A framework for standardized qPCR-targets and protocols for quantifying antibiotic resistance in surface water, recycled water and wastewater

Keenum, Ishi; Liguori, Krista; Calarco, Jeanette; Davis, Benjamin C.; Milligan, Erin; Harwood, Valerie J.; Pruden, Amy

doi:10.1080/10643389.2021.2024739

Cited by 44 publications

(42 citation statements)

References 125 publications

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“…The results of this study highlight that ARGs are prevalent in surface and groundwater samples that are used for drinking, bathing, and other household activities. A recent critical review highlighted the suitability of sul1, intI1, tet (A), vanA , and bla CTX–M as potential ARG targets to standardize the ARG monitoring in surface water and wastewater ( Keenum et al, 2022 ). In this study, sul1, intI1, tet (A), and vanA were quantified not only in surface water but also in groundwater samples.…”

Section: Discussionmentioning

confidence: 99%

Prevalence of antibiotic resistance genes in drinking and environmental water sources of the Kathmandu Valley, Nepal

et al. 2022

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Antibiotic-resistant bacteria-associated infections are responsible for more than 1.2 million annual deaths worldwide. In low- and middle-income countries (LMICs), the consumption of antibiotics for human and veterinary uses is not regulated effectively. Overused and misused antibiotics can end up in aquatic environments, which may act as a conduit for antibiotic resistance dissemination. However, data on the prevalence of antibiotic resistance determinants in aquatic environments are still limited for LMICs. In this study, we evaluated the prevalence and concentration of antibiotic resistance genes (ARGs) in different drinking and environmental water sources collected from the Kathmandu Valley, Nepal, using droplet digital polymerase chain reaction to understand the current situation of ARG contamination. River water and shallow dug well water sources were the most contaminated with ARGs. Almost all samples contained sul1 (94%), and intI1 and tet(A) were detected in 83 and 60% of the samples, respectively. Maximum ARG concentration varied between 4.2 log10 copies/100 ml for mecA and 9.3 log10 copies/100 ml for sul1. Significant positive correlations were found between ARGs (r > 0.5, p < 0.01), except for mecA, qnrS, and vanA. As sul1 and intI1 were detected in almost all samples, the presence of these genes in a given sample may need to be considered as background antibiotic resistance in LMICs. Therefore, monitoring of ARGs, such as β-lactam ARGs, quinolone resistance genes, and vancomycin resistance genes, may provide a better picture of the antibiotic resistance determinants in aquatic environments of LMICs.

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Section: Discussionmentioning

confidence: 99%

Prevalence of antibiotic resistance genes in drinking and environmental water sources of the Kathmandu Valley, Nepal

et al. 2022

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“…aadA , aadB , aacA4 , bla CTX‐M , bla TEM ), while another ( qnrS ) is at ‘high‐risk’ and a ‘future threat’ (risk rank II) because not yet present in human pathogens but of high risk of being transferred into these bacteria. Only sul1 has been assigned to rank IV (lowest risk) but this marker is commonly monitored in environmental studies about antibiotic resistance (Keenum et al ., 2021), and its monitoring allowed us to compare our results with the literature. About the two MGEs monitored, the important role of class 1 integrons in disseminating ARGs as gene cassettes in pathogenic bacteria is well known (Gillings, 2014), reason why they are frequently used as a proxy for antibiotic resistance in the environment (Gillings et al ., 2015).…”

Section: Resultsmentioning

confidence: 83%

Bacteriophages vehiculate a high amount of antibiotic resistance determinants of bacterial origin in the Orne River ecosystem

Sagrillo

Changey

Bellanger

2022

Environmental Microbiology

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Aquatic environments are important dissemination routes of antibiotic resistance genes (ARGs) from and to pathogenic bacteria. Nevertheless, in these complex matrices, identifying and characterizing the driving microbial actors and ARG dissemination mechanisms they are involved in remain difficult. We here explored the distribution/compartmentalization of a panel of ARGs and mobile genetic elements (MGEs) in bacteria and bacteriophages collected in the water, suspended material and surface sediments from the Orne River ecosystem (France). By using a new bacteriophage DNA extraction method, we showed that, when packaging bacterial DNA, bacteriophages rather encapsidate both ARGs and MGEs than 16S rRNA genes, i.e. chromosomal fragments. We also show that the bacteria and bacteriophage capsid contents in ARGs/MGEs were similarly influenced by seasonality but that the distribution of ARGs/MGEs between the river physical compartments (water vs. suspended mater vs. sediment) is more impacted when these markers were carried by bacteria. These demonstrations will likely modify our understanding of the formation and fate of transducing viral particles in the environment. Consequently, they will also likely modify our estimations of the relative frequencies of the different horizontal gene transfer mechanisms in disseminating antibiotic resistance by reinforcing the roles played by environmental bacteriophages and transduction.

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“…The search terms and protocol for the literature review are provided in the Supporting Information (section 1a), with the portion devoted to qPCR recently being published. 95 The workshop took place on four days over a two-week period (May 2021) and was attended by 49 (43 U.S., 6 international) experts representing academia (17), industry (8), federal governmental agencies (e.g., EPA, FDA, USDA) (13), state and local governmental organizations (2), United Nations agencies (WHO) (1), and water utilities (9). In addition to the literature review, the workshop participants were provided with a summary of the results of the online survey.…”

Section: A Way Forward: Guidance From An Expert Survey and Workhopmentioning

confidence: 99%

Antimicrobial Resistance Monitoring of Water Environments: A Framework for Standardized Methods and Quality Control

Liguori

Keenum

Davis

et al. 2022

Environ. Sci. Technol.

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Antimicrobial resistance (AMR) is a grand societal challenge with important dimensions in the water environment that contribute to its evolution and spread. Environmental monitoring could provide vital information for mitigating the spread of AMR; this includes assessing antibiotic resistance genes (ARGs) circulating among human populations, identifying key hotspots for evolution and dissemination of resistance, informing epidemiological and human health risk assessment models, and quantifying removal efficiencies by domestic wastewater infrastructure. However, standardized methods for monitoring AMR in the water environment will be vital to producing the comparable data sets needed to address such questions. Here we sought to establish scientific consensus on a framework for such standardization, evaluating the state of the science and practice of AMR monitoring of wastewater, recycled water, and surface water, through a literature review, survey, and workshop leveraging the expertise of academic, governmental, consulting, and water utility professionals.

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A framework for standardized qPCR-targets and protocols for quantifying antibiotic resistance in surface water, recycled water and wastewater

Cited by 44 publications

References 125 publications

Prevalence of antibiotic resistance genes in drinking and environmental water sources of the Kathmandu Valley, Nepal

Prevalence of antibiotic resistance genes in drinking and environmental water sources of the Kathmandu Valley, Nepal

Bacteriophages vehiculate a high amount of antibiotic resistance determinants of bacterial origin in the Orne River ecosystem

Antimicrobial Resistance Monitoring of Water Environments: A Framework for Standardized Methods and Quality Control

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