Metagenomics reveals the taxonomy and resistance mechanism of antibiotic resistance genes in bacterial communities of an aquaculture pond

Bacterial resistance is a complex scientific issue. To manage this issue, we need to deeply understand the influencing factors and mechanisms. Based on the background of livestock husbandry, this paper reviews the factors that affect the acquisition of bacterial resistance. Meanwhile, the resistance mechanism is also discussed. “Survival of the fittest” is the result of genetic plasticity of bacterial pathogens, which brings about specific response, such as producing adaptive mutation, gaining genetic material or changing gene expression. To a large extent, bacterial populations acquire resistance genes directly caused by the selective pressure of antibiotics. However, mobile resistance genes may be co-selected by other existing substances (such as heavy metals and biocides) without direct selection pressure from antibiotics. This is because the same mobile genetic elements as antibiotic resistance genes can be co-located by the resistance determinants of some of these compounds. Furthermore, environmental factors are a source of resistance gene acquisition. Here, we describe some of the key measures that should be taken to mitigate the risk of antibiotic resistance. We call on the relevant governments or organizations around the world to formulate and improve the monitoring policies of antibiotic resistance, strengthen the supervision, strengthen the international cooperation and exchange, and curb the emergence and spread of drug-resistant strains.

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Pharmaceutical exposure changed antibiotic resistance genes and bacterial communities in soil-surface- and overhead-irrigated greenhouse lettuce

Environment International ◽

10.1016/j.envint.2019.105031 ◽

2019 ◽

Vol 131 ◽

pp. 105031 ◽

Cited By ~ 7

Author(s):

Yike Shen ◽

Robert D. Stedtfeld ◽

Xueping Guo ◽

Gemini D. Bhalsod ◽

Sangho Jeon ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Bacterial Communities ◽

Antibiotic Resistance Genes ◽

Soil Surface

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Antibiotic Resistance Genes in Phage Particles from Antarctic and Mediterranean Seawater Ecosystems

Microorganisms ◽

10.3390/microorganisms8091293 ◽

2020 ◽

Vol 8 (9) ◽

pp. 1293

Author(s):

Pedro Blanco-Picazo ◽

Gabriel Roscales ◽

Daniel Toribio-Avedillo ◽

Clara Gómez-Gómez ◽

Conxita Avila ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Bacterial Communities ◽

Anthropogenic Activities ◽

Antibiotic Resistance Genes ◽

Mediterranean Area ◽

Mediterranean Coast ◽

Anthropogenic Pressure ◽

The Mediterranean ◽

The Antarctic

Anthropogenic activities are a key factor in the development of antibiotic resistance in bacteria, a growing problem worldwide. Nevertheless, antibiotics and resistances were being generated by bacterial communities long before their discovery by humankind, and might occur in areas without human influence. Bacteriophages are known to play a relevant role in the dissemination of antibiotic resistance genes (ARGs) in aquatic environments. In this study, five ARGs (blaTEM, blaCTX-M-1, blaCTX-M-9, sul1 and tetW) were monitored in phage particles isolated from seawater of two different locations: (i) the Mediterranean coast, subjected to high anthropogenic pressure, and (ii) the Antarctic coast, where the anthropogenic impact is low. Although found in lower quantities, ARG-containing phage particles were more prevalent among the Antarctic than the Mediterranean seawater samples and Antarctic bacterial communities were confirmed as their source. In the Mediterranean area, ARG-containing phages from anthropogenic fecal pollution might allow ARG transmission through the food chain. ARGs were detected in phage particles isolated from fish (Mediterranean, Atlantic, farmed, and frozen), the most abundant being β-lactamases. Some of these particles were infectious in cultures of the fecal bacteria Escherichia coli. By serving as ARG reservoirs in marine environments, including those with low human activity, such as the Antarctic, phages could contribute to ARG transmission between bacterial communities.

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Occurrence and removal of antibiotics, antibiotic resistance genes, and bacterial communities in hospital wastewater

Environmental Science and Pollution Research ◽

10.1007/s11356-021-14735-3 ◽

2021 ◽

Author(s):

Shijie Yao ◽

Jianfeng Ye ◽

Qing Yang ◽

Yaru Hu ◽

Tianyang Zhang ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Bacterial Communities ◽

Antibiotic Resistance Genes ◽

Hospital Wastewater

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Shotgun metagenomics reveals differences in antibiotic resistance genes among bacterial communities in Western Balkans glacial lakes sediments

Journal of Water and Health ◽

10.2166/wh.2020.227 ◽

2020 ◽

Vol 18 (3) ◽

pp. 383-397

Author(s):

Brankica Filipic ◽

Katarina Novovic ◽

David J. Studholme ◽

Milka Malesevic ◽

Nemanja Mirkovic ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Bacterial Communities ◽

