Comparison of Culture- and Quantitative PCR-Based Indicators of Antibiotic Resistance in Wastewater, Recycled Water, and Tap Water

Standardized methods are needed to support monitoring of antibiotic resistance in environmental samples. Culture-based methods target species of human-health relevance, while the direct quantification of antibiotic resistance genes (ARGs) measures the antibiotic resistance potential in the microbial community. This study compared measurements of tetracycline-, sulphonamide-, and cefotaxime-resistant presumptive total and fecal coliforms and presumptive enterococci versus a suite of ARGs quantified by quantitative polymerase chain reaction (qPCR) across waste-, recycled-, tap-, and freshwater. Cross-laboratory comparison of results involved measurements on samples collected and analysed in the US and Portugal. The same DNA extracts analysed in the US and Portugal produced comparable qPCR results (variation <28%), except for blaOXA-1 gene (0%–57%). Presumptive total and fecal coliforms and cefotaxime-resistant total coliforms strongly correlated with blaCTX-M and intI1 (0.725 ≤ R2 ≤ 0.762; p < 0.0001). Further, presumptive total and fecal coliforms correlated with the Escherichia coli-specific biomarkers, gadAB, and uidA, suggesting that both methods captured fecal-sourced bacteria. The genes encoding resistance to sulphonamides (sul1 and sul2) were the most abundant, followed by genes encoding resistance to tetracyclines (tet(A) and tet(O)) and β-lactams (blaOXA-1 and, blaCTX-M), which was in agreement with the culture-based enumerations. The findings can help inform future application of methods being considered for international antibiotic resistance surveillance in the environment.

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Corpse Degradation of Farmed Fish Increases the Abundance of Antibiotic Resistance Genes but Exhibits the Temporal Stability

10.21203/rs.3.rs-749577/v1 ◽

2021 ◽

Author(s):

Wanghong Su ◽

Tongtong Li ◽

Qiaoling Yu ◽

Tianshu Feng ◽

Jiawei Yang ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Large Volume ◽

Tap Water ◽

Quantitative Polymerase Chain Reaction ◽

Temporal Stability ◽

Antibiotic Resistance Genes ◽

Opportunistic Pathogens ◽

Control Groups ◽

Farmed Fish

Abstract Serious concerns have been raised regarding resistomes causing by corpse decomposition in the aquatic environment, which pose threats to the water environment and human health. However, antibiotic resistance genes (ARGs) in large-volume tap water and their temporal stability during corpse decay are poorly explored. Here, high-throughput quantitative polymerase chain reaction (HT-qPCR) and amplicon sequencing were applied to profile ARGs and bacterial communities in experimental and control groups containing 50 L of tap water at 7th, 15th and 100th day during corpse decomposition. We found that most of the ARGs in experimental groups had higher abundance compared with the control groups independent of time. And the absolute abundance of some ARGs in the carcass groups was even enriched by 259 to 413,640-folds. The tetracycline and beta-lactamase resistance genes of the experimental groups were obviously enriched compared with control groups, and the ARG profiles were convergent during different decay stages, which indicated the long-term persistence of ARGs. Treatment, dissolved oxygen (DO) and pH were three important factors determining ARG profiles during corpse decomposition. Twelve opportunistic pathogens, especially Burkholderia, Legionella and Halomonas, remarkably increased as decomposition proceeded. Network analysis showed that opportunistic pathogens were significantly associated with ARGs. Our results emphasize that corpse decay increases the abundance and diversity of ARGs in large-volume drinking water independent of time while exhibits temporal persistence of ARGs, thereby uncovering the harmful effects of animal cadavers. It also provides valuable suggestions for the risk assessment and management of source water caused by corpse decay.

