Dear scientists,
Out of my curiosity, when i analysed a patient harbouring pseudomonas strain with higher resistance, i have taken the toilet swab, wash basin swab and air sampling of the patient room and other environmental samples from the patients house.
I could identify the pseudomonas from environment and toilet swab, but they are not resistant to drug as the strain from patient shows?
How could we can justify that patient got the infection from any source i mentioned? or how to prove a patient harboured infection from a specific source, with the proper clinical as well as bilogical experiment results.
I can do NGS also for the both strain.
Kindly suggest me in this regard, i will be very much thankful to you.
Thanks in advance.
Drawing a phylogenetic tree can give you a clue if there is any mutations that took place in the specified environs and also it can show if the strains from the said environs are from the same ancestral line.
Hi, I think the subject can get a bit tricky. I can not really figure out if you isolated the Pseudomonas strains from the environment, but I guess so, since you've checked them for antibiotic resistance (did you try to isolate them on selective medium; like adding the antibiotic your strain is supposed to be resistant to?). That's also a good hint that these strains are not the one from the patient. Be aware that Pseudomans are highly abundant in the environment and also are very similar in their genetic make up. Probably you isolate or detect only the most abundant or most adaptable ones (inside the host organism is a totally different environment with unique selction pressures, favoring maybe only a certain very low abundant strain within in the hosts environment to establish an infection). I would also think that even NGS on 16S wouldn't give you enough phylogenetic resolution to find the source of your strain. More appropriate would be genotyping methods like SBT (Sequence Based Typing), microsatellite analyses like MLVA (Multiple Loci VNTR Analysis) ore even WGS (Whole Genome Sequencing). We use MLVA to genotype Legionella pneumophila strains. But only on isolates, since you surely get ambivalent results using these methods on environmental DNA samples. Check the literature for various genotyping methods for Pseudomonas or which gene(s) they use for high resolution phylogenetic discrimination. Good luck!
I thank Mr, Rene, and Johnstone for their valuable suggestions.
Especially Rene explaining about SBT, MLVA is new to me, which i will try to goahead.
I have seen even a patient carrying strain and wash basin swab strain or both similar by phenotypic and genotypically.
But my question is how to prove that the patient harboured the strain from the hospital source by contact with experimental evidence.
Or we could think even the environment can get contaminated by his fluids or others?
Well, I think this is quite difficult. In case of Legionella pneumophila there are many strains, serotypes, genotypes and even single clones in the environment that can cause disease. But often an outbreak is caused by a single clone from a certain contaminated source. It's a matter of virulence factors that the strain is expressing, ecological conditions that favor its abundance and expression of virulence factors and of cause to what extent the patient was exposed to the strain (=contact rates). Special well-trained investigators put a lot of (sampling and isolating) effort in pinpointing the source of infection. Means the environmental source where exactly the outbreak strain is coming from. Doing so, they find a lot of environmental Legionella pneumophila isolates that might be closely related to but not identical to the (clinical) outbreak strain. Certainty is only given by high resolution genotyping methods as mentioned above. I reckon that the situation is quite similar to Pseudomonas species. You won't be able to avoid genotyping to really prove the source and spreading of that special strain you are looking for. (That's just my point of view, maybe someone else can provide a more simpler approach)
Ya i agree with your view Rene, will expect an additional information who is working on this kind of issues will be helpful to all researchers and community.
i thank once again for your valuable input
Regards
Murugan N
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