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Antimicrobial resistance monitoring results complementing the EU Overview Summary Report on AMR in zoonotic and indicator bacteria from humans, animals and food in 2017/2018 - Spain

This dataset contains AMR monitoring results in animals and food at the isolate level pursuant to Article 9 of Directive 2003/99/EC and to Annex, part B, of Commission implementing Decision 2013/652/EU. In addition, the dataset includes any other results from isolates than the ones mentioned in the Commission implementing Decision 2013/652/EU. The quantitative minimum inhibitory concentration (MIC) data from dilution methods are included. REPORTING AUTHORITIES CONTRIBUTING TO EACH DATA COLLECTION: AMR_2018_ES_20200204: >> Agencia Espaola de Consumo, Seguridad Alimentaria y Nutricin >> Ministerio de Agricultura, Pesca y Alimentacin

Specific monitoring results of ESBL-/AmpC-/carbapenemase-producing bacteria and specific monitoring of carbapenemase-producing bacteria, in the absence of isolates detected complementing the European Union Overview Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2017/2018

This dataset derives from the specific monitoring of E. coli producers of ESBLs/AmpC/carbapenemases, as well as the specific monitoring of carbapenemase-producers (voluntary reporting), in the absence of any isolates detected. This dataset contains only data when Total units positive equals zero '0'.

Antimicrobial resistance monitoring results complementing the EU Overview Summary Report on AMR in zoonotic and indicator bacteria from humans, animals and food in 2017/2018 - Cyprus

This dataset contains AMR monitoring results in animals and food at the isolate level pursuant to Article 9 of Directive 2003/99/EC and to Annex, part B, of Commission implementing Decision 2013/652/EU. In addition, the dataset includes any other results from isolates than the ones mentioned in the Commission implementing Decision 2013/652/EU. The quantitative minimum inhibitory concentration (MIC) data from dilution methods are included. REPORTING AUTHORITIES CONTRIBUTING TO EACH DATA COLLECTION: AMR_2018_CY_20200204: >> Ministry of Agriculture, Natural Resources and Evironment - Veterinary Services

Antimicrobial resistance monitoring results complementing the EU Overview Summary Report on AMR in zoonotic and indicator bacteria from humans, animals and food in 2017/2018 - Iceland

This dataset contains AMR monitoring results in animals and food at the isolate level pursuant to Article 9 of Directive 2003/99/EC and to Annex, part B, of Commission implementing Decision 2013/652/EU. In addition, the dataset includes any other results from isolates than the ones mentioned in the Commission implementing Decision 2013/652/EU. The quantitative minimum inhibitory concentration (MIC) data from dilution methods are included. REPORTING AUTHORITIES CONTRIBUTING TO EACH DATA COLLECTION: AMR_2018_IS_20200204: >> Icelandic Food and Veterinary Authority

opencc-by-4.0Mar 2017View details →

Dataset for Antimicrobial resistance of Neisseria gonorrhoeae in Germany: low levels of cephalosporin resistance but rising azithromycin resistance

This is Dataset used for Publication "Antimicrobial resistance of Neisseria gonorrhoeae in Germany: low levels of cephalosporin resistance but rising azithromycin resistance" and contains data on Information on performed Neisseria gonorrhoeae AMR tests in sentinel Laboratories as well as AMR testing in consiliary Laboratory.

opencc-by-4.0Oct 2023View details →

Phytochemical Analysis and Antimicrobial Studies of Leaves and Roots of P. angulata

Quantifying the bioactive compounds present in plant parts (leaves and roots). This study aimed to perform comprehensive qualitative phytochemical analysis  and antimicrobial  analysis of extract of leaves and roots of p.angulata. phytochemicals test where carried out on the extracts to detect the presence of phytochemicals such as phenols, flavonoids, saponins, alkaloids, tannins and terpenoids etc. Different chemical tests were employed to confirm the presence of these compounds. The color change indicates the presence of specific phytochemicals. The results obtained from the qualitative analysis revealed the presence of phenols, flavonoids, saponins, alkaloids, tannins, terpenoids, phlobatannins, anthraquinones, glycosides and steroids in both the leaves and roots part of the plant. However the results of the antimicrobial test obtained from the extracts of  both leaves and roots extracts of Physalis angulata revealed that both the crude extracts of the leaves and roots inhibited Anti-microbial activities against Bacillus species, Styphylococcus aureus, Plasmodium parasites and Streptococcus species except the leaves  extract of acetone which does not act against Styphylococcus aureus. The facts that the plant was active against laboratory isolates are also an indication that the plant parts has medicinal values and Potential therapeutic or pharmacological properties. The findings of this analysis can be further utilized for developing drugs, functional foods, or dietary supplements with specific phytochemical.

opencc-zeroDec 2023View details →

Data from: Targeted treatment of injured nestmates with antimicrobial compounds in an ant society

