City-wide metagenomics uncover antibiotic resistance reservoirs in urban beach and sewage waters

Abstract

41Background: Microbial communities present in environmental waters constitute a reservoir for antibiotic-42 resistant pathogens that impact human health. For this reason a diverse variety of water environments are 43 being analyzed using metagenomics to uncover public health threats. However, the composition of these 44 communities along the coastal environment of a whole city where sewage and beach waters are mixed, is 45 poorly understood. 47Results: We shotgun-sequenced 20 coastal areas from the city of Montevideo (capital of Uruguay) including 48 beach and sewage water samples to characterize bacterial communities and their virulence and antibiotic 49 resistance repertories. We found that sewage and beach environments presented significantly different 50 bacterial communities. Sewage waters harbored a higher prevalence and a more diverse repertory of virulence 51 and antibiotic resistant genes mainly from well-known enterobacteria, including carbapenemases and 52 extended-spectrum betalactamases reported in hospital infections in Montevideo. Additionally, we were able 53 to genotype the presence of both globally-disseminated pathogenic clones as well as emerging antibiotic-54 resistant bacteria in sewage waters. 56Conclusions: Our study represents the first in using metagenomics to jointly analyze beaches and the sewage 57 system from an entire city, allowing us to characterize antibiotic-resistant pathogens circulating in urban 58 waters. The data generated in this initial study represent a baseline metagenomic exploration to guide future 59 longitudinal (time-wise) studies, whose systematic implementation will provide useful epidemiological 60 information to improve public health surveillance. 61 62

Structure of Bacterial Community with Resistance to Antibiotics in Aquatic Environments. A Systematic Review

“…The study carried out by Lambirth et al [ 58 ] reports the existence of genes for resistance to carbapenems and broad-spectrum β-lactamases. In accordance with the data provided around the world, the reports in Latin America, such as those made by Collins-Fairclough et al [ 23 ], Delgado-Gardea et al [ 34 ], Coutinho et al [ 45 ] and Fresia et al [ 56 ], present the same trend in the frequency of ARGs, with a predominance of resistance to β-lactams, aminoglycosides and macrolides.…”

“…Of these, there were 128 duplicates, and 16,013 were excluded on the basis of title and abstract screening. A total of 68 studies [ 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , ...…”

“…These bacteria are abundant in WWTPs in cities in Portugal, Spain, Germany, Sweden, South Korea, and Brazil [ 11 , 41 , 42 , 47 , 48 , 49 , 59 ]. However, they were also determined in treated waters and in natural water systems of marine environments, rivers and lagoons, mainly in Latin American countries [ 34 , 45 , 49 , 50 , 56 , 60 ].…”

“…According to the articles reviewed, several authors suggest that the diversity of anti-biotic-resistant bacteria in aquatic habitats can be influenced by anthropogenic contamination. In wastewater and in WWTP, bacteria are exposed to multiple antibiotics, these being released into treated water until it reaches natural water systems, facilitating the spread of antibiotic resistance [ 29 , 56 , 76 ]. The uncontrolled discharge of untreated municipal waste can contribute to an overall increase in the abundance and diversity of ARGs in the environment, including those that confer resistance to last-resort antibiotics [ 18 ].…”