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ARS Home » Southeast Area » Athens, Georgia » U.S. National Poultry Research Center » Egg and Poultry Production Safety Research Unit » Research » Publications at this Location » Publication #383869

Research Project: Reduction of Foodborne Pathogens and Antimicrobial Resistance in Poultry Production Environments

Location: Egg and Poultry Production Safety Research Unit

Title: AT homopolymer strings in salmonella enterica subspecies I contribute to speciation and serovar diversity

item Guard, Jean
item Rivers, Adam
item Vaughn, Justin
item Rothrock, Michael
item Oladeinde, Adelumola - Ade
item SHAH, DEVENDRA - Washington State University

Submitted to: Microorganisms
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/27/2021
Publication Date: 10/1/2021
Citation: Guard, J.Y., Rivers, A.R., Vaughn, J.N., Rothrock Jr, M.J., Oladeinde, A.A., Shah, D. 2021. AT homopolymer strings in salmonella enterica subspecies I contribute to speciation and serovar diversity. Microorganisms. 9(10):2075.

Interpretive Summary: Salmonella enterica subspecies I is a persistent cause of foodborne human illness, and little progress has been made in the past decade in reducing its incidence. S. enterica subspecies I has over 1,500 serovars. Only about 30 serotypes cause most of the illness from S. enterica; thus, just a few serovars have genomes optimized by selection pressure to maintain the ability to cause frequent foodborne illness. We propose that strings of at least 8 adenines, and by inference complementary thymine, is a biologically impactful motif in the chromosome of S. enterica, and it is referred to as an AT 8+mer. AT 8+mers are theorized to contribute to both serovar heterogeneity and stability of prevalent serovars by facilitating homologous recombination. Understanding the biological flexibility of the S. enterica genome helps to focus interventions intended to reduce human illness from foodborne pathogens.

Technical Abstract: Salmonella enterica subspecies I (S. enterica) was analyzed to characterize adenine (A), and complementary thymine (T), homopolymer strings of at least 8 nucleotides (AT 8+mers). Eubacterial genera were reviewed for the motif in comparison to S. enterica, and Salmonella serovars Typhimurium, Enteritidis, and Gallinarum were analyzed in detail. The reference genome for Typhimurium LT2 had a total of 293 AT 8+mers, and 135 (46.1%) were intergenic, 144 (49.1.0%) were in genes, and 13 (4.4%) were in regulatory regions. The median distance between 8mers was 11,578nt, and the average was 16,634nt. Random number analysis calculated that serovar Typhimurium with 4,600 genes could have 1 in 40 genes (2.5%) with an AT 8+mer, and the motif was observed in 1 out of 31 genes (3.2%). AT 8+mers occurred significantly more often in the reference genome of Typhimurium than did GC 8+mers as well as other serovar; however, other genera differed. A total of 481 loci with AT 8+mers were compiled from serovars Typhimurium, Enteritidis, and Gallinarum, and 35 of these loci (12.3%) had an altered AT 8+mer. Results indicate that analysis of AT 8+mers identifies genes undergoing natural mutation in Salmonella. Physicochemical properties of homopolymers was applied to develop a theory that the AT 8+mer is a motif that facilitates homologous recombination, which preserves replication fidelity, repairs mutated sections of the genome, and then also produces variable serovars. The impact of the tandem theory is that it originates new serotypes as well as maintaining an optimal gene content for causing foodborne illness.