Fresh water is fundamental for survival of life, yet it is one of the most limited and abused resources on Earth. This is particularly true in sub-Saharan Africa, where severe and persistent droughts limit water abundance and urbanization and subsequent land degradation threaten water quality. The Chobe River is one of the few permanent water sources in northern Botswana, with seven human settlements and a large wildlife population reliant on it for survival. Previous research in our study site has shown that wildlife populations can significantly impact the quality of the river, with high fecal loading and Escherichia coli levels contributing to its decline. To increase our understanding about the coupled dynamics of this shared and highly connected system, and to advance our understanding of microbial dynamics and water quality, we evaluate antibiotic resistance among E. coli isolates collected bimonthly from surface water (n=2082) and sediment (n=~1040) sampled across land use (Town/Urban, Mixed/Semi-urban and Park/Protected) and season from the Chobe River in northern Botswana (n= 414 (water) and n=~173 (sediment); July 2011- May 2012).
Over a quarter of E. coli isolated from water samples were multi-drug resistant (MDR; 25.5% (95% CI 23.6-27.4%)), and 80.9% (95% CI 79.2-82.6%) were resistant to at least one antibiotic. Urban land use exhibited the highest levels of MDR E. coli in the Chobe River (40.6% of isolates), followed by semi-urban (30.3%) and protected (16.2%) areas. Preliminary data from sediment samples suggest that MDR E. coli is only seen in urban land use (16.6%), with no evidence in semi-urban or protected areas. Sediment is known to be one of the major reservoirs of antibiotic resistant bacteria, with hydrology and meteorological factors driving distribution into surface water. However, in our study, sediment does not appear to play the same role. Rather, focal drivers underlie observed patterns of MDR E. coli. In light of this, we evaluate factors that may drive temporal and spatial patterns of antibiotic resistance in this system, including wildlife population dynamics, stormwater runoff, as well as human health behaviors and pit latrine use. The escalating accumulation of antibiotic resistance in the environment is considered a key component of the growing global health threat. Understanding microbial dynamics in complex landscapes will be essential in developing appropriate intervention strategies.