Evolutionary Relationships and Antimicrobial Resistance of Staphylococcus aureus in Humans, Ruminants and Companion Animals
Description
Staphylococcus aureus is a bacterial pathogen with broad host range, which has been associated with a wide spectrum of diseases both in humans and animals. The domestication of animals and the recent intensification of livestock farming have provided increased opportunities for the transfer of pathogens between humans and animals. Also, the overuse and misuse of antibiotics in human medicine, veterinary medicine and livestock production have led to the emergence of several antibiotic resistant strains. Based on a previous study by Richardson et al. (2018), this project aims to explore the dynamics of Staphylococcus aureus at the human-ruminant-companion animal interface, and to specifically provide answers to questions pertaining to the evolutionary relationships, host jumps and antimicrobial resistance of isolates across selected host groups. Using bioinformatics tools, the genomes of 513 Staphylococcus aureus isolates across 5 continents were downloaded from the NCBI repository, assembled, annotated, aligned, and built into a phylogenetic tree. The data were subsequently imported into R for further statistical analyses and visualization. The study provided evidence for S. aureus transmission among humans, companion animals and ruminants, identifying humans as the major reservoirs for S. aureus transmission, and as the host with the most abundant antimicrobial genes. The findings also reveals Tet38, a gene conferring resistance to tetracycline as the most common AMR gene, and the presence of significant resistance to fosfomycin and penicillins across host groups. Overall, this study establishes the existence of zoonosis as well as reverse-zoonosis, and underscores the need for antimicrobial stewardship in human and veterinary medicine. It also highlights the indication for surveillance in the early detection of emerging clones of pathogens and spill-over among human and animal hosts.
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Steps to reproduce
The metadata and sequences for this project were retrieved from a manuscript by Richardson et al. (2018) , which revealed the capacity of Staphylococcus aureus as a multi-host bacterial pathogen to undergo genetic adaptations and spread widely across several host species. Subject species were categorized into three host groups namely; humans, ruminants and companion animals. Cattle, sheep, goats were grouped as ruminants, while dogs, cats, horses and rabbits were grouped as companion animals. Bioinformatic analysis was executed on Linux, and generated data imported into RStudio for visualization. On the command line, genomes of Staphylococcus aureus isolates from selected host groups and across five continents were downloaded from the NCBI repository using the sratoolkit. With the downloaded raw reads, genomes were assembled using a program called Spades, and the genomes were annotated with a software tool known as Prokka. Subsequently, a pan genome pipeline called Panaroo was used to create a core genome alignment, which was then analyzed with the RAxML program to build a phylogenetic tree. The metadata and phylogenetic tree were loaded into RStudio for plotting representative figures, including barplots, boxplots, heatmaps and a phylogenetic tree. This was done following the installation of needed packages such as ape, devtools, dplyr, plyr, ggplot2, readr, ggpubr, rcompanion, tidyverse, ggsignif, reshape, ggtree, phytools, gridExtra, RColorBrewer, scales, tidyr. Also, for plotting antimicrobial resistance (AMR) genes and markov jumps, already generated ABRicate and StarBeast results were loaded into RStudio and subsequently merged with the metadata. The merged datasets were then used to plot figures to determine both the distribution of AMR genes and the pattern of host jumps.