Infected wounds pose a major mortality risk in animals. Injuries are common in the ant Megaponera analis, which raids pugnacious prey. Here we show that M. analis can determine when wounds are infected and treat them accordingly. By applying a variety of antimicrobial compounds and proteins secreted from the metapleural gland to infected wounds, workers reduce the mortality of infected individuals by 90%. Chemical analyses showed that wound infection is associated with specific changes in the cuticular hydrocarbon profile, thereby likely allowing nestmates to diagnose the infection state of injured individuals and apply the appropriate antimicrobial treatment. This study demonstrates that M. analis ant societies use antimicrobial compounds produced in the metapleural glands to treat infected wounds and reduce nestmate mortality.

opencc-zeroDec 2023View details →

Data from: Plant pathogenic bacterium Ralstonia solanacearum can rapidly evolve tolerance to antimicrobials produced by Pseudomonas biocontrol bacteria

Soil-borne plant pathogens significantly threaten crop production due to lack of effective control methods. One alternative to traditional agrochemicals is microbial biocontrol, where pathogen growth is suppressed by naturally occurring bacteria that produce antimicrobial chemicals. However, it is still unclear if pathogenic bacteria can evolve tolerance to biocontrol antimicrobials and if this could constrain the long-term efficacy of biocontrol strategies. Here we used an in vitro experimental evolution approach to investigate if the phytopathogenic Ralstonia solanacearum bacterium, which causes bacterial wilt disease, can evolve tolerance to antimicrobials produced by Pseudomonas bacteria. We further asked if tolerance was specific to pairs of R. solanacearum and Pseudomonas strain and certain antimicrobial compounds produced by Pseudomonas. We found that while all R. solanacearum strains could initially be inhibited by Pseudomonas strains, this inhibition decreased following successive subculturing with or without Pseudomonas supernatants. Using separate tolerance assays, we show that the majority of R. solanacearum strains evolved increased tolerance to multiple Pseudomonas strains. Mechanistically, evolved tolerance was most likely linked to reduced susceptibility to orfamide lipopeptide antimicrobials secreted by Pseudomonas strains in our experimental conditions. Some levels of tolerance also evolved in the control treatments, which was likely correlated response due to adaptations to the culture media. Together, these results suggest that plant-pathogenic bacteria can rapidly evolve increased tolerance to bacterial antimicrobial compounds, which could reduce the long-term efficacy of microbial biocontrol.

opencc-zeroDec 2022View details →

Genomic epidemiology of Escherichia coli: antimicrobial resistance through a One Health lens in sympatric humans, livestock and peri-domestic wildlife in Nairobi, Kenya

Background Livestock systems have been proposed as a reservoir for antimicrobial-resistant (AMR) bacteria and AMR genetic determinants that may infect or colonise humans, yet quantitative evidence regarding their epidemiological role remains lacking. Here we used a combination of genomics, epidemiology and ecology to investigate patterns of AMR gene carriage in Escherichia coli, regarded as a sentinel organism. Methods We conducted a structured epidemiological survey of 99 households across Nairobi, Kenya, and whole genome sequenced E. coli isolates from 311 human, 606 livestock, and 399 wildlife faecal samples. We used statistical models to investigate the prevalence of AMR carriage and characterise AMR gene diversity and structure of AMR genes in different host populations across the city. We also investigated house-hold level risk factors for exchange of AMR genes between sympatric humans and livestock. Findings We detected 56 unique acquired genes along with 13 point mutations present in variable proportions in human and animal isolates, known to confer resistance to nine antibiotic classes. We find that AMR gene community composition is not associated with host species, but AMR genes were frequently co-located, potentially enabling the acquisition and dispersal of multi-drug resistance in a single step. We find that whilst keeping livestock had no influence on human AMR gene carriage, the potential for AMR transmission across human-livestock interfaces is greatest when manure is poorly disposed of and in larger households. Conclusions Findings of widespread carriage of AMR bacteria in human and animal populations, including in long-distance wildlife species, in community settings, highlight the value of evidence-based surveillance to address antimicrobial resistance on a global scale. Our genomic analysis provided in-depth understanding of AMR determinants at the interfaces of One-Health sectors that will inform AMR prevention and control.

opencc-zeroApr 2024View details →

Direct synthesis, characterization, in vitro and in silico studies of simple chalcones as potential antimicrobial and antileishmanial agents

