Metagenomic Frameworks for Monitoring Antibiotic Resistance in Aquatic Environments

Port, Jesse A.; Cullen, Alison C.; Wallace, James C.; Smith, Maria W.; Faustman, Elaine M.

doi:10.1289/ehp.1307009

Cited by 87 publications

(56 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Sediments provide natural areas of high microbial density, which is of particular concern considered the elevated persistence and accumulation of antimicrobial resistance (AMR). Port et al (2014) estimated the potential for gene transfer and pathogenicity potential from sediment fecal bacteria from pyrosequencing datasets of sediments. This is pertinent for developing suitable baseline AMR/pathogenicity levels used to inform policy makers on fecally derived hazardous microorganisms/pathogens in sediments.…”

Section: Discussionmentioning

confidence: 99%

Abundance and Distribution of Enteric Bacteria and Viruses in Coastal and Estuarine Sediments—a Review

et al. 2016

View full text Add to dashboard Cite

The long term survival of fecal indicator organisms (FIOs) and human pathogenic microorganisms in sediments is important from a water quality, human health and ecological perspective. Typically, both bacteria and viruses strongly associate with particulate matter present in freshwater, estuarine and marine environments. This association tends to be stronger in finer textured sediments and is strongly influenced by the type and quantity of clay minerals and organic matter present. Binding to particle surfaces promotes the persistence of bacteria in the environment by offering physical and chemical protection from biotic and abiotic stresses. How bacterial and viral viability and pathogenicity is influenced by surface attachment requires further study. Typically, long-term association with surfaces including sediments induces bacteria to enter a viable-but-non-culturable (VBNC) state. Inherent methodological challenges of quantifying VBNC bacteria may lead to the frequent under-reporting of their abundance in sediments. The implications of this in a quantitative risk assessment context remain unclear. Similarly, sediments can harbor significant amounts of enteric viruses, however, the factors regulating their persistence remains poorly understood. Quantification of viruses in sediment remains problematic due to our poor ability to recover intact viral particles from sediment surfaces (typically <10%), our inability to distinguish between infective and damaged (non-infective) viral particles, aggregation of viral particles, and inhibition during qPCR. This suggests that the true viral titre in sediments may be being vastly underestimated. In turn, this is limiting our ability to understand the fate and transport of viruses in sediments. Model systems (e.g., human cell culture) are also lacking for some key viruses, preventing our ability to evaluate the infectivity of viruses recovered from sediments (e.g., norovirus). The release of particle-bound bacteria and viruses into the water column during sediment resuspension also represents a risk to water quality. In conclusion, our poor process level understanding of viral/bacterial-sediment interactions combined with methodological challenges is limiting the accurate source apportionment and quantitative microbial risk assessment for pathogenic organisms associated with sediments in aquatic environments.

show abstract

Section: Discussionmentioning

confidence: 99%

Abundance and Distribution of Enteric Bacteria and Viruses in Coastal and Estuarine Sediments—a Review

et al. 2016

View full text Add to dashboard Cite

show abstract

“…The in-vestment on antibiotic resistance monitoring would not be a stray effort, since it could be framed in a broader context of ongoing problems associated with water quality, related not only with pollution but also with climate variability, among other, and that require the action of regulatory authorities at local, national, and global scales (GEMS-Water 2014). In re-search laboratories, high-throughput qPCR and metagenomics analyses of ARG are increasingly the state of the art (Nesme et al 2014;Port et al 2014;Li et al 2015). and these will be important contributions to understand antibiotic resistance evolution.…”

Section: Methods Harmonization and Data Sharingmentioning

confidence: 99%

Antibiotic resistance in urban aquatic environments: can it be controlled?

Manaia

Macedo

Fatta‐Kassinos

et al. 2015

Appl Microbiol Biotechnol

185

View full text Add to dashboard Cite

Over the last decade, numerous evidences have contributed to establish a link between the natural and human-impacted environments and the growing public health threat that is the antimicrobial resistance. In the environment, in particular in areas subjected to strong anthropogenic pressures, water plays a major role on the transformation and transport of contaminants including antibiotic residues, antibiotic-resistant bacteria, and antibiotic resistance genes. Therefore, the urban water cycle, comprising water abstraction, disinfection, and distribution for human consumption, and the collection, treatment, and delivery of wastewater to the environment, is a particularly interesting loop to track the fate of antibiotic resistance in the environment and to assess the risks of its trans-mission back to humans. In this article, the relevance of different transepts of the urban water cycle on the potential enrichment and spread of antibiotic resistance is reviewed. According to this analysis, some gaps of knowledge, research needs, and control measures are suggested. The critical rationale behind the measures suggested and the desirable involvement of some key action players is also discussed.

show abstract

“…In case of coastal sea, although the contaminated waters are significantly diluted, fecal-derived bacteria, such as E. coli , remain viable ARG reservoirs of concern (Alves et al; Kappell et al; Ghaderpour et al). ARB and ARGs are known to occur in aquatic environments without antibiotic contaminations (Port et al, 2014). ARBs and ARGs flow into rivers, groundwater and marine environments by influx of WWTP effluent as mentioned above.…”

mentioning

confidence: 99%

“…Suzuki et al (2013) and Suzuki et al found that the defining features of ARGs tend to be distinct between culturable and yet-to-be cultured bacteria. The recent advent of next-generation DNA sequencing and metagenomics poises the scientific community on the verge of a major advance in understanding the behavior of ARGs in the environment (D'Costa et al, 2006; Port et al, 2014). However, deep sequencing and the capacity to perform high-throughput bioinformatics analyses are required to match ARGs with their bacterial hosts.…”

mentioning

confidence: 99%