Medical Microbiology and Genomic Pathology

[Enkidu]

subspecializing chemistry, coag, or microbiology with a main focus on these seems like a waste of resources

This quote seems to reflect the opinion of a lot of pathologists, and I tend to see things in the same way, but I wonder if a field like microbiology will begin to require more medical expertise as bacterial genomes begin to be routinely sequenced.

It would seem like a bacterial (or viral) genome sequence should be signed out by a pathologist and be accompanied by prognostic and therapeutic information information for the clinician. I would expect that this application of genomic medicine might come a lot sooner than whole genome analysis of patients (because the genomes are so small).

Do you think that this is right? Will medical microbiology become an attractive subspecialty for pathologists in the age of genomic medicine?

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[pathstudent]

This quote seems to reflect the opinion of a lot of pathologists, and I tend to see things in the same way, but I wonder if a field like microbiology will begin to require more medical expertise as bacterial genomes begin to be routinely sequenced.

It would seem like a bacterial (or viral) genome sequence should be signed out by a pathologist and be accompanied by prognostic and therapeutic information information for the clinician. I would expect that this application of genomic medicine might come a lot sooner than whole genome analysis of patients (because the genomes are so small).

Do you think that this is right? Will medical microbiology become an attractive subspecialty for pathologists in the age of genomic medicine?

No I think it will be heavily automated and run by techs and infectious disease docs know ten times as much about therapeutics.

 

[Enkidu]

No I think it will be heavily automated and run by techs and infectious disease docs know ten times as much about therapeutics.

Sure they know more about treatment, but do you think that they will learn how to interpret genomes to alter treatment? Or do you think that they will alter their treatment based on an automated report?

 

[KCShaw]

The latter, assuming such genomic reports equate to "if X result, then Y treatment/treatment options". However, as we know from other molecular/genomics a given result doesn't always mean a given diagnosis, prognosis, or treatment regimen automatically and exclusively fits. While that may represent limitations in testing right now, I think there is still a significant role for interpretation with such tests.

 

[Enkidu]

However, as we know from other molecular/genomics a given result doesn't always mean a given diagnosis, prognosis, or treatment regimen automatically and exclusively fits. While that may represent limitations in testing right now, I think there is still a significant role for interpretation with such tests.

I'm not sure exactly what you mean. My thought was that interpretation of bacterial genome would be complex and require an expert. I was hoping that a pathologist would fulfill this function by signing out the genomic analysis for the clinician. Is this what you're saying, or are you suggesting that the studies will be interpreted by clinicians directly?

 

[pathstudent]

Sure they know more about treatment, but do you think that they will learn how to interpret genomes to alter treatment? Or do you think that they will alter their treatment based on an automated report?

Can you give a example of what you mean by a bacteria's genomics determining "therapeutics and prognosis"?

What are the advantages over culturing and testing for drug sensitivity?

 

[scienceguy19]

i suppose PCR (with many different probes for different bacterial genomes) could potentially give a faster result rather than waiting on the results of culture for days. would require a lot of high skilled technicians though, at least for the current technology. also at a high cost

Can you give a example of what you mean by a bacteria's genomics determining "therapeutics and prognosis"?

What are the advantages over culturing and testing for drug sensitivity?

 

[KCShaw]

I'm not sure exactly what you mean. My thought was that interpretation of bacterial genome would be complex and require an expert. I was hoping that a pathologist would fulfill this function by signing out the genomic analysis for the clinician. Is this what you're saying, or are you suggesting that the studies will be interpreted by clinicians directly?

I'm saying it depends on the specific test. In theory a certain genomic outcome could be automatically compared against known genomes and a very specific treatment algorithm would be known for it. In reality I think the interpretation will be much more complex and situation dependent, at least in many cases. PCR and the like is already available and in use, allowing a certain amount of rapid "definitive" diagnosis now, but it's not used for every bug because there are simply too many things we don't know.

 

[Enkidu]

Can you give a example of what you mean by a bacteria's genomics determining "therapeutics and prognosis"?

What are the advantages over culturing and testing for drug sensitivity?

Well, I think it's easier to see how viral genomics can be used to determine prognosis and treatment.

I'm not much of a microbiologist, but my sense is that genomics can tell us everything we want to know about species and drug sensitivity that we currently know from culturing, and then more.

I'm not suggesting that we wouldn't ever do cultures again, but that when appropriate a bacterial (or viral) genome may provide information that cultures don't, and that information may be fairly complex and require an expert to interpret it. Whether that expert will be a pathologist or infectious disease guy, I don't know.

 

[pathstudent]

Well, I think it's easier to see how viral genomics can be used to determine prognosis and treatment.

I'm not much of a microbiologist, but my sense is that genomics can tell us everything we want to know about species and drug sensitivity that we currently know from culturing, and then more.

I'm not suggesting that we wouldn't ever do cultures again, but that when appropriate a bacterial (or viral) genome may provide information that cultures don't, and that information may be fairly complex and require an expert to interpret it. Whether that expert will be a pathologist or infectious disease guy, I don't know.

We will see. A pathologist should have the upper hand if this comes to fruition.

 

[KCShaw]

I think there is likely to be utility in both, depending on the circumstances, for a long while yet. In most cases we simply don't know all of the influences on gene expression, which basically means that having a "resistance" gene doesn't necessarily mean a bug automatically will or won't be resistant to a given drug at a certain concentration. Culture & sensitivities tell us that. On the other hand, isolated C&S doesn't automatically tell us about inducible resistance, which molecular/genetic studies could. I suspect some bugs are going to show themselves as amenable to molecular/genetic interpretation while others aren't, or will adapt about as quickly as we think we have them figured out.