ABOUT  

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We are microbiologists dedicated to improving microbial food safety.

We work in the interdisciplinary areas among microbiology, public health and agriculture.

We play with computers and food. 

We deal with tens of thousands of genomes in silico as well as single bacterial cells in situ.

We are part of the Food Safety Informatics Group at Center for Food Safety, University of Georgia. 

Credit: Philip Paternall/Springer Nature

NEWS

Salmonella population genomics and source attribution study published in Emerging Infectious Diseases, highlighted by a CDC podcast, reported by The Verge, referred to as
"a new era of smarter food safety and epidemiology"  by FDA Deputy Commissioner,
and featured by Nature Reviews Microbiology.  
 
Yan Qi joined The Coca-Cola Company in Shanghai as a senior scientist. Congrats!
 
Xiangyu delivered talks on zoonotic source tracking of Salmonella by WGS and machine learning at FDA CFSAN, CIFSQ 2019, bioMerieux Annual Food Safety Symposium, Mars Global Food Safety Center, and Institute of Microbiology, Chinese Academy of Sciences. (Slides)
Dual papers (Salmonella MGE, SeqSero2)published in Applied and Environmental Microbiology. SeqSero2 paper featured by AEM spotlight.
Yingshu He joined Bio-Rad Laboratories as a senior scientist. Well done Yingshu! 

Past news

Xiangyu gave a plenary talk at GenomeTrakr 2021 on geographic attribution of Salmonella.
Study on global spread of Salmonella Enteritidis published in Nature Communications, covered by Nature Reviews Microbiology, ProPublica, and Civil Eats.  
SeqSero2 approved by FDA Microbiology Methods Validation Subcommittee, officially implemented by 7 FDA Office of Regulatory Affairs labs, and incorporated into NCBI Pathogen Detection ("computed types" for Salmonella).
SeqSero2 for Salmonella serotyping becomes the first bioinformatic/genotyping method officially validated by the FDA for inclusion in the FDA Bacteriological  Analytical Manual (BAM).
 ​Shaoting Li joined Guangdong University of Technology as an assistant professor and received a research award from National Natural Science Foundation of China. Congrats Shaoting! 
Study on quat tolerance in Listeria featured by Applied and Environmental Microbiology Spotlight Selection. Congrats Yingshu and coauthors!

RESEARCH

Serotyping forms the basis of Salmonella surveillance and becomes an integral part of Salmonella nomenclature. SeqSero provides a push-button solution to serotype prediction from WGS data. So easy that you can run it on a cell phone. SeqSero is used worldwide for public health surveillance of Salmonella. 

Our quasi-metagenomics approach combines pathogen detection and subtyping (fingerprinting) in a single workflow. It shortens the turnaround from contaminated food to strain-level pathogen ID from weeks to hours, particularly using Oxford nanopore for sequencing.