scholarly journals Microbiome and Antimicrobial Resistance Gene Dynamics in International Travelers

2018 ◽  
Author(s):  
Charles Langelier ◽  
Michael Graves ◽  
Katrina Kalantar ◽  
Saharai Caldera ◽  
Robert Durrant ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Antimicrobial Resistance ◽  
Gut Microbiota ◽  
Microbial Communities ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Antimicrobial Resistance Genes ◽  
Antimicrobial Resistance Gene ◽  
Global Exchange ◽  
Generation Sequencing

AbstractWe engaged metagenomic next generation sequencing to longitudinally assess the gut microbiota and antimicrobial resistomes of international travelers to understand global exchange of resistant organisms. Travel resulted in an increase in antimicrobial resistance genes and a greater proportion of Escherichia species within gut microbial communities without impacting diversity.

scholarly journals Antimicrobial resistance gene prevalence in a population of patients with advanced dementia is related to specific pathobionts

2019 ◽  
Author(s):  
Aislinn D. Rowan-Nash ◽  
Rafael Araos ◽  
Erika M.C. D’Agata ◽  
Peter Belenky
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Gene ◽  
Resistance Genes ◽  
High Frequency ◽  
Multidrug Resistant ◽  
Advanced Dementia ◽  
Dementia Patients ◽  
Antimicrobial Resistance Genes ◽  
Antimicrobial Resistance Gene ◽  
Multidrug Resistant Organisms

ABSTRACTBackgroundThe issue of antimicrobial resistance continues to grow worldwide, and long-term care facilities are significant reservoirs of antimicrobial-resistant organisms, in part due to high frequency of antimicrobial use. Patients with advanced dementia are particularly vulnerable to multidrug-resistant organism acquisition and antimicrobial overuse, which has negative consequences for the gut microbiome and can contribute to the selection and propagation of antimicrobial resistance genes. In this study, we longitudinally examined a group of advanced dementia patients treated with the fluoroquinolone antimicrobial levofloxacin, finding a correlation between abundance of pathogens and antimicrobial resistance genes, which we confirmed in a larger cohort of subjects with advanced dementia.ResultsWe observed significant inter- and intra-subject heterogeneity in the composition of the microbiota of the longitudinal levofloxacin cohort, suggesting temporal instability. Within this dataset, we did not find significant impacts of levofloxacin on the diversity, composition, function, or resistome of the gut microbiota of this population. However, we were able to link the antimicrobial resistance gene burden in a sample with the relative abundance of several pathobionts – particularly Escherichia coli, Proteus mirabilis, and Enterococcus faecalis, as well as less-prevalent species including Providencia stuartii and Staphylococcus haemolyticus. Furthermore, we used metagenomic assembly and binning to demonstrate that these species had higher genomic resistance gene levels than common gut commensals, and we were able to predict antimicrobial resistance gene burden from the relative abundances of these species in a separate, larger cohort from the same population.ConclusionsWe found that the relative abundances of several pathobionts were correlated with and were even predictive of the level of antimicrobial resistance genes in corresponding samples, and that these species carried high levels of resistances genes in their assembled genomes. In order to test this observation, we utilized a larger metagenomics dataset from a similar population and confirmed the association between pathobiont abundance and antimicrobial resistance genes. Given the high frequency with which these species were found at high levels in this population and the underlying vulnerability to infection with multidrug resistant organisms of advanced dementia patients, attention to microbial blooms of these species may be warranted. Additionally, in this study, we were able to utilize genomic assembly from metagenomic data to more definitively associate antimicrobial resistance gene levels with specific assembled species; as this technology continues to develop, assembly could prove to be a valuable method to monitor both specific resistance genes and blooms of multidrug-resistant organisms.

scholarly journals Metagenomic Profiling and Identification of Antimicrobial Resistance Genes from Airborne Microbial Communities

2015 ◽  
Vol 7 (1) ◽  
Author(s):  
Tamar Dickerson ◽  
Jonathan L. Jacobs ◽  
Nicole Waybright ◽  
Danielle Swales ◽  
Peggy Lowary ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Antimicrobial Resistance ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Temporal Dynamics ◽  
Animal Health ◽  
Functional Metagenomics ◽  
Antimicrobial Resistance Genes ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Antimicrobial resistance (AMR) is recognized as a severe threat to human and animal health worldwide, yet relatively little is known regarding the bioavailability of AMR genes in airborne microbial communities. Hence, the objective of our study is to use next generation sequencing (NGS) to assess the temporal dynamics of airborne bacterial communities as well as functional metagenomics to investigate the dispersion of AMR genes present within them.

