Current Issue, Infectious Disease, Jail, Staph, Staphylococcus aureus

Overcoming Institutional, Scientific, and Cross-disciplinary Barriers for Healthcare and Disease Transmission Research in County Jail Settings: Integrating Genomics, Survey Data, and Biological Data Collection Strategies By Viacheslav Y. Fofanov, Crystal M. Hepp, Jill Hager Cocking, and Robert T. Trotter II


More than 20 million Americans are currently or have been previously incarcerated and 12 million cycle in and out of the criminal justice system each year. Despite the importance of the jail populations, there are a number of barriers to conducting research in this setting. Challenges in recruiting jail inmates without undue coercion while ensuring proper consent are significant. Even simple things like participant compensation are complicated in an environment when participants do not have direct access to cash or choices for places to spend it. Finally, simply carrying out survey and biological specimen collection is complicated by the requirement of not introducing contraband into a controlled jail environment. Over the last two years, we have designed and carried out a study within a county detention facility in Arizona. We have successfully enrolled, surveyed, and collected bio-specimens from 200 currently incarcerated individuals, facing and resolving the challenges outlined above. Our solutions to these can be of great benefit to other researchers attempting cross-disciplinary analyses in jail settings.


In the last two decades, jail and prison populations of the United States have increased considerably. In fact, more than 20 million Americans are currently or have been previously incarcerated, with 12 million cycling in and out of jails each year (Ahalt et al. 2015). Nationwide, jail and prison populations are disproportionately impacted by infectious, chronic, and mental diseases. In addition to substance abuse and mental health problems, incarcerated populations are also burdened by higher rates of chronic and infectious diseases, with significant rates of co-morbidity of multiple health problems—as high as 70 percent (Binswanger et al. 2012). Despite the well-established disproportional burdens of disease in incarcerated populations (Cuellar and Cheema 2014; Klevens et al. 2007), infectious disease detection and transmission research in this setting is very rare. For example, searching the United States National Library of Medicine’s central publication repository,, for “prison/jail infectious disease” results in less than 500 articles over the last fifty years. In contrast, more than 245,000 published articles were tagged as “infectious disease” in that same time period. Part of the challenge in doing infectious disease research in prison and jail settings is the fact that the traditional processes and research teams are not enough—the process demands an extremely inter-disciplinary approach. It requires seamless collaboration between anthropologists, statisticians, psychologists, and molecular biologists, as well as extensive support from local Criminal Justice governing bodies, Sheriff, and corrections officials. Here, we highlight some of the challenges and potential solutions from our recent disease detection and transmission study, carried out at a local county detention facility over the course of almost six months. We hope that these will be of great benefit to other researchers attempting cross-disciplinary analyses in jail settings.

The Study in Brief

The Converging Epidemics project (Trotter et al. 2018) consisted of three primary data collection and integrated data analysis elements: (1) linking Criminal Justice datasets, such as arrest and incarceration records, with General Health Care system datasets from emergency departments, county infectious disease records, and primary care facilities’ patient records to identify when and where the frequently incarcerated individuals receive their health care; (2) a prospective survey of the current jail populations to identify the multiple diagnosis characteristics and impacts of health care needs and health care service utilization for the county jail population; and (3) biological specimen collection to characterize the differences in the incarcerated and general populations of the rates and genomics of Staphylococcus aureus, a causative agent of “staph” infections common in Northern Arizona. With the support of the county criminal justice governing body and the corrections officials, all the data collection components of the study were successfully completed.

Testing S. aureus bacteria for antibiotic resistance
S. aureus showing up as purple on the bacterial culturing media

…Continue reading in Volume 41 No.4 of Practicing Anthropology

VYF_croppedViacheslav Fofanov ( is an Assistant Professor with the School of Informatics, Computing, and Cyber Systems at Northern Arizona University. He holds Ph.D. and M.S. degrees in Statistics from Rice University and a B.S. degree from University of Washington, Seattle. His primary research area is bioinformatics and the new algorithms, data structures, and analytic methods needed to store, process, and visualize the immense amounts of genomics data used in this field. Most recently,  Fofanov is focusing on pathogen detection and transmission, particularly as it relates to disease transmission in underserved or vulnerable populations.

Hepp HeadshotCrystal Hepp ( is an Assistant Professor with the School of Informatics, Computing, and Cyber Systems at Northern Arizona University. She holds a Ph.D. degree in Molecular and Cellular Biology from Arizona State University, Tempe, AZ and a B.S. degree from Montana State University, Bozeman, MT. Her primary research area is bioinformatics with a focus on using both pathogen genomics and electronic medical record data to identify populations that are disproportionately impacted by various clinical outcomes, with a strong focus on infectious diseases.

cockingJill Hager Cocking ( is a Research Specialist, Senior in the School of Informatics, Computing, and CyberSystems. Cocking has a BS in microbiology along with a master’s in biology from NAU and has worked in a variety of scientific fields including breast cancer at the University of Arizona and forensic mitochondrial DNA analysis at an FBI lab at the Arizona Department of Public Safety Crime Laboratory in Phoenix, AZ. Cocking’s work in SICCS involves the study of West Nile Virus, pathogen detection, and DNA sequencing.

Trotter HeadshotRobert T. Trotter II ( is an Arizona Regents’ Professor in the Department of Anthropology, Northern Arizona University. He is a medical anthropologist with research interests and publications within the confluence of issues in cross-cultural health care delivery, prevention science, organizational research, ethnographic methods, social network analysis, ethics, alcohol and drug abuse, evaluation research, community-based participatory research, rapid ethnographic assessment HIV/AIDS prevention, culturally competent interventions, and cultural models research. His recent research efforts focus on mixed methods research designs targeted at understanding the factors that create complex public health conditions for vulnerable populations within the context of environmental health and environmental justice. He is currently serving as Lead Director for the Research Infrastructure Core for the Southwest Health Equities Research Collaborative (NIH U54) and as PI for the Health Disparities in Jail Populations: Converging Epidemics. The latter research is focused on the intersection of co-morbidities of Behavioral Health, Infectious Disease, and Chronic Illness, and substance abuse in Jail Populations, as well as genomic analysis of transmission of infectious disease in incarcerated populations.

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