Genomic surveillance of multidrug-resistant bacteria and antimicrobial resistance genes in urban-impacted rivers: the need for a One Health AMR Surveillance approach
1
Mycobacterial and other bacterial diseases, Armauer Hansen ResearchInstitute, Addis Ababa, Ethiopia
2
College of Health Sciences, School of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
3
School of Science and Technology, The Life Science Center - Biology, Örebro University, Örebro, Sweden
Popul. Med. 2026;8(Supplement Supplement 1):
ABSTRACT
BACKGROUND:
The persistence and spread of antibiotic-resistant bacteria in aquatic environments represent a serious One Health threat. This study investigated genomic surveillance of multidrug-resistant bacteria and antimicrobial resistance genes (ARGs) in Ethiopia’s urban-impacted Akaki River.
METHODS:
Water samples from five sites along the Akaki River were analyzed for bacterial pathogens and ARGs. ARG diversity and abundance were assessed using qPCR. Bacterial pathogens were isolated on selective agar, identified by MALDI-TOF mass spectrometry, tested for antibiotic resistance, and further characterized by whole-genome sequencing and PCR.
RESULTS:
Genes associated with resistance to fluoroquinolones, aminoglycosides, β-lactams, macrolides, tetracyclines, and vancomycin, as well as genes for multidrug and tetracycline efflux pumps, were detected. The majority of these ARGs were located near sites of anthropogenic activity, such as hospitals, irrigation systems, and industrial areas. Sites proximate to hospitals exhibited the highest abundance of ARGs in both water and sediment. Escherichia coli strains isolated from the Akaki river were most frequently resistant to erythromycin (97%), doxycycline (78.5%), tetracycline (75.6%), and amoxicillin (75.6%). Resistance to cephalosporins and carbapenems was 7.9% and 5%, respectively, with 80.9% of E. coli isolates being MDR. The β-lactamase genes were the commonly detected resistance genes in E. coli. The most prominent plasmid sequence replicons detected were from the IncF family (65%), Col (10%), and IncX3 (7.5%). Aeromonas spp. from the Akaki River showed high antibiotic resistance, most notably to amoxicillin (100%), ampicillin (99%), amoxicillin/clavulanate (81%), imipenem (52%), ertapenem (92%), and doxycycline (93%). P. aeruginosa were resistant to multiple antibiotic classes, mainly via multidrug efflux system ARGs.
CONCLUSIONS:
These findings indicate that the Akaki River serves as a reservoir and conduit for the dissemination of antibiotic-resistant bacteria and ARGs. The prevalence of resistance in clinically relevant pathogens underscores the critical need for integrated, One Health-based surveillance and containment strategies for AMR.
The persistence and spread of antibiotic-resistant bacteria in aquatic environments represent a serious One Health threat. This study investigated genomic surveillance of multidrug-resistant bacteria and antimicrobial resistance genes (ARGs) in Ethiopia’s urban-impacted Akaki River.
METHODS:
Water samples from five sites along the Akaki River were analyzed for bacterial pathogens and ARGs. ARG diversity and abundance were assessed using qPCR. Bacterial pathogens were isolated on selective agar, identified by MALDI-TOF mass spectrometry, tested for antibiotic resistance, and further characterized by whole-genome sequencing and PCR.
RESULTS:
Genes associated with resistance to fluoroquinolones, aminoglycosides, β-lactams, macrolides, tetracyclines, and vancomycin, as well as genes for multidrug and tetracycline efflux pumps, were detected. The majority of these ARGs were located near sites of anthropogenic activity, such as hospitals, irrigation systems, and industrial areas. Sites proximate to hospitals exhibited the highest abundance of ARGs in both water and sediment. Escherichia coli strains isolated from the Akaki river were most frequently resistant to erythromycin (97%), doxycycline (78.5%), tetracycline (75.6%), and amoxicillin (75.6%). Resistance to cephalosporins and carbapenems was 7.9% and 5%, respectively, with 80.9% of E. coli isolates being MDR. The β-lactamase genes were the commonly detected resistance genes in E. coli. The most prominent plasmid sequence replicons detected were from the IncF family (65%), Col (10%), and IncX3 (7.5%). Aeromonas spp. from the Akaki River showed high antibiotic resistance, most notably to amoxicillin (100%), ampicillin (99%), amoxicillin/clavulanate (81%), imipenem (52%), ertapenem (92%), and doxycycline (93%). P. aeruginosa were resistant to multiple antibiotic classes, mainly via multidrug efflux system ARGs.
CONCLUSIONS:
These findings indicate that the Akaki River serves as a reservoir and conduit for the dissemination of antibiotic-resistant bacteria and ARGs. The prevalence of resistance in clinically relevant pathogens underscores the critical need for integrated, One Health-based surveillance and containment strategies for AMR.
| eISSN: | 2654-1459 |
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