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Introduction: Exercise therapy is the most recommended treatment for chronic low back pain (LBP), with evidence supporting modest effects, likely due to the heterogeneity of patient presentations. Evidence suggests that matching individuals to the most appropriate exercise type could improve outcomes. Systematic reviews also emphasise that effective exercise interventions should be patient centred, target paraspinal muscle health and be of sufficient duration. This study addresses these gaps using a targeted care approach to identify a homogenous sample that is more likely to respond to our interventions. The inclusion of a sample with predominant nociceptive pain profile will be performed with the integration of the Pain and Disability Drivers Management Model (PDDM) and the Lumbar Spine Instability Questionnaire (LSIQ). The primary aim of this two-arm randomised controlled trial is to compare the effectiveness of motor control plus isolated lumbar extension exercises (MC+ILEX, arm 1) to free-weight resistance training (arm 2) in reducing LBP-related disability. Secondary aims include examining whether changes in multifidus composition mediate disability improvements comparing intervention effects on muscle size and quality, strength, mobility, pain, quality of life, sleep, physical activity and satisfaction; exploring baseline LSIQ scores and sex/gender as moderators of treatment response; and investigating participants' perceptions and experiences of exercise therapy.

Methods and analysis: A total of 106 participants will be recruited through primary and secondary care and randomised (1:1) to receive either MC+ILEX or free-weight resistance training. Both groups will complete 48 exercise sessions over 16 weeks. The primary outcome will be disability at 16 weeks, measured by the Oswestry Disability Index. Secondary outcomes include multifidus muscle composition and size, lumbar and gluteal muscle strength, hip range of motion, pain, physical and mental function, satisfaction and recovery, health-related quality of life, sleep quality and physical activity levels. Linear mixed-effects models will be used to assess primary and secondary outcomes. Regression analyses will explore whether baseline LSIQ scores moderate treatment effects on multifidus composition and other outcomes. A subsample of participants will undergo semistructured interviews before and after the intervention to explore their illness perceptions, illness mindsets, perceptions of exercise therapy, as well as their experiences and satisfaction with the two exercise interventions. Reflexive thematic analysis will be used to analyse qualitative data.

Ethics and dissemination: This study received ethics approval from the Central Ethics Research Committee of the Quebec Minister of Health and Social Services (CCER-25-26-14). Results will be submitted to peer-reviewed journals and scientific meetings.

Trial registration number: ISRCTN14864451.