scholarly journals One Health genomic surveillance ofEscherichia colidemonstrates distinct lineages and mobile genetic elements in isolates from humans versus livestock

2018 ◽  
Author(s):  
Catherine Ludden ◽  
Kathy E. Raven ◽  
Dorota Jamrozy ◽  
Theodore Gouliouris ◽  
Beth Blane ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Bloodstream Infection ◽  
Resistance Genes ◽  
One Health ◽  
Core Genome ◽  
Mobile Genetic Elements ◽  
E Coli ◽  
Genetic Elements ◽  
Antimicrobial Resistance Genes ◽  
Livestock Farms

ABSTRACTLivestock have been proposed as a reservoir for drug-resistantEscherichia colithat infect humans. We isolated and sequenced 431E. coli(including 155 ESBL-producing isolates) from cross-sectional surveys of livestock farms and retail meat in the East of England. These were compared with the genomes of 1517E. coliassociated with bloodstream infection in the United Kingdom. Phylogenetic core genome comparisons demonstrated that livestock and patient isolates were genetically distinct, indicating thatE. colicausing serious human infection do not directly originate from livestock. By contrast, we observed highly related isolates from the same animal species on different farms. Analysis of accessory (variable) genomes identified a virulence cassette associated previously with cystitis and neonatal meningitis that was only present in isolates from humans. Screening all 1948 isolates for accessory genes encoding antibiotic resistance revealed 41 different genes present in variable proportions of humans and livestock isolates. We identified a low prevalence of shared antimicrobial resistance genes between livestock and humans based on analysis of mobile genetic elements and long-read sequencing. We conclude that in this setting, there was limited evidence to support the suggestion that antimicrobial resistant pathogens that cause serious infection in humans originate from livestock.ImportanceThe increasing prevalence ofE. colibloodstream infections is a serious public health problem. We used genomic epidemiology in a One Health study conducted in the East of England to examine putative sources ofE. coliassociated with serious human disease.E. colifrom 1517 patients with bloodstream infection were compared with 431 isolates from livestock farms and meat. Livestock-associated and bloodstream isolates were genetically distinct populations based on core genome and accessory genome analyses. Identical antimicrobial resistance genes were found in livestock and human isolates, but there was little overlap in the mobile elements carrying these genes. In addition, a virulence cassette found in humans isolates was not identified in any livestock-associated isolate. Our findings do not support the idea thatE. colicausing invasive disease or their resistance genes are commonly acquired from livestock.

scholarly journals One Health Genomic Surveillance ofEscherichia coliDemonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock

mBio ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Catherine Ludden ◽  
Kathy E. Raven ◽  
Dorota Jamrozy ◽  
Theodore Gouliouris ◽  
Beth Blane ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
One Health ◽  
Core Genome ◽  
Bloodstream Infections ◽  
Mobile Genetic Elements ◽  
Human Infection ◽  
Content Type ◽  
E Coli ◽  
Antimicrobial Resistance Genes

ABSTRACTLivestock have been proposed as a reservoir for drug-resistantEscherichia colithat infect humans. We isolated and sequenced 431E. coliisolates (including 155 extended-spectrum β-lactamase [ESBL]-producing isolates) from cross-sectional surveys of livestock farms and retail meat in the East of England. These were compared with the genomes of 1,517E. colibacteria associated with bloodstream infection in the United Kingdom. Phylogenetic core genome comparisons demonstrated that livestock and patient isolates were genetically distinct, suggesting thatE. colicausing serious human infection had not directly originated from livestock. In contrast, we observed highly related isolates from the same animal species on different farms. Screening all 1,948 isolates for accessory genes encoding antibiotic resistance revealed 41 different genes present in variable proportions in human and livestock isolates. Overall, we identified a low prevalence of shared antimicrobial resistance genes between livestock and humans based on analysis of mobile genetic elements and long-read sequencing. We conclude that within the confines of our sampling framework, there was limited evidence that antimicrobial-resistant pathogens associated with serious human infection had originated from livestock in our region.IMPORTANCEThe increasing prevalence ofE. colibloodstream infections is a serious public health problem. We used genomic epidemiology in a One Health study conducted in the East of England to examine putative sources ofE. coliassociated with serious human disease.E. colifrom 1,517 patients with bloodstream infections were compared with 431 isolates from livestock farms and meat. Livestock-associated and bloodstream isolates were genetically distinct populations based on core genome and accessory genome analyses. Identical antimicrobial resistance genes were found in livestock and human isolates, but there was limited overlap in the mobile elements carrying these genes. Within the limitations of sampling, our findings do not support the idea thatE. colicausing invasive disease or their resistance genes are commonly acquired from livestock in our region.

scholarly journals Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder

2020 ◽  
Vol 76 (1) ◽  
pp. 101-109 ◽  
Author(s):  
Markus H K Johansson ◽  
Valeria Bortolaia ◽  
Supathep Tansirichaiya ◽  
Frank M Aarestrup ◽  
Adam P Roberts ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Salmonella Enterica ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Mobile Genetic Elements ◽  
Metal Resistance ◽  
Animal Origin ◽  
Genetic Elements ◽  
Antimicrobial Resistance Genes

