Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics

Bengtsson‐Palme, Johan; Hammarén, Rickard; Pal, Chandan; Östman, Marcus; Björlenius, Berndt; Flach, Carl-Fredrik; Fick, Jerker; Kristiansson, Erik; Tysklind, Mats; Larsson, D. G. Joakim

doi:10.1016/j.scitotenv.2016.06.228

Cited by 227 publications

(156 citation statements)

References 85 publications

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“…The metagenomic datasets (Additional file 5: Table S3) consisted of raw Illumina sequence reads from the human gut microbiome (“Human gut 1” [59], “Human gut 2” [60]), and the human microbiome (“HMP” [53]). In addition, datasets from various polluted environments were included and consisted of oil-exposed marine sediments (“oil spill” [61]), a pharmaceutical-polluted lake (“polluted lake” [13]), Swedish waste water treatment plants (“WWTP” [14]), and pharmaceutical-polluted river sediments (“Isakavagu river” [15]). We also included samples from bacterial communities in soil and well water (“Patancheru soil,” “Patancheru well” [62]) and from river sediments in Pune (“Pune river,” [63]).…”

Section: Methodsmentioning

confidence: 99%

Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data

et al. 2017

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BackgroundMetallo-β-lactamases are bacterial enzymes that provide resistance to carbapenems, the most potent class of antibiotics. These enzymes are commonly encoded on mobile genetic elements, which, together with their broad substrate spectrum and lack of clinically useful inhibitors, make them a particularly problematic class of antibiotic resistance determinants. We hypothesized that there is a large and unexplored reservoir of unknown metallo-β-lactamases, some of which may spread to pathogens, thereby threatening public health. The aim of this study was to identify novel metallo-β-lactamases of class B1, the most clinically important subclass of these enzymes.ResultsBased on a new computational method using an optimized hidden Markov model, we analyzed over 10,000 bacterial genomes and plasmids together with more than 5 terabases of metagenomic data to identify novel metallo-β-lactamase genes. In total, 76 novel genes were predicted, forming 59 previously undescribed metallo-β-lactamase gene families. The ability to hydrolyze imipenem in an Escherichia coli host was experimentally confirmed for 18 of the 21 tested genes. Two of the novel B1 metallo-β-lactamase genes contained atypical zinc-binding motifs in their active sites, which were previously undescribed for metallo-β-lactamases. Phylogenetic analysis showed that B1 metallo-β-lactamases could be divided into five major groups based on their evolutionary origin. Our results also show that, except for one, all of the previously characterized mobile B1 β-lactamases are likely to have originated from chromosomal genes present in Shewanella spp. and other Proteobacterial species.ConclusionsThis study more than doubles the number of known B1 metallo-β-lactamases. The findings have further elucidated the diversity and evolutionary history of this important class of antibiotic resistance genes and prepare us for some of the challenges that may be faced in clinics in the future.Electronic supplementary materialThe online version of this article (10.1186/s40168-017-0353-8) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data

et al. 2017

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“…It is well known that wastewater treatment reduces the bacterial abundance, in addition a recent metagenomic study has shown that the bacterial community in wastewater is very different to the human gut community and that the number of detected genera is reduced in the wastewater 9 . Consequently, our expectation was that the genomic diversity of Escherichia coli should be reduced.…”

Section: Discussionmentioning

confidence: 99%

“…Therefore the current information on the genomic diversity of antibiotic resistant Escherichia coli in wastewater is very limited. Recent metagenomic studies have documented that human-associated bacteria are strongly reduced in the wastewater and its treatment process 9 . To investigate the genomic diversity as well as virulence genes and resistance determinants for wastewater Escherichia coli , we proceeded as sketched in Fig.…”

Section: Introductionmentioning

confidence: 99%

High genomic diversity of multi-drug resistant wastewater Escherichia coli

Mahfouz

Caucci

Achatz

et al. 2017

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19Wastewater treatment plants play an important role in the release of antibiotic resistance into the 20 environment. It has been shown that wastewater contains multi-drug resistant Escherichia coli, 21 but information on strain diversity is surprisingly scarce. Here we present an exceptionally large 22 dataset on multidrug resistant Escherichia coli, originating from wastewater, over a thousand 23 isolates were phenotypically characterized for twenty antibiotics and for 103 isolates whole 24 genomes were sequenced. To our knowledge this is the first study documenting such a 25 comprehensive diversity of multi-drug resistant Escherichia coli in wastewater. The genomic 26 diversity of the isolates was unexpectedly high and contained a high number of resistance and 27 virulence genes. To illustrate the genomic diversity of the isolates we calculated the pan genome 28 of the wastewater Escherichia coli and found it to contain over sixteen thousand genes. To 29 analyse this diverse dataset, we devised a computational approach correlating genotypic variation 30 and resistance phenotype, this way we were able to identify not only known, but also candidate 31 resistance genes. Finally, we could verify that the effluent of a wastewater treatment plant will 32

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“…Various studies advocate the abundance of distinct antibiotic resistance genes (ARGs) and their reservoirs. There are several environmental sources i.e., soil [39, 40], sediments [41, 42], sewage [43], activated sludge [44], human gut microbiota [45], human feces [46], animal waste [46], drinking water [47], surface water [48, 49], river water [50], wastewater treatment plants (WWTPs) [51, 52], glaciers [53] etc. are known to have diverse type of ARGs and considered to be hotspots for same.…”

Section: Introductionmentioning

confidence: 99%

Abundance and diversity of phages, microbial taxa and antibiotic resistance genes in the sediments of the river Ganges through metagenomic approach

Kumar

Gupta

Sudan

et al. 2020

Preprint

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14In the present study, we have analyzed the metagenomic DNA from the pooled sediment 15 sample of the river Ganges to explore the abundance and diversity of phages, microbial 16 community and antibiotic resistance genes. Utilizing data from Illumina platform, 4174 17 (~0.0013%) reads were classified for the 285 different DNA viruses largely dominated by the 18 group of 260 distinctive phages (3602 reads, ~86.3%). Among all, Microcystis (782 hits), 19

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Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics

Cited by 227 publications

References 85 publications

Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data

Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data

High genomic diversity of multi-drug resistant wastewater Escherichia coli

Abundance and diversity of phages, microbial taxa and antibiotic resistance genes in the sediments of the river Ganges through metagenomic approach

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