Shiga toxin-producing E. coli v1

Query purpose: 

Created by the CDC National Syndromic Surveillance Program (NSSP) for use with emergency department data to develop queries for all National Notifiable Diseases defined by the National Notifiable Diseases Surveillance System (NNDSS). Please note that while the disease queries are developed using the NNDSS case definition as the basis for identifying patient visits of interest, the queried patient visits themselves may or may not represent a case patient in NNDSS and further public health investigation will most often be required. This query is intended to be a version 1 and may be further improved upon by the NSSP community of practice in the future. This query is intended to be narrow and capture visits with specific terms to support greater monitoring and actionable public health data. More complex and/or broader queries may exist that more broadly capture symptoms or travel-based terms.

How it was developed: 

1. The CDC team used the NNDSS case definition of Shiga toxin-producing E. coli to identify diagnostic codes (International Classification of Diseases, 9th & 10th Revision (ICD-9-CM, ICD-10-CM), SNOMED Clinical Terms (CT)) and chief complaint free-text for syndrome development.
2. The codes and free text were then categorized as inclusion or exclusion terms. These terms were formatted for querying in ESSENCE.
3. Text analysis was conducted on the initial query to find additional inclusion or exclusion terms.
4. The query was cross-checked internally as NSSP and by CDC subject matter experts as needed.

How it works:

The Chief Complaint Discharge Diagnosis (CCDD) parsed field is used to query both the discharge diagnosis codes and chief complaint free text, and exclusions are incorporated as necessary.

• Inclusion based on Shiga toxin-producing E. coli complaint free text terms:
  • The visit is included if it contains:
    1. A chief complaint related to disease name – (“shiga” OR “shinga”)
    2. Nested chief complaint terms indicating E. coli (“ecoli” OR “e coli” OR “escherichia coli” OR “O157”) AND mention of toxin - (“toxin” OR “txn”)) OR
    3. A chief complaint related to abbreviation of disease name – (“STEC” or “VTEC” or “EHEC”) OR
• Inclusion based on ICD-10 discharge diagnosis codes related to Shiga toxin-producing E. coli:
  • The visit is included if it contains:
    1. A discharge diagnosis code for Shiga toxin-producing Escherichia coli – (B96.21 OR B96.22 OR B96.23) OR
• Inclusion based on ICD-9 discharge diagnosis codes related to Shiga toxin-producing E. coli:
  • The visit is included if it contains:
    1. A discharge diagnosis code for Shiga toxin-producing Escherichia coli – (041.41 OR 041.42 OR 041.43) OR
• Inclusion based on SNOMED discharge diagnosis codes related to Shiga toxin-producing E. coli:
  • The visit is included if it contains:
    1. A discharge diagnosis code for Shiga toxin-producing Escherichia coli – (838549008) OR
    2. A discharge diagnosis code for Shiga toxin – (255835006) OR
    3. A discharge diagnosis code for infections caused by Shiga toxin-producing Escherichia coli – (328291000119103)
• There are no exclusions in this query.

Plain Language Description:

The definition uses discharge diagnosis codes and free-text chief complaint terms. The definition requires that an emergency department visit contains a reference to the disease by its discharge diagnosis code (in at least one of the following: ICD-10-CM, ICD-9-CM, SNOMED diagnostic codes), or by the disease or pathogen name listed in the chief complaint text. Therefore, the Shiga toxin-producing E. coli surveillance definition includes ICD-10-CM, ICD-9-CM, and SNOMED diagnostic codes for Shiga toxin-producing E. coli, along with direct mentions of Shiga toxin-producing E. coli using “shiga”,potential misspellings (“shinga”), abbreviations (“STEC”, “VTEC”, “EHEC”), and combinations of E. coli (“E coli”, “Escherichia coli”) with a mention of a toxin (“toxin”, “txn”) in the chief complaint field.