Advancements in wastewater monitoring in Houston are being used to assess levels of Human Papillomavirus (HPV), a common virus that can cause cancers later in life, and bacterial targets for chlamydia, syphilis, and gonorrhea.
The research will be led by geneticist Rachel Keener, a postdoctoral fellow in Lauren Stadler’s laboratory at Rice University, through the 12-month James A. Ferguson Emerging Infectious Diseases RISE Fellowship.
The Ferguson RISE Fellowship Program, funded by a partnership between the Kennedy Kreiger Institute and the Centers for Disease Control and Prevention (CDC), appoints fellows to institutions to conduct applied public health research that improves health outcomes and reduces health disparities in communities in the U.S.
Keener’s research project is highly translatable and involves collaborating with investigators and institutions with Houston Wastewater Epidemiology, a CDC National Wastewater Surveillance System Center of Excellence.
“I am excited to extend my research experiences in genetics and infectious disease to integrate advanced molecular detection methods and wastewater analysis to monitor emerging infectious diseases of high consequence,” said Keener.
In addition to the research component, the Ferguson RISE Fellowship Program focuses on increasing knowledge and interest in public health research careers, which was a big draw for Keener, who earned her doctorate in genetics and genomics in May 2025 from Duke University’s School of Medicine with a certificate in global health. She has a B.S. in genetics from the University of Georgia, where she graduated with honors and research distinction.
Keener’s doctoral work in Dennis Ko’s group focused on evolutionary medicine and human genetic resistance to infectious diseases. She is the lead author on a paper with Ko published this September on Yersinia pestis – the bacterium responsible for plague. She has also studied the genetic basis for differences in susceptibility to Chlamydia trachomatis.
When people are infected with certain STIs, they shed viral or bacterial DNA particles from their gastrointestinal tracts into their stool, urine, and saliva, making pathogens detectable in municipal wastewater.
By testing wastewater samples from manholes and wastewater treatment plants, Keener and principal investigators at Rice and the Houston Health Department can identify areas where screening clinics and healthcare interventions are needed.
Keener began her postdoctoral work this past summer with members of Stadler’s environmental engineering group to detect and analyze genetic markers of chlamydia, syphilis, and gonorrhea, three of the most common and consequential STIs, in Houston’s wastewater.
“A primary goal of public health departments is to prevent and treat outbreaks, especially in vulnerable and medically underserved populations,” said Keener. “In addition to providing a picture of disease prevalence, wastewater analysis can test for the prevalence of antibiotic-resistant genes, which is a growing problem in helping people with chronic STI cases.”
Social stigmas behind STIs often prevent or delay individuals from getting clinically tested and seeking care. By monitoring community infection levels, privacy can be protected, as population-level shedding of pathogen genes cannot be traced back to any individual.
“Over the last five years, Harris County has had disproportionately high case rates of sexually transmitted infections compared to the rest of Texas, with Chlamydia trachomatis being the most prevalent and syphilis cases doubling,” said Keener. “If not treated properly, these infections can lead to blindness and infertility. The disease can be passed from an infected mother to her child during birth and manifest as eye infections or breathing difficulties or cause stillbirths.”
A major component of Keener’s Ferguson RISE Fellowship will also involve novel detection tools for HPV in municipal wastewater samples.
“There are approximately 40 mucosal HPV types with 14 high-risk disease types that can lead to cell changes that may ultimately lead to the development of genital or throat and mouth cancers,” Keener said. “These cancers can be prevented through HPV vaccination; however, underutilization and awareness of the vaccine are issues, especially in Texas.”
Genetic assays Keener and the Stadler lab will be developing and applying to wastewater analysis are expected to include all high-risk HPV types and two that cause 90 percent of genital warts.
Insights gained from the study will include an understanding of infection prevalence. Through collaboration with the Houston Health Department and health departments across Texas and the U.S., data from wastewater-based epidemiology can be used to increase knowledge about HPV and improve vaccination rates among youth.
- Shawn Hutchins, Communications Specialist