Urban metagenomics uncover antibiotic resistance reservoirs in coastal beach and sewage waters

Abstract

Background Microbial communities present in environmental waters constitute a reservoir for antibiotic-resistant pathogens that impact human health. For this reason, a diverse variety of water environments are being analyzed using metagenomics to uncover public health threats. However, the composition of these communities along the coastal environment of a whole city, where sewage and beach waters are mixed, is poorly understood. Results We shotgun-sequenced 20 coastal areas from the city of Montevideo (capital of Uruguay) including beach and sewage water samples to characterize bacterial communities and their virulence and antibiotic resistance repertories. As expected, we found that sewage and beach environments present significantly different bacterial communities. This baseline allowed us to detect a higher prevalence and a more diverse repertory of virulence and antibiotic-resistant genes in sewage samples. Many of these genes come from well-known enterobacteria and represent carbapenemases and extended-spectrum betalactamases reported in hospital infections in Montevideo. Additionally, we were able to genotype the presence of both globally disseminated pathogenic clones and emerging antibiotic-resistant bacteria in sewage waters. Conclusions Our study represents the first in using metagenomics to jointly analyze beaches and the sewage system from an entire city, allowing us to characterize antibiotic-resistant pathogens circulating in urban waters. The data generated in this initial study represent a baseline metagenomic exploration to guide future longitudinal (time-wise) studies, whose systematic implementation will provide useful epidemiological information to improve public health surveillance. Electronic supplementary material The online version of this article (10.1186/s40168-019-0648-z) contains supplementary material, which is available to authorized users.

Diversity and Prevalence of Antibiotic Resistance Genes, Virulence Factors, and the Microbiome in Aquaculture in Southern China Revealed by Metagenomic Sequencing

“…Fresia et al reported that the abundance and diversity of VFs in sewage samples were higher than those in beach samples, and VFs involving bacterial motility, cell adherence, iron uptake, and secretion were predominant in the sewage samples. They concluded that urban waters served as a reservoir and medium for VFs responsible for clinically relevant bacteria and their transport [29]. Unlike the results of Fresia et al [29], VFs such as Capsule with the antiphagocytosis function, LPS, with the endotoxin function, and Flagella, with the invasion function, were predominant in our study.…”

“…They concluded that urban waters served as a reservoir and medium for VFs responsible for clinically relevant bacteria and their transport [29]. Unlike the results of Fresia et al [29], VFs such as Capsule with the antiphagocytosis function, LPS, with the endotoxin function, and Flagella, with the invasion function, were predominant in our study. HPB carrying VFs with diverse functions were observed in each aquaculture sample, even in the reared shrimp, posing high risks to human health and food safety.…”

“…The presence of ARGs in chromosomes or plasmids was determined using BLAST+ blastx against 1,044,458 complete plasmid sequences from the NCBI RefSeq database (updated in October 2019) following Fresia et al [29]. Hits with query coverage of over 90% amino and acid identi cation of over 70% were retained.…”

Antimicrobial Profiles of Selected Gram-Negative Bacteria Recoverable from Sewage and Sludge from Juja and Kibera Informal Settlements of the Larger Nairobi Metropolis

“…As a result of over-use and misuse of antibiotics in human and animal health, domestic waste is likely to be highly contaminated with fecal materials which in turn have bacteria that are resistant to multiple antimicrobials due to their possible clinical origin [2]. Previous studies have documented sludge and sewage effluents as major sources of antimicrobial resistant bacteria strains in the environmental compartment [3] [4].…”

Analysis of interdomain taxonomic patterns in urban street mats

“…Four OTUs were assigned to Candidatus Odyssela, a bacterial genus with members that live intracellularly in Amoebozoa (Birtles et al, 2000). We are aware that to further characterize the presence of putative pathogens in the street surfaces, the complete bacterial community should be analysed (using 0.2 μm filters), along with the virome (Fresia et al, 2019).…”