Wastewater treatment plants (WWTPs) provide optimal conditions for the maintenance and spread of ... more Wastewater treatment plants (WWTPs) provide optimal conditions for the maintenance and spread of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). In this work we describe the occurrence of antibiotic resistant faecal coliforms and their mechanisms of antibiotic resistance in the effluent of two urban WWTPs in Ireland. Effluent samples were collected from two WWTPs in Spring and Autumn of 2015 and 2016. The bacterial susceptibility patterns to 13 antibiotics were determined. The phenotypic tests were carried out to identify AmpC or extended-spectrum β-lactamase (ESBL) producers. The presence of ESBL genes were detected by PCR. Plasmids carrying ESBL genes were transformed into Escherichia coli DH5α recipient and underwent plasmid replicon typing to identify incompatibility groups. More than 90% of isolated faecal coliforms were resistant to amoxicillin and ampicillin, followed by tetracycline (up to 39.82%), ciprofloxacin (up to 31.42%) and trimethoprim (up...
The antibiotic resistome in European UWTPs mirrors the gradient of north-to-south clinical antibi... more The antibiotic resistome in European UWTPs mirrors the gradient of north-to-south clinical antibiotic resistance prevalence.
Irrigation water is a major source of fresh produce contamination with undesired microorganisms i... more Irrigation water is a major source of fresh produce contamination with undesired microorganisms including antibiotic-resistant bacteria (ARB), and contaminated fresh produce can transfer ARB to the consumer especially when consumed raw. Nevertheless, no legal guidelines exist so far regulating quality of irrigation water with respect to ARB. We therefore examined irrigation water from major vegetable growing areas for occurrence of antibioticresistant indicator bacteria Escherichia coli and Enterococcus spp., including extendedspectrum β-lactamase (ESBL)-producing E. coli and vancomycin-resistant Enterococcus spp. Occurrence of ARB strains was compared to total numbers of the respective species. We categorized water samples according to total numbers and found that categories with higher total E. coli or Enterococcus spp. numbers generally had an increased proportion of respective ARB-positive samples. We further detected high prevalence of ESBL-producing E. coli with eight positive samples of thirty-six (22%), while two presumptive vancomycinresistant Enterococcus spp. were vancomycin-susceptible in confirmatory tests. In disk diffusion assays all ESBL-producing E. coli were multidrug-resistant (n = 21) and wholegenome sequencing of selected strains revealed a multitude of transmissible resistance genes (ARG), with bla CTX-M-1 (4 of 11) and bla CTX-M-15 (3 of 11) as the most frequent ESBL genes. Overall, the increased occurrence of indicator ARB with increased total indicator bacteria suggests that the latter might be a suitable estimate for presence of respective ARB strains. Finally, the high prevalence of ESBL-producing E. coli with transmissible ARG emphasizes the need to establish legal critical values and monitoring guidelines for ARB in irrigation water.
Waste water and waste water treatment plants can act as reservoirs and environmental suppliers of... more Waste water and waste water treatment plants can act as reservoirs and environmental suppliers of antibiotic resistance. They have also been proposed to be hotspots for horizontal gene transfer, enabling the spread of antibiotic resistance genes between different bacterial species. Waste water contains antibiotics, disinfectants, and metals which can form a selection pressure for antibiotic resistance, even in low concentrations. Our knowledge of antibiotic resistance in waste water has increased tremendously in the past few years with advances in the molecular methods available. However, there are still some gaps in our knowledge on the subject, such as how active is horizontal gene transfer in waste water and what is the role of the waste water treatment plant in the environmental resistome? The purpose of this review is to briefly describe some of the main methods for studying antibiotic resistance in waste waters and the latest research and main knowledge gaps on the issue. In a...
In this article, the current knowledge and knowledge gaps in the emergence and spread of antimicr... more In this article, the current knowledge and knowledge gaps in the emergence and spread of antimicrobial resistance (AMR) in livestock and plants and importance in terms of animal and human health are discussed. Some recommendations are provided for generation of the data required in order to develop risk assessments for AMR within agriculture and for risks through the food chain to animals and humans.
Antibiotic resistance is a threat to human and animal health worldwide, and key measures are requ... more Antibiotic resistance is a threat to human and animal health worldwide, and key measures are required to reduce the risks posed by antibiotic resistance genes that occur in the environment. These measures include the identification of critical points of control, the development of reliable surveillance and risk assessment procedures, and the implementation of technological solutions that can prevent environmental contamination with antibiotic resistant bacteria and genes. In this Opinion article, we discuss the main knowledge gaps, the future research needs and the policy and management options that should be prioritized to tackle antibiotic resistance in the environment.
