Prevalence of Antibiotic Resistance Genes and Bacterial Pathogens in Long-Term Manured Greenhouse Soils As Revealed by Metagenomic Survey

2014 ◽  
Vol 49 (2) ◽  
pp. 1095-1104 ◽  
Author(s):  
Hua Fang ◽  
Huifang Wang ◽  
Lin Cai ◽  
Yunlong Yu
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Bacterial Pathogens ◽  
Antibiotic Resistance Genes ◽  
Greenhouse Soils

scholarly journals The resistome of common human pathogens

2017 ◽  
Author(s):  
Christian Munck ◽  
Mostafa M. Hashim Ellabaan ◽  
Michael Schantz Klausen ◽  
Morten O.A. Sommer
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Bacterial Pathogens ◽  
Antibiotic Resistance Genes ◽  
Gene Clusters ◽  
Species Level ◽  
Natural Environments ◽  
Human Pathogens ◽  
Bacterial Genomes ◽  
Risk Ranking

AbstractGenes capable of conferring resistance to clinically used antibiotics have been found in many different natural environments. However, a concise overview of the resistance genes found in common human bacterial pathogens is lacking, which complicates risk ranking of environmental reservoirs. Here, we present an analysis of potential antibiotic resistance genes in the 17 most common bacterial pathogens isolated from humans. We analyzed more than 20,000 bacterial genomes and defined a clinical resistome as the set of resistance genes found across these genomes. Using this database, we uncovered the co-occurrence frequencies of the resistance gene clusters within each species enabling identification of co-dissemination and co-selection patterns. The resistance genes identified in this study represent the subset of the environmental resistome that is clinically relevant and the dataset and approach provides a baseline for further investigations into the abundance of clinically relevant resistance genes across different environments. To facilitate an easy overview the data is presented at the species level at www.resistome.biosustain.dtu.dk.

Microplastics act as vectors for antibiotic resistance genes in landfill leachate: The enhanced roles of the long-term aging process

2021 ◽  
Vol 270 ◽  
pp. 116278
Author(s):  
Yinglong Su ◽  
Zhongjian Zhang ◽  
Jundong Zhu ◽  
Jianhong Shi ◽  
Huawei Wei ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Landfill Leachate ◽  
Aging Process ◽  
Antibiotic Resistance Genes

scholarly journals Cohorting KPC+ Klebsiella pneumoniae (KPC-Kp)–positive patients: A genomic exposé of cross-colonization hazards in a long-term acute-care hospital (LTACH)

2020 ◽  
Vol 41 (10) ◽  
pp. 1162-1168
Author(s):  
Shawn E. Hawken ◽  
Mary K. Hayden ◽  
Karen Lolans ◽  
Rachel D. Yelin ◽  
Robert A. Weinstein ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Klebsiella Pneumoniae ◽  
Acute Care ◽  
Resistance Genes ◽  
Acute Care Hospital ◽  
Antibiotic Resistance Genes ◽  
Care Hospital ◽  
Cross Transmission ◽  
The Impact

AbstractObjective:Cohorting patients who are colonized or infected with multidrug-resistant organisms (MDROs) protects uncolonized patients from acquiring MDROs in healthcare settings. The potential for cross transmission within the cohort and the possibility of colonized patients acquiring secondary isolates with additional antibiotic resistance traits is often neglected. We searched for evidence of cross transmission of KPC+ Klebsiella pneumoniae (KPC-Kp) colonization among cohorted patients in a long-term acute-care hospital (LTACH), and we evaluated the impact of secondary acquisitions on resistance potential.Design:Genomic epidemiological investigation.Setting:A high-prevalence LTACH during a bundled intervention that included cohorting KPC-Kp–positive patients.Methods:Whole-genome sequencing (WGS) and location data were analyzed to identify potential cases of cross transmission between cohorted patients.Results:Secondary KPC-Kp isolates from 19 of 28 admission-positive patients were more closely related to another patient’s isolate than to their own admission isolate. Of these 19 cases, 14 showed strong genomic evidence for cross transmission (<10 single nucleotide variants or SNVs), and most of these patients occupied shared cohort floors (12 patients) or rooms (4 patients) at the same time. Of the 14 patients with strong genomic evidence of acquisition, 12 acquired antibiotic resistance genes not found in their primary isolates.Conclusions:Acquisition of secondary KPC-Kp isolates carrying distinct antibiotic resistance genes was detected in nearly half of cohorted patients. These results highlight the importance of healthcare provider adherence to infection prevention protocols within cohort locations, and they indicate the need for future studies to assess whether multiple-strain acquisition increases risk of adverse patient outcomes.

scholarly journals F Plasmids Are the Major Carriers of Antibiotic Resistance Genes in Human-Associated Commensal Escherichia coli

mSphere ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Craig Stephens ◽  
Tyler Arismendi ◽  
Megan Wright ◽  
Austin Hartman ◽  
Andres Gonzalez ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Transposable Elements ◽  
Dna Sequencing ◽  
Resistance Genes ◽  
Bacterial Pathogens ◽  
Acquired Resistance ◽  
Antibiotic Resistance Genes ◽  
Content Type ◽  
E Coli

