Precipitation influences pathogenic bacteria and antibiotic resistance gene abundance in storm drain outfalls in coastal sub-tropical waters

Ahmed, Warish; Zhang, Qian; Lobos, Aldo; Senkbeil, Jacob K.; Sadowsky, Michael J.; Harwood, Valerie J.; Saeidi, Nazanin; Marinoni, Oswald; Ishii, Satoshi

doi:10.1016/j.envint.2018.04.005

Cited by 106 publications

(66 citation statements)

References 61 publications

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“…Different approaches have been used to handle this problem. Approaches have included replacing the nondetects with 0 (Muziasari et al, 2016), with 1/2 LOQ (Sandberg et al, 2017), or by imputing values (Zhang et al, 2016a; Ahmed et al, 2018). In the present study, an “in‐house” criteria‐based approach was used to replace the nondetects, based on results from an in‐house simulation study (unpublished data).…”

Section: Discussionmentioning

confidence: 99%

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Antibiotic Resistance Genes in Freshwater Trout Farms in a Watershed in Chile

et al. 2019

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Point sources such as wastewater treatment plants, terrestrial agriculture, and aquaculture may release antibiotic residues, antibiotic resistant bacteria, and antibiotic resistance genes (ARGs) into aquatic ecosystems. However, there is a lack of quantitative studies attributing environmental ARG abundance to specific sources. The goal of this study was to evaluate the role of freshwater trout farms in the release and dissemination of ARGs into the environment. Sediment samples upstream and downstream from five rainbow trout farms were collected over time in southern Chile. A microfluidic quantitative polymerase chain reaction approach was used to quantify an ARG array covering different mechanisms of resistance, and data were analyzed using principal component analysis (PCA) and linear mixed regression models. Surveys were also conducted to obtain information about management practices, including antibiotic use, at the farms. Florfenicol and oxytetracycline were used at these farms, although at different rates. A total of 93 samples were analyzed. In the PCA, strB, sul1, sul2, qacG, tet(A), tet(B), tet(C), tet(W), and floR grouped together. A statistically significant increase in abundance of qacG, strB, sul1, and several tet genes was found downstream from the farms compared with upstream sites, and retention ponds had the highest ARG abundance at each site. Antibiotic resistance gene levels returned to baseline at an average distance of 132.7 m downstream from the farms. Although results from this study indicate an influence of trout farms on the presence of ARGs in the immediate environment, the extent of their contribution to ARG dissemination is unknown and deserves further investigation. Core Ideas Point sources contribute to antimicrobial resistance (AMR) in the environment. Antibiotic resistance genes (ARG) were quantified in river sediment samples. Freshwater trout farms in southern Chile increased ARG abundance in the watershed. The extent of the contribution of the trout farms on ARG dissemination is uncertain. Epidemiological methods are needed to attribute environmental AMR to specific point sources.

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Section: Discussionmentioning

confidence: 99%

“…The MF‐qPCR was performed on two technical replicates of DNA from each sample after pre‐amplifying the target genes with a specific target amplification. A more detailed explanation of this method can be found elsewhere (Ishii et al, 2013; Sandberg et al, 2017; Ahmed et al, 2018; Zhang and Ishii, 2018). …”

Section: Methodsmentioning

confidence: 99%

Antibiotic Resistance Genes in Freshwater Trout Farms in a Watershed in Chile

et al. 2019

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“…ARGs are readily acquired by human pathogenic bacteria (HPB) to generate superbacteria. ARGs are carried in agricultural products due to the agricultural application of manure, which can eventually eliminate the e cacy of antibiotics used in the treatment and prevention of human bacterial infections [4][5][6][7]. It has been suggested that if appropriate measures are not taken to address the important health issues associated with antimicrobial resistance, then the number of deaths due to antibiotic-resistant infections will exceed 10 million by 2050 [8,9].…”

Section: Introductionmentioning

confidence: 99%

Metagenomic analysis of effects of oxytetracycline and copper on antibiotic resistance genes and associated pathogenic hosts in swine manure compost