Understanding the soil bacterial resistome is essential to understanding the evolution and develo... more Understanding the soil bacterial resistome is essential to understanding the evolution and development of antibiotic resistance, and its spread between species and biomes. We have identified and characterized multi-drug resistance (MDR) mechanisms in the culturable soil antibiotic resistome and linked the resistance profiles to bacterial species. We isolated 412 antibiotic resistant bacteria from agricultural, urban and pristine soils. All isolates were multi-drug resistant, of which greater than 80% were resistant to 16-23 antibiotics, comprising almost all classes of antibiotic. The mobile resistance genes investigated, (ESBL, bla NDM-1 , and plasmid mediated quinolone resistance (PMQR) resistance genes) were not responsible for the respective resistance phenotypes nor were they present in the extracted soil DNA. Efflux was demonstrated to play an important role in MDR and many resistance phenotypes. Clinically relevant Burkholderia species are intrinsically resistant to ciprofloxacin but the soil Burkholderia species were not intrinsically resistant to ciprofloxacin. Using a phenotypic enzyme assay we identified the antibiotic specific inactivation of trimethoprim in 21 bacteria from different soils. The results of this study identified the importance of the efflux mechanism in the soil resistome and variations between the intrinsic resistance profiles of clinical and soil bacteria of the same family.
The plasmids of the incompatibility (Inc) group IncP-1, also called IncP, as extrachromosomal gen... more The plasmids of the incompatibility (Inc) group IncP-1, also called IncP, as extrachromosomal genetic elements can transfer and replicate virtually in all Gram-negative bacteria. They are composed of backbone genes that encode a variety of essential functions and accessory genes that have implications for human health and environmental bioremediation. Broadhost-range IncP plasmids are known to spread genes between distinct phylogenetic groups of bacteria. These genes often code for resistances to a broad spectrum of antibiotics, heavy metals, and quaternary ammonium compounds used as disinfectants. The backbone of these plasmids carries modules that enable them to effectively replicate, move to a new host via conjugative transfer and to be stably maintained in bacterial cells. The adaptive, resistance, and virulence genes are mainly located on mobile genetic elements integrated between the functional plasmid backbone modules. Environmental studies have demonstrated the wide distribution of IncP-like replicons in manure, soils and wastewater treatment plants. They also are present in strains of pathogenic or opportunistic bacteria, which can be a cause for concern, because they may encode multiresistance. Their broad distribution suggests that IncP plasmids play a crucial role in bacterial adaptation by utilizing horizontal gene transfer. This review summarizes the variety of genetic information and physiological functions carried by IncP plasmids, which can contribute to the spread of antibiotic and heavy metal resistance while also mediating the process of bioremediation of pollutants. Due to the location of the resistance genes on plasmids with a broad-hostrange and the presence of transposons carrying these genes it seems that the spread of these genes would be possible and quite hazardous in infection control. Future studies are required to determine the level of risk of the spread of resistance genes located on these plasmids.
Antibiotic application in plant agriculture is primarily used to control fire blight caused by Er... more Antibiotic application in plant agriculture is primarily used to control fire blight caused by Erwinia amylovora in pome fruit orchards. In order to facilitate environmental impact assessment for antibiotic applications, we developed and validated culture-independent quantitative real-time PCR multiplex assays for streptomycin (strA, strB, aadA and insertion sequence IS1133) and tetracycline (tetB, tetM and tetW) resistance elements in plant and soil samples. The qPCR were reproducible and consistent whether the DNA was extracted directly from bacteria, plant and soil samples inoculated with bacteria or soil samples prior to and after manure slurry treatment. The genes most frequently identified in soils pre-and post-slurry treatment were strB, aadA, tetB and tetM. All genes tested were detected in soils pre-slurry treatment, and a decrease in relative concentrations of tetB and the streptomycin resistance genes was observed in samples taken post-slurry treatment. These multiplex qPCR assays offer a cost-effective, reliable method for simultaneous quantification of antibiotic resistance genes in complex, environmental sample matrices.
In this study, the frequency of extended-spectrum b-lactamases (ESBL) and plasmid-mediated quinol... more In this study, the frequency of extended-spectrum b-lactamases (ESBL) and plasmid-mediated quinolone resistance (PMQR) mechanisms were investigated in 206 clinical isolates of thirdgeneration cephalosporin (3GC)-resistant Enterobacteriaceae in four hospitals in the Republic of Ireland. bla CTX-M-15 was the predominant ESBL gene. Of these 3GC resistant isolates, 54 % were also resistant to ciprofloxacin. Investigation of the PMQR mechanisms revealed that the aac(69) Ib-cr gene predominated in fluoroquinolone-resistant (FQR) strains of Escherichia coli and Klebsiella pneumoniae, while the qnrA gene predominated in the FQR strains of Enterobacter. The bla CTX-M-15 gene was frequently identified with the aac(69)Ib-cr gene but was not always on the same plasmid. The prevalence of the bla CTX-M-15 gene appeared to be hospital-dependent. The epidemiology of both ESBL-producing and PMQR strains within the four hospitals indicated that their prevalence is not due to the spread of these resistance genes between isolates from different hospitals.
International Journal of Antimicrobial Agents, 2010
HAL is a multidisciplinary open access archive for the deposit and dissemination of scientific re... more HAL is a multidisciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.