scholarly journals Occupational Exposure and Carriage of Antimicrobial Resistance Genes (tetW, ermB) in Pig Slaughterhouse Workers

2019 ◽  
Vol 64 (2) ◽  
pp. 125-137 ◽  
Author(s):  
Liese Van Gompel ◽  
Wietske Dohmen ◽  
Roosmarijn E C Luiken ◽  
Martijn Bouwknegt ◽  
Lourens Heres ◽  
...  
Keyword(s):  
Occupational Exposure ◽  
Antimicrobial Resistance ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Macrolide Resistance ◽  
Resistant Bacteria ◽  
Linear Regression Models ◽  
Faecal Samples ◽  
Antimicrobial Resistance Genes ◽  
Antimicrobial Resistance Gene

Abstract Objectives Slaughterhouse staff is occupationally exposed to antimicrobial resistant bacteria. Studies reported high antimicrobial resistance gene (ARG) abundances in slaughter pigs. This cross-sectional study investigated occupational exposure to tetracycline (tetW) and macrolide (ermB) resistance genes and assessed determinants for faecal tetW and ermB carriage among pig slaughterhouse workers. Methods During 2015–2016, 483 faecal samples and personal questionnaires were collected from workers in a Dutch pig abattoir, together with 60 pig faecal samples. Human dermal and respiratory exposure was assessed by examining 198 carcass, 326 gloves, and 33 air samples along the line, next to 198 packed pork chops to indicate potential consumer exposure. Samples were analyzed by qPCR (tetW, ermB). A job exposure matrix was created by calculating the percentage of tetW and ermB positive carcasses or gloves for each job position. Multiple linear regression models were used to link exposure to tetW and ermB carriage. Results Workers are exposed to tetracycline and macrolide resistance genes along the slaughter line. Tetw and ermB gradients were found for carcasses, gloves, and air filters. One packed pork chop contained tetW, ermB was non-detectable. Human faecal tetW and ermB concentrations were lower than in pig faeces. Associations were found between occupational tetW exposure and human faecal tetW carriage, yet, not after model adjustments. Sampling round, nationality, and smoking were determinants for ARG carriage. Conclusion We demonstrated clear environmental tetracycline and macrolide resistance gene exposure gradients along the slaughter line. No robust link was found between ARG exposure and human faecal ARG carriage.

scholarly journals ResistoXplorer: a web-based tool for visual, statistical and exploratory data analysis of resistome data

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Achal Dhariwal ◽  
Roger Junges ◽  
Tsute Chen ◽  
Fernanda C Petersen
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Gene ◽  
High Throughput ◽  
Resistance Genes ◽  
Visual Analytics ◽  
Gene List ◽  
Metagenomic Sequencing ◽  
High Throughput Analysis ◽  
Antimicrobial Resistance Genes ◽  
Antimicrobial Resistance Gene

Abstract The study of resistomes using whole metagenomic sequencing enables high-throughput identification of resistance genes in complex microbial communities, such as the human microbiome. Over recent years, sophisticated and diverse pipelines have been established to facilitate raw data processing and annotation. Despite the progress, there are no easy-to-use tools for comprehensive visual, statistical and functional analysis of resistome data. Thus, exploration of the resulting large complex datasets remains a key bottleneck requiring robust computational resources and technical expertise, which creates a significant hurdle for advancements in the field. Here, we introduce ResistoXplorer, a user-friendly tool that integrates recent advancements in statistics and visualization, coupled with extensive functional annotations and phenotype collection, to enable high-throughput analysis of common outputs generated from metagenomic resistome studies. ResistoXplorer contains three modules—the ‘Antimicrobial Resistance Gene Table’ module offers various options for composition profiling, functional profiling and comparative analysis of resistome data; the ‘Integration’ module supports integrative exploratory analysis of resistome and microbiome abundance profiles derived from metagenomic samples; finally, the ‘Antimicrobial Resistance Gene List’ module enables users to intuitively explore the associations between antimicrobial resistance genes and the microbial hosts using network visual analytics to gain biological insights. ResistoXplorer is publicly available at http://www.resistoxplorer.no.

scholarly journals ResistoXplorer: a web-based tool for visual, statistical and exploratory data analysis of resistome data

