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The '''pathogens''' are a list of possible entries that make up the sub-code for diagnoses categorized as [[Infections]].
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 are drawn from the '''[[S_Pathogens]]''' table on your PDA and in the [[CCMDB.mdb]].
{{subcat collapsible|supercategory = Pathogens}}


== Pathogen Table ==
Pathogens are coded as their own diagnosis codes:
For an up-to-date list of pathogens, see your PDA. This is the list as of May 08 and for orientation only.
{{ListICD10Category | categoryName = Pathogens}}
===Bacteria===
*Acinetobacter --  R
*Actinobacillus actinomycetemcomitans --  C-B
*Bacteriods fragilis --  R
*Campylobacter --  R
*Citrobacter diversus --  R
*Citrobacter feundii --  R
*Clostridium botulinum +  R
*Clostridium difficle +  R
*Clostridium perfingens +  R
*Clostridium tentani +  R
*Corynebacterium diphtheriae +  R
*E Coli --  R
*Enterobacter --  R
*Enterococcus faecalis +  C
*Haemophlilus  influenzae --  R  C  B
*Haemophilus ducreyi --  R
*Haemophilus  parainfluenzae --  R
*Kebsiella pneumoniae --  R
*Legionella sp – legionella pneumophilia     R
*Listeria monocytogenes +  R
*Moraxella catarrhalis --  R
*Morganella morganii --  R
*Mycoplasma pneumoniae
*Neisseria gonorrhoeae --  C
*Proteus mirabilis --  R
*Pseudomonas aeruginosa --  R
*Salmonella --  R
*Serratia --  R
*Shigella --  R
*Staphylococcus aureus +  C
*Staphylococcus epidermidis +  C
*Streptococcus agalactiae  Group B +  C
*Streptococcus pneumoniae +  C
*Streptococcus pyogenes  Group A +  C
*Streptococcus viridans +  C


===Fungi===
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.
Aspergillus species
Blastomyces,
Candida,
Crytococcus,
Histoplasma


===Virus===
Information about pathogens can be found in the patient's chart's [[Lab and culture reports]]; see that page for specific use instructions.
Adenoviruses,
Cytomegaloviruses,
Epstein-Barr virus,
Herpes simplex,
Herpes zoster,
West Nile


===Parasites===
== NOS pathogens ==
Cryptosporidium,
*In each of those categories there are a number of specific bugs with their own codes (e.g. B95.3 is Strep pneumoniae)
Giardia Lamblia,
*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:
Malaria,
**[[Bacteria, NOS]]
Pneumocystis carinii (PCP),
**[[Virus, NOS]]
Toxoplasma gondii
**[[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 ===
* [[Not an Infection (ICD10 pathogen alternative)]] - included for [[cross check]]s when entering [[:Category:Potential infection]]s
* [[Infectious organism, unknown]] - eg for negative culture


== Discussion ==
{{Data Integrity Check List}}
* how do we capture neuro syphyllis???  The pathogen that causes syphyllis treponema pallidum is not on the available pathogen list.  59990 was used as an alternative.  please help--[[User:JHutton|JHutton]] 14:38, 12 June 2008 (CDT)
*New codes added.  Please see [[CCMDB.mdb Change Log]] October 29, 2008[[User:TOstryzniuk|TOstryzniuk]] 21:46, 17 November 2008 (CST)


* 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)
== Related Articles ==
** Fran, what's an AFB, and how does this entry relate to the pathogens? Can you give a little more detail? Thanks--[[User:Ttenbergen|Ttenbergen]] 16:09, 6 August 2008 (CDT)
{{Related Articles}}
***AFB is defined as Acid Fast Bacilli, which is a laboratory test used to identify certain types of bacteria such as mycobacteria that cause TB.  There was a question from data collectors about how to capture this sputum sample.  I guess the fact that the sputum sample is used to categorize the pathogen is why the discussion was placed here.--[[User:JHutton|JHutton]] 12:49, 11 August 2008 (CDT)
 
****The pathogen list can only encode pathogens that were found, not negative findings, right? If that is the case, and if no other pathogen is found, would you not code this as a 68 - Unknown pathogen? Trish? [[User:Ttenbergen|Ttenbergen]] 13:33, 12 August 2008 (CDT)
[[Category:ICD10]]
* How do we code scabies ?cellulitis other parasite? Please let me know Thanks[[User:SKiesman|SKiesman]] 13:30, 17 November 2008 (CST)
[[Category:Pathogens| *]]
**Don't code.  We haven't been tracking incidence of  scabies nor are we going to start. [[User:TOstryzniuk|TOstryzniuk]] 21:21, 17 November 2008 (CST)
[[Category:Infectious disease| *]]
{{stub}}
[[Category:Data_Collection_Guide]]
[[Category:Data Integrity Rules]]
[[Category: Questions]]

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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