Guo

Wang

et al. 2020

Preprint

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Background: The proliferation of antibiotic resistance genes (ARGs) in compost and their horizontal transfer to human pathogenic bacteria (HPB) may lead to the failure of human antibiotics. However, the antibiotic resistome in compost has not been comprehensively characterized. This study used a metagenomic approach to obtain new insights into the effects of oxytetracycline (OTC) and copper (Cu) on the antibiotic resistome during swine manure composting and the risks posed to human health. Results: The results showed that composting reduced the abundances and diversity of ARGs and HPB in swine manure. In total, 289 ARG subtypes and 19 ARG types were detected in the samples with abundances ranging from 1.08 ´ 10 –1 to 9.39 ´ 10 –1 copies/16S rRNA, which mainly encoded tetracycline, aminoglycoside, and macrolide–lincosamide–streptogramin (MLS) resistance genes. The application of OTC and Cu, especially the combined application, exacerbated the compost resistome risk scores and specific ARG subtypes responded differently. Tetracycline, multidrug, and MLS resistance genes mainly affected resistance profiles of HPB throughout the composting process. HPB and intI1 had significant positive effects on determining the ARG profiles during the composting process, and the co-selective effect of heavy metals may increase the abundances of ARGs via strong positive effects on intI1 . In addition, the effect of mobile genetic elements on the horizontal gene transfer of ARGs should not be ignored. Conclusions: This study of the antibiotic resistome in compost indicates the need for effective regulation of the misuse of livestock and poultry feed additives in order to minimize the spread of the antibiotic resistome in agro-ecosystems and decrease the potential risk to public health. Keywords: Antibiotic resistome; Composting; Metagenome; Pathogenic host; Swine manure

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“…Given its high abundance, it can be used in metagenomic studies for estimating the human fecal pollution levels in the environment (Ahmed et al, 2018a;Stachler and Bibby, 2014). crAssphage has been shown to correlate moderately with only a few ARGs in storm drain outfalls (Ahmed et al, 2018b) and thus, could be a good candidate for estimating the effect of fecal pollution in ARG dynamics. Moreover, it is not physically linked to resistance genes like integrons are and hence likely independent from ARGs and thus, could enable the determination of ARG horizontal gene transfer and selection patterns in receiving environments.…”

Section: Introductionmentioning

confidence: 99%

Fecal pollution explains antibiotic resistance gene abundances in anthropogenically impacted environments

Karkman

Pärnänen

Larsson

2018

Preprint

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Discharge of treated sewage leads to release of antibiotic resistant bacteria, resistance genes and antibiotic residues to the environment. Such pollution can directly contribute to increased morbidity caused by the transmission of resistant fecal pathogens. Residual antibiotics in wastewaters have been speculated to select for resistant bacteria and thereby promote the evolution and emergence of new resistance factors. Increased abundance of antibiotic resistance genes in sewage and sewage-impacted environments may, however, simply be a result of fecal contamination with resistant bacteria rather than caused by an on-site selection pressure. In this study we have disentangled these two alternative scenarios by relating the relative resistance gene abundance to the accompanying extent of fecal pollution in publicly available metagenomic data. This was possible by analyzing the abundance of a newly discovered phage which is exceptionally abundant in, and specific to, human feces. The presence of resistance genes could largely be explained by fecal pollution, with no clear signs of selection in the environment, the only exception being environments polluted by very high levels of antibiotics from manufacturing where selection is evident. Our results demonstrate the necessity to take in to account the fecal pollution levels to avoid making erroneous assumptions regarding environmental selection of antibiotic resistance. The presence or absence of selection pressure has major implications for what the risk scenarios are (transmission versus evolution) and for what mitigations (reducing pathogenic bacteria or selective agents) should be prioritized to reduce health risks related to antibiotic resistance in the environment.

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Precipitation influences pathogenic bacteria and antibiotic resistance gene abundance in storm drain outfalls in coastal sub-tropical waters

Cited by 106 publications

References 61 publications

Antibiotic Resistance Genes in Freshwater Trout Farms in a Watershed in Chile

Antibiotic Resistance Genes in Freshwater Trout Farms in a Watershed in Chile

Metagenomic analysis of effects of oxytetracycline and copper on antibiotic resistance genes and associated pathogenic hosts in swine manure compost

Fecal pollution explains antibiotic resistance gene abundances in anthropogenically impacted environments

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