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PRO: Carbapenems should be used for ALL infections caused by ceftriaxone-resistant Enterobacterales

JAC-Antimicrobial Resistance ◽

10.1093/jacamr/dlab013 ◽

2021 ◽

Vol 3 (1) ◽

Author(s):

David L Paterson ◽

Burcu Isler ◽

Patrick N A Harris

Keyword(s):

Antibiotic Resistance ◽

Observational Studies ◽

Randomized Trials ◽

Antibiotic Resistance Genes ◽

Definitive Treatment ◽

In Vitro Activity ◽

Genes Encoding ◽

Amoxicillin Clavulanate ◽

Trial Outcomes

Abstract Ceftriaxone resistance in the Enterobacterales is typically the result of production of ESBLs or AmpC β-lactamases. The genes encoding these enzymes are often co-located with other antibiotic resistance genes leading to resistance to aminoglycosides, quinolones and trimethoprim/sulfamethoxazole. Carbapenems are stable to ESBLs and AmpC giving them reliable in vitro activity against producers of these β-lactamases. In contrast, piperacillin/tazobactam and amoxicillin/clavulanate are compromised by co-production of OXA-1, which is not inhibited by tazobactam or clavulanate. These in vitro findings provide an explanation for the MERINO trial outcomes, where 3.7% (7/191) randomized to meropenem died compared with 12.3% (23/187) randomized to piperacillin/tazobactam as definitive treatment of bloodstream infection due to ceftriaxone-resistant organisms. No randomized trials have yet put cefepime and carbapenems head to head, but some observational studies have shown worse outcomes with cefepime. We argue that carbapenems are the antibiotics of choice for ceftriaxone-resistant Enterobacterales.

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Environmental Spread of New Delhi Metallo-β-Lactamase-1-Producing Multidrug-Resistant Bacteria in Dhaka, Bangladesh

Applied and Environmental Microbiology ◽

10.1128/aem.00793-17 ◽

2017 ◽

Vol 83 (15) ◽

Cited By ~ 32

Author(s):

Mohammad Aminul Islam ◽

Moydul Islam ◽

Rashedul Hasan ◽

M. Iqbal Hossain ◽

Ashikun Nabi ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Tap Water ◽

Antibiotic Resistance Genes ◽

Multidrug Resistant ◽

Resistant Bacteria ◽

New Delhi ◽

Multidrug Resistant Bacteria ◽

Content Type ◽

Wastewater Samples

ABSTRACT Resistance to carbapenem antibiotics through the production of New Delhi metallo-β-lactamase-1 (NDM-1) constitutes an emerging challenge in the treatment of bacterial infections. To monitor the possible source of the spread of these organisms in Dhaka, Bangladesh, we conducted a comparative analysis of wastewater samples from hospital-adjacent areas (HAR) and from community areas (COM), as well as public tap water samples, for the occurrence and characteristics of NDM-1-producing bacteria. Of 72 HAR samples tested, 51 (71%) samples were positive for NDM-1-producing bacteria, as evidenced by phenotypic tests and the presence of the bla NDM-1 gene, compared to 5 of 41 (12.1%) samples from COM samples (P < 0.001). All tap water samples were negative for NDM-1-producing bacteria. Klebsiella pneumoniae (44%) was the predominant bacterial species among bla NDM-1-positive isolates, followed by Escherichia coli (29%), Acinetobacter spp. (15%), and Enterobacter spp. (9%). These bacteria were also positive for one or more other antibiotic resistance genes, including bla CTX-M-1 (80%), bla CTX-M-15 (63%), bla TEM (76%), bla SHV (33%), bla CMY-2 (16%), bla OXA-48-like (2%), bla OXA-1 (53%), and bla OXA-47-like (60%) genes. Around 40% of the isolates contained a qnr gene, while 50% had 16S rRNA methylase genes. The majority of isolates hosted multiple plasmids, and plasmids of 30 to 50 MDa carrying bla NDM-1 were self-transmissible. Our results highlight a number of issues related to the characteristics and source of spread of multidrug-resistant bacteria as a potential public health threat. In view of the existing practice of discharging untreated liquid waste into the environment, hospitals in Dhaka city contribute to the potential dissemination of NDM-1-producing bacteria into the community. IMPORTANCE Infections caused by carbapenemase-producing Enterobacteriaceae are extremely difficult to manage due to their marked resistance to a wide range of antibiotics. NDM-1 is the most recently described carbapenemase, and the bla NDM-1 gene, which encodes NDM-1, is located on self-transmissible plasmids that also carry a considerable number of other antibiotic resistance genes. The present study shows a high prevalence of NDM-1-producing organisms in the wastewater samples from hospital-adjacent areas as a potential source for the spread of these organisms to community areas in Dhaka, Bangladesh. The study also examines the characteristics of the isolates and their potential to horizontally transmit the resistance determinants. The significance of our research is in identifying the mode of spread of multiple-antibiotic-resistant organisms, which will allow the development of containment measures, leading to broader impacts in reducing their spread to the community.

