A cross-sectional study was conducted from July to November 2021. Of all general hospitals in Indonesia, 20% (N = 475) were selected using stratified random sampling on the basis of class and region. Hospitals in Indonesia are classified into four classes (A, B, C and D) based on the number of beds and services (Additional file 2) [7]. There were 2,373 general hospitals in Indonesia (per February 2021): class A, 24 hospitals (1.0%), class B, 376 hospitals (15.8%), class C, 1146 hospitals (48.3%) and class D, 827 hospitals (34.9%) [8]. Since Indonesia is a large country, regions were taken into consideration to ensure all regions were well represented. The regions, as defined by the National Development Agency, were used [9]: region 1 (Sumatra, Java, and Bali), region 2 (Kalimantan, Sulawesi, and West Nusa Tenggara), and region 3 (East Nusa Tenggara, Papua, West Papua, and Maluku). Of the participating hospitals, 10% were selected for two additional semi-structured interviews; one with the management and one with the IPC team or committee. For the selection, stratified random sampling by class and region of the hospitals was applied as well. The interviews were conducted after the IPCAF assessment was completed. The study was approved by the Health Research Ethical Board of National Health Research and Development (No: LB.02.01/2/KE.494/2021).

The WHO IPCAF questionnaire was translated into Indonesian by the first author and an independent researcher (both Indonesian native speakers) and adapted to the situation in hospitals in Indonesia (Additional file 3). The most important adaptation was the ratio of IPC nurse (IPCN) per number of beds. In the WHO IPCAF, this is set at a minimum of 1 IPCN per 250 beds, while the Indonesian government has mandated a minimum of 1 IPCN per 100 beds. Several discussions were held to review the questions with local IPC experts from the National Committee of IPC, the Ministry of Health, and the WHO.

Several questions were added regarding the characteristics of the hospitals, challenges, and recommendations for the improvement of IPC implementation on a hospital and national level, but these were kept separate from the IPCAF questions in such a way that the scoring as per the original IPCAF tool could be performed (Additional file 4). For the implementation challenge questions, 11 challenges were given in the questionnaire, and each hospital was asked to rank these challenges in order from high to low priority based on the situation in their hospital. A low number corresponded with a high priority. Subsequently, the median rank of each challenge was determined from all hospitals.

The questionnaire used for the semi-structured interviews with managers and IPC committees was translated into Indonesian from the questionnaires previously used in a study from Georgia that described the challenges and opportunities in implementing IPC [10]. Additional open questions about recommendations for implementing IPC in hospitals were asked to the management of the hospital. Translated questionnaires were entered into an online collection tool (Lime Survey). To obtain complete questionnaires, answering all questions was mandatory. Translated questionnaires for the semi-structured interviews can be found in Additional file 5 (interview for management of hospitals) and Additional file 6 (interview for IPC team/committee).

A pilot study was conducted to test the online questionnaires and interviews in four hospitals (one of each class) in Java, which were not included in the study sample selection. An online introduction meeting was organized to provide the four hospitals with information needed to properly conduct the pilot study. The steps for filling out the questionnaires were explained and shown in an instructional video that was uploaded on YouTube (https://youtu.be/pyykZCY_H0A). Telephone numbers and emails were provided to the hospitals to contact organizing staff when they encountered any difficulty in filling out the questionnaires. A link to the questionnaire was sent to all hospitals and interviews were conducted with the management and IPC committee of the hospitals. Focus group discussions were held with all four hospitals for the improvement of data collection and questionnaire procedures.

Data collection was performed by a team consisting of IPC experts who received training about the IPCAF CCs, study protocols, and interview technique. Data were collected from August until November 2021. The steps for collecting data were the same as those carried out in the pilot study. Introduction meetings for the selected hospitals were conducted and informed consent to use the data was also included in the questionnaires and obtained from all participants. Participation was voluntary, the facility data were kept confidential, access was restricted to the research team, and results would not affect the participating hospitals’ accreditation status.

The questionnaires were filled in by members of management, the IPC committee, and other units that were involved in the implementation of IPC. Reminders by WhatsApp, telephone, text messages, and email were sent once a week. Submitted complete questionnaires were checked and, in case of any unclarity, the team contacted the respective hospital. Interviews with management of the hospitals and IPC committees were organized after all questionnaires had been submitted. These interviews were all conducted separately and online. The questions in the interview with the IPC committee focused on the three CCs that had the lowest score in the IPCAF scores of all hospitals taken together. The interviewer also asked for proof of documents (pictures, video documentation, certificates) when applicable during the interviews. The flow of the study is presented in Additional file 7.

Based on the total score of the eight CCs, a healthcare facility can be assigned to one of four levels of implementation: inadequate (score of 0–200), basic (score of 201–400), intermediate (score of 401–600) and advanced (score of 601–800) (Additional file 8).

Data from IPCAF questionnaires were analyzed using SPSS version 28.0 (IBM, Armonk, NY, USA). Hospital characteristics are presented as absolute numbers and proportions. Quantitative IPCAF scores are presented as medians with a range of minimum and maximum. ANOVA, Kruskal–Wallis, Welch, and Mann–Whitney U tests were used where appropriate to test for differences between questionnaire scores and hospital characteristics such as hospital class, region/island, ownership (private/government), accreditation status, and/or presence of a microbiological laboratory. Post-hoc analyses were performed using the Tukey, Mann–Whitney U, and Games-Howell test where appropriate. A P value of < 0.05 was considered statistically significant.