General description and methods:

These data were used to produce the results of the meta-analysis of the following article: "Prevalence and risk factors for colonisation during the first three months of life with three critical antibiotic-resistant pathogens in low- and middle-income countries: a systematic review, meta-analysis, and meta-regression study". All articles published between 1 January 2000 and 29 July 2024 were searched in: PubMed, Scopus, Web of Science, and WHO Global Index Medicus. The search strategy was divided in two parts: one to identify studies reporting risk factors or prevalence of 3GC-R-E and/or CRE colonisation; and another for MRSA colonisation. This was supplemented by hand searching the reference lists of all eligible studies. Cohort and cross-sectional studies were eligible if they (1) reported the prevalence or risk factors for 3GC-R-E, CRE, or MRSA colonisation, (2) included a population from birth to three months of age and (3) were conducted in an LMIC (according to the World Bank Classification of study period). Exclusion criteria were outbreak reports, studies focusing on a specific resistance enzyme subpopulation, sample size less than 10. Of note, (quasi-) experimental studies were not an exclusion criterion if they included a baseline cross-sectional survey. Studies focusing on specific Enterobacterales (e.g. E. coli) and case-control studies were included in the descriptive review but excluded from the prevalence meta-analysis. Two investigators (Bich-Tram Huynh, Anne-Lise Beaumont) independently screened titles and abstracts to identify relevant studies. Then, they assessed full-text articles for eligibility, extracted data and evaluated methodological quality using a modified version of Joanna Briggs Institute Critical Appraisal Checklist for Prevalence Studies tailored to the research question. If data could not be extracted directly from the article, the authors were contacted up to four times. Any discrepancies were resolved by discussion with other authors of the papers. Parameters such as study design, year, setting, sampling site, inclusion and exclusion criteria, prevalence, laboratory methods and guidelines used to detect resistance, bacterial species, resistance genes, and results of risk factors analysis were extracted. Sub-studies within the same publication were treated as separate studies when reporting results. For cohort studies, data were extracted from the initial collection to ensure comparability with cross-sectional studies.

File naming convention:

The databases have been divided between the 3 antibiotic-resistant pathogens studied: third generation-cephalosporin-resistant Enterobacterales (3GC-R-E), carbapenem-resistant Enterobacterales (CRE), and methicillin-resistant Staphylococcus aureus (MRSA). For every pathogen of interest, there are two files : - The database itself : date of file creation_META_codenumber_database_name of pathogen_publication. - The associated data dictionary : data dictionary _ database _ name of pathogen Additional, a fourth database "20241009_META_S02_database_RF_publication" contains the data of studies included in the meta-analysis of risk factors associated with third generation-cephalosporin-resistant Enterobacterales (3GC-R-E) colonisation prevalence. Of note, there was not enough data to perform meta-analysis of risk factors associated with carbapenem-resistant Enterobacterales (CRE) and methicillin-resistant Staphylococcus aureus (MRSA).