Kruif or read the initial release).  I earned a degree in Chemical Engineering because I’ve always been a “belt and suspenders” kind of person and wanted to have a profession to fall back on if I was not able to get into med school.  While in medical school at Baylor College of Medicine (a few years before Dr. Cortes-Penfield – also a Baylor grad), I thought I wanted to be a surgeon.  I ended up going into Internal Medicine due to the very broad career choices available and eventually came around to ID because “you just got to love them bugs!”    

-Dr. Mark E. Rupp

Clinical Guidance for Next-Generation Sequencing of Infectious Diseases: Q&A from the Antimicrobial Stewardship Team

photo of Dr. Cichon smiling. her hair is long and blonde, and she is wearing a black blazer with a white blouse

The UNMC/Nebraska Medicine Antimicrobial Stewardship team has developed a new clinical guidance regarding use of infectious disease next generation sequencing diagnostic tests. There is currently no national consensus regarding the use of ID-NGS tests, nor have they been systematically compared to a diagnostic gold standard. The UNMC Antimicrobial Stewardship team reviewed the literature and evaluated UNMC’s most common uses of ID-NGS tests to develop this set of practical guidelines. The guidelines project and this blog post were led by one of our recent graduates, Dr. Cathy Cichon, MD, MPH, during her fellowship.

What is NGS?

Next-generation sequencing (NGS) is a culture-free method of analyzing the microbes within a sample. These tests sequence all or part of the microbial DNA or RNA in a patient specimen (such as serum, tissue, or cerebrospinal fluid [CSF]). 

What NGS tests are currently available?

All NGS tests are send-out studies. The most common NGS tests that Nebraska Medicine clinicians order are the Karius Test, University of Washington Broad-Range PCR, and Delve Bio (previously UCSF Center for Next-Gen precision diagnostics) CSF cell-free DNA. 

What are the advantages of NGS testing verses conventional microbiology?

The benefits of NGS testing include the potential detection of obscure or rare pathogens, detection of pathogens that are difficult to grow using conventional methods, or detection of pathogens in patients previously treated with antimicrobials. 

What are the drawbacks of NGS testing verses conventional microbiology?

The limitations of NGS testing include high cost (>$1000), long turnaround times due to shipping requirements, the detection of commensal/non-pathogenic organisms, and lack of antimicrobial susceptibility testing. Additionally, they have not been compared to a diagnostic gold standard and their performance (sensitivity, specificity, etc.) is unknown. 

When are NGS tests useful?

NGS tests have been proposed as a diagnostic tool for a variety of clinical syndromes. While studies are still ongoing, to date the Karius Test has been most useful for culture-negative endovascular infections (i.e. endocarditis or mycotic aneurysm) and the University of Washington Broad-Range PCR has been most useful for biopsies of focal infections (i.e. culture-negative osteomyelitis) where traditional cultures have been negative. They can be considered in other limited circumstances when traditional testing is unrevealing, as detailed in the new guidance document. They are not useful for undifferentiated clinical syndromes (i.e. febrile neutropenia, polyarthritis, etc.). They should only be considered where the result will change care such as if the patient is expected to need >14 days of antibiotics or there is concern that empiric antibiotics will be inadequate. 

Who can order NGS tests?

Due to the complexity of interpretation and cost, these tests can only be ordered by infectious diseases (ID) clinicians. If you think your patient would benefit from an NGS test, please consult the appropriate ID team. 

Where can I find the guidelines?

The guidelines are in the clinical microbiology section of the antimicrobial stewardship website: https://www.unmc.edu/intmed/_documents/id/asp/ngs.pdf

Antimicrobial Stewardship logo with a pill bottle and pill encircled by a polygon outlined in red, and a red rectangular shape to the right with the words Antimicrobial Stewardship written in it

UNMC ID Seeking Applications for Solid Organ Transplant/Oncology ID Faculty

Are you an exceptional infectious diseases physician specialized in the care of immunocompromised patients and dedicated to teaching and making a significant impact within a diverse and collaborative environment? If yes, we invite you to consider joining our world-class team as a Solid Organ Transplant (SOT)/Oncology ID (OncID) faculty member in the Infectious Diseases (ID) Division at the University of Nebraska Medical Center (UNMC).

