Validating the NCBI AMRFinder Tool and Resistance Gene Database Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of NARMS Isolates.

Validating the NCBI AMRFinder Tool and Resistance Gene Database Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of NARMS Isolates. Antimicrob Agents Chemother. 2019 Aug 19;: Authors: Feldgarden M, Brover V, Haft DH, Prasad AB, Slotta DJ, Tolstoy I, Tyson GH, Zhao S, Hsu CH, McDermott PF, Tadesse DA, Morales C, Simmons M, Tillman G, Wasilenko J, Folster JP, Klimke W Abstract Antimicrobial resistance (AMR) is a major public health problem that requires publicly available tools for rapid analysis. To identify AMR genes in whole genome sequences, the National Center for Biotechnology Information (NCBI) has produced AMRFinder, a tool that identifies AMR genes using a high-quality curated AMR gene reference database. The Bacterial Antimicrobial Resistance Reference Gene Database consists of up-to-date gene nomenclature, a set of hidden Markov models (HMMs), and a curated protein family hierarchy. Currently, it contains 4,579 antimicrobial resistance proteins and more than 560 HMMs.Here, we describe AMRFinder and its associated database. To assess the predictive ability of AMRFinder, we measured the consistency between predicted AMR genotypes from AMRFinder and resistance phenotypes of 6,242 isolates from the National Antimicrobial Resistance Monitoring System (NARMS). This included 5,425 Salmonella enterica, 770 Campylobacter spp., and 47 Escherichia coli phenotypically tested against various antimicrobial agents. Of 87,679 susce...
Source: Antimicrobial Agents and Chemotherapy - Category: Microbiology Authors: Tags: Antimicrob Agents Chemother Source Type: research

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ConclusionsWhen fed at approved dosages for typical durations, tylosin increases the proportion of macrolide-resistant enterococci in the cattle gastrointestinal tract, which could pose a zoonotic risk to human beef consumers. Feeding tylosin for short durations may mitigate the impact on macrolide-resistant enterococci and further studies are encouraged to determine the effect of minimizing or eliminating tylosin use in beef cattle. There may also be an impact on other bacteria and other antimicrobial resistances but additional details or data are needed to strengthen these comparisons. We encourage authors of antimicrobi...
Source: Preventive Veterinary Medicine - Category: Veterinary Research Source Type: research
Abstract Wild birds have been the focus of a great deal of research investigating the epidemiology of zoonotic bacteria and antimicrobial resistance in the environment. While enteric pathogens (e.g. Campylobacter, Salmonella, and E. coli O157:H7) and antimicrobial resistant bacteria of public health importance have been isolated from a wide variety of wild bird species, there is a considerable variation in the measured prevalence of a given microorganism from different studies. This variation may often reflect differences in certain ecological and biological factors such as feeding habits and immune status. Variat...
Source: Animal Health Research Reviews - Category: Veterinary Research Authors: Tags: Anim Health Res Rev Source Type: research
te; T Abstract Bacteria within biofilms are more resistant to antibiotics and chemical agents than planktonic bacteria in suspension. Treatment of biofilm-associated infections inevitably involves high dosages and prolonged courses of antimicrobial agents; therefore, there is a potential risk of the development of antimicrobial resistance (AMR). Due to the high prevalence of AMR and its association with biofilm formation, investigation of more effective anti-biofilm agents is required. From ancient times, herbs and spices have been used to preserve foods, and their antimicrobial, anti-biofilm and anti-quorum sensi...
Source: Current Pharmaceutical Design - Category: Drugs & Pharmacology Authors: Tags: Curr Pharm Des Source Type: research
Publication date: Available online 10 October 2019Source: Comparative Immunology, Microbiology and Infectious DiseasesAuthor(s): Bárbara Martín-Maldonado, Laura Montoro-Dasi, Maria Teresa Pérez-Gracia, Jaume Jordá, Santiago Vega, Francisco Marco-Jiménez, Clara MarinAbstractWild birds have repeatedly been found to be involved in the dissemination of enteric bacterial pathogens in the environment. The aim of this study was to determine the occurrence of Salmonella and Campylobacter as well as the antimicrobial resistance in wild Bonelli’s eagles nestlings in Eastern Spain. In addition...