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Characterization of a Multiresistant Mosaic Plasmid from a Fish Farm Sediment Exiguobacterium sp. Isolate Reveals Aggregation of Functional Clinic-Associated Antibiotic Resistance Genes

Applied and Environmental Microbiology ◽

10.1128/aem.03257-13 ◽

2013 ◽

Vol 80 (4) ◽

pp. 1482-1488 ◽

Cited By ~ 9

Author(s):

Jing Yang ◽

Chao Wang ◽

Jinyu Wu ◽

Li Liu ◽

Gang Zhang ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Mobile Elements ◽

Fish Farms ◽

Significant Similarity ◽

Content Type ◽

Genes Encoding ◽

The Mean

ABSTRACTThe genusExiguobacteriumcan adapt readily to, and survive in, diverse environments. Our study demonstrated thatExiguobacteriumsp. strain S3-2, isolated from marine sediment, is resistant to five antibiotics. The plasmid pMC1 in this strain carries seven putative resistance genes. We functionally characterized these resistance genes inEscherichia coli, and genes encoding dihydrofolate reductase and macrolide phosphotransferase were considered novel resistance genes based on their low similarities to known resistance genes. The plasmid G+C content distribution was highly heterogeneous. Only the G+C content of one block, which shared significant similarity with a plasmid fromExiguobacterium arabatum, fit well with the mean G+C content of the host. The remainder of the plasmid was composed of mobile elements with a markedly lower G+C ratio than the host. Interestingly, five mobile elements located on pMC1 showed significant similarities to sequences found in pathogens. Our data provided an example of the link between resistance genes in strains from the environment and the clinic and revealed the aggregation of antibiotic resistance genes in bacteria isolated from fish farms.

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The Occurrence of Antibiotic Resistance Genes in an Urban River in Nepal

Water ◽

10.3390/w12020450 ◽

2020 ◽

Vol 12 (2) ◽

pp. 450 ◽

Cited By ~ 3

Author(s):

Ocean Thakali ◽

Sarmila Tandukar ◽

John Brooks ◽

Samendra Sherchan ◽

Jeevan Sherchand ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Anthropogenic Activities ◽

Quantitative Polymerase Chain Reaction ◽

Antibiotic Resistance Genes ◽

Urban River ◽

Class 1 Integron ◽

Upstream Site ◽

Class 1 ◽

The Impact

Urban rivers affected by anthropogenic activities can act as reservoirs of antibiotic resistance genes (ARGs). This study aimed to describe the occurrence of selected ARGs (blaTEM, ermF, mecA, and tetA) and a class 1 integron (intI1) in an urban river in Nepal. A total of 18 water samples were collected periodically from upstream, midstream, and downstream sites along the Bagmati River over a 1-year period. All ARGs except mecA and intI1 were consistently detected by a quantitative polymerase chain reaction in the midstream and downstream sites, with concentrations ranging from 3.1 to 7.8 log copies/mL. ARG abundance was significantly lower at the upstream site (p < 0.05), reflecting the impact of anthropogenic activities on increasing concentrations of ARGs at midstream and downstream sites. Our findings demonstrate the presence of clinically relevant ARGs in the urban river water of Nepal, suggesting a need for mitigating strategies to prevent the spread of antibiotic resistance in the environment.

