Research Interests
(1) Use of germfree soil and germfree lettuce models to study the evolution and development of resistomes and their interactions with the human pathogen, Salmonella Typhimurium
Our earlier work on a germfree soil model was published in 2021 [mSystems, 6(6), e00988-21]. This was a collaborative project between GTIIT and Technion (Prof. Sima Yaron). The germfree soil model was expanded to germfree lettuce to study the microbiome and resistome development. We plan to investigate how the initial bacterial loads shape the microbiomes and resistomes in soils and lettuce plants under tetracycline antibiotic selection pressures. Additionally, we are also studying the persistence of S. Typhimurium under tetracycline treatments to elucidate the transfer of antibiotic resistant genes (ARGs) from the soil and lettuce resistomes to S. Typhimurium and other bacteria. This research seeks to explain how ARGs spread between environments and the human food chain via food-borne pathogens (such as Salmonella) and other opportunistic pathogens (such as the family of Burkholderiaceae). This research has potential to lead to the development of novel methods to prevent farm-to-hospital transmission of ARGs and to give insights for bio-restoration of ARG contaminated environments.
Germfree soil model design
ARGs and their bacterial hosts in the germfree soil
(2) Frog farm resistome studies and horizontal plasmid transfer
(2A) Frog farms are hotspots of antibiotics and chemicals overuse. Horizontal plasmid transfer (HPT) is a leading driver shaping the development of frog farm resistomes. We collected fecal samples and soil sediments from five frog farms in the Shantou area of Guangdong Province in China. Metagenomic studies of frog farm soil samples identified the core microbiome and core ARGs. Genomes of 95 antibiotic resistant isolates of Escherichia coli, Edwardsiella tarda, and other bacteria were sequenced to identify ARGs carried on chromosomes and plasmids. The goal of this study was to connect the resistome in frog farms to the plasmidome of host bacteria such as E. coli and E. tarda.
Frog farm studies at Shantou, Guangdong, China
(2B) Mechanisms of plasmid exclusion and co-transfer in frog-farm resistomes. This is a collaborative project between GTIIT and Hebrew University (Profs. Ilan Rosenshine and Sigal Ben-Yehuda). Using plasmids from our 250 plasmid collection from frog farms, new plasmid constructs with new antibiotic resistant genes (ARGs) and GFP/mCherry markers were engineered to tag some of the conjugative and non-conjugative plasmids. Confocal microscopy and flow cytometry were then used to reveal plasmid transfer in real time. PCR and antibiotic markers were used to track the transfer of various plasmids in different bacterial hosts. The genetic determinants that govern plasmid transfer from a donor to recipient as well as how plasmids co-transfer from one bacterium to another are not known. These studies will explain the mechanisms of co-transfer of different plasmids (with different ARGs) and lead to novel methods to prevent the spread of plasmids or ARGs and other virulent resistance.
Visualization of co-transfer of plasmids from one bacterium to another
(2C) Pan-genome and comparative genomics studies of the 250 frog-farm plasmids and 95 antibiotic resistant bacteria (ARB). This work will be carried out with our Shantou University collaborator (Prof. Liang Chen).