Hi everyone, currently I' m doing a course "Whole-genome sequencing and its applications" from the technical university of Denmark, working on a final project
So I have five unknown samples,
And those five unknown samples, they are in the sample genomes.
That means they are in FASTA format, not FASTQ or RARI.
They already assembled.
And in those five genomes that will get,
three of them are the outbreak strains.
So, what I have to find out from the five strains, I have to find out which one are the three outbreak strains. So in order to identify which one are the outbreak strains.
Of course, because they're unknown, I have to know what they are.
Then I have to know how to treat them.
To know those questions, they give me some hint.
For example, what they are?
I can use KmerFinder to know a species and once I know species I also can know sequence type by using MLST tool.
And then I can see if my samples contain any plasmid using PlasmidFinder.
And if my sample contains plasmid and what kind of plasmid in my sample,
I can do Pm(t) or plasma typing.
Your question is not quite clear enough for me to understand. It sounds like you would be asking about bacteria infecting humans. But it could possibly be an agricultural (pigs, cattle, horses, chickens, fish etc) or other type of outbreak. And even within human bacterial infections or "outbreaks" there is a large difference between different types of bacteria. The Escherchia coli that carry a shiga toxin gene on a plasmid (STEC), for example, are quite different from Klebsiella pneumoniae or other "outbreak" bacteria.
Some plasmids (or phages carried on plasmids) are rather promiscuous and can travel between rather diverse host bacterial "species", while others are usually associated with a single bacterial lineage. Sometimes it is a drug resistance issue, making the infection more difficult to treat, and sometimes it is a bacterial toxin causing a more accute issue. Some bacteria are spread by wastewater or other unsanitary conditions, and some are food-borne or require close human-to-human contact.
Anyway, the type of "detective work" needed in the databases to sort this out can be quite different for the different bacteria.
- Badges
- Science topic