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The '''pathogens''' are a list of possible entries that make up the sub-code for diagnoses categorized as [[:Category: Infection | Infection]]. 
The [[ICD10 Diagnosis List]] contains specific codes for a number of different bacteria, viruses, fungi/yeast, mycobacteria and miscellaneous types of organisms. The entire list can be found in category and subcategories:
*Refer to: [[UPL]] - [[Universal Pathogen List]], for a list of "bugs" we track.
{{subcat collapsible|supercategory = Pathogens}}


*The pathogen subcodes are drawn from the '''[[S_Pathogens]]''' which is table in [[HanDBase]] on the PDA and also in also in the Access database also know as: [[CCMDB.mdb]].
Pathogens are coded as their own diagnosis codes:
{{ListICD10Category | categoryName = Pathogens}}


They are always entered as [[Combined ICD10 codes]] with an [[Infections in ICD10|infection]], but not all infections require pathogens. See [[Template:ICD10 Guideline Infection]], [[Infections in ICD10]] for more info.


Information about pathogens can be found in the patient's chart's [[Lab and culture reports]]; see that page for specific use instructions.


=== Special Codes ===
== NOS pathogens ==
Could someone please fill in specifics about how or when these are to be used? Specifically, if we know specific bugs, are there any that should be coded implicitly even if there are others (ie precedence rules)?
*In each of those categories there are a number of specific bugs with their own codes (e.g. B95.3 is Strep pneumoniae)
 
*But obviously we can't list every bug of any type, so for each of those categories there is also a "wastebasket" code for "NOS".  For example, if the bug is a specific bacteria but it's not in our list, then use [[Bacteria, NOS]], etc.  These are:
 
**[[Bacteria, NOS]]
 
**[[Virus, NOS]]
* Sputums for AFB (Acid Fast Bacilli).  As per Dr. Kumar: a negative AFB culture is considered a '''negative culture''' and should '''not''' to be coded as '''NO C&S culture sent'''.--[[User:FLindell|FLindell]] 15:33, 6 August 2008 (CDT)
**[[Fungus or yeast, NOS]]
 
**[[Nontuberculous mycobacteria]]
===Discussion===
**[[Other type of infectious organism, NOS]]
{{discussion}}
Question:
*''should be be tracking Swine flu''? - Laura Kolesar, STB
 
**FROM DR. KUMAR:
***''Trish, don’t add a new code for swine flu.  We already have a subcode in the pathogen list: use subcode (#75) for '''influenza virus''', this is good enough.  We get few enough cases that if we want to review, we can just look at more closely during the period that swine flu hit....within a few years, it’ll just be another influenza case'' --Dr. Anand Kumar, June 1.09
****What are we supposed to do with the CAP cases that are presumed to be H1N1(Swine flu) but are discharged or die prior to notification from Cadham lab that they are indeed positive for the virus? The information won't be on KEA.Please advise as I have 2 cases and 1 patient has left the hospital without confirmation yet from the lab.I think if we are treating them for flu virus we should code it even if the results aren't in. Then if those charts need review they could be pulled.
 
== Data Integrity Rules==
The [[CCMDB.mdb]] runs checks for the following:
*'''no infections without pathogens'''
*'''no non-infections with pathogens'''
For details, see the coding in Access.


=== NOS vs Unknown in the context of pathogens  ===
*We must distinguish '''NOS''' from '''unknown'''.
**''NOS'' means that we do know the bug, but it's not in our list of specific pathogens
**''[[Infectious organism, unknown]]'' means we assume that there IS in fact a pathogen, but we have no idea about it's actual identity.


=== Special Codes ===
* [[Not an Infection (ICD10 pathogen alternative)]] - included for [[cross check]]s when entering [[:Category:Potential infection]]s
* [[Infectious organism, unknown]] - eg for negative culture


{{Data Integrity Check List}}


== Related Articles ==
{{Related Articles}}


{{stub}}
[[Category:ICD10]]
[[Category: Infection|*]]
[[Category:Pathogens| *]]
[[Category: Infection]]
[[Category:Infectious disease| *]]
[[Category:Diagnosis Coding]]
[[Category:Data Integrity Rules]]
[[Category: Questions Diagnosis]]

Latest revision as of 11:56, 30 July 2025

The ICD10 Diagnosis List contains specific codes for a number of different bacteria, viruses, fungi/yeast, mycobacteria and miscellaneous types of organisms. The entire list can be found in category and subcategories:

Pathogens

Pathogens are coded as their own diagnosis codes:

Pathogens codes:

They are always entered as Combined ICD10 codes with an infection, but not all infections require pathogens. See Template:ICD10 Guideline Infection, Infections in ICD10 for more info.

Information about pathogens can be found in the patient's chart's Lab and culture reports; see that page for specific use instructions.

NOS pathogens

NOS vs Unknown in the context of pathogens

  • We must distinguish NOS from unknown.
    • NOS means that we do know the bug, but it's not in our list of specific pathogens
    • Infectious organism, unknown means we assume that there IS in fact a pathogen, but we have no idea about it's actual identity.

Special Codes

Data Integrity Checks (automatic list)

 AppStatus
Query check ICD10 Inf Potential Infection must have pathogen or altCCMDB.accdbdeclined
Check Inf Antibiotic resistance must have pathogen or Infection with implied pathogenCCMDB.accdbimplemented
Check Inf Infection with implied pathogen must not have a pathogen combined codeCCMDB.accdbimplemented
Query check ICD10 Inf Infection req Pathogen must have oneCCMDB.accdbimplemented
Query Check Inf Pathogens must have Infection requiring pathogen or Potential InfectionCCMDB.accdbimplemented

Related Articles

Related articles:
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