Comprehensive Phylogenetic Analysis of Bovine Non-aureus Staphylococci Species Based on Whole-Genome Sequencing

Abstract

Non-aureus staphylococci (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, and tuf genes 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.

Bacteriocins of Non-aureus Staphylococci Isolated from Bovine Milk

“…Lastly, 4 lasso peptide clusters were identified in 2 noninhibiting S. fleurettii genomes, a noninhibiting S. sciuri genome, and an inhibiting S. sciuri genome. Putative bacteriocin-associated genes were distributed throughout the phylogeny of NAS (22) (Fig. 1), although no isolates from S. agnetis (n ϭ 13), S. arlettae (n ϭ 15), S. auricularis (n ϭ 2), S. caprae (n ϭ 1), S. devriesei (n ϭ 8), S. hominis (n ϭ 11), S. kloosii (n ϭ 1), S. nepalensis (n ϭ 2), and S. pasteuri (n ϭ 6) contained putative bacteriocin gene clusters.…”

“…Distribution of bacteriocin biosynthetic gene clusters in species of non-aureus staphylococci isolated from milk of Canadian dairy cows, displayed on the phylogenetic tree from Naushad et al (22). Bacteriocin types are indicated by the following abbreviations: L, lanthipeptide; S, sactipeptide; Ls, lasso peptide; II, class II double glycine leader peptides; C, circular bacteriocins; Lt, lactococcin-like.…”

Staphylococcal species less frequently isolated from human clinical specimens - are they a threat for hospital patients?

“…Up to now, another S. hominis subspecies, S. hominis subsp. novosepticus, was [39,40] considered as multi-resistant [74]. Similarly to S. epidermidis, S. hominis is present on human skin more often than other CoNS [39].…”

Molecular epidemiology and distribution of antimicrobial resistance genes of Staphylococcus species isolated from Chinese dairy cows with clinical mastitis

“…For S. aureus, several typing methods have been used, including ribotyping, random amplification of polymorphic DNA (RAPD), pulsed field gel electrophoresis (PFGE), multilocus sequence typing, spa typing, and multiple-locus variable number tandem repeat analysis methods . The environmental and contagious nature of some NAS species have been similarly explored by strain typing methods such as PFGE, amplified fragment length polymorphism, RAPD (Gillespie et al, 2009;Piessens et al, 2012), and whole-genome sequencing (Naushad et al, 2016). Among them, RAPD analysis has been successfully used to detect polymorphisms of both S. aureus and NAS strains from bovine mastitis (Piessens et al, 2012;Wang et al, 2016).…”