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United States Department of Agriculture

Agricultural Research Service

Research Project: Molecular Identification and Characterization of Bacterial and Viral Pathogens Associated with Foods

Location: Produce Safety and Microbiology Research

Title: Comparative genomic analysis identifies a Campylobacter clade deficient in selenium metabolism

Author
item Miller, William - Bill
item Yee, Emma
item Lopes, Bruno
item Chapman, Mary
item Huynh, Steven
item Bono, James - Jim
item Parker, Craig
item Strachan, Norval Jc
item Forbes, Ken

Submitted to: Genome Biology and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/6/2017
Publication Date: 5/10/2017
Citation: Miller, W.G., Yee, E., Lopes, B.S., Chapman, M.H., Huynh, S., Bono, J.L., Parker, C., Strachan, N., Forbes, K.J. 2017. Comparative genomic analysis identifies a Campylobacter clade deficient in selenium metabolism. Genome Biology and Evolution. doi: 10.1093/gbe/evx093.

Interpretive Summary: Campylobacter fetus is a human and veterinary pathogen associated with spontaneous abortion in cattle. C. fetus-related species are also isolated from cattle and other food animals, livestock and other grazing animals. Together these species form a related cluster within Campylobacter. Previous typing studies of this cluster identified three putative new species within the group, also isolated from foraging and grazing animals. Analysis in this study further confirmed that these organisms are in fact members of three new species, which are most similar to the C. fetus-related species C. lanienae. Genetic analysis of the entire C. fetus group indicated that C. lanienae and the three new species represent a distinct subcluster within the group. This subcluster is defined by a reduction in chromosome size, potential differences in cellular motility and a complete absence of all genes related to selenium metabolism.

Technical Abstract: The non-thermotolerant Campylobacter species C. fetus, C. hyointestinalis, C. iguaniorum and C. lanienae form a distinct phylogenetic cluster within the genus. These species are primarily isolated from foraging (swine) or grazing (e.g. cattle, sheep) animals and cause sporadic and infrequent human illness. Previous typing studies identified three putative novel C. lanienae-related taxa, based on either MLST or atpA sequence data. To further characterize these putative novel taxa and the C. fetus group as a whole, 76 genomes were sequenced, either to completion or to draft level. These genomes represent 26 C. lanienae strains and 50 strains of the three novel taxa. C. fetus, C. hyointestinalis and C. iguaniorum genomes were previously sequenced to completion; therefore, a comparative genomic analysis across the entire C. fetus group could be conducted. Analysis of the C. fetus group genomes further supports the initial identification of three novel Campylobacter species. Furthermore, C. lanienae and the three putative novel species form a discrete clade within the C. fetus group, which we have termed the C. lanienae clade. This clade is distinguished from other members of the C. fetus group by a reduced genome size and CRISPR/Cas system differences. However, there are two signature characteristics of the C. lanienae clade. C. lanienae clade genomes carry four to ten unlinked and similar, but non-identical, flagellin genes. Additionally, all 76 C. lanienae clade genomes sequenced demonstrate a complete absence of genes related to selenium metabolism, including genes encoding the selenocysteine insertion machinery, selenoproteins and the selenocysteinyl tRNA

Last Modified: 06/22/2017
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