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Wastewater-Based Surveillance of Antimicrobial Resistance in Niger: An Exploratory Study
Sani Ousmane1, Issifi A Kollo1, Ronan Jambou1
1Centre de Recherche Médicale et Sanitaire, Niamey, Niger.
Abstract:
Wastewater-based surveillance is increasingly recognized as an important approach to monitoring population-level antimicrobial resistance (AMR). In this exploratory study, we examined the use of metagenomics to evaluate AMR using untreated wastewater samples routinely collected by the Niger national polio surveillance program. Forty-eight stored samples from two seasons each year over 4 years (2016-2019) in three regions were selected for inclusion in this study and processed using unbiased DNA deep sequencing. Normalized number of reads of genetic determinants for different antibiotic classes were compared over time, by season, and by location. Correlations in resistance were examined among classes. Changes in reads per million per year were demonstrated for several classes, including decreases over time in resistance determinants for phenicols (-3.3, 95% CI: -8.7 to -0.1, P = 0.029) and increases over time for aminocoumarins (3.8, 95% CI: 0.0 to 11.4, P = 0.043), fluoroquinolones (6.8, 95% CI: 0.0 to 20.5, P = 0.048), and beta-lactams (0.85, 95% CI: 0.1 to 1.7, P = 0.006). Sulfonamide resistance was higher in the post-rainy season compared with the dry season (5.2-fold change, 95% CI: 3.4 to 7.9, P < 0.001). No differences were detected when comparing other classes by season or by site for any antibiotic class. Positive correlations were identified in genetic determinants of resistance among several antibiotic classes. These results demonstrate the potential utility of leveraging existing wastewater sample collection in this setting for AMR surveillance.
Insights
Wastewater surveillance using metagenomics in Niger revealed changing antimicrobial resistance (AMR) patterns over time and seasons. This approach effectively monitors AMR trends using existing polio surveillance infrastructure.
Area of Science:
- Environmental microbiology
- Public health surveillance
- Genomics
Background:
- Antimicrobial resistance (AMR) is a growing global health threat.
- Wastewater-based surveillance offers a population-level monitoring strategy for AMR.
- Existing infrastructure, like polio surveillance, can potentially be leveraged for broader health monitoring.
Purpose of the Study:
- To explore the utility of metagenomics for evaluating AMR in wastewater.
- To analyze AMR trends over time, by season, and by region in Niger.
- To assess correlations between different antibiotic resistance genes.
Main Methods:
- Utilized metagenomic deep sequencing on 48 stored wastewater samples from Niger (2016-2019).
- Analyzed untreated wastewater samples collected through the national polio surveillance program.
- Compared normalized read counts of resistance genes across different antibiotic classes, seasons, and locations.
Main Results:
- Observed temporal changes in resistance determinants: phenicols decreased, while aminocoumarins, fluoroquinolones, and beta-lactams increased.
- Sulfonamide resistance was significantly higher in the post-rainy season compared to the dry season.
- Identified positive correlations among genetic determinants for several antibiotic classes, suggesting co-selection.
Conclusions:
- Metagenomics applied to wastewater is a viable tool for monitoring AMR in settings with established surveillance programs.
- Leveraging existing polio surveillance infrastructure in Niger can provide valuable insights into population-level AMR.
- Findings highlight the dynamic nature of AMR in wastewater and the need for ongoing surveillance.
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