suspicion-of-infection

name	suspicion-of-infection
description	Identify suspected infection events using antibiotic administration plus culture timing. Use as a component of Sepsis-3 definition or for infection research.
tier	validated
category	clinical

Suspicion of Infection

This concept identifies when clinicians suspected infection based on clinical actions: systemic antibiotic administration combined with culture collection within a defined time window. It operationalizes the infection component of the Sepsis-3 definition (Seymour et al. 2016).

M4Bench Use

In M4Bench, target concept tables listed in the task configuration are removed or unavailable in the agent database. Use this skill as procedural guidance and derive the requested output from available source or intermediate tables; do not rely on a precomputed target table or bundled SQL script.

When to Use This Skill

• Building Sepsis-3 cohorts (infection component)
• Antibiotic stewardship research
• Time-to-treatment studies
• Infection onset timing
• Culture yield research

Definition Logic

Suspected infection requires BOTH:

1. Antibiotic administration (systemic, not topical)
2. Culture collection within time window:
   • Culture obtained up to 72h BEFORE antibiotic, OR
   • Culture obtained up to 24h AFTER antibiotic

Suspected Infection Time

The suspected_infection_time is defined as:

• The culture time if culture was obtained BEFORE antibiotic
• The antibiotic time if antibiotic was given BEFORE culture

This represents when infection was first clinically suspected.

Culture Matching Logic

Each antibiotic is matched to cultures in two directions:

Culture Before Antibiotic (Primary)

• Culture obtained within 72 hours before antibiotic start
• If multiple cultures, uses the EARLIEST culture before the antibiotic

Culture After Antibiotic (Secondary)

• Culture obtained within 24 hours after antibiotic start
• If multiple cultures, uses the EARLIEST culture after the antibiotic

Priority: Culture-before-antibiotic takes precedence when both exist.

Critical Implementation Notes

1. One Row Per Antibiotic: Each antibiotic prescription gets its own row, potentially matched to one culture. A single culture may be matched to multiple antibiotics.

2. Culture Positivity Not Required: Negative cultures still count as suspected infection — the flag captures clinical suspicion, not confirmed infection.

3. All Culture Types Included: Blood, urine, sputum, wound, CSF, etc. The specimen column identifies the type.

4. Systemic Antibiotics Only: Topical formulations (eye drops, ear drops, creams, ointments) must be excluded. The specific route codes vary by dataset.

General Limitations

1. Proxy for Clinical Suspicion: Not all antibiotic + culture pairs represent true infection suspicion. Routine screening cultures (e.g., weekly surveillance) paired with prophylactic antibiotics may be misclassified as suspected infection.

2. Time Window Is an Operationalization: The 72h/24h windows are from the Seymour et al. operationalization. There is no biological basis for these specific cutoffs — they are pragmatic choices that balance sensitivity and specificity.

3. Misses Antibiotic-Only or Culture-Only Events: Patients treated empirically without cultures sent, or cultures obtained without subsequent antibiotics, will not be flagged.

4. Does Not Distinguish Empiric vs Targeted Therapy: The concept captures the initial antibiotic-culture pairing regardless of whether the antibiotic was empiric (before results) or targeted (after susceptibility).

Dataset-Specific Implementation Notes

MIMIC-IV

MIMIC-IV implementation details:

• Antibiotics are sourced from systemic medication orders. When a curated antibiotic concept is available, it filters the prescriptions table for systemic routes, excluding topical routes: OU, OS, OD, AU, AS, AD, TP, and topical formulations like creams, gels, ophthalmic ointments.
• Cultures from mimiciv_hosp.microbiologyevents. Positive culture identified by non-null org_name excluding itemid 90856 ("NEGATIVE").
• stay_id is populated when antibiotic timing overlaps with an ICU stay. May be NULL for floor patients.
• Chart dates vs times: Microbiology cultures sometimes only have dates (not times). When charttime is null, the query falls back to chartdate with day-level matching (72h becomes 3 days, 24h becomes 1 day).

MIMIC-IV limitations:

• Prescription duplication: each ICU stay in a hospitalization gets a copy of all prescriptions for that admission, which the query handles via unique ab_id per patient.
• Antibiotic route filtering relies on MIMIC's route coding. Miscoded routes could include topical antibiotics or exclude systemic ones.

eICU

For eICU, both components must be derived from raw tables:

Component	eICU Table	Columns	Notes
Antibiotics	medication	drugname, routeadmin, drugstartoffset, drugstopoffset	Free-text drugname; drugstartoffset in minutes from unit admission
Cultures	microlab	culturetakenoffset, culturesite, organism	culturetakenoffset in minutes from unit admission; positive culture = non-null organism

eICU limitations:

• Center variability in missingness: Medication documentation and culture practices vary substantially across the 208 hospitals. Some sites have near-complete medication records; others have significant gaps. This non-random missingness affects infection identification rates.
• Medication naming: drugname is free-text and varies across sites. The same antibiotic may appear as "Vancomycin", "VANCOMYCIN", "vancomycin 1g IV", etc. Building a reliable antibiotic identification filter requires extensive text matching and validation.
• Route coding: routeadmin also varies by site. Excluding topical routes requires site-aware filtering.
• Offset-based timing: Both drugstartoffset and culturetakenoffset are in minutes from unit admission (not absolute timestamps). The antibiotic-culture pairing logic must use offset arithmetic rather than datetime comparisons.
• No upstream antibiotic table: Unlike MIMIC installations that have a curated antibiotic concept, eICU requires building the antibiotic filtering from scratch.

Related Skills

• sepsis-3-cohort — Combines this concept with SOFA >= 2 for Sepsis-3 identification
• sofa-score — Organ dysfunction component of Sepsis-3
• sirs-criteria — Historical inflammatory response criteria (pre-Sepsis-3)

References

• Singer M et al. "The Third International Consensus Definitions for Sepsis and Septic Shock (Sepsis-3)." JAMA. 2016;315(8):801-810.
• Seymour CW et al. "Assessment of Clinical Criteria for Sepsis." JAMA. 2016;315(8):762-774.