Christopher Grim
, U.S. Food and Drug Administration–CFSAN
, Laurel
, MD
Meimin Wang
, U.S. Food and Drug Administration–CFSAN
, Laurel
, MD
Susan Leonard
, U.S. Food and Drug Administration–CFSAN
, Laurel
, MD
Erin Lipp
, University of Georgia
, Athens
, GA
John Maurer
, University of Georgia
, Athers
, GA
Michele Ray-Russell
, University of California-Davis
, Davis
, CA
George Vellidis
, University of Georgia
, Tifton
, GA
Mark Mammel
, U.S. Food and Drug Administration–CFSAN
, Laurel
, MD
Christopher Elkins
, U.S. Food and Drug Administration–CFSAN
, Laurel
, MD
Baoguang Li
, U.S. Food and Drug Administration–CFSAN
, Laurel
, MD
Introduction: There has been and continues to be a significant investment in environmental surveillance activities to detect human health hazards, such as presence, frequency and abundance of bacterial pathogens. Traditionally, these types of studies are conducted and reported by a single research group. Whole genome sequencing (WGS) has gained wide usage as a tool for epidemiological and evolutionary investigations.
Purpose: The purpose of this study was to compare and determine relatedness among isolates of Salmonella serovar Newport from three distinct surveillance activities, which all took place in a discrete geographical area, namely the rivers and surface waters of Southern and Central Georgia, USA in agricultural areas.
Methods: Forty-one isolates of S. Newport were compared by reference-based whole genome SNP analysis, average nucleotide identity, and tetranucleotide frequency to determine relatedness. Representative strains from each identified cluster were compared by reciprocal BLASTP analysis to determine unique and clade specific genomic features.
Results: WGS-based SNP analysis separated the isolates into two major clades, one with 16 members (Lineage II) and the other with 25 (Lineage III). All the Lineage II isolates came from a single study and single source. They all harbor a large plasmid of approximately 142 kb, which is highly homologous with the antibiotic resistance plasmid, pSN254, from Newport strain SL254. The Lineage III clade was further divided into three subclades, with two of them comprising isolates from more than one study. Comparative genomics corroborated these results with sub-clade members possessing group-specific, as well as inter-group specific, prophage and other mobilome elements.
Significance: These results suggest that certain strains of S. Newport can persist in defined geographic areas over time.
