scholarly journals Survival of Antibiotic Resistant Bacteria and Horizontal Gene Transfer Control Antibiotic Resistance Gene Content in Anaerobic Digesters

2016 ◽  
Vol 7 ◽  
Author(s):  
Jennifer H. Miller ◽  
John T. Novak ◽  
William R. Knocke ◽  
Amy Pruden
Keyword(s):  
Antibiotic Resistance ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Resistance Gene ◽  
Antibiotic Resistance Gene ◽  
Gene Content ◽  
Resistant Bacteria ◽  
Antibiotic Resistant Bacteria ◽  
Anaerobic Digesters ◽  
Antibiotic Resistant

scholarly journals Horizontal gene transfer facilitates the spread of extracellular antibiotic resistance genes in soil

2021 ◽  
Author(s):  
Heather A. Kittredge ◽  
Kevin M. Dougherty ◽  
Sarah E. Evans
Keyword(s):  
Antibiotic Resistance ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Resistance Genes ◽  
Natural Transformation ◽  
Antibiotic Resistance Genes ◽  
Live Cells ◽  
Resistant Bacteria ◽  
Antibiotic Resistant Bacteria ◽  
Antibiotic Resistant

AbstractAntibiotic resistance genes (ARGs) are ubiquitous in the environment and pose a serious risk to human and veterinary health. While many studies focus on the spread of live antibiotic resistant bacteria throughout the environment, it is unclear whether extracellular ARGs from dead cells can transfer to live bacteria to facilitate the evolution of antibiotic resistance in nature. Here, we inoculate antibiotic-free soil with extracellular ARGs (eARGs) from dead Pseudeononas stutzeri cells and track the evolution of antibiotic resistance via natural transformation – a mechanism of horizontal gene transfer involving the genomic integration of eARGs. We find that transformation facilitates the rapid evolution of antibiotic resistance even when eARGs occur at low concentrations (0.25 μg g-1 soil). However, when eARGs are abundant, transformation increases substantially. The evolution of antibiotic resistance was high under soil moistures typical in terrestrial systems (5%-30% gravimetric water content) and was only inhibited at very high soil moistures (>30%). While eARGs transformed into live cells at a low frequency, exposure to a low dose of antibiotic allowed a small number of transformants to reach high abundances in laboratory populations, suggesting even rare transformation events pose a risk to human health. Overall, this work demonstrates that dead bacteria and their eARGs are an overlooked path to antibiotic resistance, and that disinfection alone is insufficient to stop the spread of antibiotic resistance. More generally, the spread of eARGs in antibiotic-free soil suggests that transformation allows genetic variants to establish at low frequencies in the absence of antibiotic selection.ImportanceOver the last decade, antibiotics in the environment have gained increasing attention because they can select for drug-resistant phenotypes that would have otherwise gone extinct. To counter this effect, bacterial populations exposed to antibiotics often undergo disinfection. However, the release of extracellular antibiotic resistance genes (eARGs) into the environment following disinfection can promote the transfer of eARGs through natural transformation. This phenomenon is well-documented in wastewater and drinking water, but yet to be investigated in soil. Our results directly demonstrate that eARGs from dead bacteria are an important, but often overlooked source of antibiotic resistance in soil. We conclude that disinfection alone is insufficient to prevent the spread of ARGs. Special caution should be taken in releasing antibiotics into the environment, even if there are no live antibiotic resistant bacteria in the community, as transformation allows DNA to maintain its biological activity past microbial death.

scholarly journals Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Amy Langdon ◽  
◽  
Drew J. Schwartz ◽  
Christopher Bulow ◽  
Xiaoqing Sun ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Gut Microbiota ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Multidrug Resistant ◽  
Resistant Bacteria ◽  
Antibiotic Resistant Bacteria ◽  
Open Label ◽  
Antibiotic Resistant ◽  
Clostridioides Difficile

Abstract Background Once antibiotic-resistant bacteria become established within the gut microbiota, they can cause infections in the host and be transmitted to other people and the environment. Currently, there are no effective modalities for decreasing or preventing colonization by antibiotic-resistant bacteria. Intestinal microbiota restoration can prevent Clostridioides difficile infection (CDI) recurrences. Another potential application of microbiota restoration is suppression of non-C. difficile multidrug-resistant bacteria and overall decrease in the abundance of antibiotic resistance genes (the resistome) within the gut microbiota. This study characterizes the effects of RBX2660, a microbiota-based investigational therapeutic, on the composition and abundance of the gut microbiota and resistome, as well as multidrug-resistant organism carriage, after delivery to patients suffering from recurrent CDI. Methods An open-label, multi-center clinical trial in 11 centers in the USA for the safety and efficacy of RBX2660 on recurrent CDI was conducted. Fecal specimens from 29 of these subjects with recurrent CDI who received either one (N = 16) or two doses of RBX2660 (N = 13) were analyzed secondarily. Stool samples were collected prior to and at intervals up to 6 months post-therapy and analyzed in three ways: (1) 16S rRNA gene sequencing for microbiota taxonomic composition, (2) whole metagenome shotgun sequencing for functional pathways and antibiotic resistome content, and (3) selective and differential bacterial culturing followed by isolate genome sequencing to longitudinally track multidrug-resistant organisms. Results Successful prevention of CDI recurrence with RBX2660 correlated with taxonomic convergence of patient microbiota to the donor microbiota as measured by weighted UniFrac distance. RBX2660 dramatically reduced the abundance of antibiotic-resistant Enterobacteriaceae in the 2 months after administration. Fecal antibiotic resistance gene carriage decreased in direct relationship to the degree to which donor microbiota engrafted. Conclusions Microbiota-based therapeutics reduce resistance gene abundance and resistant organisms in the recipient gut microbiome. This approach could potentially reduce the risk of infections caused by resistant organisms within the patient and the transfer of resistance genes or pathogens to others. Trial registration ClinicalTrials.gov, NCT01925417; registered on August 19, 2013.