Human Population ◽

Antibiotic Resistance Genes ◽

Efflux Pumps ◽

Mobile Genetic Elements ◽

Glacial Lakes ◽

Western Balkans ◽

Shotgun Metagenomics

Abstract Long-term overuse of antibiotics has driven the propagation and spreading of antibiotic resistance genes (ARGs) such as efflux pumps in the environment, which can be transferred to clinically relevant pathogens. This study explored the abundance and diversity of ARGs and mobile genetic elements within bacterial communities from sediments of three Western Balkans glacial lakes: Plav Lake (high impact of human population), Black Lake (medium impact of human population) and Donje Bare Lake (remote lake, minimal impact of human population) via shotgun metagenomics. Assembled metagenomic sequences revealed that Resistance-Nodulation-Division (RND) efflux pumps genes were most abundant in metagenome from the Plav Lake. The Integron Finder bioinformatics tool detected 38 clusters of attC sites lacking integron-integrases (CALIN) elements: 20 from Plav Lake, four from Black Lake and 14 from Donje Bare Lake. A complete integron sequence was recovered only from the assembled metagenome from Plav Lake. Plasmid contents within the metagenomes were similar, with proportions of contigs being plasmid-related: 1.73% for Plav Lake, 1.59% for Black Lake and 1.64% for Donje Bare Lake. The investigation showed that RNDs and mobile genetic elements content correlated with human population impact.

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The formation mechanism of antibiotic-resistance genes associated with bacterial communities during biological decomposition of household garbage

Journal of Hazardous Materials ◽

10.1016/j.jhazmat.2020.122973 ◽

2020 ◽

Vol 398 ◽

pp. 122973 ◽

Cited By ~ 2

Author(s):

Zhishu Liang ◽

Yuna Zhang ◽

Tao He ◽

Yun Yu ◽

Wen Liao ◽

...

Keyword(s):

Antibiotic Resistance ◽

Formation Mechanism ◽

Resistance Genes ◽

Bacterial Communities ◽

Antibiotic Resistance Genes ◽

Biological Decomposition

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HflXr, a homolog of a ribosome-splitting factor, mediates antibiotic resistance

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1810555115 ◽

2018 ◽

Vol 115 (52) ◽

pp. 13359-13364 ◽

Cited By ~ 14

Author(s):

Mélodie Duval ◽

Daniel Dar ◽

Filipe Carvalho ◽

Eduardo P. C. Rocha ◽

Rotem Sorek ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Antibiotic Resistance Gene ◽

Resistance Mechanism ◽

Antibiotic Resistance Genes ◽

Amino Acid Peptide ◽

Splitting Factor ◽

A Genome ◽

Attenuation Mechanism ◽

Drug Modification

To overcome the action of antibiotics, bacteria have evolved a variety of different strategies, such as drug modification, target mutation, and efflux pumps. Recently, we performed a genome-wide analysis ofListeria monocytogenesgene expression after growth in the presence of antibiotics, identifying genes that are up-regulated upon antibiotic treatment. One of them,lmo0762, is a homolog ofhflX, which encodes a heat shock protein that rescues stalled ribosomes by separating their two subunits. To our knowledge, ribosome splitting has never been described as an antibiotic resistance mechanism. We thus investigated the role oflmo0762in antibiotic resistance. First, we demonstrated thatlmo0762is an antibiotic resistance gene that confers protection against lincomycin and erythromycin, and that we renamedhflXr(hflXresistance). We show thathflXrexpression is regulated by a transcription attenuation mechanism relying on the presence of alternative RNA structures and a small ORF encoding a 14 amino acid peptide containing the RLR motif, characteristic of macrolide resistance genes. We also provide evidence that HflXr is involved in ribosome recycling in presence of antibiotics. Interestingly,L. monocytogenespossesses another copy ofhflX,lmo1296, that is not involved in antibiotic resistance. Phylogenetic analysis shows several events ofhflXrduplication in prokaryotes and widespread presence ofhflXrin Firmicutes. Overall, this study reveals theListeria hflXras the founding member of a family of antibiotic resistance genes. The resistance conferred by this gene is probably of importance in the environment and within microbial communities.

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Occurrence and distribution of antibiotic resistance genes in lakes and reservoirs from water-receiving area of Eastern Route of the South-to-North Water Diversion Project, Northern China

Water Science & Technology Water Supply ◽

10.2166/ws.2020.190 ◽

2020 ◽

Vol 20 (8) ◽

pp. 3029-3037

Author(s):

Wei Hou ◽

Fang Hu ◽

Shaohua Sun ◽

Xiaotong Dong ◽

Mingquan Wang ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Local Level ◽

Resistance Mechanism ◽

Antibiotic Resistance Genes ◽

Northern China ◽

Water Diversion ◽

Contamination Level ◽

North Water ◽

Study Sites

Abstract To characterize antibiotic resistance genes (ARGs) in surface waterbodies in Shandong Province, and to understand the occurrence, diversity and resistance mechanism of ARGs, nine aquatic ecosystems were selected and evaluated regarding occurrence of ARGs in the period from 2018 to 2019. Thirty-three types and 242 subtypes of ARGs were detected in the nine waterbodies with the most subtypes in Wohushan (242) and Jihongtan (235), and the fewest ARGs in Datun (213) and Mishan (221). Among the top nine ARG types, MacB, BcrA, CarA and TetW were the dominant ARGs in these samples. Four groups of the study sites were distinguished by cluster analysis, indicating different distribution characteristics of ARGs in these waterbodies, and regional differences in ARG contamination. Efflux pumps were the predominant resistance mechanism in all the waterbodies in terms of both subtype number (49.2%) and abundance (70.4%), followed by operon, antibiotic inactivation and others. Our findings provide comprehensive information to better understand the contamination level of ARGs on a local level as well as for global considerations, and may be practically helpful for the prevention and control of ARG pollution.

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