Chalcone represents a vital biosynthetic scaffold owing to its numerous therapeutic effects. The present study was intended to synthesize seventeen chalcone derivatives (3a-q) by direct coupling of substituted acetophenones and benzaldehyde. The target chalcones were characterized by spectroscopic analyses followed by their in vitro antimicrobial, and antileishmanial investigations with reference to standard drugs. The majority of the chalcones displayed good to excellent biological activities. Chalcone 3q (1000 μg/mL) exhibited the most potent antibacterial effect with its zone of inhibition values of 30, 33, and 34 mm versus Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa respectively. The results also confirmed chalcone 3q to be the most potent versus Leishmania major with the lowest IC50 value of 0.59±0.12 μg/mL. Chalcone 3i (500 μg/mL) was noticed to be the most potent antifungal agent with its zone of inhibition being 29 mm against Candida albicans. Computational studies of chalcones 3i and 3q supported the preliminary in vivo results. The existence of the amino moiety and bromine atom on ring-A and methoxy moieties on ring-B caused better biological effects of the chalcones. In brief, the investigations reveal that chalcones (3i and 3q) can be employed as building blocks to discover novel antimicrobial agents.

opencc-by-4.0Mar 2024View details →

Comprehensive study of antimicrobial polycaprolactone/clay nanocomposite films: preparation, characterization, properties and degradation in simulated body fluid

Even though the biodegradability of polycaprolactone (PCL) and its nanocomposites is lower compared to other biodegradable polyesters, this property and good biocompatibility are used for development of materials for drug delivery with a long-term effect. We prepared novel PCL/clay nanocomposite films with antimicrobials chlorhexidine (CH) or octenidine (OCT) combined with ZnO anchored on vermiculite (VER). The intercalation of CH and OCT into the interlayer of VER/ZnOVER was confirmed by XRD, FTIR and SEM. The organically modified nanofillers compared to VER (−46.0 mV) or ZnOVER (−34.9 mV) showed a positive ζ-potential (+30.7 mV (VER_CH), +21.9 mV (VER_OCT), +24.6 mV (ZnOVER_CH)) indicating a relatively stable materials, except ZnOVER_OCT (+8.6 mV), which strongly agglomerated. Thin PCL/clay films were prepared by solvent casting method and the effect of used nanofillers on structural, thermal, mechanical and antimicrobial properties followed by degradation under hydrolytic conditions was studied. The results showed that presence of ZnO significantly decreases thermal and mechanical stability. The nanofillers with the higher hydrophilic character are responsible for the fastest degradation of PCL matrix. Films possessed high antimicrobial efficiency in long time intervals, hence these nanocomposites open new avenues for the possible application of such materials for the drug delivery with a long-term effect.

opencc-by-4.0Nov 2024View details →

Data from: Antimicrobial resistance of Staphylococcus and Enterococcus bacteria in rural dogs in Hungary - a preliminary report

Antimicrobial resistance (AMR) is one of the most relevant health challenges globally. Since resistant bacteria and their resistance genes circulate through the ecosystem, AMR is among the main focuses of One Health. Dogs are the best friends of humans, therefore their relationships with the owners are mostly very close. This connection can make the dogs vehicles of AMR between the environment and humans. Based on this hypothesis, we investigated faecal samples from 37 dogs in Inner Somogy, Hungary. We isolated and investigated for antibiotic susceptibility 21 and 6 strains of Staphylococcus and Enterococcus genera, respectively. Among staphylococci and enterococci, 12 and 3 strains proved to be resistant to at least one antibiotic. Multidrug resistant strains were detected only among coagulase negative staphylococci, mainly in S. sciuri species. The antibiotics that proved to be inefficient against the most strains were benzylpenicillin (8 strains), moxifloxacin (6 strains), clindamycin (5 S. sciuri strains), and fusidic acid (12 strains). In the case of moxifloxacin and fusidic acid, the MIC excessed the EUCAST clinical breakpoint. Analysing the epidemiological background of the animals, outdoors keeping and higher income level of the owners seemed risk factors of AMR carrying, though the sample size of this study could not confirm statistically the apparent interdependence.

opencc-by-4.0Jun 2024View details →

E. coli ribosome phenotypes for antimicrobial susceptibility testing

This repository contains the anonymised images, masks, and metadata for "Ribosome Phenotypes Enable Rapid Antibiotic Susceptibility Testing in Escherichia coli". Code for training neural networks using these images can be found at <a href="https://github.com/KapanidisLab/ribosome_phenotype_classification">https://github.com/KapanidisLab/ribosome_phenotype_classification</a>. The data contains fluorescence microscopy images of E. coli MG1655 and clinical isolates, details of which can be found in the manuscript.

opencc-zeroDec 2020View details →

Data from: Chicken gut microbiome members limit the spread of an antimicrobial resistance plasmid in Escherichia coli

