4.4 Article

Metagenomic profiling of antibiotic resistance genes in Red Sea brine pools

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Genetics & Heredity

Metagenomic and Recombination Analyses of Antimicrobial Resistance Genes from Recreational Waters of Black Sea Coastal Areas and Other Marine Environments Unveil Extensive Evidence for Their both Intrageneric and Intergeneric Transmission across Genetically Very Diverse Microbial Communities

Ekaterine Gabashvili et al.

Summary: Microbial communities in marine coastal recreation waters are reservoirs of antimicrobial resistance genes (ARGs), leading to the emergence and spread of antibiotic-resistant infections. The study analyzed ARGs in the Black Sea coastal recreation waters using metagenomics approaches and identified genetic recombination and transmission of ARGs among diverse microbial communities.

MARINE GENOMICS (2022)

Article Infectious Diseases

Occurrence of Virulence and Antimicrobial Resistance Determinants in Vibrio harveyi Isolated from Marine Food Fish Cultured in Korea

Liyana Arachchilage Dinithi S. De Silva et al.

Summary: Vibrio harveyi isolated from marine food fish cultured in Korea showed high virulence factors and antimicrobial resistance, with most classified as multidrug resistant, posing a threat to the effectiveness of antimicrobial treatments. Various virulence genes and antimicrobial resistance genes were detected in the isolates, indicating the potential development of more virulent strains with increased antimicrobial resistance.

MICROBIAL DRUG RESISTANCE (2022)

Article Environmental Sciences

Metagenomic analysis reveals microbiome and resistome in the seawater and sediments of Kongsfjorden (Svalbard, High Arctic)

Tao Zhang et al.

Summary: This study analyzed the diversity and distribution of bacterial communities and antibiotic resistance genes (ARGs) in seawater and sediments of Kongsfjorden in the Arctic through metagenomic analysis. The results showed significant differences in bacterial community compositions and ARG profiles between seawater and sediment samples. Geographic and geochemical factors greatly influenced the bacterial communities and ARG profiles, with Procrustes analysis revealing a significant correlation between the two.

SCIENCE OF THE TOTAL ENVIRONMENT (2022)

Article Microbiology

Characteristics of Antibiotic Resistance Genes and Antibiotic-Resistant Bacteria in Full-Scale Drinking Water Treatment System Using Metagenomics and Culturing

Qihui Gu et al.

Summary: This study investigated the profile of antibiotic resistance genes (ARGs) in a drinking water treatment system (DWTS) in South China using a metagenomic approach. The study found a wide presence of various ARG subtypes in the DWTS, with Acidovorax, Polynucleobacter, Pseudomonas, Escherichia, and Klebsiella as the main hosts. Stenotrophomonas maltophilia and Pseudomonas aeruginosa were the most common pathogens, and the study highlighted the need for more effective disinfection methods to remove ARGs.

FRONTIERS IN MICROBIOLOGY (2022)

Article Chemistry, Medicinal

Evaluation of a Thermophilic, Psychrostable, and Heavy Metal-Resistant Red Sea Brine Pool Esterase

Shimaa F. Ahmed et al.

Summary: This study comprehensively evaluates the extreme properties of EstATII-TM lipase isolated from the Red Sea Atlantis II brine pool, showing its tolerance to high temperatures, stability to hot and cold conditions, and resistance to toxic heavy metals. EstATII-TM exhibits superior catalytic activity and resistance/enhancement to metal ions compared to commercial esterases.

MARINE DRUGS (2022)

Article Biotechnology & Applied Microbiology

Bioprospecting the microbiome of Red Sea Atlantis II brine pool for peptidases and biosynthetic genes with promising antibacterial activity

Laila Ziko et al.

Summary: In this study, two clones with antibacterial and anticancer effects were identified through screening of DNA from marine environments. These clones showed promising antibacterial activity against challenging bacterial strains and also exhibited inhibitory effects on cancer cells. Additionally, potential proteases and biosynthetic genes were detected. Therefore, searching for new molecules in extreme marine environments is of great importance.