Abstract Objectives Antimicrobial resistance (AMR) in clinically relevant bacteria is a growing threat to public health globally. In these bacteria, antimicrobial resistance genes are often associated with mobile genetic elements (MGEs), which promote their mobility, enabling them to rapidly spread throughout a bacterial community. Methods The tool MobileElementFinder was developed to enable rapid detection of MGEs and their genetic context in assembled sequence data. MGEs are detected based on sequence similarity to a database of 4452 known elements augmented with annotation of resistance genes, virulence factors and detection of plasmids. Results MobileElementFinder was applied to analyse the mobilome of 1725 sequenced Salmonella enterica isolates of animal origin from Denmark, Germany and the USA. We found that the MGEs were seemingly conserved according to multilocus ST and not restricted to either the host or the country of origin. Moreover, we identified putative translocatable units for specific aminoglycoside, sulphonamide and tetracycline genes. Several putative composite transposons were predicted that could mobilize, among others, AMR, metal resistance and phosphodiesterase genes associated with macrophage survivability. This is, to our knowledge, the first time the phosphodiesterase-like pdeL has been found to be potentially mobilized into S. enterica. Conclusions MobileElementFinder is a powerful tool to study the epidemiology of MGEs in a large number of genome sequences and to determine the potential for genomic plasticity of bacteria. This web service provides a convenient method of detecting MGEs in assembled sequence data. MobileElementFinder can be accessed at https://cge.cbs.dtu.dk/services/MobileElementFinder/.

scholarly journals Virulence potential of a multidrug-resistant Escherichia coli strain belonging to the emerging clonal group ST101-B1 isolated from bloodstream infection

2019 ◽  
Author(s):  
Ana Carolina de Mello Santos ◽  
Rosa Maria Silva ◽  
Tiago Barcelos Valiatti ◽  
Fernanda Fernandes dos Santos ◽  
José Francisco Santos-Neto ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Bloodstream Infection ◽  
Resistance Genes ◽  
Multidrug Resistant ◽  
Phylogenetic Group ◽  
E Coli ◽  
Extraintestinal Infection ◽  
Virulence Potential ◽  
Antimicrobial Resistance Genes

AbstractEscherichia coli EC121 is a multidrug-resistant (MDR) strain isolated from bloodstream infection of an inpatient with persistent gastroenteritis and Zone T lymphoma, that died due to septic shock. Despite causing an extraintestinal infection, it harbors few known virulence factors and was assigned into phylogenetic group B1. To evaluate if the EC121 was pathogenic or opportunistic, its genome was sequenced, and an in vitro characterization of some pathogenicity-associated properties was performed. The data retrieved from genome analysis showed that E. coli strain EC121 belongs to the O154:H25 serotype, and to ST101-B1, which was epidemiologically linked to extraintestinal infections and antimicrobial resistance spread as well. Moreover, it was closely related to Shiga-toxin producing E. coli (STEC). Besides, strain EC121 is an MDR strain harboring 14 antimicrobial resistance genes, including blaCTX-M-2, and more than 50 complete virulence genetic clusters, which are reported to be associated either with DEC or ExPEC. The strain also displays the capacity to adhere to a variety of cell lineages, and invade T24 bladder cells, as well as the ability to form biofilms on abiotic surfaces, and survive the bactericidal serum complement activity. Additionally, it is virulent in the Galleria mellonella model. Altogether, E. coli EC121 unveiled to be a pathogen powered by its multi-drug resistance characteristic. Carry out studies providing accurate information about the virulence potential of all kinds of MDR strains are essential because these studies will help in the development of alternative therapies of infection management and spread control of MDR strains.Authors summaryThe phylogenetic origin of extraintestinal pathogenic Escherichia coli is mostly associated with phylogroup B2, and the majority of the studies regarding extraintestinal infection focus on the most virulent strains, which might also present multidrug-resistant (MDR) phenotype. Strains belonging to phylogroup B1 and isolated from extraintestinal infections are considered as opportunist pathogens and have their virulence neglected. We focus our study in one MDR strain isolated from bloodstream infection that belongs to phylogenetic group B1 to enlarge the knowledge about the virulence of this kind of strain. We demonstrated that the EC121 is capable of adheres to intestinal and bladder human cells, and invades the latter one; it survives to human serum bactericidal effects and produces biofilm. Additionally, the in vivo assay confirmed the EC121 virulence, showing that it should be considered a pathogenic strain. The genetic analyzes highlighted important aspects of EC121 which are typical from strains of sequence type 101, like its involvement in the spread of antimicrobial resistance genes and its relationship with extraintestinal infection from diverse sources. Information concerning the virulence of MDR strains is important for the development of global actions treating the spread of antimicrobial resistance, as well as to elucidate the pathogenesis of strains that were considered as an opportunist.

scholarly journals Comparison of microbiota, antimicrobial resistance genes and mobile genetic elements in flies and the feces of sympatric animals