UNMC’s robust solid organ transplant programs perform lung, heart, liver, kidney, pancreas, intestinal and multi-visceral organ transplants and attract patients from across the region and nation. UNMC’s Fred and Pamela Buffett Cancer Center is NCI-designated and provides specialty care to patients with solid tumors and hematologic malignancies, including autologous and allogeneic hematopoietic cell transplants and CAR T cell therapies. As a SOT/OncID faculty member, you will work in collaboration with faculty from the Transplant and Cancer Centers to provide excellent clinical care, foster a stimulating learning environment, and engage in impactful research initiatives. You will also play a crucial role in educating and mentoring future medical professionals while contributing to the advancement and success of UNMC. 

Responsibilities:

  • Deliver exceptional care for solid organ transplant and oncology patients to optimize clinical outcomes.
  • Provide high-quality instruction and mentorship to medical students, residents, and fellows in a positive, inclusive, and dynamic learning environment.
  • Collaborate with faculty colleagues, specialty APPs, and multidisciplinary staff. 
  • Conduct and contribute to clinical and translational research. 

Desired Characteristics: 

  • Advanced degree in a relevant field (MD, DO, MBBS, or equivalent).
  • Board certified or board eligible in Infectious Diseases.
  • Proven ability to teach and mentor medical students, residents, or fellows.
  • Strong communication skills, with proficiency in conveying complex information effectively.
  • Demonstrated research experience and a track record of scholarly publications.
  • Capability to work collaboratively in a team-oriented setting.

To learn more about UNMC ID: https://www.unmc.edu/intmed/divisions/id/index.html.

We look forward to your application and the opportunity to explore how your expertise and excellence can contribute to our vibrant academic community. If you are interested in this opportunity, please apply at https://unmc.peopleadmin.com/postings/86084

UNMC ID Recognizes National Immunization Awareness Month

As we close out August 2024, we want to take a moment as a Division to recognize National Immunization Awareness Month. Held every August, this observance gives healthcare professionals and the public a chance to highlight the incredible importance of vaccination and to encourage conversations with providers to ensure that all are up to date on their vaccinations.

From the yearly flu vaccine to those targeted at serious pathogens of different stages of life, like the Pneumococcal οr Varicella (chickenpox) vaccines, staying up to date on these critical medical interventions is one of the best things we can do to protect ourselves from serious diseases.

The Centers for Disease Control and Prevention (CDC) and the American College of Physicians (ACP) have great resources to facilitate the goal of increased vaccine compliance, which are linked below. These resources can answer vaccine-related questions or help providers identify and offer appropriate vaccinations.

With the 2025 flu season nearly upon us, the Advisory Committee on Immunization Practices (ACIP) and CDC have also updated their vaccination recommendations for the prevention of COVID-19, RSV, and influenza, among others. Additionally, the FDA has just approved updated mRNA COVID-19 vaccines targeting the currently circulating Omicron variant KP.2 strain of SARS-CoV-2. For more information about these changes and the upcoming respiratory virus season, attend the Infectious Diseases Society of America (IDSA) webinar later this week (August 29th @ 12pm CST; register here).

More Helpful Links:

  • APC Adult Immunization Center, which provides patient and provider education material on vaccines as well as up-to-date information on vaccine schedules and new formulations
  • CDC National Immunization Awareness Month Hub, which provides practical tips for talking to patients about vaccinations, as well as resources for patients to identify if and which vaccines they or their children may be missing

Thinking about training with UNMC ID? Fellows share why they chose UNMC

Fellowship application season is well underway, and our fellowship directors can’t wait to review applications. We have recently posted about the benefits of a UNMC ID fellowship (see here) and how to thrive in interviews (link here). But today, we wanted to highlight the words of fellows as they explain why they wanted to train at UNMC.


