Understanding of the phylogeny and interrelationships genera within order 'Enterobacteriales' has proven difficult using 16S rRNA gene other single-gene or limited multi-gene approaches. In this work, we have completed comprehensive comparative genomic analyses members which includes phylogenetic reconstructions based on 1548 core proteins, 53 ribosomal proteins four multilocus sequence analysis as well examining overall genome similarity amongst order. The results these all support...

The Halobacteria constitute one of the largest groups within Archaea. hierarchical relationship among members this large class, which comprises a single order and family, has proven difficult to determine based upon 16S rRNA gene trees morphological physiological characteristics. This work reports detailed phylogenetic comparative genomic studies on >100 halobacterial (haloarchaeal) genomes containing representatives from 30 genera investigate their evolutionary relationships. In...

Emergence and spread of antimicrobial resistance is a major concern for the dairy industry worldwide. Objectives were to determine: 1) phenotypic genotypic prevalence drug-specific 25 species non-aureus staphylococci, 2) associations between presence determinants resistance. Broth micro-dilution was used determine profiles 1,702 isolates from 89 herds. Additionally, 405 sequenced screen determinants. Antimicrobial clearly species-dependent. Resistance quinupristin/dalfopristin common in...

Genome sequences are enabling applications of different approaches to more clearly understand microbial phylogeny and systematics. Two these involve identification conserved signature indels (CSIs) proteins (CSPs) that specific for lineages. These molecular markers provide novel definitive means demarcation prokaryotic taxa species from groups. also determination phylogenetic relationships among based upon multiple proteins. In this work, we have used all studying the phytopathogenic...

ABSTRACT Non- aureus staphylococci (NAS), the bacteria most commonly isolated from bovine udder, potentially protect udder against infection by major mastitis pathogens due to bacteriocin production. In this study, we determined inhibitory capability of 441 NAS isolates (comprising 26 species) Staphylococcus . Furthermore, inhibiting were tested a human methicillin-resistant S. (MRSA) isolate using cross-streaking method. We presence clusters in whole genomes genome mining tools, BLAST, and...

Non-aureus staphylococci (NAS), a heterogeneous group of large number species and subspecies, are the most frequently isolated pathogens from intramammary infections in dairy cattle. Phylogenetic relationships among bovine NAS controversial have mostly been determined based on single-gene trees. Herein, we analyzed phylogeny using whole-genome sequencing (WGS) 441 distinct isolates. In addition, evolutionary were estimated multilocus data 16S rRNA, hsp60, rpoB, sodA, tuf genes sequences...

Staphylococcus aureus, a common cause of bovine mastitis, is known for its ability to acquire antimicrobial resistance and secrete numerous virulence factors that can exacerbate inflammation. In addition, alpha-hemolysin has an important role in S. aureus infections, diversity the hla gene (that produces alpha-hmolysin) isolated from mastitis not been well characterized. The objective was, therefore, determine genes, sequences, clonal profiles Chinese dairy herds, evaluate...

Staphylococcus aureus causes persistent clinical and subclinical bovine intramammary infections (IMI) worldwide. However, there is a lack of comprehensive information regarding genetic diversity, the presence antimicrobial resistance (AMR), virulence genes for S. in milk Canada. Here, we performed whole-genome sequencing (WGS) 119 Canadian isolates determined they belonged to 8 sequence types (ST151, ST352, ST351, ST2187, ST2270, ST126, ST133, ST8), 5 clonal complexes (CC151, CC97, CC126,...

Non- aureus staphylococci (NAS) are the most frequently isolated pathogens from milk in dairy cattle worldwide. The virulence factors (VFs) and mechanisms by which these bacteria cause udder infection not fully known. We determined distribution associations of 191 VFs 25 NAS species investigated relationship between disease. Although overall number was associated with disease severity, increasing numbers toxin host immune evasion genes specifically were more severe outcomes. These findings...

The species from the order Xanthomonadales, which harbors many important plant pathogens and some human pathogens, are currently distinguished primarily on basis of their branching in 16S rRNA tree. No molecular or biochemical characteristic is known that specific for these bacteria. Phylogenetic comparative analyses were conducted 26 sequenced Xanthomonadales genomes to delineate identify signatures consisting conserved signature indels (CSIs) protein sequences In a phylogenetic tree based...

Digital dermatitis (DD) presents as painful, ulcerative or proliferative lesions that lead to bovine lameness affecting economic efficiency and animal welfare. Although DD etiological agent(s) have not been established, it is widely accepted a polymicrobial disease significantly associated with species of Treponema the non-linear progression may be attributed interactions among infecting bacteria. We postulated morphological changes lesion grades are related Treponema. developed novel...

Bovine digital dermatitis (DD) is a skin disorder that significant cause of infectious lameness in cattle around the world. However, very little known about etiopathogenesis disease and microbiota associated with DD beef cattle. In this study, we provide comprehensive characterization healthy feedlot We also developed validated novel multiplex quantitative PCR (qPCR) assay to quantify distribution DD-associated bacterial species across lesion stages. determined deep amplicon sequencing V3-V4...

Infections with protozoan parasites associated the consumption of fresh produce is an on-going issue in developed countries but mitigating risk hampered by lack adequate methods for their detection and identification. We a metagenomic next-generation sequencing (mNGS) assay using MinION sequencer identification intentionally contaminated lettuce to achieve more accurate rapid method than traditional molecular microscopy commonly used regulatory purposes. Lettuce (25 g) was spiked varying...

Salmonella Infantis, a common contaminant of poultry products, is known to harbor mobile genetic elements that confer multi-drug resistance (MDR) and have been detected in many continents. Here, we report four MDR S. Infantis strains recovered from house environments Santa Cruz Island the Galapagos showing extended-spectrum β-lactamase (ESBL) reduced fluoroquinolone susceptibility. Whole-genome sequencing (WGS) revealed presence ESBL-conferring blaCTX-M-65 gene an IncFIB-like plasmid three...

The genera Actinobacillus, Haemophilus, and Pasteurella exhibit extensive polyphyletic branching in phylogenetic trees do not represent coherent clusters of species. In this study, we have utilized molecular signatures identified through comparative genomic analyses conjunction with genome based multilocus sequence to clarify the taxonomic boundary these genera. We large species which "sensu stricto" members 3, 7, 6 conserved signature indels (CSIs), are specifically shared by sensu stricto...

Abstract Background Bacteriophages are bacterial parasites and considered the most abundant diverse biological entities on planet. Previously we identified 154 prophages from 151 serovars of Salmonella enterica subsp. . A detailed analysis prophage genomics is required given influence phages their hosts should provide a broader understanding biology virulence contribute to practical applications as vectors antibacterial agents. Results Here comparative full genome sequences 142 which...