Metagenomic and metatranscriptomic analyses reveal activity and hosts of antibiotic resistance genes in activated sludge

Liu, Zongbao; Klümper, Uli; Liu, Yang; Yang, Yuchun; Wei, Qiaoyan; Lin, Jium-Ming; Gu, Ji Dong; Li, Meng

doi:10.1016/j.envint.2019.05.036

Cited by 186 publications

(82 citation statements)

References 75 publications

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“…With the growing use of MAG methods in infectious disease research [73][74][75][76][77] and the public-health and agrifood importance of the LGT of AMR and VF genes, we also specifically evaluated the binning of these gene classes. The majority of these genes were correctly assembled across assemblers, but were either not assigned or incorrectly assigned to MAG bins during binning.…”

Section: Discussionmentioning

confidence: 99%

Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands

et al. 2020

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Metagenomic methods enable the simultaneous characterization of microbial communities without time-consuming and bias-inducing culturing. Metagenome-assembled genome (MAG) binning methods aim to reassemble individual genomes from this data. However, the recovery of mobile genetic elements (MGEs), such as plasmids and genomic islands (GIs), by binning has not been well characterized. Given the association of antimicrobial resistance (AMR) genes and virulence factor (VF) genes with MGEs, studying their transmission is a public-health priority. The variable copy number and sequence composition of MGEs makes them potentially problematic for MAG binning methods. To systematically investigate this issue, we simulated a low-complexity metagenome comprising 30 GI-rich and plasmid-containing bacterial genomes. MAGs were then recovered using 12 current prediction pipelines and evaluated. While 82–94 % of chromosomes could be correctly recovered and binned, only 38–44 % of GIs and 1–29 % of plasmid sequences were found. Strikingly, no plasmid-borne VF nor AMR genes were recovered, and only 0–45 % of AMR or VF genes within GIs. We conclude that short-read MAG approaches, without further optimization, are largely ineffective for the analysis of mobile genes, including those of public-health importance, such as AMR and VF genes. We propose that researchers should explore developing methods that optimize for this issue and consider also using unassembled short reads and/or long-read approaches to more fully characterize metagenomic data.

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Section: Discussionmentioning

confidence: 99%

Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands

et al. 2020

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“…With the growing use of MAG methods in infectious disease research (e.g., [51,52,53,54,55]) and the public-health importance of the LGT of AMR and VF genes, we also speci cally evaluated the binning of these gene classes. The majority of these genes were correctly assembled across assemblers but were either not assigned or incorrectly assigned to MAG bins during binning.…”

Section: Discussionmentioning

confidence: 99%

Metagenome-Assembled Genome Binning Methods with Short Reads Disproportionately Fail for Plasmids and Genomic Islands

Maguire

Jia²,

Gray³

et al. 2020

Preprint

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MotivationMetagenomic methods have emerged as a key tool in public-health microbiology for surveillance of virulence factor (VF) and antimicrobial resistance (AMR) genes. However, metagenomic data, even when assembled, typically results in complex, mixed sets DNA sequence fragments rather than fully resolved individual genomes. Recently, metagenome-assembled genomes (MAGs) have emerged as a promising approach that groups sequences into bins that are likely derived from the same underlying genome. However, MAGs have not been well assessed for their ability to identify some of the key sequences of interest for infectious disease surveillance purposes: AMR and VFs associated with mobile genetic elements (MGEs) such as plasmids and genomic islands (GIs). We hypothesized that due to the di erent copy number and sequence composition of plasmids and GIs compared to core genome sequence, such sequences will be under-represented in MAG-based approaches. ResultsTo evaluate the impact of MAG recovery methods on recovery of AMR genes and MGEs, we generated a simulated metagenomic dataset comprised of 30 genomes with up to 16.65% of the chromosomal DNA consisting of GIs and 65 associated plasmids. MAGs were then recovered from this data using 12 di erent MAG pipelines and evaluated for recovery accuracies. Across all pipelines, 81.9-94.3% of chromosomes were recovered and binned. However, only 37.8-44.1% of GIs and 1.5-29.2% of plasmids were recovered and correctly binned at >50% coverage. In terms of AMR and VF genes associated with MGEs, 0-45% of GI-associated AMR genes and 0-16% of GI-associated VF genes were correctly assigned. More strikingly, 0% of plasmid-borne VF or AMR genes were recovered. This work shows that regardless of the MAG recovery approach used, plasmid and GI dominated sequences will disproportionately be left unbinned or incorrectly binned. From a public-health perspective, this means MAG approaches are less suited for analysis of mobile genes, especially key groups such as AMR and VF genes. This underlines the utility of read-based and long-read approaches to thoroughly evaluate the resistome in metagenomic data.

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“…The sul1 gene was also the most abundant of the 20 resistant genes tested. Currently, sulfa antibiotics are widely used in aquatic products and animal husbandry industries and discharged with feces, but they are not easily degraded in the environment [25], resulting in high levels of sulfonamide resistance gene residues. The sul1 genes are located on large binding plasmids, and the sul2 genes are located on widely distributed plasmids and small unbound plasmids in the host.…”

Section: Absolute Abundance Of Argsmentioning

confidence: 99%

Distribution of Antibiotic Resistance Genes in Three Different Natural Water Bodies-A Lake, River and Sea

Su¹,

Li²,

Yang

et al. 2020

IJERPH

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Currently, due to abuse in the use of human antibiotics and the weak regulatory control that the authorities have over sewage discharge and manure management, antibiotic resistance genes (ARGs) have become a new type of environmental pollutant. Three different natural water bodies (Poyang Lake, Haihe River and Qingdao No.1 Bathing Beach seawater) were sampled during the same periods to conduct a longitudinal comparison of distribution. The distribution and expression of 11 ARGs in 20 species were studied, and the correlations between the expression and the distribution of time and space of the ARGs in different water bodies were also analyzed. With the exception of ermA, blaNDM-1 and vanA, which were not detected in seawater, the other ARGs could be detected in all three water bodies. Tetracycline resistance genes (tetC, tetM and tetQ) in the seawater and Haihe River had even reached 100%, and sulfa ARGs (sul1 and sul2) in the seawater and Poyang Lake, as well as sul2 and sul3 in the Haihe River, had also reached 100%. The ARG pollution in Haihe River was much more serious, since 14 and 17 of 20 ARG species were significantly higher compared with seawater and Poyang Lake, respectively. Some ARGs also had a high absolute abundance. The absolute abundance of macrolide resistance genes (ermB) in seawater was as high as 8.61 × 107 copies/L, and the anti-tuberculosis resistant genes (rpoB and katG) in the Haihe River Basin were highly abundant at 1.32 × 106 copies/L and 1.06 × 107 copies/L, respectively. This indicates that ARGs have gradually become more diverse and extensive in natural water bodies. The results of a redundancy analysis (RDA) of the three water bodies showed that although each water body is affected by different factors in space and time, overall, the presence of AGRs is closely related to the production and life of human beings and the migration of animals.

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Metagenomic and metatranscriptomic analyses reveal activity and hosts of antibiotic resistance genes in activated sludge

Cited by 186 publications

References 75 publications

Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands

Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands

Metagenome-Assembled Genome Binning Methods with Short Reads Disproportionately Fail for Plasmids and Genomic Islands

Distribution of Antibiotic Resistance Genes in Three Different Natural Water Bodies-A Lake, River and Sea

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