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.

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.

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 Antimicrobial Resistance and CRISPR Typing Among Salmonella Isolates From Poultry Farms in China

2021 ◽  
Vol 12 ◽  
Author(s):  
Cui Li ◽  
Yulong Wang ◽  
Yufeng Gao ◽  
Chao Li ◽  
Boheng Ma ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Direct Repeat ◽  
Epidemiological Data ◽  
Multidrug Resistant ◽  
Typing Method ◽  
Crispr Locus ◽  
Research Areas

Although knowledge of the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas system has been applied in many research areas, comprehensive studies of this system in Salmonella, particularly in analysis of antibiotic resistance, have not been reported. In this work, 75 Salmonella isolates obtained from broilers or broilers products were characterized to determine their antimicrobial susceptibilities, antibiotic resistance gene profiles, and CRISPR array diversities, and genotyping was explored. In total, 80.00% (60/75) of the strains were multidrug resistant, and the main pattern observed in the isolates was CN-AZM-AMP-AMC-CAZ-CIP-ATM-TE-SXT-FOS-C. The resistance genes of streptomycin (aadA), phenicol (floR-like and catB3-like), β-lactams (blaTEM, blaOXA, and blaCTX), tetracycline [tet(A)-like], and sulfonamides (sul1 and sul2) appeared at higher frequencies among the corresponding resistant isolates. Subsequently, we analyzed the CRISPR arrays and found 517 unique spacer sequences and 31 unique direct repeat sequences. Based on the CRISPR spacer sequences, we developed a novel typing method, CRISPR locus three spacer sequences typing (CLTSST), to help identify sources of Salmonella outbreaks especially correlated with epidemiological data. Compared with multi-locus sequence typing (MLST), conventional CRISPR typing (CCT), and CRISPR locus spacer pair typing (CLSPT), discrimination using CLTSST was weaker than that using CCT but stronger than that using MLST and CLSPT. In addition, we also found that there were no close correlations between CRISPR loci and antibiotics but had close correlations between CRISPR loci and antibiotic resistance genes in Salmonella isolates.

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 Removal of Antibiotic Resistance Gene-Carrying Plasmids from Lactobacillus reuteri ATCC 55730 and Characterization of the Resulting Daughter Strain, L. reuteri DSM 17938

2008 ◽  
Vol 74 (19) ◽  
pp. 6032-6040 ◽  
Author(s):  
Anna Rosander ◽  
Eamonn Connolly ◽  
Stefan Roos
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Lactobacillus Reuteri ◽  
Antibiotic Resistance Gene ◽  
Genetically Modify ◽  
Antibiotic Resistance Genes ◽  
Probiotic Strain ◽  
Probiotic Properties ◽  
Food Borne

ABSTRACT The spread of antibiotic resistance in pathogens is primarily a consequence of the indiscriminate use of antibiotics, but there is concern that food-borne lactic acid bacteria may act as reservoirs of antibiotic resistance genes when distributed in large doses to the gastrointestinal tract. Lactobacillus reuteri ATCC 55730 is a commercially available probiotic strain which has been found to harbor potentially transferable resistance genes. The aims of this study were to define the location and nature of β-lactam, tetracycline, and lincosamide resistance determinants and, if they were found to be acquired, attempt to remove them from the strain by methods that do not genetically modify the organism before subsequently testing whether the probiotic characteristics were retained. No known β-lactam resistance genes was found, but penicillin-binding proteins from ATCC 55730, two additional resistant strains, and three sensitive strains of L. reuteri were sequenced and comparatively analyzed. The β-lactam resistance in ATCC 55730 is probably caused by a number of alterations in the corresponding genes and can be regarded as not transferable. The strain was found to harbor two plasmids carrying tet(W) tetracycline and lnu(A) lincosamide resistance genes, respectively. A new daughter strain, L. reuteri DSM 17938, was derived from ATCC 55730 by removal of the two plasmids, and it was shown to have lost the resistances associated with them. Direct comparison of the parent and daughter strains for a series of in vitro properties and in a human clinical trial confirmed the retained probiotic properties of the daughter strain.

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