A Pharmacist-Driven Deprescribing Protocol for Negative Urine and Sexually Transmitted Infection Cultures

Introduction

Antibiotics for suspected urinary tract infection (UTI) and sexually transmitted infection (STI) are frequently started empirically in the emergency department, before the confirmatory urine culture or nucleic-acid amplification test (NAAT) results. Because those results usually finalize after the patient is discharged, there is a structural gap: no one is reliably reviewing the result and adjusting therapy.

Two failure modes this creates

Overtreatment — antibiotics continued when the culture/NAAT is negative (or when the finding is asymptomatic bacteriuria that should never have been treated). In two ED cohorts, 86–88% of patients empirically treated for gonorrhea/chlamydia ultimately tested negative.
Undertreatment — a positive result in a patient who was not empirically treated, who then does not return. Roughly 39% of laboratory-positive STI patients across U.S. EDs received no antibiotics, and many are lost to follow-up.

A pharmacist-driven culture/lab follow-up (“callback”) program closes this gap on both ends — and, increasingly, is being extended to actively deprescribe (stop or narrow) unnecessary antibiotics when the culture returns negative.

Clinical Detail

A deprescribing protocol framework

A pharmacist-driven protocol — typically operating under a collaborative practice agreement (CPA) — systematically reviews post-discharge culture/NAAT results and takes one of a small set of actions. Confirm your institution’s CPA scope and local protocol before acting on any of these steps.

Review every pending urine culture and STI NAAT ordered from the ED once it finalizes.
Deprescribe (stop) empiric antibiotics when the culture/NAAT is negative and there is no clear ongoing clinical indication.
De-escalate / narrow when a pathogen is identified — match the agent to susceptibilities and the narrowest effective spectrum.
Initiate or change therapy for a positive result in an untreated patient (the undertreatment gap), with documented patient outreach.
Do not treat asymptomatic bacteriuria outside the accepted exceptions (see guideline box).

Guideline anchors

Asymptomatic bacteriuria (IDSA 2019): screen for and treat ASB only in (1) pregnant patients and (2) patients before an invasive urologic procedure with anticipated mucosal trauma. Do not treat ASB in healthy or older adults, patients with diabetes, indwelling catheters, or spinal cord injury.
STIs (CDC 2021): uncomplicated gonorrhea — ceftriaxone 500 mg IM × 1 (1 g if ≥150 kg); if chlamydia is not excluded, add doxycycline 100 mg PO BID × 7 days. Chlamydia — doxycycline 100 mg PO BID × 7 days (preferred over single-dose azithromycin).

Regimens per the CDC 2021 STI Treatment Guidelines and the IDSA 2019 ASB guideline (see references). Confirm current CDC/IDSA guidance and local antibiogram before prescribing.

Evidence

Pharmacist-driven follow-up & deprescribing

Author, Year	Design (n)	Key finding
Dumkow, 2014	Quasi-experimental pre/post ED culture follow-up (197 cultures)	Antimicrobial therapy modified in 25.5% of reviewed cultures. Combined 72-h ED revisit + 30-d admission fell 16.9% → 10.2% (P=0.079); in the uninsured, 72-h revisits fell 15.3% → 2.4% (P=0.044).
Dumkow, 2017	Retrospective, pharmacist-led CPA follow-up, ED + urgent care (1,461 cultures)	320 (22%) required intervention; urine cultures and STIs were the most frequent (~25% each); a median of 15 min and one call per intervention.
Shealy, 2020	Single-center pre/post culture + STI RDT follow-up (127 patients)	Mean time to culture/RDT review fell 36.3% (75.2 → 47.9 h, P<0.001); fluoroquinolone prescribing fell 18.1% → 5.4% (P=0.036). 30-day revisits/admissions unchanged.
Wu, 2020	Retrospective, health-system-wide, 13 EDs (7,663 encounters)	39.8% of ED encounters required a post-discharge intervention (3,049 interventions). Urine cultures were 50.6% and STIs 15.2% of reviewed results.
Geyer, 2023	Retrospective feasibility of a CPA to deprescribe after ED/UC (398 cultures)	208 (52%) were negative urine cultures or chlamydia tests; 50 of those patients (24%) had received empiric antibiotics (median 7-day course) while cultures finalized in a median of 2 days — an opportunity to save a median of 5 antibiotic days per patient. No ADRs.
Kooda, 2022	Systematic review + meta-analysis (24 studies, 9,984 patients)	Appropriate prescribing more likely with a pharmacist: OR 3.47 (95% CI 2.39–5.03); UTI-specific OR 1.76 (1.24–2.50). Time-to-appropriate antibiotic shortened by ~18.9 h.

The problem being solved: over- and under-treatment

Author, Year	Design (n)	Key finding
Levitt, 2003	Prospective, county teaching ED (1,260 women)	Of 426 women empirically treated for gonorrhea/chlamydia, 376 (88.3%) tested negative (overtreatment). Separately, 38.3% of positives were untreated initially and 64.5% of those did not return.
Holley, 2015	Retrospective, 2 inner-city EDs (522 visits)	Overtreatment rate for gonorrhea/chlamydia was 86% (87/101 treated patients tested negative). Undertreatment was low (17/412 untreated were positive, 4%).
Solnick, 2025	Systematic review + meta-analysis, U.S. EDs (19 studies, 32,593 patients)	Among negative-test patients, 38% received antibiotics (overtreatment); among laboratory-positive patients, 39% received none (undertreatment). Females were 3.5× more likely than males to be undertreated.
Childers, 2022	Observational cohort, ED patients at risk of UTI misdiagnosis	UTI treatment rate was more than double the positive-culture rate; only ~15% of patients treated for UTI met symptom-plus-culture criteria. Urine testing added ≥30 min to ED length of stay.
Monje, 2025	Quasi-experimental, clinical-pharmacist-led education + audit, tertiary ED (195 patients)	Median cases of asymptomatic bacteriuria with unnecessary antibiotics fell from 19 to 9 per month (P=0.018); urine-culture requests fell 16.1%; 30-day mortality unchanged.