MICROBIAL CELL FACTORIES (2022)

Article Environmental Sciences

Abundance and diversity of antibiotic resistance genes and bacterial communities in the western Pacific and Southern Oceans

Jiyi Jang et al.

Summary: This study investigated the abundance and diversity of antibiotic resistance genes (ARGs) and bacterial communities in the western Pacific Ocean to the Southern Ocean. The results showed that the absolute abundance of ARGs was higher in the western Pacific Ocean and slightly increased towards Terra Nova Bay in Antarctica. Beta-lactam and tetracycline resistance genes were dominant in all samples. Certain bacterial communities were found to be positively correlated with ARGs. This study highlights the latitudinal profile of ARG distribution in the open ocean system.

SCIENCE OF THE TOTAL ENVIRONMENT (2022)

Article Microbiology

IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella

Bertrand Neron et al.

Summary: Integrons are flexible gene-exchanging platforms that play a crucial role in spreading antibiotic resistance genes among nosocomial pathogens. IntegronFinder, a widely used software, lacks functionality to handle large datasets. This study introduces IntegronFinder version 2, which improves efficiency and usability, allows for analysis of incomplete genome data, and includes new functions. The relevance of IntegronFinder is demonstrated by analyzing integron distribution across 20,000 genomes and identifying integrons and antibiotic resistance genes in 4,000 Klebsiella pneumoniae genomes.

MICROORGANISMS (2022)

Article Microbiology

Prevalence and Antimicrobial Resistance of Bacteria Isolated from Marine and Freshwater Fish in Tanzania

Esther Marijani

Summary: This study aimed to determine the prevalence and antimicrobial resistance of bacteria isolated from retail fish and shrimp in Tanzania. The results showed that the majority of samples were contaminated, with E. coli, Klebsiella spp., and Salmonella spp. being the most common bacterial species.

INTERNATIONAL JOURNAL OF MICROBIOLOGY (2022)

Article Environmental Sciences

Ecological insights into the elevational biogeography of antibiotic resistance genes in a pristine river: Metagenomic analysis along the Yarlung Tsangpo River on the Tibetan Plateau

Sheng Liu et al.

Summary: This study analyzed the biogeographical pattern of ARGs along the pristine Yarlung Tsangpo River on the Tibetan Plateau using metagenomics approaches, revealing the distribution characteristics of ARGs at different elevations. The study found that bacA, resistant to bacitracin, dominated the ARGs in the pristine river, and elevational gradients could influence the assembly processes of ARGs.

ENVIRONMENTAL POLLUTION (2021)

Review Genetics & Heredity

Metagenomic Approaches to Analyze Antimicrobial Resistance: An Overview

Vinicius A. C. de Abreu et al.

Summary: Antimicrobial resistance is a significant global public health issue, primarily caused by pathogens acquiring resistance genes through horizontal gene transfer. High-throughput sequencing technologies and metagenomics have helped identify community antimicrobial resistance, with challenges in analyzing microbial diversity, functional gene analysis, and searching for relevant resistome databases.

FRONTIERS IN GENETICS (2021)

Article Biology

Twelve years of SAMtools and BCFtools

Petr Danecek et al.

Summary: SAMtools and BCFtools are widely used tools for processing high-throughput sequencing data, with a history of 12 years of continuous development and improvement. These packages have been utilized in various software projects and genomic pipelines and are freely available on GitHub.

GIGASCIENCE (2021)

Article Biotechnology & Applied Microbiology

Functional metagenomic analysis of quorum sensing signaling in a nitrifying community

Chuan Hao Tan et al.

Summary: By conducting metagenomic screening and functional validation of AHL genes in the activated sludge microbial community from the Ulu Pandan wastewater treatment plant in Singapore, functional QS genes LuxI and LuxR were identified, indicating that Nitrospira spp. may be active in the activated sludge community.

NPJ BIOFILMS AND MICROBIOMES (2021)

Article Biochemical Research Methods

Sensitive protein alignments at tree-of-life scale using DIAMOND

Benjamin Buchfink et al.

