Verotoxin-producing Escherichia coli (VTEC) of serotype O157:H7 is a pathogen causing illness in humans worldwide. The path and nature of transmission from and among cattle is important knowledge when it comes to preventing cases of disease in humans. Two concepts potentially playing an important role in transmission of VTEC O157:H7 are super-shedding and super-spreading. Super-shedders are individuals (here calves) shedding a high amount of bacteria. Super-spreaders are individuals (here calves) spreading the disease in a higher extent compared to the rest of the population investigated. Little is known about these phenomenons’ effect on transmission as well as the relation between them. Therefore, it is important to investigate this further. The purpose of this master thesis was to get a better understanding of how super-spreaders can be identified. One way to identify super-spreaders and explore the transmission of a pathogen is to investigate molecular data using computational methods. Here, a literature study with a systematic approach was conducted in order to scan the literature for such methods. In this first phase of the master thesis three methods, all constructing transmission trees, were identified as relevant methods for the second phase. These methods are called outbreaker2, phybreak and TransPhylo. In the second phase of the master thesis, 32 whole genome sequences of VTEC O157:H7 collected from four different cattle farms were investigated using the methods outbreaker2 and phybreak. Both methods were able to identify samples infecting more secondary cases compared to the rest of the investigated population. Some of these samples came from the environment, possibly shedding light on the importance of the pathogen's ability to survive outside of the host, and therefore playing an important role in transmission of the disease. The rest of the samples infecting more secondary cases were from calves, and a minority of these were super-shedders. From this the importance of the relation between super-shedders and super-spreaders can neither be confirmed nor denied. Outbreaker2 suggested that the spread of the pathogen is frequently occurring between the four neighbouring farms, while phybreak instead suggested that the spread mostly occurs within the farms. From this, a scenario explaining that the transmission possibly occurs within farms is presented.
| Identifer | oai:union.ndltd.org:UPSALLA1/oai:DiVA.org:uu-479471 |
| Date | January 2022 |
| Creators | Wallskog, Amanda |
| Publisher | Uppsala universitet, Institutionen för biologisk grundutbildning |
| Source Sets | DiVA Archive at Upsalla University |
| Language | English |
| Detected Language | English |
| Type | Student thesis, info:eu-repo/semantics/bachelorThesis, text |
| Format | application/pdf |
| Rights | info:eu-repo/semantics/openAccess |
| Relation | UPTEC X ; 22008 |
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