Plasmid-mediated antimicrobial resistance is a major contributor to the spread of resistance genes within bacterial communities. Successful plasmid spread depends upon a balance between plasmid fitness effects on the host and rates of horizontal transmission. While these key parameters are readily quantified in vitro, the influence of interactions with other microbiome members is largely unknown. Here, we investigated the influence of three genera of lactic acid bacteria (LAB) derived from the chicken gastrointestinal microbiome on the spread of an epidemic narrow-range ESBL resistance plasmid, IncI1 carrying blaCTX-M-1, in mixed cultures of isogenic Escherichia coli strains. Secreted products of LAB decreased E. coli growth rates in a genus-specific manner but did not affect plasmid transfer rates. Importantly, we quantified plasmid transfer rates by controlling for density-dependent mating opportunities. Parametrization of a mathematical model with our in vitro estimates illustrated that small fitness costs of plasmid carriage may tip the balance towards plasmid loss under growth conditions in the gastrointestinal tract. This work shows that microbial interactions can influence plasmid success and provides an experimental-theoretical framework for further study of plasmid transfer in a microbiome context.

opencc-by-4.0Jul 2021View details →

Assessment of animal diseases caused by bacteria resistant to antimicrobials: Cattle- Appendix B: Excel file with all data extracted

Information on all the full-text studies that were assessed, including the reason for exclusion for those that were excluded at the full-text screening and the data extracted from the included studies, can be consulted here.  The extensive literature review was carried out by the University of Copenhagen under the contract OC/EFSA/ALPHA/2020/02 – LOT 1 (https://ted.europa.eu/udl?uri=TED:NOTICE:457654-2020:TEXT:EN:HTML)

opencc-zeroOct 2021View details →

DRIAMS: Database of Resistance Information on Antimicrobials and MALDI-TOF Mass Spectra

Early administration of effective antimicrobial treatments is critical for the outcome of infections and the prevention of treatment resistance. Antimicrobial resistance testing enables the selection of optimal antibiotic treatments, but current culture-based techniques can take up to 72 hours to generate results. We have developed a novel machine learning approach to predict antimicrobial resistance directly from MALDI-TOF mass spectra profiles of clinical samples. We trained calibrated classifiers on a newly-created publicly available database of mass spectra profiles from clinically most relevant isolates with linked antimicrobial susceptibility phenotypes. The dataset combines more than 300,000 mass spectra with more than 750,000 antimicrobial resistance phenotypes from four medical institutions. Validation against a panel of clinically important pathogens, including Staphylococcus aureus, Escherichia coli, and Klebsiella pneumoniae, resulting in AUROC values of 0.80, 0.74, and 0.74 respectively, demonstrated the potential of using machine learning to substantially accelerate antimicrobial resistance determination and change of clinical management. Furthermore, a retrospective clinical case study found that implementation of this approach would have resulted in a beneficial change in the clinical treatment in 88% (8/9) of cases. MALDI-TOF mass spectra based machine learning may thus be an important new tool for treatment optimization and antibiotic stewardship.

opencc-by-4.0Jul 2021View details →

Assessment of animal diseases caused by bacteria resistant to antimicrobials: Fishes - Appendix B: Excel file with all data extracted

opencc-by-4.0Jul 2021View details →

Assessment of animal diseases caused by bacteria resistant to antimicrobials: Rabbits - Appendix B: Excel file with all data extracted

opencc-zeroMar 2022View details →

The lower airways microbiota and antimicrobial peptides indicate dysbiosis in sarcoidosis

Rationale: The role of the pulmonary microbiome in sarcoidosis is unknown. Objectives: The objectives of the current study was to: 1) Examine whether the pulmonary fungal and bacterial microbiota differed in patients with sarcoidosis compared with controls. 2) Examine whether there was an association between the microbiota and levels of the antimicrobial peptides (AMPs) in protected bronchoalveolar lavage (PBAL), indicating an interaction with the innate immune response. Methods: 35 sarcoidosis patients and 35 healthy controls underwent bronchoscopy and were sampled with oral wash (OW), protected BAL (PBAL) and left protected sterile brushes (LPSB). The fungal ITS1 region and the V3V4 region of the bacterial 16SrDNA gene were sequenced. Bioinformatic analyses were performed with QIIME 2. The AMPs secretory leucocyte protease inhibitor (SLPI) and human beta defensins 1 and 2 (hBD-1 & hBD-2), were measured in PBAL by enzyme linked immunosorbent assay (ELISA). Measurements and Main Results: Aspergillus dominated the PBAL samples in sarcoidosis. Differences in bacterial taxonomy were minor. There was no significant difference in fungal alpha diversity between sarcoidosis and controls, but the bacterial alpha diversity in sarcoidosis was significantly lower in OW (p=0.047) and PBAL (p=0.03) compared with controls. The beta diversity for sarcoidosis compared with controls differed for both fungi and bacteria. AMP levels were significantly lower in sarcoidosis compared to controls (SLPI & hBD-1: p<0.01). No significant correlations were found between a-diversity and AMPs. Conclusions: The pulmonary fungal and bacterial microbiota in sarcoidosis differed from controls, with lower antimicrobial peptides levels in sarcoidosis.