Interestingly, I ended up coming to UNMC because they have a phenomenal Emergency Medicine Residency! My significant other enjoyed his away rotation in UNMC’s ED so much we ended up couples matching into their IM and ED residencies. Initially, I thought I would pursue Rheumatology, but I abruptly changed my mind after a phenomenal ID rotation during my intern year. I subsequently rotated on ID two more times during residency and enjoyed working with the UNMC ID family so much I wanted to stay for fellowship.

Dr. Casey Zelus (Left, with a bagel she baked herself that is as big as her face!)


After researching the program for infectious diseases fellowship, I was especially struck at how both comprehensive and well-organized the training program appeared to be. Having dedicated clinical experiences in orthopedics, oncology, and transplant, for example, caught my eye.  After my interview day, I learned that the program’s strong points were largely the result of dedicated program leadership and faculty.  There is a sincere interest at UNMC in helping me become the clinician I hope to be.   

Image of ID fellow Dr. Bryan Walker wearing a red shirt and blue jacket and dark blue jeans and sunglasses leaning against a brick wall

– Dr. Bryan Walker


I chose UNMC for Internal Medicine residency in part because of the strong Infectious Diseases fellowship program. During residency, I was able to form strong mentorship bonds that truly made leaving the program incredibly hard. Working with the incredible faculty throughout my three years made staying at UNMC the right decision for my career. My interest in ID is antimicrobial stewardship. Our stewardship team is one of the best in the country (maybe I’m biased?), and I look forward to training under them throughout my fellowship. Furthermore, having access to the biocontainment unit and leaders in the field of emerging pathogens is an experience I don’t know I would be able to get anywhere else. Our training here is well balanced between general ID, immunocompromised services, and antimicrobial stewardship, so I know that when I come out of fellowship, I will be prepared for whatever position I decide to take.

– Dr. Mackenzie Keintz


UNMC has a rich tradition of being a center of clinical and scholarly excellence while promoting education through mentorship and fostering initiative and collaboration. The Medical Center is also committed to providing empathetic, evidence-based, and patient-centered care while serving a diverse and often medically underrepresented population. I look forward to experiencing this collegial and supportive atmosphere during fellowship training. The HEAL track also represents an amazing opportunity to further advance my knowledge and skills in medical education and leadership!

– Dr. Nabil Al-Kourainy


(1)  The infectious disease training here is highly regarded, and I wanted to train at a location where I could learn from all branches of ID – from emerging infectious diseases (check this out) to antimicrobial stewardship to transplant ID…even pediatrics ID!

(2)  I have family here in Omaha, and Omaha is much closer to my family in Colorado. It’s great to be close to your support system!

(3)  Omaha itself is a great city! There is so much to eat, do, and see here. The affordable cost of living adds to the attraction.

– Dr. Catherine Cichon and her dog Loki


Before the COVID pandemic began, I had visited UNMC and Omaha for internal medicine residency interviews, and I was considerably impressed by the medical facilities, the strength of the educational program, and the tranquility of the city. One of the faculty that I had interviewed with for residency interviews was Dr. Mark Rupp, the chief of the ID division, and I had promised him that regardless of where I ended up for residency, I would apply to UNMC for ID fellowship. So when I matched to UNMC for ID fellowship, I knew I had matched to the right place!

– Dr. Timothy Jang

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UNMC ID Research: Where to find us at the NIDS Meeting

The Nebraska Infectious Diseases Society (NIDS) annual meeting is this Friday, August 23rd. If you still need to register, check out our previous posts on the meeting and the keynote address for more information.

One of the most anticipated events held during the meeting is the poster session, which continues to grow each year and features fascinating cases and novel research, most of which is led by trainees, residents, and fellows. This year, the top abstracts in each category will also be presented orally. A huge congratulations to our top abstract winners: John Glassmann, who will present Data-driven strategies towards case management utilizing Tableau dashboard reporting and automation from the research category, and Sarah Uhm & Kari Havyer, who will present their clinical vignette Extrapulmonary Osteoarticular and CNS Tuberculosis: A Case Report. In addition to these talks, dozens of other fascinating projects will be presented as part of the poster session. Read on below for a digest of presenters to help plan your day.