International Journal of Antimicrobial Agents, 2003
Faropenem is a new oral penem with a structure different from current b-lactams including carbape... more Faropenem is a new oral penem with a structure different from current b-lactams including carbapenems. The susceptibility of Streptococcus pneumoniae , Haemophilus influenzae and Moraxella catarrhalis to faropenem, a macrolide, a b-lactam, a b-lactam/blactamase inhibitor combination and two fluoroquinolones was investigated. S. pneumoniae was the most susceptible of the three species to faropenem. The MIC 90 s of faropenem against M. catarrhalis and H. influenzae were 0.5 and 1 mg/l, respectively. They were similar to amoxiclav (MIC 90 s of 0.25 and 0.5 mg/l). The quinolones showed strong activity against H. influenzae. A cluster analysis of the activities of amoxycillin and faropenem demonstrated a direct relationship between the two antimicrobial agent's activities and resistance profiles against both S. pneumoniae and H. influenzae .
International Journal of Antimicrobial Agents, 2013
Antibiotic resistance concerns have been compounded by a report that soil bacteria can catabolise... more Antibiotic resistance concerns have been compounded by a report that soil bacteria can catabolise antibiotics, i.e. break down and use them as a sole carbon source. To date this has not been verified or reproduced, therefore in this study soil bacteria were screened to verify and reproduce this hypothesis. Survival in high concentrations of antibiotics was initially observed; however, on further analysis these bacteria either did not degrade the antibiotics or they used an intrinsic resistance mechanism (lactamases) to degrade the -lactams, as demonstrated by high-performance liquid chromatography. These results did not verify or reproduce the hypothesis that bacteria subsist on antibiotics or catabolise antibiotics as previously reported. This study identified that bacteria with a catabolising phenotype did not degrade streptomycin or trimethoprim and therefore could not utilise the antibiotics as a nutrient source. Therefore, we conclude that soil bacteria do not catabolise antibiotics.
Streptomycin is used as a first-line defense and tetracycline as a second-line defense, in the fi... more Streptomycin is used as a first-line defense and tetracycline as a second-line defense, in the fight against fire blight disease in apple and pear orchards. We have performed the first study to quantitatively analyze the influence of streptomycin use in agriculture on the abundance of streptomycin and tetracycline resistance genes in apple orchards. Flowers, leaves, and soil were collected from three orchard sites in 2010, 2011, and 2012. Gene abundance distribution was analyzed using two-way ANOVA and principal component analysis to investigate relationships between gene abundance data over time and treatment. The mobile antibiotic resistance genes, strA, strB, tetB, tetM, tetW, and the insertion sequence IS1133, were detected prior to streptomycin treatment in almost all samples, indicating the natural presence of these resistance genes in nature. Statistically significant increases in the resistance gene abundances were occasional, inconsistent, and not reproducible from one year to the next. We conclude that the application of streptomycin in these orchards was not associated with sustained increases in streptomycin or tetracycline resistance gene abundances.
This study examined differences in antibiotic-resistant soil bacteria and the presence and quanti... more This study examined differences in antibiotic-resistant soil bacteria and the presence and quantity of resistance genes in soils with a range of management histories. We analyzed four soils from agricultural systems that were amended with manure from animals treated with erythromycin and exposed to streptomycin and/or oxytetracycline, as well as non-manure-amended compost and forest soil. Low concentrations of certain antibiotic resistance genes were detected using multiplex quantitative real-time PCR (qPCR), with tet (B), aad (A), and str (A) each present in only one soil and tet (M) and tet (W) detected in all soils. The most frequently detected resistance genes were tet (B), tet (D), tet (O), tet (T), and tet (W) for tetracycline resistance, str (A), str (B), and aac for streptomycin resistance, and erm (C), erm (V), erm (X), msr (A), ole (B), and vga for erythromycin resistance. Transposon genes specific for Tn 916 , Tn 1549 , Tn B1230 , Tn 4451 , and Tn 5397 were detected in so...
All supporting data, code and protocols have been provided within the article or through suppleme... more All supporting data, code and protocols have been provided within the article or through supplementary data files.One supplementary file and four supplementary tables are available with the online version of this article.
In this article, the current knowledge and knowledge gaps in the emergence and spread of antimicr... more In this article, the current knowledge and knowledge gaps in the emergence and spread of antimicrobial resistance (AMR) in livestock and plants and importance in terms of animal and human health are discussed. Some recommendations are provided for generation of the data required in order to develop risk assessments for AMR within agriculture and for risks through the food chain to animals and humans.
Tackling antibiotic resistance: the environmental framework.
Antibiotic resistance is a threat to human and animal health worldwide, and key measures are requ... more Antibiotic resistance is a threat to human and animal health worldwide, and key measures are required to reduce the risks posed by antibiotic resistance genes that occur in the environment. These measures include the identification of critical points of control, the development of reliable surveillance and risk assessment procedures, and the implementation of technological solutions that can prevent environmental contamination with antibiotic resistant bacteria and genes. In this Opinion article, we discuss the main knowledge gaps, the future research needs and the policy and management options that should be prioritized to tackle antibiotic resistance in the environment.
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