2020 ◽  
Author(s):  
Achal Dhariwal ◽  
Roger Junges ◽  
Tsute Chen ◽  
Fernanda Cristina Petersen
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Gene ◽  
High Throughput ◽  
Resistance Genes ◽  
Visual Analytics ◽  
Gene List ◽  
Metagenomic Sequencing ◽  
High Throughput Analysis ◽  
Antimicrobial Resistance Genes ◽  
Antimicrobial Resistance Gene

ABSTRACTThe study of resistomes using whole metagenomic sequencing enables high throughput identification of resistance genes in complex microbial communities, such as the human microbiome. Over recent years, sophisticated and diverse pipelines have been established to facilitate raw data processing and annotation. Despite the progress, there are no easy-to-use tools for comprehensive visual, statistical, and functional analysis of resistome data. Thus, exploration of the resulting large complex datasets remains a key bottleneck requiring robust computational resources and technical expertise, which creates a significant hurdle for advancements in the field. Here, we introduce ResistoXplorer, a user-friendly tool that integrates recent advancements in statistics and visualization, coupled with extensive functional annotations and phenotype collection, to enable high-throughput analysis of common outputs generated from metagenomic resistome studies. ResistoXplorer contains three modules- the ‘Antimicrobial Resistance Gene Table’ module offers various options for composition profiling, functional profiling and comparative analysis of resistome data; the ‘Integration’ module supports integrative exploratory analysis of resistome and microbiome abundance profiles derived from metagenomic samples; finally, the ‘Antimicrobial Resistance Gene List’ module enables users to intuitively explore the associations between antimicrobial resistance genes and the microbial hosts using network visual analytics to gain biological insights. ResistoXplorer is publicly available at http://www.resistoxplorer.no.

scholarly journals Metagenomics Analysis Reveals the Microbial Communities, Antimicrobial Resistance Gene Diversity and Potential Pathogen Transmission Risk of Two Different Landfills in China

Diversity ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 230
Author(s):  
Shan Wan ◽  
Min Xia ◽  
Jie Tao ◽  
Yanjun Pang ◽  
Fugen Yu ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Microbial Communities ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Gene Diversity ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Pathogen Transmission ◽  
Transmission Risk ◽  
Antimicrobial Resistance Gene

In this study, we used a metagenomic approach to analyze microbial communities, antibiotic resistance gene diversity, and human pathogenic bacterium composition in two typical landfills in China. Results showed that the phyla Proteobacteria, Bacteroidetes, and Actinobacteria were predominant in the two landfills, and archaea and fungi were also detected. The genera Methanoculleus, Lysobacter, and Pseudomonas were predominantly present in all samples. sul2, sul1, tetX, and adeF were the four most abundant antibiotic resistance genes. Sixty-nine bacterial pathogens were identified from the two landfills, with Klebsiella pneumoniae, Bordetella pertussis, Pseudomonas aeruginosa, and Bacillus cereus as the major pathogenic microorganisms, indicating the existence of potential environmental risk in landfills. In addition, KEGG pathway analysis indicated the presence of antibiotic resistance genes typically associated with human antibiotic resistance bacterial strains. These results provide insights into the risk of pathogens in landfills, which is important for controlling the potential secondary transmission of pathogens and reducing workers’ health risk during landfill excavation.

scholarly journals Impact of UV and Peracetic Acid Disinfection on the Prevalence of Virulence and Antimicrobial Resistance Genes in Uropathogenic Escherichia coli in Wastewater Effluents

2014 ◽  
Vol 80 (12) ◽  
pp. 3656-3666 ◽  
Author(s):  
Basanta Kumar Biswal ◽  
Ramzi Khairallah ◽  
Kareem Bibi ◽  
Alberto Mazza ◽  
Ronald Gehr ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Peracetic Acid ◽  
Content Type ◽  
E Coli ◽  
Antimicrobial Resistance Genes ◽  
Antimicrobial Resistance Gene ◽  
Municipal Wastewaters ◽  
The Impact

