Deciphering the mobility and bacterial hosts of antibiotic resistance genes under antibiotic selection pressure by metagenomic assembly and binning approaches

Zhao, Renxin; Yu, Ke; Zhang, Jiayu; Zhang, Guijuan; Huang, Jin; Ma, Liping; Deng, Chunfang; Li, Xiaoyan; Li, Bing

doi:10.1016/j.watres.2020.116318

Cited by 209 publications

(63 citation statements)

References 95 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…With the successful investigation on microbial communities in diverse environments, massive metagenomic datasets have been produced to investigate the taxonomical and functional compositions of microbial communities, obtain an in-depth understanding of functional traits, such as nitrogen cycle (Jansson and Hofmockel, 2018;Miao and Liu, 2018) and ARGs (Stalder et al, 2019;Xiang et al, 2020), and explore the driving factors for the dynamic changes of functional traits (Pan et al, 2020). For example, based on metagenomic datasets, ARG profiles in different environments have been investigated and explored, such as activated sludge under high selective pressure with different antibiotics (Zhao et al, 2019) and seed activated sludge collected from a municipal wastewater treatment plant and five experiment groups with different antibiotics (Zhao et al, 2020) and a deep subtropical lake (Carnevali et al, 2021). These studies revealed that metagenomic sequencing creates an opportunity for capturing the majority of ARGs and their potential hosts.…”

Section: Metagenomic Data In Antibiotics Resistance Gene Studiesmentioning

confidence: 99%

“…CARD is currently a bioinformatic database and a compressive platform for identifying resistance genes, including their products and associated phenotypes (https:// card.mcmaster.ca/). In 2016, SARG was constructed with a hierarchical structure (type-subtype-reference sequence) by integrating the two most commonly used ARG databases ARDB and CARD, removing their redundant sequences, and re-selecting the query sequences based on the similarity of sequences; this database can identify ARG sequences through similarity search (Yang et al, 2016) and has been widely used in ARG studies (Zhao et al, 2019;Zhao et al, 2020). The latest version of SARG (v2.0) has tripled the sequences of the first version, improved the coverage of ARG detection, and annotated the high-throughput raw reads by using a similarity search strategy in diverse environmental metagenomes (Zhao et al, 2020).…”

Section: Bioinformatic Databases Used For Identifying Antibiotics Resistance Genes and Mgesmentioning

confidence: 99%

See 1 more Smart Citation

Utilizing Metagenomic Data and Bioinformatic Tools for Elucidating Antibiotic Resistance Genes in Environment

Peng

Mao

Zhang

et al. 2021

Front. Environ. Sci.

View full text Add to dashboard Cite

Antibiotics resistance genes (ARGs) are mainly caused by the extensive use and abuse of antibiotics and have become a global public health concern. Owing to the development of high-throughput sequencing, metagenomic sequencing has been widely applied to profile the composition of ARGs, investigate their distribution pattern, and track their sources in diverse environments. However, the lack of a detailed transmission mechanism of ARGs limits the management of its pollution. Hence, it’s essential to introduce how to utilize the metagenomic data to obtain an in-depth understanding of the distribution pattern and transmission of ARGs. This review provides an assessment of metagenomic data utilization in ARG studies and summarizes current bioinformatic tools and databases, including ARGs-OAP, ARG analyzer, DeepARG, CARD, and SARG, for profiling the composition of ARGs and tracking the source of ARGs. Several bioinformatic tools and databases were then benchmarked. Our results showed that although SARG is a good database, the application of two or more bioinformatic tools and databases could provide a comprehensive view of ARG profiles in diverse environmental samples. Finally, several perspectives were proposed for future studies to obtain an in-depth understanding of ARGs based on metagenomic data. Our review of the utilization of metagenomic data together with bioinformatic tools and databases in ARG studies could provide insights on exploring the profiles and transmission mechanism of ARG in different environments that mitigate the spread of ARGs and manage the ARGs pollution.

show abstract

Section: Metagenomic Data In Antibiotics Resistance Gene Studiesmentioning

confidence: 99%

Section: Bioinformatic Databases Used For Identifying Antibiotics Resistance Genes and Mgesmentioning

confidence: 99%

Utilizing Metagenomic Data and Bioinformatic Tools for Elucidating Antibiotic Resistance Genes in Environment

Peng

Mao

Zhang

et al. 2021

Front. Environ. Sci.

