METAGENOMIC SEQUENCING IN INTEGRATED ANTIMICROBIAL RESISTANCE SURVEILLANCE

Abstract

Objectives. Antimicrobial resistance surveillance requires comparing resistance profiles across the human population, the animal sector, and the environment, under reproducible sampling and analysis conditions.

Methods. A narrative review with standardized extraction of quantitative data was conducted to identify metagenomic surveillance models. We searched PubMed/MEDLINE, PubMed Central, and Europe PMC for studies published between 1^st January 2019 and 14^th July 2026. Of 48 records, six duplicates were removed, nine publications were excluded based on title and/or abstract, and 15 were excluded after full-text review. Eighteen studies reporting quantitative data and including a resistome-surveillance component were included.

Results. Four studies (22.2%) focused on human populations, six (33.3%) on animals or One Health interfaces, and eight (44.4%) on the environment. Twelve studies (66.7%) had a cross-sectional and/or ecological design, four (22.2%) were longitudinal or paired-sample studies, and two (11.1%) were global bioinformatic reanalyses. Sample sizes ranged from 59 to 490 participants and from 90 to 592 animal or One Health samples, reaching 757 wastewater samples from 101 countries. Only two studies used long reads or hybrid assembly; in the hybrid approach, Oxford Nanopore Technologies long reads were combined with short Illumina reads to resolve gene–mobile genetic element–host associations.

Conclusions. Priority should be given to expanding shotgun sequencing to eligible human biospecimens, conducting longitudinal and multi-site sampling of wastewater, operationalizing the animal component, and validating results through culture, antibiotic susceptibility testing, and sequencing of isolates. Versioned bioinformatics pipelines and standardized metadata are prerequisites for comparability.