Summary: We are at the beginning of a genomic revolution where all known species are planned to be sequenced. The improved version of DIAMOND allows for quick tree-of-life scale protein alignments.

NATURE METHODS (2021)

Article Environmental Sciences

Antibiotic residues in wastewaters from sewage treatment plants and pharmaceutical industries: Occurrence, removal and environmental impacts

Kun Wang et al.

Summary: This study investigated wastewater samples from two STPs and two PMFs in eastern China, revealing higher antibiotic concentrations in PMFs. The MBR system showed the best performance in antibiotic removal, while certain SAs and FQs antibiotics were consistently detected at high concentrations in effluent samples.

SCIENCE OF THE TOTAL ENVIRONMENT (2021)

Article Biochemistry & Molecular Biology

The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities

I-Min A. Chen et al.

Summary: The Integrated Microbial Genomes & Microbiomes system at the DOE's Joint Genome Institute contains annotated genome datasets and metagenome bins, with advanced search functions and a new statistical analysis tool available in IMG v 6.0. The updated web user interface includes a Help page and webinar tutorials to assist users in understanding and utilizing various IMG functions and tools in their research. New datasets have been processed with an extended prokaryotic annotation pipeline v.5, featuring expanded protein family assignments.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

Pfam: The protein families database in 2021

Jaina Mistry et al.

Summary: The Pfam database has recently added a large number of protein families and domains, made revisions for COVID-19 research, and introduced Pfam-B as a supplement. These updates and improvements can help researchers classify protein sequences more effectively and conduct related studies.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database

Brian P. Alcock et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Multidisciplinary Sciences

Discovery of Afifi, the shallowest and southernmost brine pool reported in the Red Sea

Carlos M. Duarte et al.

SCIENTIFIC REPORTS (2020)

Editorial Material Critical Care Medicine

Key Takeaways From the US CDC's 2019 Antibiotic Resistance Threats Report for Frontline Providers

Sameer S. Kadri

CRITICAL CARE MEDICINE (2020)

Article Biotechnology & Applied Microbiology

Antibacterial and anticancer activities of orphan biosynthetic gene clusters from Atlantis II Red Sea brine pool

Laila Ziko et al.

MICROBIAL CELL FACTORIES (2019)

Article Environmental Sciences

Understanding drivers of antibiotic resistance genes in High Arctic soil ecosystems

Clare M. McCann et al.

ENVIRONMENT INTERNATIONAL (2019)

Article Biochemistry & Molecular Biology

Plasmid detection and assembly in genomic and metagenomic data sets

Dmitry Antipov et al.

GENOME RESEARCH (2019)

Article Biotechnology & Applied Microbiology

Molecular Adaptations of Bacterial Mercuric Reductase to the Hypersaline Kebrit Deep in the Red Sea

Eman Ramadan et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2019)

Article Biochemical Research Methods

fastp: an ultra-fast all-in-one FASTQ preprocessor

Shifu Chen et al.

BIOINFORMATICS (2018)

Article Environmental Sciences

Baseline screening for the presence of antimicrobial resistance in E. coli isolated from Kuwait's marine environment

Hanan A. Al-Sarawi et al.

MARINE POLLUTION BULLETIN (2018)

Article Biochemistry & Molecular Biology

Insertion sequences enrichment in extreme Red sea brine pool vent

Ali H. A. Elbehery et al.

EXTREMOPHILES (2017)

Article Biotechnology & Applied Microbiology

Novel thermostable antibiotic resistance enzymes from the Atlantis II Deep Red Sea brine pool

Ali H. A. Elbehery et al.

MICROBIAL BIOTECHNOLOGY (2017)

Article Multidisciplinary Sciences

Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data

Nicolas F. Fernandez et al.

SCIENTIFIC DATA (2017)

Article Microbiology

Continental-scale pollution of estuaries with antibiotic resistance genes

Yong-Guan Zhu et al.

NATURE MICROBIOLOGY (2017)

Review Microbiology

The impact of insertion sequences on bacterial genome plasticity and adaptability

Joachim Vandecraen et al.