View full text Add to dashboard Cite

show abstract

“…The advantage of MAGs versus traditional metagenome gene catalogs is manifold; the most apparent is the high accuracy of phylogenetic affiliations and often complete gene clusters, revealing gene synteny. The latter is of high interest when studying ARGs since the genetic environment often reveals the potential for the genetic mobility of ARGs, e.g., their location on genetic islands or plasmids [22]. Besides, it is also possible to investigate the presence of multi-drug-resistant (MDR) bacteria by detecting more than one ARG in the same bacterial genome or contig [9] when using the MAG based approach.…”

Section: Introductionmentioning

confidence: 99%

Putative mobilized colistin resistance genes in the human gut microbiome

et al. 2021

View full text Add to dashboard Cite

Background The high incidence of bacterial genes that confer resistance to last-resort antibiotics, such as colistin, caused by mobilized colistin resistance (mcr) genes, poses an unprecedented threat to human health. Understanding the spread, evolution, and distribution of such genes among human populations will help in the development of strategies to diminish their occurrence. To tackle this problem, we investigated the distribution and prevalence of potential mcr genes in the human gut microbiome using a set of bioinformatics tools to screen the Unified Human Gastrointestinal Genome (UHGG) collection for the presence, synteny and phylogeny of putative mcr genes, and co-located antibiotic resistance genes. Results A total of 2079 antibiotic resistance genes (ARGs) were classified as mcr genes in 2046 metagenome assembled genomes (MAGs), distributed across 1596 individuals from 41 countries, of which 215 were identified in plasmidial contigs. The genera that presented the largest number of mcr-like genes were Suterella and Parasuterella. Other potential pathogens carrying mcr genes belonged to the genus Vibrio, Escherichia and Campylobacter. Finally, we identified a total of 22,746 ARGs belonging to 21 different classes in the same 2046 MAGs, suggesting multi-resistance potential in the corresponding bacterial strains, increasing the concern of ARGs impact in the clinical settings. Conclusion This study uncovers the diversity of mcr-like genes in the human gut microbiome. We demonstrated the cosmopolitan distribution of these genes in individuals worldwide and the co-presence of other antibiotic resistance genes, including Extended-spectrum Beta-Lactamases (ESBL). Also, we described mcr-like genes fused to a PAP2-like domain in S. wadsworthensis. These novel sequences increase our knowledge about the diversity and evolution of mcr-like genes. Future research should focus on activity, genetic mobility and a potential colistin resistance in the corresponding strains to experimentally validate those findings.

show abstract

“…The advantage of MAGs versus traditional metagenome gene catalogs is manifold; the most apparent is the high accuracy of phylogenetic affiliations and often complete gene clusters, revealing gene synteny. Especially the latter is of high interest when studying ARGs since the genetic environment often shows the genetic mobility of ARGs, e.g., their location on genetic islands or plasmids 22 . Besides, it is also possible to investigate the presence of multi-drug-resistant (MDR) bacteria by detecting more than one ARG in the same bacterial genome or contig 9 when using the MAGs approach.…”

Section: Introductionmentioning

confidence: 99%

Putative mobilized colistin resistance genes in the human gut microbiome

Andrade

Goris

Afli

et al. 2021

Preprint

View full text Add to dashboard Cite

BackgroundThe high incidence of bacterial genes that confer resistance to last-resort antibiotics, such as colistin caused by MCR genes, poses an unprecedented threat to our civilization’s health. To understand the spread, evolution, and distribution of such genes among human populations, with the final goal of diminishing their occurrence in human environments should be a priority. To tackle this problem, we investigated the distribution and prevalence of potential mcr genes in the human gut microbiome we used a set of bioinformatics tools to screen the Unified Human Gastrointestinal Genome (UHGG) collection for the presence, synteny and phylogeny of putative mcr genes, and co-located antibiotic resistance genes.ResultsA total of 2,079 ARGs were classified as different MCR in 2,046 Metagenome assembled genomes (MAGs), present in 1,596 individuals from 41 countries, of which 215 MCRs were identified in plasmidial contigs. The genera that presented the largest number of MCR-like genes were Suterella and Parasuterella, prevalent human gut bacteria of which Suterella wadsworthensis is associated with autism. Other potential pathogens carrying MCR genes belonged to the genus Vibrio, Escherichia and Campylobacter. Finally, we identified a total of 22,746 ARGs belonging to 21 different classes in the same 2,046 MAGs, suggesting multi-resistance potential in the corresponding bacterial strains, increasing the concern of ARGs impact in the clinical settings.ConclusionThis study uncovers the diversity of MCR-like genes in the human gut microbiome. We showed the cosmopolitan distribution of these genes in individuals worldwide and the co-presence of other antibiotic resistance genes, including Extended-spectrum beta-lactamases (ESBL). Also, we described mcr-like genes fused to a PAP2-like domain in S. wadsworthensis. Although these novel sequences increase our knowledge about the diversity and evolution of mcr-like genes, their activity and a potential colistin resistance in the corresponding strains has to be experimentally validated.

show abstract

Deciphering the mobility and bacterial hosts of antibiotic resistance genes under antibiotic selection pressure by metagenomic assembly and binning approaches

Cited by 209 publications

References 95 publications

Utilizing Metagenomic Data and Bioinformatic Tools for Elucidating Antibiotic Resistance Genes in Environment

Utilizing Metagenomic Data and Bioinformatic Tools for Elucidating Antibiotic Resistance Genes in Environment

Putative mobilized colistin resistance genes in the human gut microbiome

Putative mobilized colistin resistance genes in the human gut microbiome

Contact Info

Product

Resources

About