ABSTRACT The evolution and propagation of antibiotic resistance by bacterial pathogens are significant threats to global public health. Contemporary DNA sequencing tools were applied here to gain insight into carriage of antibiotic resistance genes in Escherichia coli, a ubiquitous commensal bacterium in the gut microbiome in humans and many animals, and a common pathogen. Draft genome sequences generated for a collection of 101 E. coli strains isolated from healthy undergraduate students showed that horizontally acquired antibiotic resistance genes accounted for most resistance phenotypes, the primary exception being resistance to quinolones due to chromosomal mutations. A subset of 29 diverse isolates carrying acquired resistance genes and 21 control isolates lacking such genes were further subjected to long-read DNA sequencing to enable complete or nearly complete genome assembly. Acquired resistance genes primarily resided on F plasmids (101/153 [67%]), with smaller numbers on chromosomes (30/153 [20%]), IncI complex plasmids (15/153 [10%]), and small mobilizable plasmids (5/153 [3%]). Nearly all resistance genes were found in the context of known transposable elements. Very few structurally conserved plasmids with antibiotic resistance genes were identified, with the exception of an ∼90-kb F plasmid in sequence type 1193 (ST1193) isolates that appears to serve as a platform for resistance genes and may have virulence-related functions as well. Carriage of antibiotic resistance genes on transposable elements and mobile plasmids in commensal E. coli renders the resistome highly dynamic. IMPORTANCE Rising antibiotic resistance in human-associated bacterial pathogens is a serious threat to our ability to treat many infectious diseases. It is critical to understand how acquired resistance genes move in and through bacteria associated with humans, particularly for species such as Escherichia coli that are very common in the human gut but can also be dangerous pathogens. This work combined two distinct DNA sequencing approaches to allow us to explore the genomes of E. coli from college students to show that the antibiotic resistance genes these bacteria have acquired are usually carried on a specific type of plasmid that is naturally transferrable to other E. coli, and likely to other related bacteria.

scholarly journals Evolution of Antibiotic Resistance and the Relationship between the Antibiotic Resistance Genes and Microbial Compositions under Long-Term Exposure to Tetracycline and Sulfamethoxazole

2019 ◽  
Vol 16 (23) ◽  
pp. 4681 ◽  
Author(s):  
Bingbing Du ◽  
Qingxiang Yang ◽  
Ruifei Wang ◽  
Ruimin Wang ◽  
Qiang Wang ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Wastewater Treatment ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
The Core ◽  
Aerobic Wastewater Treatment ◽  
The Relationship ◽  
Bacterial Groups ◽  
Wastewater Treatment Systems

The removal of antibiotics and widespread of antibiotic resistance genes (ARGs) have received continuous attention due to the possible threats to environment. However, little information is available on the evolution of antibiotic resistance and the relationship between ARGs and microbial communities under long-term exposure to sub-inhibitory concentrations of antibiotics. In our study, two laboratory-scale anoxic-aerobic wastewater treatment systems were established and operated for 420 days to investigate the evolution of antibiotic resistance under exposure of 5 mg·L−1 tetracycline (TC) or 5 mg·L−1 TC and 1 mg·L−1 sulfamethoxazole (SMX). The average removal rates of TC and SMX were about 59% and 72%, respectively. The abundance of the main ARGs responsible for resistance to TC and SMX increased obviously after antibiotics addition, especially when TC and SMX in combination (increased 3.20-fold). The tetC and sul1 genes were the predominant genes in the development of TC and SMX resistance, in which gene sul1 had the highest abundance among all the detected ARGs. Network analysis revealed that under antibiotic pressure, the core bacterial groups carrying multiple ARGs formed and concentrated in about 20 genera such as Dechloromonas, Candidatus Accumulibacter, Aeromonas, Rubrivivax, in which intI1 played important roles in transferring various ARGs except sul3.

Long-term application of swine manure and sewage sludge differently impacts antibiotic resistance genes in soil and phyllosphere

Geoderma ◽  
2022 ◽  
Vol 411 ◽  
pp. 115698
Author(s):  
Xue-Mei Han ◽  
Hang-Wei Hu ◽  
Jin-Yang Li ◽  
He-Lian Li ◽  
Fang He ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Sewage Sludge ◽  
Resistance Genes ◽  
Swine Manure ◽  
Antibiotic Resistance Genes

scholarly journals Community structure explains antibiotic resistance gene dynamics over a temperature gradient in soil

2017 ◽  
Author(s):  
Taylor K Dunivin ◽  
Ashley Shade
Keyword(s):  
Antibiotic Resistance ◽  
Community Structure ◽  
Temperature Gradient ◽  
Resistance Genes ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Reference Surface ◽  
Ambient Temperatures ◽  
Concomitant Reduction

Soils are reservoirs of antibiotic resistance genes, but dynamics of antibiotic resistance genes in the environment are largely unknown. Long-term disturbances offer extended opportunities to examine microbiome responses at scales relevant for both ecological and evolutionary processes, and therefore can be insightful for studying the dynamics of antibiotic resistance genes in the environment. We examined antibiotic resistance genes in soils overlying the underground coal seam fire in Centralia, PA, which has been burning since 1962. As the fire progresses, previously hot soils can recover to ambient temperatures, which creates a gradient of contemporary and historical fire impact. We examined metagenomes from fire-affected, recovered, and reference surface soils to examine gene-resolved dynamics of antibiotic resistance using a gene-targeted assembler. We targeted 35 distinct types of clinically-relevant antibiotic resistance genes and two horizontal gene transfer-related genes (intI and repA). We detected 17 antibiotic resistance genes in Centralia, including AAC6-Ia, adeB, bla_A, bla_B, bla_C, cmlA, dfra12, intI, sul2, tetA, tetW, tetX, tolC, vanA, vanH, vanX, and vanZ. The diversity and abundance of several antibiotic resistance genes (bla_A, bla_B, dfra12, tolC) decreased with soil temperature, and changes in ARGs could largely be explained by associated changes in community structure. We also observed sequence-specific dynamics along the temperature gradient and observed compositional shifts in bla_A, dfra12, and intI. These results suggest that increased temperatures can reduce soil antibiotic resistance genes but that this is largely due to a concomitant reduction in community-level diversity.

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