Monitoring microbes in the built environment: I have recently started collaborating with Christopher E. Mason of PathoMap developing sampling protocols and analysis pipelines to monitor the microbiota of hospitals with the goal of decreasing the rate of hospital acquired infections.


Motivation: Hospital acquired infections (HAIs) are a high priority problem, resulting in prolonged patient stays, readmission, and death, as well as great economic burden. One in twenty patients get an infection in hospitals, and 99,000 deaths occur each year, in the US alone, due to HAIs. Many of the bacteria causing HAIs, including Clostridium difficile (C. diff), live on surfaces for prolonged periods and are being transmitted to patients from these surfaces. While it is not yet an established practice, there is a clear need for regular environmental testing to identify the microbial populations in hospitals.

Striking advances have been made recently in DNA sequencing technology, giving us the ability to rapidly sequence and analyze big data sets to identify and monitor the microbes in our environments. This technology has effectively been used to monitor and determine the source of the recent Ebola outbreak. Additionally, my collaborator Christopher E. Mason has used this technology to swab and sequence the DNA collected in the New York City subway (see Pathomap study). This was the first study to establish a baseline of the microbial population at the city scale, and it received international press (e.g. Wall Street Journal, and New York Times articles).

Similarly to the Pathomap study, we are using a DNA sequencing based approach to monitor the hospital environment to identify microbes and characterize microbial dynamics including distribution of antibiotic resistance. Long term, our ultimate goal is to identify and alert the hospital to help stop pathogenic microbes, before patients catch infections.


Questions: With this study, we are addressing the following questions:

1) What does a healthy hospital microbiome look like?

2) What does the microbiome look like when an infection occurs, are there predictors or environmental signals that we can detect?

3) What microbes are left behind after cleaning using bleach wipes? What about after UV disinfection?

4) Can we detect if the infection is coming from the community or the hospital?

5) What are the vectors and paths of movement of microbial populations through the hospital?

6) Do we see evidence of drug resistance in these microbial populations?


*If you are a hospital interested in learning more about our research or are interested in being included in a study please email


Project Baseline: I am part of the Project Baseline Team at Fordham University. We are collecting and cataloguing seed from natural plant populations undergoing environmental changes. This collection will allow researchers to directly study how these populations are evolving by using a resurrection approach. See more about the project here.

Genomics of flowering time: In collaboration with Steven J. Franks, Joshua S. Rest, Nolan Kane, and Silas Tittes, I am studying the genomic basis of an observed evolutionary shift in flowering time. Using shotgun sequencing, we have sequenced the genomes of 205 Brassica rapa plants from two populations at two time points. We are characterizing the genetic diversity in these populations across the genome, exploring how 7 years of drought might shape genomes, and identifying candidate genes that have evolved in these populations in response to drought. 

 The cost of adaptation to droughtI have used a resurrection approach in the greenhouse to test how drought adaptation in a natural Brassica rapa population affects disease susceptibility to a fungal pathogen, Alternaria brassicae. I have found that drought adapted plants, which flower earlier, have thinner leaves and are more susceptible to a pathogenic fungus, an ecological cost of adaptation.



Genomics of a cost of adaptation: I have also analyzed the sequence data from the 205 Brassica rapa plants mentioned above and am characterizing divergence and diversity in pathogen related genes. I am focusing on jasmonic acid related genes, which underly necrotrophic fungal pathogen response, to see if they have evolved and exploring the potential role that pleiotropy may have played in an increase in disease susceptibility observed following a natural drought.

 Environmental factors influencing disease in natural populations: I have conducted field work in natural Brassica rapa populations along a moisture gradient along the west coast of the U.S. to characterize the environmental factors contributing to Alternaria brassicae disease distribution.