Protocol · Pharmaceutical · 05

Antibiotic Protocols

There is no single antibiotic regimen for Lyme disease. Which one your doctor reaches for depends almost entirely on which country and which guideline they were trained under.

By country

Guideline Comparison

United States — IDSA (2020)

Short-course, single-agent

Regimen: Doxycycline 100 mg BID × 10–14 days for early Lyme; ceftriaxone 2 g IV daily × 14–28 days for neuroborreliosis.

Does not recognise chronic Lyme; retreatment discouraged.

PubMed reference (PMID 33417672)

United States — ILADS (2014)

Long-course, combination, individualised

Regimen: Doxycycline 200 mg BID + cefuroxime/azithromycin, 4–6 weeks minimum; extended if symptoms persist.

Allows clinical diagnosis; supports retreatment for persistent symptoms.

PubMed reference (PMID 25077519)

Germany — DBG / Deutsche Borreliose-Gesellschaft

Pulsed, combination

Regimen: Doxycycline + hydroxychloroquine; minocycline + tinidazole for cyst-form coverage; rotated 3–6 months.

Cyst-form/persister coverage central. Often combined with herbals.

PubMed reference (PMID 32354067)

United Kingdom — NICE NG95 (2018)

Single-agent, defined courses

Regimen: Doxycycline 100 mg BID × 21 days first line; amoxicillin or azithromycin as alternatives. IV ceftriaxone for CNS disease.

Updated to recognise post-treatment Lyme symptoms but limits retreatment.

PubMed reference (PMID 29632062)

Switzerland

Conservative, mainstream

Regimen: Doxycycline 200 mg/day × 14–21 days; ceftriaxone IV for late neuroborreliosis.

Aligned with EFNS guidelines.

PubMed reference (PMID 20132514)

Poland & Eastern Europe

Aggressive, combination, longer-course

Regimen: Doxycycline + amoxicillin or ceftriaxone, often 6+ weeks; metronidazole pulses for persisters.

Influence from Burrascano and ILADS schools; Lyme-Borreliosis Society guidelines.

PubMed reference (PMID 23097222)
By coinfection

Coinfection Regimens

PathogenStandard courseExtended / chronicPubMed
BabesiaAtovaquone 750 mg BID + azithromycin 500 mg daily × 7–10 days (mild); clindamycin + quinine for severe.Atovaquone + azithromycin × 4–6 weeks; add proguanil or methylene blue in refractory cases.PMID 32651583
BartonellaDoxycycline + rifampin; or azithromycin + rifampin; 4–6 weeks.Triple therapy with methylene blue or clarithromycin; 3–6 months.PMID 32760465
Ehrlichia / AnaplasmaDoxycycline 100 mg BID × 10–14 days. First-line in pregnancy as well (CDC, 2016).Rifampin if doxycycline-intolerant.PMID 27172113
MycoplasmaDoxycycline or azithromycin × 3–6 weeks.Combination with moxifloxacin or minocycline for chronic cases.PMID 29438949
Rickettsia (RMSF, typhus group)Doxycycline 100 mg BID × 7 days minimum (or until afebrile + 3 days).Chloramphenicol as alternative in true doxycycline allergy.PMID 27172113

Do antibiotics actually work?

The honest answer from the literature is: often, but not always, and rarely on the first try in late disease. The four pivotal NIH-funded retreatment trials (Klempner 2001, Krupp 2003, Fallon 2008, Berende 2016) showed only modest, mixed benefits from a further 10–12 weeks of antibiotics. Yet later work — Sapi 2011 (PMID 21993564), Feng 2014 (PMID 25337473), and the daptomycin/doxycycline/cefuroxime combination by Feng & Zhang 2020 (PMID 32175334) — demonstrates that persister Borrelia survive standard monotherapy and require combination, pulsed regimens.