Question: how to identify gene expression and genes responsible for virulence
gravatar for bhavya.v
9 months ago by
bhavya.v0 wrote:

Hi, I have clinical urine samples from which i need to identify the gene expression changes in the pathogen after treatment. (i know the bacteria present in urine through urine culture test)

Q1. Should I do 16s DNA sequencing to identify the strain of the bacteria? How do I know the genes present in the DNA? Can I do annotation of the data and identify the genes to see which genes are virulent or responsible for biofilm formation?

Q2. I will be doing Rna-Seq to identify the expression of the genes. Do i need to provide the reference genome as the one sequenced above?

Do I need to do DNA sequencing and rna expression profiling to make my data look validated? What exactly is the right route to go to conclude my result.

Totally confused, I am new to this and this is my first bioinformatics clubbed project.

rna-seq • 268 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by bhavya.v0

Could you tell us if the bacteria is a known or novel one? Meaning does it have a reference genome? A gene annotation database? You can try searching NCBI's database but I'd also recommend googling and looking for papers.

ADD REPLYlink written 9 months ago by kristoffer.vittingseerup3.2k

I am working on Urinary tract infection causing bacteria from clinical patient samples. I know which bacteria caused infection just by name as i did bacterial urine culture to check the count of bacteria (eg. I know if it is e.coli or streptococcus, etc) but I dont know its sequence. It has reference genome at NCBI most definitely. But, do i need to sequence the isolated bacteria and use its genome as reference for identification of gene-expression from rna-seq

ADD REPLYlink written 9 months ago by bhavya.v0

I dont know the strain of the bacteria, all I know from urine culture report is that the bacteria present in urine sample is E.coli with >100000cfu/ml count, and the resistant-sensitivity pattern against antibiotics before and after treatment.

So, I want to see if the reason for change in the sensitivity against antibiotics can be checked through DNA sequencing by identifying SNP and genes responsible for the change

ADD REPLYlink written 9 months ago by bhavya.v0
gravatar for Buffo
9 months ago by
Buffo1.8k wrote:

Q1. Yes, you can identify bacteria by 16S amplification and sequencing. Q2. Yes, you can perform differential expression analysis before treatment/after treatment (do not forget replicates, at least 3). Genome reference is recommended but if it does not exist you can perform a de novo transcriptome assembly.

Do I need to do DNA sequencing?

Just for the 16S, if the bacterial genome does not exist and you have money you can sequence it and assembly :)

ADD COMMENTlink written 9 months ago by Buffo1.8k
gravatar for kristoffer.vittingseerup
9 months ago by
European Union
kristoffer.vittingseerup3.2k wrote:

If your bacteria of interest already have an annotated genome (and you are sure exactly which bacteria and strain etc it is) you dont need to sequence DNA - you can just use RNASeq directly and map it against the known genome and already annotated genes.

ADD COMMENTlink written 9 months ago by kristoffer.vittingseerup3.2k
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