Environmental contamination in a high-income country (France) by antibiotics, antibiotic-resistant bacteria, and antibiotic resistance genes: Status and possible causes

Haenni, Marisa; Dagot, Christophe; Chesneau, O.; Bibbal, Delphine; Labanowski, Jérôme; Vialette, Michèle; Bouchard, Damien; Martin-Laurent, Fabrice; Calsat, Louisiane; Nazaret, Sylvie; Petit, Fabienne; Pourcher, Anne‐Marie; Togola, Anne; Bachelot, Morgane; Topp, Edward; Hocquet, Didier

doi:10.1016/j.envint.2021.107047

Cited by 100 publications

(71 citation statements)

References 149 publications

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“…Important studies have described AMR in water and effluents [3][4][5][26][27][28][29][30][31][32][33][34][35][36], but lack of a consensus set of tools to harmonize methodologies and analyses across multiple groups' efforts (from water collection and laboratory processing to bioinformatic analysis and reporting) leaves us without a ready, common source of information to support local, national and global AMR monitoring of the environment. Metagenomic approaches provide valuable surveillance of species such as Mycobacterium, Mycoplasma and Neisseria (as shown in Figure 11), but for surveillance of NARMS critically important gene targets, metagenomics should be coupled with microbial pre-enrichment using relevant bacterial growth media.…”

Section: Discussionmentioning

confidence: 99%

Advancing antimicrobial resistance monitoring in surface waters with metagenomic and quasimetagenomic methods

Ottesen

Kocurek

Ramachandran

et al. 2022

Preprint

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Surface waters present a unique challenge for the monitoring of critically important antimicrobial resistance. Metagenomic approaches provide unbiased descriptions of taxonomy and antimicrobial resistance genes in many environments, but for surface water, culture independent data is insufficient to describe critically important resistance. To address this challenge and expand resistome reporting capacity of antimicrobial resistance in surface waters, we apply metagenomic and quasimetagenomic (enriched microbiome) data to examine and contrast water from two sites, a creek near a hospital, and a reservoir used for recreation and municipal water. Approximately 30% of the National Antimicrobial Resistance Monitoring System’s critically important resistance gene targets were identified in enriched data contrasted to only 1% in culture independent data. Four different analytical approaches consistently reported substantially more antimicrobial resistance genes in quasimetagenomic data compared to culture independent data across most classes of antimicrobial resistance. Statistically significant differential fold changes (p<0.05) of resistance determinants were used to infer microbiological differences in the waters. Important pathogens associated with critical antimicrobial resistance were described for each water source. While the single time-point for only two sites represents a small pilot project, the successful reporting of critically important resistance determinants is proof of concept that the quasimetagenomic approach is robust and can be expanded to multiple sites and timepoints for national and global monitoring and surveillance of antimicrobial resistance in surface waters.

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Section: Discussionmentioning

confidence: 99%

Advancing antimicrobial resistance monitoring in surface waters with metagenomic and quasimetagenomic methods

Ottesen

Kocurek

Ramachandran

et al. 2022

Preprint

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“…Although the direct discharge of untreated human waste containing many ARB and ARGs into the soil and water environment is one of the major contributors to environmental AMR contamination in LMICs [9,12], in HICs, where the sanitation infrastructure is welldeveloped, most human waste is released into the water environment (rivers or oceans) after being treated at sewage treatment plants (STPs) [13][14][15][16][17]. STPs were developed to ensure the removal of harmful microorganisms, so they play a pivotal role in reducing AMR [5].…”

Section: Introductionmentioning

confidence: 99%

“…As in other HICs, in Japan, most of the large centralized STPs use a conventional activated sludge (CAS) process, and most of the small to medium-sized STPs use an oxidation ditches (OD) process, usually combined with chlorination [16,[23][24][25]. In STPs, wastewater is treated until it meets National Effluent Standards, which define the permissible limit of coliform bacteria in STP effluent as a daily average of 3000 colonies/cm 3 [26]; however, no regulations limit the discharge of AMR or antimicrobial residues, and the actual amount of them in STP effluent is still unknown.…”

Section: Introductionmentioning

confidence: 99%

Review of Antimicrobial Resistance in Wastewater in Japan: Current Challenges and Future Perspectives

et al. 2022

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Antimicrobial resistance (AMR) circulates through humans, animals, and the environments, requiring a One Health approach. Recently, urban sewage has increasingly been suggested as a hotspot for AMR even in high-income countries (HICs), where the water sanitation and hygiene infrastructure are well-developed. To understand the current status of AMR in wastewater in a HIC, we reviewed the epidemiological studies on AMR in the sewage environment in Japan from the published literature. Our review showed that a wide variety of clinically important antibiotic-resistant bacteria (ARB), antibiotic resistance genes (ARGs), and antimicrobial residues are present in human wastewater in Japan. Their concentrations are lower than in low- and middle-income countries (LMICs) and are further reduced by sewage treatment plants (STPs) before discharge. Nevertheless, the remaining ARB and ARGs could be an important source of AMR contamination in river water. Furthermore, hospital effluence may be an important reservoir of clinically important ARB. The high concentration of antimicrobial agents commonly prescribed in Japan may contribute to the selection and dissemination of AMR within wastewater. Our review shows the importance of both monitoring for AMR and antimicrobials in human wastewater and efforts to reduce their contamination load in wastewater.

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“…The highest detection rate of antibiotics in the world, reaching almost 100% in soils and 98% in surface water, has been reported in China [ 27 ]. A far better situation is observed in the European countries [ 33 ]. According to Conde-Cid et al [ 23 ], antibiotics can be detected in approximately 40% of manures and 17% of soils therein.…”

Section: Introductionmentioning

confidence: 99%

The Role of Grass Compost and Zea Mays in Alleviating Toxic Effects of Tetracycline on the Soil Bacteria Community

Wyszkowska

Borowik

Kucharski

2022

IJERPH

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Given their common use for disease treatment in humans, and particularly in animals, antibiotics pose an exceptionally serious threat to the soil environment. This study aimed to determine the response of soil bacteria and oxidoreductases to a tetracycline (Tc) contamination, and to establish the usability of grass compost (G) and Zea mays (Zm) in mitigating adverse Tc effects on selected microbial properties of the soil. The scope of microbiological analyses included determinations of bacteria with the conventional culture method and new-generation sequencing method (NGS). Activities of soil dehydrogenases and catalase were determined as well. Tc was found to reduce counts of organotrophic bacteria and actinobacteria in the soils as well as the activity of soil oxidoreductases. Soil fertilization with grass compost (G) and Zea mays (Zm) cultivation was found to alleviate the adverse effects of tetracycline on the mentioned group of bacteria and activity of oxidoreductases. The metagenomic analysis demonstrated that the bacteria belonging to Acidiobacteria and Proteobacteria phyla were found to prevail in the soil samples. The study results recommend soil fertilization with G and Zm cultivation as successful measures in the bioremediation of tetracycline-contaminated soils and indicate the usability of the so-called core bacteria in the bioaugmentation of such soils.

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Environmental contamination in a high-income country (France) by antibiotics, antibiotic-resistant bacteria, and antibiotic resistance genes: Status and possible causes

Cited by 100 publications

References 149 publications

Advancing antimicrobial resistance monitoring in surface waters with metagenomic and quasimetagenomic methods

Advancing antimicrobial resistance monitoring in surface waters with metagenomic and quasimetagenomic methods

Review of Antimicrobial Resistance in Wastewater in Japan: Current Challenges and Future Perspectives

The Role of Grass Compost and Zea Mays in Alleviating Toxic Effects of Tetracycline on the Soil Bacteria Community

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