High-Resolution Identification of Multiple Salmonella Serovars in a Single Sample by Using CRISPR-SeroSeq

Applied and Environmental Microbiology
Cameron P ThompsonNikki W Shariat

Abstract

Salmonella enterica is represented by >2,600 serovars that can differ in routes of transmission, host colonization, and in resistance to antimicrobials. S. enterica is the leading bacterial cause of foodborne illness in the United States, with well-established detection methodology. Current surveillance protocols rely on the characterization of a few colonies to represent an entire sample; thus, minority serovars remain undetected. Salmonella contains two CRISPR loci, CRISPR1 and CRISPR2, and the spacer contents of these can be considered serovar specific. We exploited this property to develop an amplicon-based and multiplexed sequencing approach, CRISPR-SeroSeq (serotyping by sequencing of the CRISPR loci), to identify multiple serovars present in a single sample. Using mixed genomic DNA from two Salmonella serovars, we were able to confidently detect a serovar that constituted 0.01% of the sample. Poultry is a major reservoir of Salmonella spp., including serovars that are frequently associated with human illness, as well as those that are not. Numerous studies have examined the prevalence and diversity of Salmonella spp. in poultry, though these studies were limited to culture-based approaches and therefore only identified a...Continue Reading

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Citations

Dec 7, 2019·Microbiology Resource Announcements·Daniela MillerMaria Hoffmann
Dec 28, 2019·Nucleic Acids Research·Rafael Pinilla-RedondoShiraz A Shah
Sep 16, 2019·Microbial Pathogenesis·Tayyab RehmanPing Ouyang
Dec 5, 2020·Scientific Reports·Simran Krishnakant KushwahaSandhya Amol Marathe
Jan 6, 2021·Applied and Environmental Microbiology·Abigail M DeavenNikki W Shariat
Mar 31, 2021·Antimicrobial Agents and Chemotherapy·Amy T SiceloffNikki W Shariat
Jun 15, 2021·EcoSal Plus·Eric W BrownMarc W Allard

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