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Studies on Bd0934 and Bd3507, Two Secreted Nucleases from Bdellovibrio bacteriovorus, Reveal Sequential Release of Nucleases during the Predatory Cycle

Journal of Bacteriology ◽

10.1128/jb.00150-20 ◽

2020 ◽

Vol 202 (18) ◽

Author(s):

Ewa Bukowska-Faniband ◽

Tilde Andersson ◽

Rolf Lood

Keyword(s):

Antibiotic Resistance ◽

Life Cycle ◽

Antibiotic Resistance Genes ◽

Human Pathogens ◽

Temporal Expression ◽

Bdellovibrio Bacteriovorus ◽

Exogenous Dna ◽

Content Type ◽

Genes Encoding ◽

Predatory Bacteria

ABSTRACT Bdellovibrio bacteriovorus is an obligate predatory bacterium that invades and kills a broad range of Gram-negative prey cells, including human pathogens. Its potential therapeutic application has been the subject of increased research interest in recent years. However, an improved understanding of the fundamental molecular aspects of the predatory life cycle is crucial for developing this bacterium as a “living antibiotic.” During intracellular growth, B. bacteriovorus secretes an arsenal of hydrolases, which digest the content of the host cell to provide growth nutrients for the predator, e.g., prey DNA is completely degraded by the nucleases. Here, we have, on a genetic and molecular level, characterized two secreted DNases from B. bacteriovorus, Bd0934 and Bd3507, and determined the temporal expression profile of other putative secreted nucleases. We conclude that Bd0934 and Bd3507 are likely a part of the predatosome but are not essential for the predation, host-independent growth, prey biofilm degradation, and self-biofilm formation. The detailed temporal expression analysis of genes encoding secreted nucleases revealed that these enzymes are produced in a sequential orchestrated manner. This work contributes to our understanding of the sequential breakdown of the prey nucleic acid by the nucleases secreted during the predatory life cycle of B. bacteriovorus. IMPORTANCE Antibiotic resistance is a major global concern with few available new means to combat it. From a therapeutic perspective, predatory bacteria constitute an interesting tool. They not only eliminate the pathogen but also reduce the overall pool of antibiotic resistance genes through secretion of nucleases and complete degradation of exogenous DNA. Molecular knowledge of how these secreted DNases act will give us further insight into how antibiotic resistance, and the spread thereof, can be limited through the action of predatory bacteria.

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Synthesis of CeO2 as promising adsorbent for the management of free-DNA harboring antibiotic resistance genes from tap-water

Chemical Engineering Journal ◽

10.1016/j.cej.2020.125562 ◽

2020 ◽

Vol 401 ◽

pp. 125562 ◽

Cited By ~ 3

Author(s):

Eric Tobechukwu Anthony ◽

Mike O. Ojemaye ◽

Anthony I. Okoh ◽

Omobola O. Okoh

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Tap Water ◽

Antibiotic Resistance Genes ◽

Free Dna

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The antibiotic resistance of heterotrophic bacteria in tap waters in London

Water Science & Technology Water Supply ◽

10.2166/ws.2018.065 ◽

2018 ◽

Vol 19 (1) ◽

pp. 179-190

Author(s):

R. Destiani ◽

M. R. Templeton

Keyword(s):

Antibiotic Resistance ◽

Stenotrophomonas Maltophilia ◽

Heterotrophic Bacteria ◽

Tap Water ◽

Antibiotic Resistance Genes ◽

Resistant Bacteria ◽

Opportunistic Pathogens ◽

Antibiotic Resistant ◽

Sampling Locations ◽

The City

Abstract This study assessed the occurrence and prevalence of antibiotic-resistant bacteria (ARBs) and antibiotic resistance genes (ARGs) in tap water sampled across London, United Kingdom. Sampling was conducted seasonally from nine locations spread geographically across the city. ARBs and ARGs (tet(A), dfrA7, and sul1) were detected in all sampling locations in all sampling rounds. Resistance to trimethoprim was the highest among the tested antibiotics and the sul1 gene was the most abundant resistance gene detected. Several opportunistic pathogens were identified amongst the ARBs in the water samples, including Pseudomonas aeruginosa and Stenotrophomonas maltophilia.

