Much of in silico pathogen studies involve culture of the clinical isolates, NGS sequencing followed by SNP calling . The novel polymorphisms are associated with drug resistance.
But, the genomic impact of the shift from host milieu to culture medium hardly gets attention. Would not the the change in growth conditions be causing acquisition of SNPs, indels and the chromosomal aberrations in the pathogen?
If drug stressor causes resistance development in the pathogens, the host immune pressure determines adaptation of pathogens too. In culture medium, the immune pressure and other competing microbes are lacking. Also the nutrient composition is much much different than host bio-fluid.
I will be surprised if not, for most of us are aware how mere optimization of growth medium substantially improves industrially-important microbial metabolite production.
Discussions and expert opinions are appreciated.
I think you need to differentiate between long-term culture (i.e. culture-adapted strains) and short-term culture. The latter is usually done to increase the amount of template (i.e. genomes) for sequencing.
It is very likely that long-term culture has led to accumulation and finally fixation of certain mutations. Thus culture-adapted strains do not fully reflect clinical isolates. This is however very unlikely in the case of short term culture. Mutations will always occur at a similar rate (i.e. they will not occur faster by culturing a pathogen), thus they will not reach high frequency in only a few generations of culture. Thus it is very unlikely that you will detect novel mutations when sequencing.
The situation presents different if you try to culture a pathogen, and let's say only 1 in 10 isolates grow. In that case you should think whether the culture selects for a certain genotype, and consider sequencing without a culture step.
Thank you.
Consider M. tuberculosis H37rv, the strain used as worldwide reference for susceptible pathogen. It was isolated in 1905 and whole genome sequenced in 1998. I think its too long a period to cause multiple mutations and genome shuffling.
I am not an expert in Mycobacterium evolution, but I agree that in this case I think it is likely that the long-term culture has affected the genome.
- Badges
- Science topic
- Similar topics
- Agriculture