STUDENTS

Lauren’s main research focus is using computational tools to analyze whole-genome sequencing (WGS) data to determine population structure and genotypic characteristics of foodborne pathogens (Listeria, Salmonella, Campylobacter) to improve public health surveillance and aid in epidemiological outbreak investigations. She works closely with the Tennessee Department of Health and the Tennessee Integrated Food Safety Center of Excellence (CoE) in her research and other efforts (training, outreach, and teaching), with the goal of bridging the gap between foodborne pathogen genomics and state public health epidemiologists.

Genomic characterization and phylogenetic analysis of Salmonella enterica serovar Javiana

Salmonella enterica serovar Javiana is the fourth most reported serovar of laboratory-confirmed human Salmonella infections in the U.S. and in Tennessee (TN). To better understand Salmonella ser. Javiana microbial population structure within the state, we completed a phylogenetic analysis of Salmonella ser. Javiana clinical isolates from TN and found that the population structure consisted of three genetic clades. We performed a pan-genome-wide association study (pan-GWAS) to compare gene content between clades and found that the majority of genes that were over-represented in specific clades were located in mobile genetic element (MGE) regions. Using a 5, 10, and 25 hqSNP distance threshold, nine, 12, and 10 potential epidemiologically-relevant clusters were identified, respectively.

Additionally, we completed phylogenetic analyses of global Salmonella ser. Javiana datasets to gain a broader insight into the population structure of this serovar. We found that the global phylogeny consisted of three major clades (one of which all of the TN isolates belonged to) and two cgMLST eBurstGroups (ceBGs) and that the branch length between the two Salmonella ser. Javiana ceBGs was comparable to those from other serovars that have been reported as polyphyletic. This study demonstrates the population structure of TN and global Salmonella ser. Javiana isolates, a clinically important Salmonella serovar and can provide guidance for phylogenetic cluster analyses for public health surveillance and response. https://peerj.com/articles/10256/

Phylogenetic Analysis Reveals Source Attribution Patterns for Campylobacter spp. in Tennessee and Pennsylvania

Campylobacteriosis is the most common bacterial foodborne illness in the United States and is frequently associated with foods of animal origin. The goals of this study were to compare clinical and non-clinical Campylobacter populations from Tennessee (TN) and Pennsylvania (PA), use phylogenetic relatedness to assess source attribution patterns, and identify potential outbreak clusters. Campylobacter isolates studied included TN clinical isolates collected and sequenced for routine surveillance, PA clinical isolates collected from patients at the University of Pennsylvania Health System facilities, and non-clinical isolates from both states. Phylogenetic analyses were conducted to determine the population structure of each species. Most isolates were C. jejuni (69.2%) and C. coli (29.9%), while the remaining were C. lari, C. upsaliensis, and C. fetus. The C. jejuni group consisted of three clades; most non-clinical isolates were of poultry (62.7%) or cattle (35.8%) origin, and 59.7 and 16.5% of clinical isolates were in subclades associated with poultry or cattle, respectively. The C. coli isolates grouped into two clades; most non-clinical isolates were from poultry (61.2%) or swine (29.0%) sources, and 74.5, 9.2, and 6.1% of clinical isolates were in subclades associated with poultry, cattle, or swine, respectively. Based on genomic similarity, we identified 42 C. jejuni and one C. coli potential outbreak clusters. The C. jejuni clusters contained 19.6% of the total C. jejuni clinical isolates, suggesting that a larger proportion of campylobacteriosis may be associated with outbreaks than previously determined. https://www.mdpi.com/2076-2607/9/11/2300

Phylogeny and Genomic Characterization of Clinical Salmonella enterica Serovar Newport Collected in Tennessee

Salmonella enterica subsp. enterica serovar Newport (S. Newport) is the second most prevalent clinically isolated Salmonella serovar in the United States, and it can contaminate a wide variety of food products. The goal of this study was to provide insight on the genomic diversity of epidemiologically relevant serovar. Specifically, we explored the diversity of human clinical isolates from a localized region (Tennessee) and compared this level of diversity with the global context. In this study, we evaluated the population structure of S. Newport clinical isolates obtained by the Tennessee Department of Health during routine surveillance, along with a diverse set of other global clinical isolates. Most of these clinical isolates belonged to established lineages II and III. Additionally, we performed lineage-specific phylogenetic analyses and were able to identify 18 potential epidemiological clusters among the isolates from Tennessee, including one that was predicted to be multidrug resistant. We showed that a greater proportion of TN isolates were associated with putative epidemiological clusters (based on genomic relatedness) than historical estimates. The findings of this study provide insight on Salmonella enterica serovar Newport that can impact public health surveillance and responses and serve as a foundational context for the Salmonella research community. https://journals.asm.org/doi/full/10.1128/spectrum.03876-22