Research in Microbial Safety of Food and Environment

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Our interdisciplinary research program in microbial food safety runs in collaboration with US FDA, USDA, state and local government agencies, industry, major US and International Universities. Several masters and doctoral students are involved in these research projects.  

The microbial community structure of retail foods available in areas with higher food insecurity and low socioeconomic status (SES) may differ significantly from high SES areas. Since the microbial ecology of foods may be associated with the potential presence of pathogens, a comprehensive evaluation of the microbiota of foods sold at retail stores from different SES areas is important to understand the potential risk of getting foodborne illness resulting from consumption of such foods. We used Next Generation Sequencing (NGS) of the 16S rRNA genes as well as culture-dependent methods to evaluate the bacterial community of selected foods procured from retail outlets located at different SES areas. In addition, metabolic pathways associated with the detected bacterial communities were also inferred from 16S rRNA sequences. We found that foods from stores in low SES areas were found to contain higher bacterial counts and a differential microbial composition as compared to stores in high SES areas. Our NGS data revealed that foods from low SES area stores contained a different bacterial composition compared to high SES area stores. Moreover, microbial metabolic pathways also differed in foods procured from stores in low SES as compared to stores in high SES areas. These differences in the microbial composition of foodborne bacteria may expose populations living in different socioeconomic conditions and food access to differential risk of contracting foodborne illness. Find our work here: Food Research International 2018; 105:29–40. 

Dissemination of pathogens/infections and human health risks and molecular epidemiology of multi-drug resistant pathogens 

With the advent of the advanced Next Generation Sequencing (NGS) technologies, it is possible to visualize the unseen diversity of microbial pathogens inhabiting in the environment surrounding us. In one of such projects, we collaborated with a Memphis-based investigative journalist and accessed the “microbial cleanliness” of the large fitness centers around Memphis metropolitan area. Check the news coverage here: http://www.wmcactionnews5.com/story/24036649/the-investigators-gyms-undercover. The first round of our findings including the bacterial diversity from gym surfaces is reported in International Journal of Environmental Research and Public Health 2014, 11(12), 12544-12561. In an extension of this project, Dr. Banerjee’s group has recently reported the prevalence of multi-drug resistant (MDR) methicillin-resistant Staphylococcus aureus (MRSA) in indoor surfaces, and the molecular characterization of a MRSA type (CC59) found for the first time in the US. This is reported in the American Journal of Infection Control 2016, 44(12):1681-1683.  

Microbial ecology and prevalence of multi-drug resistant organisms in in human and food environment 

In collaboration with SCHD, this project aims to assess microbiological quality and safety of retail foods commodities available in low- and high-socioeconomic neighborhoods of Memphis metropolitan. We are using conventional microbiological as well as Next Generation Sequencing-based metagenomics techniques to evaluate microbial populations of food commodities, and presence of antibiotic resistance genes in these products. The study was featured in the University of Memphis YouTube portal and can be found here: https://www.youtube.com/watch?v=gx4rboE0fLI. 

Haiti Drinking Water Project

In a recent project, we examined the overall bacterial diversity of selected source and point-of-use water from rural areas in Central Plateau, Haiti using NGS based metagenomics methods (pyrosequencing of 16s rRNA genes). We also evaluated the impact of interventions (filtration) in removing or reducing the overall microbial loads of drinking water in the study area. You can read the full report published in PLOS ONE 2016, 11(12): e0167353.  

Environment poses stress to pathogens. Recently, we have finished an extensive study where we used whole genome sequencing to understand the differential expression of virulence genes of pathogenic E. coli O157:H7 during environmental shock (such as cold temperature). The initial findings were reported in Journal of Food Protection 2016, 79(7):1259-65. Our group is also working on to understand the relationship of virulence gene expression in multi-drug resistant and drug-sensitive bacteria. 

Biosensors for rapid detection of pathogens, toxins and hazards

We are developing novel biosensor based rapid detection methods of pathogens, toxins, and contaminants in food and environmental (water, soil, air) samples.  The overall objective is to develop and demonstrate a novel gel encapsulated cellular formulation integrated with a microfluidic device for long term storage of biosensor cells utilized for a very sensitive biosensor-based technique (called cell-based assay for rapid detection or CBARD) for detection pathogens from water and food. The sensor validation study was done using common biological toxins. (check out our relevant publications at: Toxins 2013, 5(12), 2366-2383,   

Biosensors and Bioelectronics. 2010;26(1):99–106, Trends in Biotechnology. 2009;27(3):179–88, Laboratory Investigation. 2008;88(2):196–206). 

Method development for food sample preparation 

We developed a nanotechnology-based method to mitigate the “matrix effect” of foods to enable successful detection and identification of pathogens (find our work here: International Journal of Food Microbiology 2014;189:89–97).