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Background <p>Hospital and industrial wastes act as sources of pollutants due to high antibiotic and chemical loads. However, studies exploring the presence of antimicrobial resistance (AMR) and antibiotic resistance genes (ARGs) in these wastes remain limited in Ethiopia.</p> Objective <p>This study employed shotgun metagenomic sequencing to investigate and identify antimicrobial resistance genes in assembled metagenomic DNA samples extracted from soil and wastewater originating from hospitals and the pharmaceutical industry.</p> Methods <p>Genomic DNA was extracted from wastewater and soil samples and sequenced using the high-throughput Illumina HiSeq 150 platform. The Resistance Gene Identifier (RGI), a tool within the Comprehensive Antibiotic Resistance Database (CARD), was used to predict antimicrobial resistance genes. Additionally, pathogen-of-origin identification via RGI K-mer analysis and pathway analysis performed via the Kyoto Encyclopedia of Genes and Genomes (KEGG).</p> Results <p>Analysis of metagenome sequences revealed diverse ARGs in both hospitals and pharmaceutical waste samples. The Alert Hospital (AH), Tirunash Beijing Hospital (TB), Cadila Pharmaceuticals PLC (CP), and East Africa Pharmaceuticals PLC (EP)samples contained 62, 107, 218, and 165 unique (Antibiotic resistance Ontologies)AROs, after removal of duplicates. The most prevalent ARGs identified were <i>VacY</i>,<i> qacG</i>, and <i>qacG</i>. The most common resistance mechanisms identified were antibiotic target alteration, antibiotic inactivation, and antibiotic resistance efflux. The predominant pathogens of origin included <i>Pseudomonas stutzeri</i>,<i> Acinetobacter baumannii</i>,<i> Pseudomonas putida</i>, and <i>Pseudomonas aeruginosa</i>. The KEGG pathway analysis revealed pathways related to beta-lactam resistance (<i>Bla</i> system), vancomycin resistance (<i>D-Ala-D-Lac</i> type), imipenem resistance (<i>OprD</i> repression), and more multidrug resistance efflux pumps. This study revealed that hospital and pharmaceutical industry wastes in the studied sites harbor diverse antibiotic resistance genes, indicating their potential as reservoirs that threaten human health and environmental safety.</p>

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Uncovering resistomes in hospital and pharmaceutical industry wastes: insights from shotgun metagenomic profiling

  • 期刊论文

  • 发表日期：

    2026年1月3日

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  • Niguse Kelile Lema,
  • Mesfin Tafesse Gemeda,
  • Adugna Abdi Woldesemayat

摘要

Background

Hospital and industrial wastes act as sources of pollutants due to high antibiotic and chemical loads. However, studies exploring the presence of antimicrobial resistance (AMR) and antibiotic resistance genes (ARGs) in these wastes remain limited in Ethiopia.

Objective

This study employed shotgun metagenomic sequencing to investigate and identify antimicrobial resistance genes in assembled metagenomic DNA samples extracted from soil and wastewater originating from hospitals and the pharmaceutical industry.

Methods

Genomic DNA was extracted from wastewater and soil samples and sequenced using the high-throughput Illumina HiSeq 150 platform. The Resistance Gene Identifier (RGI), a tool within the Comprehensive Antibiotic Resistance Database (CARD), was used to predict antimicrobial resistance genes. Additionally, pathogen-of-origin identification via RGI K-mer analysis and pathway analysis performed via the Kyoto Encyclopedia of Genes and Genomes (KEGG).

Results

Analysis of metagenome sequences revealed diverse ARGs in both hospitals and pharmaceutical waste samples. The Alert Hospital (AH), Tirunash Beijing Hospital (TB), Cadila Pharmaceuticals PLC (CP), and East Africa Pharmaceuticals PLC (EP)samples contained 62, 107, 218, and 165 unique (Antibiotic resistance Ontologies)AROs, after removal of duplicates. The most prevalent ARGs identified were VacY, qacG, and qacG. The most common resistance mechanisms identified were antibiotic target alteration, antibiotic inactivation, and antibiotic resistance efflux. The predominant pathogens of origin included Pseudomonas stutzeri, Acinetobacter baumannii, Pseudomonas putida, and Pseudomonas aeruginosa. The KEGG pathway analysis revealed pathways related to beta-lactam resistance (Bla system), vancomycin resistance (D-Ala-D-Lac type), imipenem resistance (OprD repression), and more multidrug resistance efflux pumps. This study revealed that hospital and pharmaceutical industry wastes in the studied sites harbor diverse antibiotic resistance genes, indicating their potential as reservoirs that threaten human health and environmental safety.