Metagenomic analysis deciphers airborne pathogens with enhanced antimicrobial resistance and virulence factors in composting facilities

• Published in: Environment international Vol. 201; p. 109569
• Main Authors: Chen, Mo, Xing, Lijun, Gao, Shanshan, Guo, Yajie, Qiu, Tianlei, Wang, Xuming, Gao, Min
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier Ltd 01.07.2025; Elsevier
• Subjects: Air Microbiology; Airborne antimicrobial resistance; Bacteria - genetics; Composting; Composting facility; Drug Resistance, Bacterial - genetics; Drug Resistance, Microbial - genetics; Enrichment; Human-pathogenic antibiotic-resistant bacteria; Humans; Metagenome-assembled genomes; Metagenomics; Microbiota; Virulence Factors - genetics; Enrichment; Metagenome-assembled genomes; Airborne antimicrobial resistance; Composting facility; Human-pathogenic antibiotic-resistant bacteria
• ISSN: 0160-4120; 1873-6750; 1873-6750
• DOI: 10.1016/j.envint.2025.109569

[Display omitted] •The first airborne HPARB in a composting facility were profiled.•Enhanced airborne HPARB carried increasing ARGs and VFGs than those in compost.•Multiple antibiotic-resistant Mycobacterium tuberculosis was prevalent in the air.•A total of 23 core ARGs were enriched in the air, with increases ranging from 2.16- to 13.36-fold.•Airborne AMR in the composting facility posed a higher risk than that in hospital and urban environment. The composting process has been shown to effectively reduce antimicrobial resistance (AMR) in animal manure, but its influence on surrounding airborne AMR remains unknown, particularly with regard to human-pathogenic antibiotic-resistant bacteria (HPARB). In this study, air and paired compost samples were collected from a full-scale composting facility, and the antibiotic resistome, microbiome, and HPARB were systematically analyzed in both two habitats using metagenomic analysis. Current result uncovered the profiles of HPARB in air, showing that significantly more airborne HPARB were assembled than that in compost samples. Airborne pathogens harboredan increased abundance and diversity of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in comparison with compost-borne HPARB. The core antibiotic resistome represents 18.58% of overall ARG subtypes, contributing to 86.31% of ARG abundance. A higher number of enriched core ARGs (2.16- to 13.36-times higher), including mexF, tetW, and vanS, were observed in air samples compared to compost samples. As an important human pathogen, Mycobacterium tuberculosis was prevalent in the air and carried more ARG (6) and VFG (130) subtypes than those in compost. A significantly higher risk score was detected for airborne AMR in the composting facility compared to that in hospital and urban environments. This study revealed the enhanced airborne HPARB through comparative experiments between air and composting habitats. It highlighted the unrecognized AMR risks associated with air in composting site and provided a scientific basis for accurately assessing health outcomes caused by occupational exposure.