Table 1.

Systematic review protocol

What are the characteristics of models for routine surveillance of pathogens with antimicrobial resistance, that utilise Whole Genome Sequencing integrated with epidemiological information?
Population	Inclusion • Human samples containing pathogens with antimicrobial resistance. • Only include studies that consider at least one of the following species:  • Carbapenem-resistant or carbapenemase-producing Enterobacterales (CRE/CPE)  • Carbapenem-resistant or carbapenemase-producing Acinetobacter spp. (CRA/CPA)  • Methicillin-resistant Staphylococcus aureus (MRSA)  • Vancomycin-resistant Enterococci (VRE) Exclusion • Other pathogens / resistances • Studies that ONLY handle food, animal or other environmental samples.
Inclusion criteria relating to content of publications	Any reported models of whole genome sequencing, integrated with epidemiological information, that are used for surveillance of antimicrobial resistance, will be included. The publication must have sufficient detail about methods, to determine that the system described meets the definition of a surveillance system (which will exclude sole outbreak reports). The WHO definition of public health surveillance will be used: ’the continuous, systematic collection, analysis and interpretation of health-related data […] guiding priority-setting and planning and evaluation public health policy and strategies’ [13]. The surveillance system must operate at a regional, national or supra-regional level. There must be detailed description of the population, including epidemiological information (has to include information on patient characteristics, such as age, sex, diagnosis, geographic location, patient location (ward/clinic), specimen type, or clinical outcome). Data covering at least one of the following four pieces of information must be available for inclusion: • Information on any countries that have started to build such systems, or have them already established • Scope of the models: for sporadic outbreak detection, for temporal and/or spatial trends, or routine monitoring of genetic properties • Transmission pathways described. • Visualisation methods applied [trees, timelines, heatmaps, networks and others].
Study types	Inclusion • Full-text primary articles of any form (including grey literature) that include a description of WGS models for surveillance of antimicrobial resistance that are in actual use. Exclusion • Papers solely discussing hypothetical systems that are not currently in use. • Secondary (i.e. review/guideline) articles and abstracts.
Dates	2012 to August 2023 (details see below)
Languages	English, Chinese (Mandarin), French, Spanish and German. Other languages will be excluded.
Stratification	Unconditional Stratification will be applied unconditionallyA for the type of pathogen (the four categories are given in the population section). Conditional Conditional stratificationB will occur for the type of additional environmental, or animal samples used (no additional samples versus additional environmental samples versus additional food samples versus additional animal samples versus other categories that reflect combinations of the additional types of sample [for example, additional food and environmental samples]). If no meta-analysis is used, then these conditional categories for additional samples will become unconditional, and the strata of the review will be formed by permutations of pathogen and additional sample categories.
Synthesis of findings	Meta-analysis will be used if appropriate, but it is envisaged that the most likely form of synthesis will be narrative (tabular).

Abbreviations: WHO = World Health Organization

A. unconditional stratification: stratified ‘up front’, prior to any initial overall meta-analysis, and therefore not conditional on any initial overall meta-analysis I² result.

B. conditional stratification: stratified after initial overall meta-analysis shows an I² value of ≥ 50%