Welcome to the project

In this step we will explore two plasmid sequences found in Shigella known to carry antibiotic resistance genes. We will introduce you to the project tasks and guide your preparation in support of your learning and completion of the assignment: a short written report (200 words maximum). This report is meant to be concise, therefore please use bullet points if you need to

First, we will learn more about Shigella and plasmids with a research article before downloading specified annotation files onto your computer.

Introduction
Shigella is a bacterium that causes shigellosis or dysentery. Symptoms of the infection usually includes, nausea, cramping, bloody or mucus containing diarrhoea and usually a fever. Shigellosis is still a major public health problem and remains endemic in Low and Middle-income countries.

Shigellosis usually resolves in 5-7 days, however in some severe cases treatment with antibiotics may be prescribed. This however comes at a cost, as resistance to the most commonly used drugs, ciprofloxacin and azithromycin, has been frequently reported and is increasing. Resistance to ciprofloxacin is usually carried on the chromosome of the bacterium, which arises due to a mutation in the DNA replication gene that the drug would target, thus making it inactive.

Resistance to azithromycin is caused by the expression of a protein that alters the drug and making it inactive. These genes are commonly, but not exclusively, found in plasmids. Plasmids are exogenous DNA molecules (see picture below) often found in bacteria, which act like parasites, as they cannot exist without a host, but they bring with them many useful genes enabling the bacterium host to survive in harsh environments e.g. antibiotic resistance. More information on plasmids can be found here: https://en.wikipedia.org/wiki/Plasmid

Image source: https://en.wikipedia.org/wiki/Plasmid

Plasmids, especially ones carrying antibiotic resistance genes are a huge concern in the scientific and medical field, because some of them have the ability to transfer between cells independent of the host bacterium cell. This transfer is known as conjugation (pictured below), and usually occurs when cells are in close proximity to each other. This mobilisation requires replication proteins and other genes that form the ‘tunnel’ structures known as pili (encoded by the tra genes) that enable the DNA molecules to pass through to the new host cell known as the recipient, leaving a copy of the same plasmid DNA molecule in the original host (donor). Other forms of plasmid transfer between cells also occur and collectively are known as horizontal gene transfer or HGT.

Image source: Nature, Furuya and Lowy (2006).

In the article you will be reading about the spread of an antibiotic resistant plasmid, known as pKSR100, between different species of the Shigella genus. An epidemic of Shigella carrying the antibiotic resistance plasmid pKSR100 emerged in 2009 and rapidly spread world wide, with further outbreaks reported in 2012 appearing to carry the same plasmid in different Shigella species. Such was the efficiency of the plasmid transfer that scientists postulated that the acquisition of this plasmid resulted in an increase in population in the bacterial strains that harboured the plasmids and subsequently the increase in azithromycin resistance.

Before continuing, please read the article: Horizontal antimicrobial resistance transfer drives epidemics of multiple Shigella species by Baker et. al. (2018), which can be found here:

Making sure to read the following sections:

• Introduction
• Results: associations with AMR
• Results: HGT of pKSR100 among MSMA sublineages
• Discussion

Getting an idea of what is discussed in these sections will give you a strong start in your quest to answering the questions in the assignment.

To begin the assignment, you will need to download the files listed in the table below from here: ftp://ftp.sanger.ac.uk/pub/resources/coursesandconferences/Online_Courses/Course4/Week3/Peer_Review/

Important – you may need to copy and paste the link in your internet browser, rather than just clicking on it. We recommend use of Chrome or Firefox browsers for downloading data files.

Please note: If you are having trouble accessing the files from the FTP site using your browser, you can use an FTP client such as Cyberduck.

If you have questions or concerns about any of the Steps or tasks, please use the comments area to ask questions, discuss your queries and seek solutions with other learners.