Fate of antimicrobial resistance genes (ARG) and ARG carriers in struvite production process from human urine

Abstract

Struvite, a human urine-derived fertilizer types, is characterized by its low water solubility that renders it a slow-releasing eco-friendly fertilizer. Knowing the fate of antibiotic resistance genes in struvite is important since human urine carries microorganisms, viruses and mobilomes. In this study, urine samples were collected and struvite production was done using MgCl₂. From the fresh, stored urine and struvite, DNA was extracted and metagenomic sequencing was done using Illumina HiSeqX. Metagenome-derived genome sequence analysis revealed the dominance of phages of Streptococcus, Bacillus and Escherichia, with nearly 50% abundance of streptococcus phage in fresh urine. Increased antibiotic resistance genes were found in the stored urine than in fresh and struvite samples. The top five resistance genes in all the three samples were to aminoglycosides, carbapenem, chloramphenicol, erythromycin and efflux pump, with key carrying pathogens including Acinetobacter, Aeromonas and Enterococcus. The identified families for carbapenem, aminoglycoside resistance and efflux pump were shown persistent in struvite with a shift in gene families. The detection of resistance-gene-laden mobilomes, including the last-resort antibiotics in the struvite sample, requires due attention before the implementation of struvite as fertilizer. Further optimization of the struvite production process with regard to the minimization of mobilomes is recommended.

Graphical Abstract

Keywords:

• Mobilomes
• antibiotics
• resistance
• genes
• plasmids
• phages
• Addis Ababa
• metagenome-derived genome
• metagenomics
• sequencing

Acknowledgments

We would like to acknowledge Ms Birtukan Getnet, Mr Elias Yassin and Mr Sisay Alemu for the urine collection and DNA extraction. Mr Johanny Girma is acknowledged for the struvite reactor design and process optimization. Mr Mesfin Diro and Mr Gebreab Teklebirhan are acknowledged for their valuable advice during R use and analysis tools. We thank Mr Mesele Admassie, Mr Eshetu Yilma and Mr Fiseha Tadesse for proof reading and Mr Natnael Demissie for assistance in developing the graphical abstract of this article.

Ethical approval

The project was submitted to the College of Natural Science Ethical Review Board (IRB) and was granted ethical approval.

Disclosure statement

None of the authors have a conflict of interest.

Data availability statement

The data that were used in this paper are going to be presented upon request. The metagenomics data will be stored at the NCBI database.

Additional information

Funding

This work was supported by the Thematic research of Addis Ababa University and PEER-USAID grant (grant number 400, subaward number 2000008797).