Abstract
16S rRNA community profiling continues to be a useful tool to study microbiome composition and dynamics, in part due to advances in next generation sequencing technology that translate into reductions in cost. Reliable taxonomic identification to the species-level, however, remains difficult, especially for short-read sequencing platforms, due to incomplete coverage of the 16S rRNA gene. This is especially true for Salmonella enterica, which is often found as a low abundant member of the microbial community, and is often found in combination with several other closely related enteric species. Here, we report on the evaluation and application of Resphera Insight, an ultra-high resolution taxonomic assignment algorithm for 16S rRNA sequences to the species level. The analytical pipeline achieved 99.7% sensitivity to correctly identify S. enterica from WGS datasets extracted from the FDA GenomeTrakr Bioproject, while demonstrating 99.9% specificity over other Enterobacteriaceae members. From low-diversity and low-complexity samples, namely ice cream, the algorithm achieved 100% specificity and sensitivity for Salmonella detection. As demonstrated using cilantro and chili powder, for highly complex and diverse samples, especially those that contain closely related species, the detection threshold will likely have to be adjusted higher to account for misidentifications. We also demonstrate the utility of this approach to detect Salmonella in the clinical setting, in this case, bloodborne infections.
Highlights
Salmonella infection is a common bacterial disease throughout the developed and developing world, causing considerable morbidity and mortality
Across the V1–V3 region (16S rRNA gene positions 27–534), Resphera Insight achieved Diagnostic True Positive rate (DTP) rates up to 99.7%, with improved accuracy correlated with increased read length (Figure 1A)
It should be noted that the DTP rates for all methods evaluated tended to dip in value across the 16S rRNA sequence that corresponds to the 3 end of the V3 region, and this reduction in diagnostic capability was more pronounced for shorter read lengths (Figure 1A)
Summary
Salmonella infection is a common bacterial disease throughout the developed and developing world, causing considerable morbidity and mortality. Salmonellosis can be categorized into two disease manifestations, a more common, and usually self-limiting, gastroenteritis due to non-typhoidal salmonellae (NTS) and the rarer, more severe, typhoid fever. It is estimated that NTS cause 94 million cases of gastroenteritis and 155,000 deaths per year (Majowicz et al, 2010), and in the United States, NTS are estimated to cause one million cases, 19,000 hospitalizations, and 380 deaths, annually (Dvir et al, 2014). The majority of non-typhoidal Salmonella cases are due to the consumption of contaminated food and water, and as such, this group of organisms is considered a major foodborne pathogen, occurring in almost all types of foods. Transmission of the organism can occur due to the handling of contaminated farm animals or reptiles
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