ABSTRACTWastewater discharges may increase the populations of pathogens, includingEscherichia coli, and of antimicrobial-resistant strains in receiving waters. This study investigated the impact of UV and peracetic acid (PAA) disinfection on the prevalence of virulence and antimicrobial resistance genes in uropathogenicEscherichia coli(UPEC), the most abundantE. colipathotype in municipal wastewaters. Laboratory disinfection experiments were conducted on wastewater treated by physicochemical, activated sludge, or biofiltration processes; 1,766E. coliisolates were obtained for the evaluation. The target disinfection level was 200 CFU/100 ml, resulting in UV and PAA doses of 7 to 30 mJ/cm2and 0.9 to 2.0 mg/liter, respectively. The proportions of UPECs were reduced in all samples after disinfection, with an average reduction by UV of 55% (range, 22% to 80%) and by PAA of 52% (range, 11% to 100%). Analysis of urovirulence genes revealed that the decline in the UPEC populations was not associated with any particular virulence factor. A positive association was found between the occurrence of urovirulence and antimicrobial resistance genes (ARGs). However, the changes in the prevalence of ARGs in potential UPECs were different following disinfection, i.e., UV appears to have had no effect, while PAA significantly reduced the ARG levels. Thus, this study showed that both UV and PAA disinfections reduced the proportion of UPECs and that PAA disinfection also reduced the proportion of antimicrobial resistance gene-carrying UPEC pathotypes in municipal wastewaters.

Formula-fed and Clostridium difficile infected neonatal piglets carry a highly diverse and abundant set of antimicrobial resistance genes

2020 ◽  
Author(s):  
Robert Pieper ◽  
Temesgen Dadi ◽  
Lukasz Grzeskowiak ◽  
Laura Pieper ◽  
Britta Siegmund ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Microbial Colonization ◽  
Metagenomic Data ◽  
Neonatal Piglets ◽  
Gut Colonization ◽  
Antimicrobial Resistance Genes ◽  
Antimicrobial Resistance Gene ◽  
Genes Encoding

Abstract Background: Clostridium difficile infection (CDI) is an increasing zoonotic health threat and has also been documented as a cause of enteritis outbreaks in neonatal pigs. Furthermore, CDI in neonatal piglets cause changes in microbial gut colonization. We hypothesized that an imbalanced microbial colonization in piglets with CDI could be associated with an altered abundance of antimicrobial resistance genes. Results: We analyzed fecal metagenomic data of lactating sows (S), their piglets during suckling (SP), the same piglets two weeks after weaning (WP), 5-day old artificially reared and formula-fed siblings (FP) and FP infected with C. difficile (FP-CD) for microbiota composition and antimicrobial resistance gene abundance. FP and FP-CD piglets had an immature-type microbiota and increased abundance of antimicrobial resistance genes. A co-occurrence of genes encoding for resistance against aminoglycosides (e.g. aph(3”)-lb, aph(6)-ld, ant(2”)-la), β-lactams (blaCTX-M, blaTEM), fluoroquinolones (pat(A) macrolides (mph(A)), sulfonamides (sul1, sul2), polypeptides (e.g. pmrB, pmrC, arnA, bac(A)) and tetracyclines (e.g. tet(A-D),) was observed. Conclusion: Increased abundance of antimicrobial resistance genes in formula feeding and concomitant CDI may be associated with therapeutic resistance later in life and warrant further studies.

scholarly journals Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle

2017 ◽  
Author(s):  
Milton Thomas ◽  
Megan Webb ◽  
Sudeep Ghimire ◽  
Amanda Blair ◽  
Kenneth Olson ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Gut Microbiota ◽  
Resistance Genes ◽  
Feedlot Cattle ◽  
Feed Additives ◽  
Gastrointestinal Microbiota ◽  
Finishing Diets ◽  
Antimicrobial Resistance Genes ◽  
Metagenome Sequencing ◽  
The Impact

AbstractIn North America, antibiotic feed additives such as monensin and tylosin are added to the finishing diets of feedlot cattle to counter the ill-effects of feeding diets with rapidly digestible carbohydrates. While these feed additives have been proven to improve feed efficiency, and reduce liver abscess incidence, how these products impact the gastrointestinal microbiota is not completely understood. Furthermore, there are concerns that antibiotic feed additives may expand the antibiotic resistome of feedlot cattle by enriching antimicrobial resistance genes in pathogenic and nonpathogenic bacteria in the gut microbiota. In this study, we analyzed the impact of providing antibiotic feed additives to feedlot cattle using metagenome sequencing of treated and untreated animals. Our results indicate that use of antibiotic feed additives does not produce discernable changes at the phylum level however treated cattle had reduced the abundance of gram-positive bacteria at the genus level. The abundance of Ruminococcus, Erysipelotrichaceae and Lachanospira in the gut of treated steers was reduced. This may impact the ability of these animals to exclude pathogens from the gut. However, our results did not show any correlation between the presence of antimicrobial resistance genes in the gut microbiota and the administration of antibiotic feed additives.

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