Temporal Genomic Phylogeny Reconstruction Indicates a Geospatial Transmission Path of Salmonella Cerro in the United States and a Clade-Specific Loss of Hydrogen Sulfide Production

Frontiers in Microbiology
Jasna KovacMartin Wiedmann

Abstract

Salmonella Cerro has become one of the most prevalent Salmonella serotypes isolated from dairy cattle in several U.S. states, including New York where it represented 36% of all Salmonella isolates of bovine origin in 2015. This serotype is commonly isolated from dairy cattle with clinical signs of salmonellosis, including diarrhea and fever, although it has also been identified in herds without evidence of clinical disease or decreased production. To better understand the transmission patterns and drivers of its geographic spread, we have studied the genomic similarity and microevolution of S. Cerro isolates from the northeast U.S. and Texas. Eighty-three out of 86 isolates were confirmed as multilocus sequence type 367. We identified core genome SNPs in 57 upstate New York (NY), 2 Pennsylvania (PA), and 27 Texas S. Cerro isolates from dairy cattle, farm environments, raw milk, and one human clinical case and used them to construct a tip-dated phylogeny. S. Cerro isolates clustered in three distinct clades, including (i) clade I (n = 3; 2013) comprising isolates from northwest Texas (NTX), (ii) clade II (n = 14; 2009-2011, 2014) comprising isolates from NY, and (iii) clade III comprising isolates from NY, PA, and central Texas ...Continue Reading

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Citations

Jun 23, 2019·BMC Evolutionary Biology·Jingqiu LiaoMartin Wiedmann
Aug 19, 2021·Applied and Environmental Microbiology·Diéssy KipperVagner R Lunge

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Datasets Mentioned

BETA
PRJNA308933

Methods Mentioned

BETA
PCA
PCR

Software Mentioned

TreeAnnotator
Orange
RaxML
ggplot2
BEAST
kSNP
BEAUti
Gubbins
PHASTER
Trimmomatic

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