RDT = rapid diagnostic technology; CPA = collaborative practice agreement; ASB = asymptomatic bacteriuria; NAAT = nucleic-acid amplification test. All sample sizes and outcome values verified against the primary PubMed records (see EVIDENCE-PACKET.md).

Conclusions

Empiric ED treatment of suspected UTI and STI produces large, well-documented rates of both overtreatment (often ~86–88% of empirically treated STI patients test negative) and undertreatment of true positives who are lost to follow-up.
A pharmacist-driven culture/NAAT follow-up program reliably catches these cases: roughly one-quarter to two-fifths of reviewed encounters require an intervention, and pharmacist involvement is associated with higher odds of appropriate prescribing (OR 3.47) (Kooda 2022).
Extending the program to deprescribe antibiotics on negative cultures is feasible and can save a meaningful number of unnecessary antibiotic-days (Geyer 2023), closing a gap that routine primary-care follow-up rarely fills.
Ground the protocol in guidelines: do not treat asymptomatic bacteriuria outside pregnancy or pre-urologic-procedure (IDSA 2019), and use current CDC-recommended STI regimens.
Confirm your institution’s collaborative practice agreement scope and local protocol before implementing pharmacist-driven deprescribing.

References

Dumkow LE, Kenney RM, MacDonald NC, et al. Impact of a Multidisciplinary Culture Follow-up Program of Antimicrobial Therapy in the Emergency Department. Infect Dis Ther. 2014 Jun;3(1):45-53. PMID: 25134811.
Dumkow LE, Beuschel TS, Brandt KL. Expanding Antimicrobial Stewardship to Urgent Care Centers Through a Pharmacist-Led Culture Follow-up Program. Infect Dis Ther. 2017 Sep;6(3):453-459. PMID: 28853035.
Shealy SC, Alexander C, Hardison TG, et al. Pharmacist-Driven Culture and Sexually Transmitted Infection Testing Follow-Up Program in the Emergency Department. Pharmacy (Basel). 2020 Apr 23;8(2):72. PMID: 32340149.
Wu JY, Balmat R, Kahle ML, et al. Evaluation of a health system-wide pharmacist-driven emergency department laboratory follow-up and antimicrobial management program. Am J Emerg Med. 2020 Dec;38(12):2591-2595. PMID: 31918897.
Geyer AC, Draper HM, Wolf LM, et al. Feasibility evaluation to expand a collaborative practice agreement and discontinue antibiotics after an emergency department or urgent care visit. Am J Health Syst Pharm. 2023 Nov 23;80(Suppl 4):S151-S156. PMID: 36975721.
Kooda K, Canterbury E, Bellolio F. Impact of Pharmacist-Led Antimicrobial Stewardship on Appropriate Antibiotic Prescribing in the Emergency Department: A Systematic Review and Meta-Analysis. Ann Emerg Med. 2022 Apr;79(4):374-387. PMID: 35039180.
Levitt MA, Johnson S, Engelstad L, et al. Clinical management of chlamydia and gonorrhea infection in a county teaching emergency department. J Emerg Med. 2003 Jul;25(1):7-11. PMID: 12865101.
Holley CE, Van Pham T, Mezzadra HM, et al. Overtreatment of gonorrhea and chlamydial infections in 2 inner-city emergency departments. Am J Emerg Med. 2015 Sep;33(9):1265-8. PMID: 26119905.
Solnick RE, Patel R, Chang E, et al. Sex disparities in chlamydia and gonorrhea treatment in U.S. adult emergency departments: A systematic review and meta-analysis. Acad Emerg Med. 2025 Sep;32(9):1003-1016. PMID: 40503872.
Childers R, Liotta B, Brennan J, et al. Urine testing is associated with inappropriate antibiotic use and increased length of stay in emergency department patients. Heliyon. 2022 Oct 12;8(10):e11049. PMID: 36281377.
Monje A, Escolá-Vergé L, Rivera A, et al. Targeting Overtreatment of Asymptomatic Bacteriuria in the Emergency Department: Results from a Quasi-Experimental Clinical Pharmacist-Led Program Based on Education and Audit. Antibiotics (Basel). 2025 Dec 14;14(12):1261. PMID: 41463763.
Nicolle LE, Gupta K, Bradley SF, et al. Clinical Practice Guideline for the Management of Asymptomatic Bacteriuria: 2019 Update by the Infectious Diseases Society of America. Clin Infect Dis. 2019 May 2;68(10):e83-e110. PMID: 30895288.
Workowski KA, Bachmann LH, Chan PA, et al. Sexually Transmitted Infections Treatment Guidelines, 2021. MMWR Recomm Rep. 2021 Jul 23;70(4):1-187. PMID: 34292926.