Research Category:

Poster #Project TitlePresenting Author
2A Quality Improvement Project to Improve Utilization of Sputum Cultures in Hospitalized Patients with PneumoniaJennifer Zimmerman
17Inconsistent Participant Demographic Reporting in Published Antibiotic Clinical Trials Targeting Multidrug-Resistant Gram-Negative OrganismsDr. Evangeline Green
22Medicaid Insurance Expansion and its Association with HIV Outcomes in Nebraska, USA: An Observational Prospective Cohort StudyEmmanuel Essam
23Urine testing in the emergency department: an analysis of the frequency of inappropriate testing and an economic analysisAlex Larson
24A retrospective review of health disparities in achieving sustained virologic response in chronic Hepatitis C infection: A single center experienceEileen Leach
28Evaluating the Effects of Hepatitis C Treatment With Direct-Acting Antivirals on Glycemic Control in Patients With Diabetes MellitusRicky Rana
29Association Between Adherence Barriers and Pharmacy Refill History in People with HIV after Medicaid Expansion in Nebraska: An observational retrospective cohort study.Elizabeth Amato-Hanner
30Data-driven strategies towards case management utilizing Tableau dashboard reporting and automationJohn Glassman
33Duration of Daptomycin and Ceftaroline Dual Therapy in Salvage Methicillin Resistant Staphylococcus aureus(MRSA) Bacteremia Prior to Monotherapy De-escalationDr. Josh Lechner

Clinical Vignettes Category:

Poster #Project TitlePresenting Author
3A Fungal Tracheitis and Epiglottitis with Bacterial Superinfection in an Immunocompromised Teenager: A Long Road to Confirmation  Haley DeWitt
4Disseminated Mycobacterium Bovis with Prosthetic Joint InfectionMadeline Helm
5A Picture Worth a Thousand Words: Incidentally Diagnosed Neurocysticercosis and Barriers to its Treatment  Dr. Emily Dyer
7A rare case of idiopathic granulomatous mastitis with Corynebacterium kroppenstedtii infection in the setting of pregnancy and erythema nodosumLauren Ziegenbein
8Syphilis-Related Glomerulopathy: A Rare Presentation of a Common DiseaseShalmali Mirajkar
9Veillonella parvula Bacteremia in a Diabetic Patient with Osteomyelitis and Soft Tissue Infection Linked to OnychophagiaEmily Ehsan
10The Diagnostic Dilemma of an Atypical Bacterial Ventriculoperitoneal Shunt Infection in an Immunocompetent ChildDr. Christian Clodfelder
11Disseminated Mycobacterium bovis with severe thrombocytopenia during treatment: A diagnostic and therapeutic dilemmaLauren Crockett
12Not quite Bacillus. Not quite an Aneurysm. Navigating diagnostic challenges of a rare pseudoaneurysm infection.Jacob Owens
13Extrapulmonary Osteoarticular and CNS Tuberculosis: A Case ReportSarah Uhm &, Kari Havyer
14A Case of Severe Mucositis Following Mycoplasma InfectionDr. Abby Wolfe
15Blastomyces dermatitidis Cervical Spine Osteomyelitis and Paraspinal Abscess in NebraskaEllie Staab
16Cutaneous Mycobacterium abscessus infection in an immunocompetent teenage femaleMatthew Muellner
194 weeks of dyspnea in immunocompromised woman; presenting symptom of disseminated Histoplasmosis CapsulatumDr. Cristina Torres
20Breakthrough osteomyelitis with opportunistic canine oral flora in an immunocompromised patientRyan Chapman
21Mycolicibacterium smegmatis: a rare cause of sternal osteomyelitisJose Ortega
25Fusobacterium nucleatum mimicking lung cancer: A case report  Sarah Maki
26Rare Case of Ignatzschineria larvae Bacteremia in a Myiatic Wound Infection: A Case ReportDr. Nicholas Mielke
31Unrecognized Complications: The Uncommon Occurrence of PJP Pneumonia in lung cancer on DurvalumabDr. Narmada Lavu