Source: Comparative Immunology, Microbiology and Infectious Diseases - Category: Infectious Diseases Source Type: research
ménez F, Marin C Abstract Wild birds have repeatedly been found to be involved in the dissemination of enteric bacterial pathogens in the environment. The aim of this study was to determine the occurrence of Salmonella and Campylobacter as well as the antimicrobial resistance in wild Bonelli's eagles nestlings in Eastern Spain. In addition, we compared the efficiency of two sampling methods (fresh faecal samples from nest and cloacal swabs from nestlings) for detection of both bacteria. A total of 28 nests with 45 nestlings were analysed. In the nest, Salmonella occurrence was 61 ± 9.2%...
Source: Comparative immunology, microbiology and infectious diseases. - Category: Allergy & Immunology Authors: Tags: Comp Immunol Microbiol Infect Dis Source Type: research
Source: European Union, European Centre for Disease Prevention and Control (ECDC). Published: 5/28/2019. This 25-page report presents the results of the third round of the external quality assessment on antimicrobial susceptibility testing for national public health laboratories for Campylobacter (Campylobacter EQA3-AST) within the Food- and Waterborne Diseases and Zoonoses Network (FWD-Net). It is part of a European Union protocol for harmonized monitoring of antimicrobial resistance in human Salmonella and Campylobacter isolates. Campylobacteriosis, followed by salmonellosis, is the leading cause of zoonotic foodborne d...
Source: Disaster Lit: Resource Guide for Disaster Medicine and Public Health - Category: International Medicine & Public Health Source Type: news
This study aims to investigate the occurrences and epidemiology of selected bacterial (Salmonella spp. and Campylobacter spp.), viral (adenovirus, norovirus GI and GII, and astrovirus), and parasitic (Entamoeba spp. and Giardia spp.) agents in stool samples from 155 child diarrheal cases enrolled between March and August 2017, in a hospital-based cross-sectional study in Thi-Qar, southeastern Iraq. Using molecular techniques and sequence-based characterization, adenovirus was the most frequently detected enteropathogen (53/155 (34.2%)), followed by Salmonella spp. (23/155 (14.8%)), Entamoeba spp. (21/155 (13.5%)), and Camp...
Source: International Journal of Environmental Research and Public Health - Category: Environmental Health Authors: Tags: Article Source Type: research
Conclusion This study confirms the in vitro antibacterial activity of BIOCITRO® against Gram-negative and Gram-positive bacteria. For most of the strains, the product reached the bactericidal effect at the same concentration of the bacteriostatic effect and maximum difference between MIC and MBC was two dilution steps. The less susceptible species of the study were S. enterica ssp. enterica and E. coli with MBC90 values of 256 and 128 μg/mL, respectively, while the most susceptible was C. perfringens with MBC90 of 16 μg/mL. After short exposition time to the product, the significant effect over the viability of ...
Source: Frontiers in Microbiology - Category: Microbiology Source Type: research
Conclusion Genomic analyses herein performed allowed us to confirm the recently (Pérez-Cataluña et al., 2018a,b) suggested amendment of A. butzleri as Al. butzlerii, comb. nov. Antimicrobial susceptibility tests defined Ab 55 and Ab 6V strains as resistant to vancomycin, tetracyclin, nalidixic acid (only Ab 55 whereas Ab 6V is intermediate resistant), erythromycin, and β-lactam antibiotics. Moreover, in our strains isolated from shellfish, we identified numerous virulence, antibiotic, and heavy metal resistance determinants, also additional to those previously found in the genome sequenced A. butzleri ...
Source: Frontiers in Microbiology - Category: Microbiology Source Type: research
In conclusion, association rule mining is an effective tool for identifying patterns of multidrug resistance within antimicrobial susceptibility testing data and evaluating the statistical and biological significance of the patterns. Rule quality measures used to sort and differentiate rules should be tested using resampling procedures to minimize the false discovery rate. Rule mining identified consistent multidrug resistance patterns involving beta-lactams, sulfisoxazole, tetracycline, gentamicin, and streptomycin in E. coli isolated from chicken carcasses and meat between 2004 and 2012. The generally low rule overlap su...
Source: Frontiers in Microbiology - Category: Microbiology Source Type: research
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