scholarly journals 1420. A One Health Approach Examining the Potential Linkage between Agricultural Livestock and Human Antibiotic Resistance at the Watershed Level

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S716-S717
Author(s):  
Linsey M Donner ◽  
Xu Li ◽  
Daniel D Snow ◽  
Jodi L Sangster ◽  
Zachery R Staley ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
One Health ◽  
Bacterial Species ◽  
Antibiotic Resistance Gene ◽  
Agricultural Watershed ◽  
Resistant Bacteria ◽  
Organic Chemical ◽  
Drug Resistant ◽  
Antibiotic Resistant Bacteria ◽  
Antibiotic Resistant

Abstract Background Antibiotic resistance is a significant public health threat and widespread use of antibiotics in agriculture is increasing the concern about agricultural contributions to the dissemination of antibiotic resistant bacteria. Of concern is the level of exposure to antibiotics and antibiotic-resistant bacteria in the watershed. Consequently, adopting a One Health approach to measure antibiotic levels and identify antibiotic resistance gene (ARG) transfer at the human, animal and environmental interfaces is essential to better understand how antibiotic resistance is spread. Methods In this project, antibiotic levels were measured using passive organic chemical integrative samplers (POCIS) for 30-day periods from August – November 2018 from Elkhorn River and Shell Creek watersheds in Nebraska (Figure 1). In addition, whole genome sequences of bacterial isolates cultured from the watersheds were assessed to identify ARGs present on mobile genetic elements (MGE) that had >95% similarity to mobile ARG present in isolates recorded in the NCBI GenBank database was identified using ResFinder. Figure 1. Sampling locations within the two watersheds. Results The study demonstrated significant antibiotic levels present throughout the watershed, with five of them associated with human usage (Table 1). In addition, seasonally based drug-resistant bacterial species was associated with specific antibiotic levels in the watershed (Figure 2). Mobile ARGs were detected in 87.5% of isolates collected from the Elkhorn River and 80.0% within Shell Creek (Figure 3). Table 1. Pharmaceutical levels in the watershed Figure 2. Antibiotic levels and drug-resistant bacteria in the watershed Figure 3. Antibiotic resistance observed from each isolate at every sampling date and site. A colored bar denotes that resistance to that antibiotic was observed. Conclusion These results present evidence of transfer of highly mobile ARGs between environment, clinical, and animal-associated bacteria and highlight the need for a One Health perspective in assessing the spread of antibiotic resistance. The presence of significant levels of antibiotics persisting in this agricultural watershed points out the need for ongoing monitoring of compliance with the Food and Drug Administration (FDA) recommendation of veterinarian oversight of the use of antibiotics in the use of veterinary feed directive applications. Disclosures All Authors: No reported disclosures

scholarly journals The effect of sequencing and assembly on the inference of horizontal gene transfer on chromosomal and plasmid phylogenies

2021 ◽  
Author(s):  
Jana Sanne Huisman ◽  
Timothy G Vaughan ◽  
Adrian Egli ◽  
Sarah Tschudin-Sutter ◽  
Tanja Stadler ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Resistance Gene ◽  
Antibiotic Resistance Gene ◽  
Sequencing Data ◽  
Short Read ◽  
Assembly Method ◽  
Long Reads ◽  
The Impact

The spread of antibiotic resistance genes on plasmids is a threat to human and animal health. Phylogenies of bacteria and their plasmids contain clues regarding the frequency of plasmid transfer events, as well as the co-evolution of plasmids and their hosts. However, whole genome sequencing data from diverse ecological or clinical bacterial samples is rarely used to study plasmid phylogenies and resistance gene transfer. This is partially due to the difficulty to extract plasmids from short-read sequencing data. Here, we use both short- and long-read sequencing data of 24 clinical extended-spectrum beta-lactamase producing Escherichia coli to estimate chromosomal and plasmid phylogenies. We compare the impact of different sequencing and assembly methodologies on these phylogenies and on the inference of horizontal gene transfer. We find chromosomal phylogenies can be estimated robustly with all methods, whereas plasmid phylogenies have more variable topology and branch lengths across the methods used. Specifically, hybrid methods that use long reads to resolve short-read assemblies (HybridSPAdes and Unicycler) perform better than those that started from long-reads during assembly graph generation (Canu). In contrast, the inference of plasmid and antibiotic resistance gene transfer using a parsimony-based criterion is mostly robust to the choice of sequencing and assembly method.

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