Research Scientist (Tenure)

Center for Human Genetics, MLR
Marshfield Clinic
1000 North Oak Avenue
Marshfield, WI 54449




Dr. Sanjay Shukla is a molecular microbiologist with research interests in the emerging infectious diseases. Dr. Shukla joined the Marshfield Clinic Research Foundation in 1998. He is a tenured Research Scientist at the MCRF and directs the Molecular Microbiology Laboratory. Dr. Shukla received his undergraduate degree with honors from the University of Calcutta, India. He obtained his master’s degree from the North Dakota State University and the doctorate degree from the University of Oklahoma in Norman, Oklahoma.



  • My research focus is on infectious diseases with emphasis on exploring the genetics underlying host-pathogen responses from the vantage of both the pathogen and human host. The overall goal of my laboratory is to advance understanding of infectious disease processes with the purpose of supporting development of new or more informed therapeutic interventions. By investigating the genetics of both the pathogen and the human host central to establishing infectious processes, we can target interventions at the level of key molecular interactions with the intention of improving human health.
  • Microbiome and Chronic Diseases: The balance between health and disease, to a large extent, depends on the dynamic interaction between the host and microbial community it harbors in different organs and environmental niches of the body. Individuals with poor dental health are at a higher risk of developing chronic diseases including type 2 diabetes mellitus, high blood pressure and heart disease. As part of oral and systemic health initiative at Marshfield Clinic, we are creating a biorepository of clinical samples from patients with periodontal disease. We plan to study patients with periodontal diseases and the dynamics of the oral microbiome under the conditions of both health and disease in order to better understand correlations between microbial representation in microbiomes and other common chronic diseases, including type 2 diabetes mellitus.
    Using the same approach to investigate the changes in the gut microbiome, we are seeking to identify biomarkers of post-exertional fatigue and are exploring whether enhanced gut permeability due to abnormal gut flora could trigger fatigue symptoms.
  • Staphylococcus aureus virulence and host susceptibility to S. aureus infection. Staphylococcus aureus and its multiple resistant phenotypes, including methicillin-resistant S. Aureus (MRSA), is a significant pathogen affecting millions worldwide. Over the last fifteen years a focus of my research has focused on determining why only certain S. aureus clones exhibit enhanced virulence compared to other clones. Some of the specific questions our group is trying to address include:
  • How do lytic bacteriophages with specificity to staphylococci modulate the S. aureus nasal colonization in anterior nares?
  • What is the mechanism of genetic regulation of newer toxin genes in S. aureus
  • How do new toxin genes respond to treatment with antimicrobials?
  • Using the unique resources of Personalized Medicine Research Project at Marshfield Clinic, we are investigating the genetic basis of susceptibility to S. aureus infection in humans. Earlier, using one of the largest biobank of S. aureus and MRSA isolates dating back to the 1980s, we have described the molecular epidemiology of MRSA strains in the Midwest and the evolutionary changes among community-associated MRSA in this region since 1990s.
  • Ehrlichiosis due to Anaplasma phagocytophilum. My laboratory is further attempting to define A. phagocytophilum genotypes isolated from both human and animal sources to evaluate their relative levels of pathogenicity.
  • Pregnancy outcomes and Corynebacterium nigricans/C. aurimucosum. My laboratory continues its research in determining the prevalence of black pigmented C. nigricans in colonizing both pregnant and non-pregnant women to determine if the organism is a pathogen contributing to complications associated with pregnancy.


Daniel Frank, Ph.D. – Division of Infectious Diseases, School of Medicine, University of Colorado - Denver
Yun-Xin Fu, Ph.D. – Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston
Warren Rose, Pharm.D. – School of Pharmacy, University of Wisconsin – Madison
Vineet Singh, Ph.D. – Department of Microbiology, A. T. Still University


Glurich I, Acharya A, Shukla SK, Nycz GR, Brilliant MH. The oral-systemic personalized medicine model at Marshfield Clinic. ORAL DIS 2013;19:1-17.
PubMed ID: 22458294

Rose WE, Eickhoff JC, Shukla SK, Pantrangi M, Rooijakkers S, Cosgrove SE, Nizet V, Sakoulas G. Elevated serum interleukin-10 at time of hospital admission is predictive of mortality in patients with Staphylococcus aureus bacteremia. J INFECT DIS 2012;206:1604-11.
PubMed ID: 22966128

Shukla SK, Pantrangi M, Stahl B, Briska AM, Stemper ME, Wagner TK, Zentz EB, Callister SM, Lovrich SD, Henkhaus JK, Dykes CW. Comparative whole-genome mapping to determine Staphylococcus aureus genome size, virulence motifs, and clonality. J CLIN MICROBIOL 2012;50:3526-33.
PubMed ID: 22915603

Rose WE, Schulz LT, Andes D, Striker R, Berti AD, Hutson PR, Shukla SK. Addition of ceftaroline to daptomycin after emergence of daptomycin-nonsusceptible Staphylococcus aureus during therapy improves antibacterial activity. ANTIMICROB AGENTS CHEMOTHER 2012;56:5296-302.
PubMed ID: 22869564

Lin Y, Barker E, Kislow J, Kaldhone P, Stemper ME, Moore FM, Hall M, Fritsche TR, Novicki T, and Shukla SK. Evidence of Infections due to Nosocomial and Community-Associated MRSA Genotypes in Companion Animals from the Upper Midwestern and Northeastern United States. CLIN MED RES 2011;9:7-16.

John J Jr, Shukla SK. Staphylococcus aureus. In Mayhall CG (Ed.), Hospital Epidemiology and Infection Control, 4th edition. Philadelphia, PA: Lippincott Williams & Wilkins; 2011;pp 385-409.