CRITICAL REVIEWS IN MICROBIOLOGY (2017)

Article Biochemical Research Methods

ISEScan: automated identification of insertion sequence elements in prokaryotic genomes

Zhiqun Xie et al.

BIOINFORMATICS (2017)

Article Biotechnology & Applied Microbiology

Red Sea Atlantis II brine pool nitrilase with unique thermostability profile and heavy metal tolerance

Sarah A. Sonbol et al.

BMC BIOTECHNOLOGY (2016)

Article Immunology

The Future of Antibiotics and Resistance: A Tribute to a Career of Leadership by John Bartlett

Brad Spellberg et al.

CLINICAL INFECTIOUS DISEASES (2014)

Article Biochemistry & Molecular Biology

A Novel Mercuric Reductase from the Unique Deep Brine Environment of Atlantis II in the Red Sea

Ahmed Sayed et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2014)

Article Multidisciplinary Sciences

Bacterial phylogeny structures soil resistomes across habitats

Kevin J. Forsberg et al.

NATURE (2014)

Article Microbiology

Aerobic methanotrophic communities at the Red Sea brine-seawater interface

Rehab Z. Abdallah et al.

FRONTIERS IN MICROBIOLOGY (2014)

Article Biochemical Research Methods

Infernal 1.1: 100-fold faster RNA homology searches

Eric P. Nawrocki et al.

BIOINFORMATICS (2013)

Article Engineering, Environmental

Metagenomic Profiles of Antibiotic Resistance Genes (ARGs) between Human Impacted Estuary and Deep Ocean Sediments

Baowei Chen et al.

ENVIRONMENTAL SCIENCE & TECHNOLOGY (2013)

Article Multidisciplinary Sciences

Isolation and characterization of a heavy metal-resistant, thermophilic esterase from a Red Sea Brine Pool

Yasmine M. Mohamed et al.

SCIENTIFIC REPORTS (2013)

Article Oceanography

Vertical, horizontal, and temporal changes in temperature in the Atlantis II and Discovery hot brine pools, Red Sea

Stephen A. Swift et al.

DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS (2012)

Article Environmental Sciences

Selective Pressure of Antibiotic Pollution on Bacteria of Importance to Public Health

Alfredo Tello et al.

ENVIRONMENTAL HEALTH PERSPECTIVES (2012)

Article Multidisciplinary Sciences

Antibiotic Resistance Is Prevalent in an Isolated Cave Microbiome

Kirandeep Bhullar et al.

PLOS ONE (2012)

Article Multidisciplinary Sciences

Antibiotic resistance is ancient

Vanessa M. D'Costa et al.

NATURE (2011)

Review Environmental Sciences

Microbiology of the Red Sea (and other) deep-sea anoxic brine lakes

Andre Antunes et al.

ENVIRONMENTAL MICROBIOLOGY REPORTS (2011)

Article Biochemical Research Methods

Prodigal: prokaryotic gene recognition and translation initiation site identification

Doug Hyatt et al.

BMC BIOINFORMATICS (2010)

Article Biochemical Research Methods

Hidden Markov model speed heuristic and iterative HMM search procedure

L. Steven Johnson et al.

BMC BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

FragGeneScan: predicting genes in short and error-prone reads

Mina Rho et al.

NUCLEIC ACIDS RESEARCH (2010)

Review Microbiology

Genomic islands: tools of bacterial horizontal gene transfer and evolution

Mario Juhas et al.

FEMS MICROBIOLOGY REVIEWS (2009)

Article Biotechnology & Applied Microbiology

The RAST server: Rapid annotations using subsystems technology

Ramy K. Aziz et al.

BMC GENOMICS (2008)

Article Microbiology

Metagenomic analysis of the microbial community associated with the coral Porites astreoides

Linda Wegley et al.

ENVIRONMENTAL MICROBIOLOGY (2007)

Article Infectious Diseases

Antibiotic selective pressure and development of bacterial resistance

M Kolár et al.

INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS (2001)