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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]]''' table in [[CCMDB.mdb]].
Pathogens are coded as their own diagnosis codes:
{{ListICD10Category | categoryName = Pathogens}}


==The 5 day post discharge RULE for Culture report follow up==
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.
Follow up all culture reports up to 5 days after discharge from unit. If pathogen is still not available then, enter [[Unknown Pathogen]].


=== Special Codes ===
Information about pathogens can be found in the patient's chart's [[Lab and culture reports]]; see that page for specific use instructions.
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)?
 
== NOS pathogens ==
*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]]
**[[Fungus or yeast, NOS]]
**[[Nontuberculous mycobacteria]]
**[[Other type of infectious organism, NOS]]


== Data Integrity Rules==
=== NOS vs Unknown in the context of pathogens  ===
The [[CCMDB.mdb]] runs checks for the following:
*We must distinguish '''NOS''' from '''unknown'''.
*'''no infections without pathogens'''  
**''NOS'' means that we do know the bug, but it's not in our list of specific pathogens
*'''no non-infections with pathogens'''  
**''[[Infectious organism, unknown]]'' means we assume that there IS in fact a pathogen, but we have no idea about it's actual identity.
For details, see the coding in Access.


==Discussion==
=== Special Codes ===
{{Discussion}}
* [[Not an Infection (ICD10 pathogen alternative)]] - included for [[cross check]]s when entering [[:Category:Potential infection]]s
*At the Vic, sputum and urine cultures are rarely ordered. Even when pathogen is unknown, antibiotic course is started and completed. A +ve urinalysis or infiltrates on CXR and other UTI or pneumonic infectious process symptoms are sufficient enough reasons to treat. This makes sense for N5 and S5 when admissions are generally those of the older adult, with a number from PCHs. Antibiotics are chosen based on likely pathogens, despite absent cultures. I've been coding them as infections. Should I stop? Thanks.
* [[Infectious organism, unknown]] - eg for negative culture
**Con, could you get a coding consult from Dr. Embil?


{{Data Integrity Check List}}


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


[[Category: UPL]]
[[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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