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Characterization of antibiotic resistance genes in the species of the rumen microbiota

Nature Communications ◽

10.1038/s41467-019-13118-0 ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 9

Author(s):

Yasmin Neves Vieira Sabino ◽

Mateus Ferreira Santana ◽

Linda Boniface Oyama ◽

Fernanda Godoy Santos ◽

Ana Júlia Silva Moreira ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Animal Health ◽

Antibiotic Resistance Genes ◽

Tetracycline Resistance ◽

Multidrug Resistant ◽

Resistant Bacteria ◽

Ruminal Bacteria ◽

Genes Encoding

AbstractInfections caused by multidrug resistant bacteria represent a therapeutic challenge both in clinical settings and in livestock production, but the prevalence of antibiotic resistance genes among the species of bacteria that colonize the gastrointestinal tract of ruminants is not well characterized. Here, we investigate the resistome of 435 ruminal microbial genomes in silico and confirm representative phenotypes in vitro. We find a high abundance of genes encoding tetracycline resistance and evidence that the tet(W) gene is under positive selective pressure. Our findings reveal that tet(W) is located in a novel integrative and conjugative element in several ruminal bacterial genomes. Analyses of rumen microbial metatranscriptomes confirm the expression of the most abundant antibiotic resistance genes. Our data provide insight into antibiotic resistange gene profiles of the main species of ruminal bacteria and reveal the potential role of mobile genetic elements in shaping the resistome of the rumen microbiome, with implications for human and animal health.

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Inside environmental Clostridium perfringens genomes: antibiotic resistance genes, virulence factors and genomic features

Journal of Water and Health ◽

10.2166/wh.2020.029 ◽

2020 ◽

Vol 18 (4) ◽

pp. 477-493

Author(s):

Johannes Cornelius Jacobus Fourie ◽

Cornelius Carlos Bezuidenhout ◽

Tomasz Janusz Sanko ◽

Charlotte Mienie ◽

Rasheed Adeleke

Keyword(s):

Antibiotic Resistance ◽

Clostridium Perfringens ◽

Resistance Genes ◽

Gc Content ◽

Antibiotic Resistance Genes ◽

Open Reading Frames ◽

Health Security ◽

Genes Encoding ◽

Integration Sites ◽

Potential Pathogenicity

Abstract Until recently, research has focused on Clostridium perfringens in clinical settings without considering environmental isolates. In this study, environmental genomes were used to investigate possible antibiotic resistance and the presence of virulence traits in C. perfringens strains from raw surface water. In silico assembly of three C. perfringens strains, DNA generated almost complete genomes setting their length ranging from 3.4 to 3.6 Mbp with GC content of 28.18%. An average of 3,175 open reading frames was identified, with the majority associated with carbohydrate and protein metabolisms. The genomes harboured several antibiotic resistance genes for glycopeptides, macrolide–lincosamide–streptogramin B, β-lactam, trimethoprim, tetracycline and aminoglycosides and also the presence of several genes encoding for polypeptides and multidrug resistance efflux pumps and 35 virulence genes. Some of these encode for haemolysins, sialidase, hyaluronidase, collagenase, perfringolysin O and phospholipase C. All three genomes contained sequences indicating phage, antibiotic resistance and pathogenic islands integration sites. A genomic comparison of these three strains confirmed high similarity and shared core genes with clinical C. perfringens strains, highlighting their health security risks. This study provides a genomic insight into the potential pathogenicity of C. perfringens present in the environment and emphasises the importance of monitoring this niche in the future.

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