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Background  The English national health system experienced a major reorganisation in April 2013. This mixed methods study examined how staff managed to deliver the national immunisation programme within a new health infrastructure and explored the role and contribution of ‘partnership working’ to programme implementation.    Methods  A cross-sectional online questionnaire survey and a qualitative evaluation of an urban immunisation board were conducted in 2016. The questionnaire included 38 questions about immunisation responsibilities, collaboration, service evaluation and programme support. It was completed by 199 immunisation providers and 70 people involved in the management of the immunisation programme. The evaluation involved 12 semi-structured interviews, 3 observations of forum meetings and the review of forum meeting minutes. Descriptive statistical analysis of the survey data was performed using SPSS version 23 and qualitative data from both study components were uploaded to NVivo 11 and analysed thematically.    Results  Screening and Immunisation Teams were cited as responsible for programme leadership by 56% of survey respondents, but concerns were raised about their capacity to oversee larger geographies and a case made for decentralised accountability mechanisms. Only 44% of immunisation managers stated that poor performance was addressed adequately, and half of respondents thought that support given to providers was inadequate. Managers reported that partnership working improved the organisation (83%) and performance (78%) of immunisation, but stated it was more beneficial for information-sharing than implementation. A preference for a  “locality working approach”  with committees covering smaller health economies rather than larger commissioning areas was voiced. The immunisation board examined in the qualitative evaluation sought to achieve this by forging links with locally based steering committees, but also had to address internal challenges related to the role of the board and contribution of members to programmatic decision-making.    Conclusions  Key challenges in delivering the immunisation programme were rooted in the new health infrastructure, which had created greater distance between commissioners and providers and resulted in the fragmentation of programme responsibilities. Partnership working bridged gaps but more needs to be done to strengthen accountability mechanisms and ensure that collaborative activities are outcome oriented and sustainable in the shifting environment of reorganisation.    Electronic supplementary material  The online version of this article (10.1186/s12889-019-6400-6) contains supplementary material, which is available to authorized users.

Is partnership the answer? Delivering the national immunisation programme in the new English health system: a mixed methods study