title: Comprehensive Phylogenetic Analysis of Bovine Non-aureusStaphylococci Species Based on Whole-Genome Sequencing.
abstract: Non-aureusstaphylococci (NAS), a heterogeneous group of a large number of species and subspecies, are the most frequently isolated pathogens from intramammary infections in dairy cattle. Phylogenetic relationships among bovine NAS species are controversial and have mostly been determined based on single-gene trees. Herein, we analyzed phylogeny of bovine NAS species using whole-genome sequencing (WGS) of 441 distinct isolates. In addition, evolutionary relationships among bovine NAS were estimated from multilocus data of 16S rRNA,hsp60, rpoB, sodA, andtufgenes and sequences from these and numerous other single genes/proteins. All phylogenies were created with FastTree, Maximum-Likelihood, Maximum-Parsimony, and Neighbor-Joining methods. Regardless of methodology, WGS-trees clearly separated bovine NAS species into five monophyletic coherent clades. Furthermore, there were consistent interspecies relationships within clades in all WGS phylogenetic reconstructions. Except for the Maximum-Parsimony tree, multilocus data analysis similarly produced five clades. There were large variations in determining clades and interspecies relationships in single gene/protein trees, under different methods of tree constructions, highlighting limitations of using single genes for determining bovine NAS phylogeny. However, based on WGS data, we established a robust phylogeny of bovine NAS species, unaffected by method or model of evolutionary reconstructions. Therefore, it is now possible to determine associations between phylogeny and many biological traits, such as virulence, antimicrobial resistance, environmental niche, geographical distribution, and host specificity.
authors.affiliation: Department of Production Animal Health, Faculty of Veterinary Medicine, University of CalgaryCalgary, AB, Canada; Canadian Bovine Mastitis and Milk Quality Research NetworkSt-Hyacinthe, QC, Canada.
authors.forename: Sohail
authors.initials: S
authors.lastname: Naushad
authors.affiliation: Department of Production Animal Health, Faculty of Veterinary Medicine, University of CalgaryCalgary, AB, Canada; Canadian Bovine Mastitis and Milk Quality Research NetworkSt-Hyacinthe, QC, Canada.
authors.forename: Herman W
authors.initials: HW
authors.lastname: Barkema
authors.affiliation: Canadian Bovine Mastitis and Milk Quality Research NetworkSt-Hyacinthe, QC, Canada; Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of SaskatchewanSaskatoon, SK, Canada.
authors.forename: Christopher
authors.initials: C
authors.lastname: Luby
authors.affiliation: Department of Production Animal Health, Faculty of Veterinary Medicine, University of CalgaryCalgary, AB, Canada; Canadian Bovine Mastitis and Milk Quality Research NetworkSt-Hyacinthe, QC, Canada.
authors.forename: Larissa A Z
authors.initials: LA
authors.lastname: Condas
authors.affiliation: Department of Production Animal Health, Faculty of Veterinary Medicine, University of CalgaryCalgary, AB, Canada; Canadian Bovine Mastitis and Milk Quality Research NetworkSt-Hyacinthe, QC, Canada.
authors.forename: Diego B
authors.initials: DB
authors.lastname: Nobrega
authors.affiliation: Department of Production Animal Health, Faculty of Veterinary Medicine, University of CalgaryCalgary, AB, Canada; Canadian Bovine Mastitis and Milk Quality Research NetworkSt-Hyacinthe, QC, Canada.
authors.forename: Domonique A
authors.initials: DA
authors.lastname: Carson
authors.affiliation: Department of Production Animal Health, Faculty of Veterinary Medicine, University of CalgaryCalgary, AB, Canada; Canadian Bovine Mastitis and Milk Quality Research NetworkSt-Hyacinthe, QC, Canada.
authors.forename: Jeroen
authors.initials: J
authors.lastname: De Buck
keywords: Non-aureus staphylococci; bovine intramammary infection; coagulase-negative staphylococci; phylogenetic trees; whole-genome sequencing