I had the following advice from Vitali Sintchenko who is director of Public Health in Sydney:
Naming of salmonella serovars is done by the World Health Organization (WHO) Collaborating Centre for Reference and Research on Salmonella at the Pasteur Institute, Paris, France (WHO Collaborating Centre), and new serotypes are listed in annual updates of the Kauffmann-White scheme. Perhaps the NEHTA could engage SNOMED CT International and the WHO CC.
I would not underestimate logistical challenges associated with this process.
In other words, unless we can get some sort of slick process going with the WHO CC,
I think having current SNOMED CT concepts for Salmonella serovars is perhaps too difficult to achieve.
I think we have to consider inter-related problems as well.
1) Staying current with WHO CC Salm (Kauffman-White scheme) is certainly a challenge. I am unaware of "annual updates" so clearly I'm not well enough connected. Even if we get WHO CC Salm updates in a timely fashion, there's a built-in time lag for editorial processes at WHO, then editorial processes and timed updates for SNOMED CT.
2) There really are "new" Salmonella serotypes discovered (even if infrequently) all the time. It is NOT POSSIBLE for any terminology to have a code waiting for an organism subtype that's never been seen before.
In the veterinary world, we created the veterinary extension so that appropriate concept classes and codes could be created DURING disease outbreaks (and distributed to labs in real time). This almost always means new specimen types, new diagnostic tests. We have never attempted to stay out in front of new organisms.
3) We don't actually have a strategy for maintaining/naming/defining serotypes in SNOMED CT. Consider one of the most common serotypes, 50136005 | S. Typhimurium. The antigenic formula listed (as a synonym) is Salmonella 1,4,[5],12:i:1,2 - the brackets indicate that O5 is optional. The antigenic formaula listed in KW is Salmonella 1,4,[5],12:i:1,2. Both O1 and O5 are optional. There are 4 actual ISOLATE (serotypes) 4,12,:i:1,2 | 1,4,12,:i:1,2 | 4,5,12,:i:1,2 | 1,4,5,12:i:1,2 (the antigenic formulas of actual Salmonella Typhimurium isolates). These formulas are NOT IN SNOMED CT. It is often not possible to look up an antigenic formula for an organism you've just isolated in the lab (no real isolate has an optional antigen - they have what they have).
The biggest problem related to our recent telecon discussion (as I see it) are reporting requirements by public health agencies that are actually IMPOSSIBLE to meet. That problem aside, we really do have an unmet editorial challenge with serotypes.
2 Comments
Michael Osborne
I had the following advice from Vitali Sintchenko who is director of Public Health in Sydney:
In other words, unless we can get some sort of slick process going with the WHO CC,
I think having current SNOMED CT concepts for Salmonella serovars is perhaps too difficult to achieve.
Jeff Wilcke
I think we have to consider inter-related problems as well.
1) Staying current with WHO CC Salm (Kauffman-White scheme) is certainly a challenge. I am unaware of "annual updates" so clearly I'm not well enough connected. Even if we get WHO CC Salm updates in a timely fashion, there's a built-in time lag for editorial processes at WHO, then editorial processes and timed updates for SNOMED CT.
2) There really are "new" Salmonella serotypes discovered (even if infrequently) all the time. It is NOT POSSIBLE for any terminology to have a code waiting for an organism subtype that's never been seen before.
In the veterinary world, we created the veterinary extension so that appropriate concept classes and codes could be created DURING disease outbreaks (and distributed to labs in real time). This almost always means new specimen types, new diagnostic tests. We have never attempted to stay out in front of new organisms.
3) We don't actually have a strategy for maintaining/naming/defining serotypes in SNOMED CT. Consider one of the most common serotypes, 50136005 | S. Typhimurium. The antigenic formula listed (as a synonym) is Salmonella 1,4,[5],12:i:1,2 - the brackets indicate that O5 is optional. The antigenic formaula listed in KW is Salmonella 1,4,[5],12:i:1,2. Both O1 and O5 are optional. There are 4 actual ISOLATE (serotypes) 4,12,:i:1,2 | 1,4,12,:i:1,2 | 4,5,12,:i:1,2 | 1,4,5,12:i:1,2 (the antigenic formulas of actual Salmonella Typhimurium isolates). These formulas are NOT IN SNOMED CT. It is often not possible to look up an antigenic formula for an organism you've just isolated in the lab (no real isolate has an optional antigen - they have what they have).
The biggest problem related to our recent telecon discussion (as I see it) are reporting requirements by public health agencies that are actually IMPOSSIBLE to meet. That problem aside, we really do have an unmet editorial challenge with serotypes.