2020 ◽  
Vol 96 (4) ◽  
Author(s):  
Anil Poudel ◽  
Yuan Kang ◽  
Rabindra K Mandal ◽  
Anwar Kalalah ◽  
Patrick Butaye ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Mobile Genetic Elements ◽  
Fecal Samples ◽  
Bacterial Phyla ◽  
Genetic Elements ◽  
Antimicrobial Resistance Genes ◽  
Microbial Analysis ◽  
Qpcr Array ◽  
Curtis Dissimilarity

ABSTRACT Flies are well-known vectors of bacterial pathogens, but there are little data on their role in spreading microbial community and antimicrobial resistance. In this study, we compared the bacterial community, antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) in flies with those in the feces of sympatric animals. A 16S rRNA-based microbial analysis identified 23 bacterial phyla in fecal samples and 25 phyla in flies; all the phyla identified in the fecal samples were also found in the flies. Bray–Curtis dissimilarity analysis showed that the microbiota of the flies were more similar to the microbiota of the feces of their sympatric animals than those of the feces from the three other animal species studied. The qPCR array amplified 276 ARGs/MGEs in fecal samples, and 216 ARGs/MGEs in the flies, while 198 of these genes were identified in both flies and feces. Long-term studies with larger sample numbers from more geospatially distinct populations and infection trials are indicated to further evaluate the possibility of flies as sentinels for antimicrobial resistance.

scholarly journals Clostridioides difficile as a Dynamic Vehicle for the Dissemination of Antimicrobial-Resistance Determinants: Review and In Silico Analysis

2021 ◽  
Vol 9 (7) ◽  
pp. 1383
Author(s):  
Philip Kartalidis ◽  
Anargyros Skoulakis ◽  
Katerina Tsilipounidaki ◽  
Zoi Florou ◽  
Εfthymia Petinaki ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
In Silico ◽  
In Silico Analysis ◽  
Mobile Genetic Elements ◽  
Genetic Elements ◽  
Clostridioides Difficile ◽  
Antimicrobial Resistance Genes ◽  
Silico Analysis

The present paper is divided into two parts. The first part focuses on the role of Clostridioides difficile in the accumulation of genes associated with antimicrobial resistance and then the transmission of them to other pathogenic bacteria occupying the same human intestinal niche. The second part describes an in silico analysis of the genomes of C. difficile available in GenBank, with regard to the presence of mobile genetic elements and antimicrobial resistance genes. The diversity of the C. difficile genome is discussed, and the current status of resistance of the organisms to various antimicrobial agents is reviewed. The role of transposons associated with antimicrobial resistance is appraised; the importance of plasmids associated with antimicrobial resistance is discussed, and the significance of bacteriophages as a potential shuttle for antimicrobial resistance genes is presented. In the in silico study, 1101 C. difficile genomes were found to harbor mobile genetic elements; Tn6009, Tn6105, CTn7 and Tn6192, Tn6194 and IS256 were the ones more frequently identified. The genes most commonly harbored therein were: ermB, blaCDD, vanT, vanR, vanG and vanS. Tn6194 was likely associated with resistance to erythromycin, Tn6192 and CTn7 with resistance to the β-lactams and vancomycin, IS256 with resistance to aminoglycoside and Tn6105 to vancomycin.

scholarly journals Antimicrobial Resistance Genes in ESBL-Producing Escherichia coli Isolates from Animals in Greece

Antibiotics ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 389
Author(s):  
Zoi Athanasakopoulou ◽  
Martin Reinicke ◽  
Celia Diezel ◽  
Marina Sofia ◽  
Dimitris C. Chatzopoulos ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Multidrug Resistance ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Wild Bird ◽  
One Health ◽  
Multidrug Resistant ◽  
E Coli ◽  
Antimicrobial Resistance Genes ◽  
Multidrug Resistance Genes

The prevalence of multidrug resistant, extended spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is increasing worldwide. The present study aimed to provide an overview of the multidrug resistance phenotype and genotype of ESBL-producing Escherichia coli (E. coli) isolates of livestock and wild bird origin in Greece. Nineteen phenotypically confirmed ESBL-producing E. coli strains isolated from fecal samples of cattle (n = 7), pigs (n = 11) and a Eurasian magpie that presented resistance to at least one class of non β-lactam antibiotics, were selected and genotypically characterized. A DNA-microarray based assay was used, which allows the detection of various genes associated with antimicrobial resistance. All isolates harbored blaCTX-M-1/15, while blaTEM was co-detected in 13 of them. The AmpC gene blaMIR was additionally detected in one strain. Resistance genes were also reported for aminoglycosides in all 19 isolates, for quinolones in 6, for sulfonamides in 17, for trimethoprim in 14, and for macrolides in 8. The intI1 and/or tnpISEcp1 genes, associated with mobile genetic elements, were identified in all but two isolates. This report describes the first detection of multidrug resistance genes among ESBL-producing E. coli strains retrieved from feces of cattle, pigs, and a wild bird in Greece, underlining their dissemination in diverse ecosystems and emphasizing the need for a One-Health approach when addressing the issue of antimicrobial resistance.

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